!_TAG_FILE_FORMAT 2 /extended format; --format=1 will not append ;" to lines/ !_TAG_FILE_SORTED 1 /0=unsorted, 1=sorted, 2=foldcase/ !_TAG_PROGRAM_AUTHOR Darren Hiebert /dhiebert@users.sourceforge.net/ !_TAG_PROGRAM_NAME Exuberant Ctags // !_TAG_PROGRAM_URL http://ctags.sourceforge.net /official site/ !_TAG_PROGRAM_VERSION 5.5.4 // A framework/base/mathutilities.h /^ enum {N = 1+BinaryExponentHelper::N};$/;" e enum:ProtoMol::Private::BinaryExponentHelper:: A framework/topology/LennardJonesParameters.h /^ Real A,B;$/;" m struct:ProtoMol::LennardJonesParameters A14 framework/topology/LennardJonesParameters.h /^ Real A14,B14;$/;" m struct:ProtoMol::LennardJonesParameters ABSTRACTENUMTYPE_H framework/base/AbstractEnumType.h 3;" d ALL framework/topology/topologyutilities.h /^ enum waterOption {IGNORE_WATER, ONLY_WATER, ALL};$/;" e enum:ProtoMol::waterOption AMBERREADER_H framework/io/AMBERReader.h 3;" d AMBERReader framework/io/AMBERReader.cpp /^ AMBERReader::AMBERReader(): $/;" f class:ProtoMol::AMBERReader AMBERReader framework/io/AMBERReader.cpp /^ AMBERReader::AMBERReader(const std::string& filename):$/;" f class:ProtoMol::AMBERReader AMBERReader framework/io/AMBERReader.h /^ class AMBERReader : public Reader {$/;" c namespace:ProtoMol AMU framework/base/pmconstants.cpp /^ const Real AMU = 1.6605655e-27; \/\/ [kg]$/;" v ANGLE framework/base/ScalarStructure.h /^ ANGLE,$/;" e enum:ProtoMol::ScalarStructure::Index ANGLE framework/io/PARReader.h /^ ANGLE,$/;" e enum:ProtoMol::PARReader::PARRecordTypeEnum ANGLEINFO_H framework/topology/AngleInfo.h 3;" d ANGLESYSTEMFORCEBASE_H framework/forces/AngleSystemForceBase.h 3;" d ANGLESYSTEMFORCE_H framework/forces/AngleSystemForce.h 3;" d ANGLE_DELTAMU framework/base/ScalarStructure.h /^ ANGLE_DELTAMU, \/\/\/< needed for iSG and oSG simulations$/;" e enum:ProtoMol::ScalarStructure::Index ANGLE_H framework/topology/Angle.h 3;" d ANGLE_NOTSET framework/topology/AngleInfo.h /^ ANGLE_NOTSET = 10003, $/;" e enum:ProtoMol::AngleInfo::AngleType ANGLE_POINTER framework/topology/AngleInfo.h /^ ANGLE_POINTER = 10002,$/;" e enum:ProtoMol::AngleInfo::AngleType ANGLE_VALUE framework/topology/AngleInfo.h /^ enum AngleType { ANGLE_VALUE = 10001,$/;" e enum:ProtoMol::AngleInfo::AngleType AObserved framework/frontend/OutputState.h /^ bool AObserved;$/;" m class:ProtoMol::OutputState ARRAYCELLSTRUCTURE_H framework/topology/ArrayCellListStructure.h 3;" d ARRAY_FASTEST_H framework/base/Array_Fastest.h 3;" d ARRAY_H framework/base/Array.h 3;" d ARRAY_NOPARTIALSPECIALIZATION_H framework/base/Array_NoPartialSpecialization.h 3;" d ATOMTYPE_H framework/base/AtomType.h 3;" d ATOM_H framework/base/Atom.h 3;" d AVOGADRO framework/base/pmconstants.cpp /^ const Real AVOGADRO = 6.022045e+23; \/\/ [1\/mol]$/;" v AbstractEnumType framework/base/AbstractEnumType.h /^ AbstractEnumType():myType(T::UNDEFINED){}$/;" f class:ProtoMol::AbstractEnumType AbstractEnumType framework/base/AbstractEnumType.h /^ AbstractEnumType(Enum n):myType(n){}$/;" f class:ProtoMol::AbstractEnumType AbstractEnumType framework/base/AbstractEnumType.h /^ AbstractEnumType(const char s[]):myType(getEnum(std::string(s))){}$/;" f class:ProtoMol::AbstractEnumType AbstractEnumType framework/base/AbstractEnumType.h /^ AbstractEnumType(const std::string& s):myType(getEnum(s)){}$/;" f class:ProtoMol::AbstractEnumType AbstractEnumType framework/base/AbstractEnumType.h /^ class AbstractEnumType : public T {$/;" c namespace:ProtoMol Acceptor framework/base/PSF.h /^ Acceptor():number(0),atom1(0),atom2(0){}$/;" f struct:ProtoMol::PSF::Acceptor Acceptor framework/base/PSF.h /^ Acceptor(int a, int b, int c):number(a),atom1(b),atom2(c){}$/;" f struct:ProtoMol::PSF::Acceptor Acceptor framework/base/PSF.h /^ struct Acceptor {$/;" s class:ProtoMol::PSF Aij framework/integrators/ModifierShadow.cpp /^ Real ModifierShadow::Aij( unsigned int i, unsigned int j ) {$/;" f class:ProtoMol::ModifierShadow AliasMapType framework/base/Configuration.h /^ typedef std::map AliasMapType;$/;" t class:ProtoMol::Configuration Angle framework/base/PAR.h /^ Angle(){} $/;" f struct:ProtoMol::PAR::Angle Angle framework/base/PAR.h /^ Angle(int a, std::string b, std::string c, std::string d, Real e, Real f, bool g, Real h, Real i):$/;" f struct:ProtoMol::PAR::Angle Angle framework/base/PAR.h /^ struct Angle{$/;" s class:ProtoMol::PAR Angle framework/base/PSF.h /^ Angle():number(0),atom1(0),atom2(0),atom3(0){}$/;" f struct:ProtoMol::PSF::Angle Angle framework/base/PSF.h /^ Angle(int a, int b, int c, int d):number(a),atom1(b),atom2(c),atom3(d){}$/;" f struct:ProtoMol::PSF::Angle Angle framework/base/PSF.h /^ struct Angle {$/;" s class:ProtoMol::PSF Angle framework/topology/Angle.h /^ Angle():atom1(-1),atom2(-1),atom3(-1),restAngle(0.0),forceConstant(0.0),$/;" f class:ProtoMol::Angle Angle framework/topology/Angle.h /^ class Angle {$/;" c namespace:ProtoMol AngleIndex framework/integrators/BSplineMOLLYIntegrator.h /^ AngleIndex(int a, int b, int c):angle(a),bond1(b),bond2(c){}$/;" f struct:ProtoMol::BSplineMOLLYIntegrator::AngleIndex AngleIndex framework/integrators/BSplineMOLLYIntegrator.h /^ struct AngleIndex {$/;" s class:ProtoMol::BSplineMOLLYIntegrator AngleInfo framework/topology/AngleInfo.cpp /^ AngleInfo::AngleInfo() {$/;" f class:ProtoMol::AngleInfo AngleInfo framework/topology/AngleInfo.h /^ class AngleInfo {$/;" c namespace:ProtoMol AngleSystemForce framework/forces/AngleSystemForce.h /^ class AngleSystemForce : public SystemForce, private AngleSystemForceBase {$/;" c namespace:ProtoMol AngleSystemForceBase framework/forces/AngleSystemForceBase.h /^ class AngleSystemForceBase {$/;" c namespace:ProtoMol AngleType framework/topology/AngleInfo.h /^ enum AngleType { ANGLE_VALUE = 10001,$/;" g class:ProtoMol::AngleInfo Array framework/base/Array_Fastest.h /^ Array()$/;" f class:ProtoMol::Array Array framework/base/Array_Fastest.h /^ Array(const Array & A)$/;" f class:ProtoMol::Array Array framework/base/Array_Fastest.h /^ class Array$/;" c namespace:ProtoMol Array framework/base/Array_Fastest.h /^ class Array$/;" c namespace:ProtoMol Array framework/base/Array_Fastest.h /^ class Array$/;" c namespace:ProtoMol Array framework/base/Array_NoPartialSpecialization.h /^ Array()$/;" f class:ProtoMol::Array Array framework/base/Array_NoPartialSpecialization.h /^ Array(const Array & A)$/;" f class:ProtoMol::Array Array framework/base/Array_NoPartialSpecialization.h /^ explicit Array(const ArraySize & Dimensions, const T & Init=T())$/;" f class:ProtoMol::Array Array framework/base/Array_NoPartialSpecialization.h /^ explicit Array(const unsigned int * Dimensions, const T & Init=T())$/;" f class:ProtoMol::Array Array framework/base/Array_NoPartialSpecialization.h /^ class Array$/;" c namespace:ProtoMol ArrayCellListStructure framework/topology/ArrayCellListStructure.cpp /^ ArrayCellListStructure::ArrayCellListStructure():valid(false),$/;" f class:ProtoMol::ArrayCellListStructure ArrayCellListStructure framework/topology/ArrayCellListStructure.h /^ class ArrayCellListStructure {$/;" c namespace:ProtoMol ArraySize framework/base/Array_Fastest.h /^ class ArraySize$/;" c namespace:ProtoMol ArraySize framework/base/Array_NoPartialSpecialization.h /^ ArraySize(std::vector & v)$/;" f class:ProtoMol::ArraySize ArraySize framework/base/Array_NoPartialSpecialization.h /^ class ArraySize$/;" c namespace:ProtoMol ArraySizes framework/base/Array_Fastest.h /^ explicit ArraySizes(size_t dim) $/;" f class:ProtoMol::ArraySizes ArraySizes framework/base/Array_Fastest.h /^ class ArraySizes$/;" c namespace:ProtoMol ArraySizes framework/base/Array_NoPartialSpecialization.h /^ explicit ArraySizes(unsigned int dim) $/;" f class:ProtoMol::ArraySizes ArraySizes framework/base/Array_NoPartialSpecialization.h /^ class ArraySizes$/;" c namespace:ProtoMol Atom framework/base/Atom.h /^ Atom():type(-1),$/;" f struct:ProtoMol::Atom Atom framework/base/Atom.h /^ struct Atom {$/;" s namespace:ProtoMol Atom framework/base/PDB.cpp /^ PDB::Atom::Atom():elementType(""), $/;" f class:ProtoMol::PDB::Atom Atom framework/base/PDB.cpp /^ PDB::Atom::Atom(std::string etype, $/;" f class:ProtoMol::PDB::Atom Atom framework/base/PDB.h /^ struct Atom{$/;" s struct:ProtoMol::PDB Atom framework/base/PSF.h /^ Atom():number(0),seg_id(""),residue_sequence(0),residue_name(""),$/;" f struct:ProtoMol::PSF::Atom Atom framework/base/PSF.h /^ Atom(int a,std::string b, int c, std::string d, std::string e, std::string f, Real g, Real h, unsigned int i):$/;" f struct:ProtoMol::PSF::Atom Atom framework/base/PSF.h /^ struct Atom {$/;" s class:ProtoMol::PSF AtomType framework/base/AtomType.h /^ AtomType():name(""),mass(0.0),charge(0.0),symbolName("") {}$/;" f struct:ProtoMol::AtomType AtomType framework/base/AtomType.h /^ struct AtomType {$/;" s namespace:ProtoMol B framework/topology/LennardJonesParameters.h /^ Real A,B;$/;" m struct:ProtoMol::LennardJonesParameters B14 framework/topology/LennardJonesParameters.h /^ Real A14,B14;$/;" m struct:ProtoMol::LennardJonesParameters BANKLENNARDJONESPARAMETERTABLE_H framework/topology/BankLennardJonesParameterTable.h 3;" d BBKINTEGRATOR_H framework/integrators/BBKIntegrator.h 3;" d BBKIntegrator framework/integrators/BBKIntegrator.cpp /^ BBKIntegrator::BBKIntegrator():$/;" f class:ProtoMol::BBKIntegrator BBKIntegrator framework/integrators/BBKIntegrator.cpp /^ BBKIntegrator::BBKIntegrator(Real timestep,$/;" f class:ProtoMol::BBKIntegrator BBKIntegrator framework/integrators/BBKIntegrator.h /^ class BBKIntegrator: public STSIntegrator {$/;" c namespace:ProtoMol BERENDSEN framework/integrators/PaulTrapIntegrator.h /^ BERENDSEN,$/;" e enum:ProtoMol::ThermostatEnum::Enum BERENDSEN_GLOBAL framework/integrators/PaulTrapIntegrator.h /^ BERENDSEN_GLOBAL,$/;" e enum:ProtoMol::ThermostatEnum::Enum BERENDSEN_IND framework/integrators/PaulTrapIntegrator.h /^ BERENDSEN_IND,$/;" e enum:ProtoMol::ThermostatEnum::Enum BERENDSEN_SHELL framework/integrators/PaulTrapIntegrator.h /^ BERENDSEN_SHELL,$/;" e enum:ProtoMol::ThermostatEnum::Enum BERENDSEN_ZERO framework/integrators/PaulTrapIntegrator.h /^ BERENDSEN_ZERO,$/;" e enum:ProtoMol::ThermostatEnum::Enum BITS framework/base/Real.h 16;" d BITSPERBYTE framework/base/Real.h 15;" d BOLTZMANN framework/base/pmconstants.cpp /^ const Real BOLTZMANN = 1.380662e-23; \/\/ [J\/K]$/;" v BOLTZMANN framework/base/pmconstants.cpp /^ const Real BOLTZMANN = 0.001987191;$/;" v BOND framework/base/ScalarStructure.h /^ BOND,$/;" e enum:ProtoMol::ScalarStructure::Index BOND framework/io/PARReader.h /^ BOND,$/;" e enum:ProtoMol::PARReader::PARRecordTypeEnum BONDSYSTEMFORCEBASE_H framework/forces/BondSystemForceBase.h 3;" d BONDSYSTEMFORCE_H framework/forces/BondSystemForce.h 3;" d BOND_DELTAMU framework/base/ScalarStructure.h /^ BOND_DELTAMU, \/\/\/< needed for iSG and oSG simulations$/;" e enum:ProtoMol::ScalarStructure::Index BOND_H framework/topology/Bond.h 3;" d BOOL framework/base/ValueType.h /^ BOOL,$/;" e enum:ProtoMol::ValueEnum::Enum BORDER framework/base/MultiGrid.h /^ static const int BORDER = 2;$/;" v BORDER_TOLERANCE framework/base/MultiGrid.h /^ static const Real BORDER_TOLERANCE = 0.0001;$/;" v BObserved framework/frontend/OutputState.h /^ bool BObserved;$/;" m class:ProtoMol::OutputState BSPLINEMOLLYINTEGRATOR_H framework/integrators/BSplineMOLLYIntegrator.h 3;" d BSPLINETYPE_H framework/base/BSplineType.h 3;" d BSPLINE_H framework/base/BSpline.h 3;" d BSpline framework/base/BSpline.cpp /^ BSpline::BSpline():myInterOrder(0),theta(NULL),dTheta(NULL){$/;" f class:ProtoMol::BSpline BSpline framework/base/BSpline.cpp /^ BSpline::BSpline(const BSpline& bspline){$/;" f class:ProtoMol::BSpline BSpline framework/base/BSpline.cpp /^ BSpline::BSpline(unsigned int order):myInterOrder(order),$/;" f class:ProtoMol::BSpline BSpline framework/base/BSpline.cpp /^ BSpline::BSpline(unsigned int order, Real w):myInterOrder(order),$/;" f class:ProtoMol::BSpline BSpline framework/base/BSpline.h /^ class BSpline {$/;" c namespace:ProtoMol BSplineEnum framework/base/BSplineType.h /^ class BSplineEnum {$/;" c namespace:ProtoMol BSplineMOLLYIntegrator framework/integrators/BSplineMOLLYIntegrator.cpp /^ BSplineMOLLYIntegrator::BSplineMOLLYIntegrator() : MOLLYIntegrator(),$/;" f class:ProtoMol::BSplineMOLLYIntegrator BSplineMOLLYIntegrator framework/integrators/BSplineMOLLYIntegrator.cpp /^ BSplineMOLLYIntegrator::BSplineMOLLYIntegrator(int cycles,$/;" f class:ProtoMol::BSplineMOLLYIntegrator BSplineMOLLYIntegrator framework/integrators/BSplineMOLLYIntegrator.h /^ class BSplineMOLLYIntegrator: public MOLLYIntegrator {$/;" c namespace:ProtoMol BSplineType framework/base/BSplineType.h /^ typedef AbstractEnumType BSplineType;$/;" t namespace:ProtoMol BUILDCELLLIST_H framework/topology/buildCellLists.h 3;" d BankLennardJonesParameterTable framework/topology/BankLennardJonesParameterTable.h /^ BankLennardJonesParameterTable(){};$/;" f struct:ProtoMol::BankLennardJonesParameterTable BankLennardJonesParameterTable framework/topology/BankLennardJonesParameterTable.h /^ struct BankLennardJonesParameterTable {$/;" s namespace:ProtoMol BinaryExponent framework/base/mathutilities.h /^ template struct BinaryExponent {$/;" s namespace:ProtoMol BinaryExponentHelper framework/base/mathutilities.h /^ template struct BinaryExponentHelper {$/;" s namespace:ProtoMol::Private BinaryExponentHelper framework/base/mathutilities.h /^ template struct BinaryExponentHelper {$/;" s namespace:ProtoMol::Private Bond framework/base/PAR.h /^ Bond(){}$/;" f struct:ProtoMol::PAR::Bond Bond framework/base/PAR.h /^ Bond(int a, std::string b, std::string c, Real d, Real e):number(a),atom1(b),atom2(c),forceConstant(d),distance(e){}$/;" f struct:ProtoMol::PAR::Bond Bond framework/base/PAR.h /^ struct Bond{$/;" s class:ProtoMol::PAR Bond framework/base/PSF.h /^ Bond():number(0),atom1(0),atom2(0){}$/;" f struct:ProtoMol::PSF::Bond Bond framework/base/PSF.h /^ Bond(int a, int b, int c):number(a),atom1(b),atom2(c){}$/;" f struct:ProtoMol::PSF::Bond Bond framework/base/PSF.h /^ struct Bond {$/;" s class:ProtoMol::PSF Bond framework/topology/Bond.h /^ Bond():atom1(-1),atom2(-1),springConstant(0.0),restLength(0.0),$/;" f class:ProtoMol::Bond Bond framework/topology/Bond.h /^ Bond(int a, int b, Real c, Real d):atom1(a),atom2(b),springConstant(c),restLength(d){}$/;" f class:ProtoMol::Bond Bond framework/topology/Bond.h /^ class Bond {$/;" c namespace:ProtoMol BondIndex framework/integrators/BSplineMOLLYIntegrator.h /^ BondIndex(int a, int b):b1(std::min(a,b)),b2(std::max(a,b)){}$/;" f struct:ProtoMol::BSplineMOLLYIntegrator::BondIndex BondIndex framework/integrators/BSplineMOLLYIntegrator.h /^ struct BondIndex {$/;" s class:ProtoMol::BSplineMOLLYIntegrator BondSystemForce framework/forces/BondSystemForce.h /^ class BondSystemForce : public SystemForce, private BondSystemForceBase{$/;" c namespace:ProtoMol BondSystemForceBase framework/forces/BondSystemForceBase.h /^ class BondSystemForceBase {$/;" c namespace:ProtoMol BoundaryConditions framework/forces/NonbondedCutoffForce.h /^ typedef typename TOneAtomPair::BoundaryConditions BoundaryConditions;$/;" t class:ProtoMol::NonbondedCutoffForce BoundaryConditions framework/forces/NonbondedCutoffMollyForce.h /^ typedef typename TOneAtomPair::BoundaryConditions BoundaryConditions;$/;" t class:ProtoMol::NonbondedCutoffMollyForce BoundaryConditions framework/forces/NonbondedCutoffSystemForce.h /^ typedef typename TOneAtomPair::BoundaryConditions BoundaryConditions;$/;" t class:ProtoMol::NonbondedCutoffSystemForce BoundaryConditions framework/forces/OneAtomPair.h /^ typedef TBoundaryConditions BoundaryConditions;$/;" t class:ProtoMol::OneAtomPair BoundaryConditions framework/forces/OneAtomPairFull.h /^ typedef TBoundaryConditions BoundaryConditions;$/;" t class:ProtoMol::OneAtomPairFull BoundaryConditions framework/forces/OneAtomPairTwo.h /^ typedef TBoundaryConditions BoundaryConditions;$/;" t class:ProtoMol::OneAtomPairTwo BoundaryConditions framework/forces/OneAtomPairTwoFull.h /^ typedef TBoundaryConditions BoundaryConditions;$/;" t class:ProtoMol::OneAtomPairTwoFull BoundaryConditions framework/forces/OneMollyPair.h /^ typedef TBoundaryConditions BoundaryConditions;$/;" t class:ProtoMol::OneMollyPair BoundaryConditions framework/forces/OneMollyPairTwo.h /^ typedef TBoundaryConditions BoundaryConditions;$/;" t class:ProtoMol::OneMollyPairTwo BoundaryConditions framework/topology/SemiGenericTopology.h /^ typedef TBoundaryConditions BoundaryConditions;$/;" t class:ProtoMol::SemiGenericTopology C framework/base/pmconstants.cpp /^ const Real C = 299792458.0; \/\/ [m\/s]$/;" v C1 framework/forces/CoulombForce.h /^ class C1 {$/;" c class:ProtoMol::CoulombForce C1SWITCHINGFUNCTIONBASE_H framework/topology/C1SwitchingFunctionBase.h 3;" d C1SWITCHINGFUNCTION_H framework/topology/C1SwitchingFunction.h 3;" d C1SwitchingFunction framework/topology/C1SwitchingFunction.cpp /^ C1SwitchingFunction::C1SwitchingFunction():myCutoff(0.0),$/;" f class:ProtoMol::C1SwitchingFunction C1SwitchingFunction framework/topology/C1SwitchingFunction.cpp /^ C1SwitchingFunction::C1SwitchingFunction(Real cutoff):myCutoff(cutoff),$/;" f class:ProtoMol::C1SwitchingFunction C1SwitchingFunction framework/topology/C1SwitchingFunction.h /^ class C1SwitchingFunction : private C1SwitchingFunctionBase {$/;" c namespace:ProtoMol C1SwitchingFunctionBase framework/topology/C1SwitchingFunctionBase.h /^ class C1SwitchingFunctionBase {$/;" c namespace:ProtoMol C2 framework/forces/CoulombForce.h /^ class C2 {$/;" c class:ProtoMol::CoulombForce C2SWITCHINGFUNCTIONBASE_H framework/topology/C2SwitchingFunctionBase.h 3;" d C2SWITCHINGFUNCTION_H framework/topology/C2SwitchingFunction.h 3;" d C2SwitchingFunction framework/topology/C2SwitchingFunction.cpp /^ C2SwitchingFunction::C2SwitchingFunction():mySwitchon(-1.0),myCutoff(0.0){}$/;" f class:ProtoMol::C2SwitchingFunction C2SwitchingFunction framework/topology/C2SwitchingFunction.cpp /^ C2SwitchingFunction::C2SwitchingFunction(Real switchon,Real cutoff):mySwitchon(switchon),$/;" f class:ProtoMol::C2SwitchingFunction C2SwitchingFunction framework/topology/C2SwitchingFunction.h /^ class C2SwitchingFunction : private C2SwitchingFunctionBase {$/;" c namespace:ProtoMol C2SwitchingFunctionBase framework/topology/C2SwitchingFunctionBase.h /^ class C2SwitchingFunctionBase {$/;" c namespace:ProtoMol C3 framework/forces/CoulombForce.h /^ class C3 {$/;" c class:ProtoMol::CoulombForce C4 framework/forces/CoulombForce.h /^ class C4 {$/;" c class:ProtoMol::CoulombForce CELLLISTENUMERATOR_H framework/topology/CellListEnumerator.h 3;" d CELLLISTENUMERATOR_PERDIOCBOUNDARIES_H framework/topology/CellListEnumerator_periodicBoundaries.h 3;" d CELLLISTENUMERATOR_STANDARD_H framework/topology/CellListEnumerator_standard.h 3;" d CHARMM19 framework/base/PAR.h /^ CHARMM19$/;" e enum:ProtoMol::PAR::CharmmTypeEnum CHARMM28 framework/base/PAR.h /^ CHARMM28,$/;" e enum:ProtoMol::PAR::CharmmTypeEnum CHDIR framework/base/systemutilities.cpp 22;" d file: CHDIR framework/base/systemutilities.cpp 9;" d file: CMPCNCNSWITCHINGFUNCTIONBASE_H framework/topology/CmpCnCnSwitchingFunctionBase.h 3;" d CMPCNCNSWITCHINGFUNCTION_H framework/topology/CmpCnCnSwitchingFunction.h 3;" d COMMUNICATION framework/base/TimerStatistic.h /^ COMMUNICATION,$/;" e enum:ProtoMol::TimerStatistic::Enum COMPAREFORCE_H framework/forces/CompareForce.h 3;" d COMPLEMENTSWITCHINGFUNCTIONBASE_H framework/topology/ComplementSwitchingFunctionBase.h 3;" d COMPLEMENTSWITCHINGFUNCTION_H framework/topology/ComplementSwitchingFunction.h 3;" d CONFIGURATIONREADER_H framework/io/ConfigurationReader.h 3;" d CONFIGURATION_H framework/base/Configuration.h 3;" d CONSTANTS_H framework/base/pmconstants.h 3;" d CONSTRAINTVALUETYPE_H framework/base/ConstraintValueType.h 3;" d COULOMB framework/base/ScalarStructure.h /^ COULOMB = FIRST,$/;" e enum:ProtoMol::ScalarStructure::Index COULOMBEWALDREALFORCE_H framework/forces/CoulombEwaldRealForce.h 3;" d COULOMBEWALDREALTABLEFORCEBASE_H framework/forces/CoulombEwaldRealTableForceBase.h 3;" d COULOMBEWALDREALTABLEFORCE_H framework/forces/CoulombEwaldRealTableForce.h 3;" d COULOMBFORCE_H framework/forces/CoulombForce.h 3;" d COULOMBMULTIGRIDDIRECTFORCEBASE_H framework/forces/CoulombMultiGridDirectForceBase.h 3;" d COULOMBMULTIGRIDDIRECTFORCE_H framework/forces/CoulombMultiGridDirectForce.h 3;" d COULOMBMULTIGRIDDIRECTTABLEFORCEBASE_H framework/forces/CoulombMultiGridDirectTableForceBase.h 3;" d COULOMBMULTIGRIDDIRECTTABLEFORCE_H framework/forces/CoulombMultiGridDirectTableForce.h 3;" d COULOMBTABLEFORCEBASE_H framework/forces/CoulombTableForceBase.h 3;" d COULOMBTABLEFORCE_H framework/forces/CoulombTableForce.h 3;" d COULOMB_DELTAMU framework/base/ScalarStructure.h /^ COULOMB_DELTAMU, \/\/\/< needed for iSG and oSG simulations$/;" e enum:ProtoMol::ScalarStructure::Index COULOMB_FACTOR framework/base/pmconstants.cpp /^ const Real COULOMB_FACTOR = C*C*1e-7; \/\/ [Vm\/C]$/;" v CQFLUCTUATION framework/base/ScalarStructure.h /^ CQFLUCTUATION, \/\/\/< needed for iSG and oSG simulations$/;" e enum:ProtoMol::ScalarStructure::Index CRDREADER_H framework/io/CRDReader.h 3;" d CRDReader framework/io/CRDReader.cpp /^ CRDReader::CRDReader():$/;" f class:ProtoMol::CRDReader CRDReader framework/io/CRDReader.cpp /^ CRDReader::CRDReader(const std::string& filename):$/;" f class:ProtoMol::CRDReader CRDReader framework/io/CRDReader.h /^ class CRDReader : public Reader {$/;" c namespace:ProtoMol CUBICCELLLOCATION_H framework/topology/CubicCellLocation.h 3;" d CUBICCELLMANAGER_H framework/topology/CubicCellManager.h 3;" d CUTOFF framework/forces/CoulombEwaldRealForce.h /^ enum {CUTOFF=0};$/;" e enum:ProtoMol::CoulombEwaldRealForce:: CUTOFF framework/forces/CoulombEwaldRealTableForce.h /^ enum {CUTOFF=1};$/;" e enum:ProtoMol::CoulombEwaldRealTableForce:: CUTOFF framework/forces/CoulombForce.h /^ enum {CUTOFF=0};$/;" e enum:ProtoMol::CoulombForce:: CUTOFF framework/forces/CoulombMultiGridDirectForce.h /^ enum {CUTOFF=0};$/;" e enum:ProtoMol::CoulombMultiGridDirectForce:: CUTOFF framework/forces/CoulombMultiGridDirectTableForce.h /^ enum {CUTOFF=1};$/;" e enum:ProtoMol::CoulombMultiGridDirectTableForce:: CUTOFF framework/forces/CoulombTableForce.h /^ enum {CUTOFF=1};$/;" e enum:ProtoMol::CoulombTableForce:: CUTOFF framework/forces/GravitationForce.h /^ enum {CUTOFF=0};$/;" e enum:ProtoMol::GravitationForce:: CUTOFF framework/forces/LennardJonesForce.h /^ enum {CUTOFF=0};$/;" e enum:ProtoMol::LennardJonesForce:: CUTOFF framework/forces/LennardJonesTableForce.h /^ enum {CUTOFF=1};$/;" e enum:ProtoMol::LennardJonesTableForce:: CUTOFF framework/forces/MagneticDipoleForce.h /^ enum {CUTOFF=0};$/;" e enum:ProtoMol::MagneticDipoleForce:: CUTOFF framework/topology/C1SwitchingFunction.h /^ enum {CUTOFF=1};$/;" e enum:ProtoMol::C1SwitchingFunction:: CUTOFF framework/topology/C2SwitchingFunction.h /^ enum {CUTOFF=1};$/;" e enum:ProtoMol::C2SwitchingFunction:: CUTOFF framework/topology/CmpCnCnSwitchingFunction.h /^ enum {CUTOFF=1};$/;" e enum:ProtoMol::CmpCnCnSwitchingFunction:: CUTOFF framework/topology/CnSwitchingFunction.h /^ enum {CUTOFF=1};$/;" e enum:ProtoMol::CnSwitchingFunction:: CUTOFF framework/topology/ComplementSwitchingFunction.h /^ enum {CUTOFF=0};$/;" e enum:ProtoMol::ComplementSwitchingFunction:: CUTOFF framework/topology/CutoffSwitchingFunction.h /^ enum {CUTOFF=1};$/;" e enum:ProtoMol::CutoffSwitchingFunction:: CUTOFF framework/topology/RangeSwitchingFunction.h /^ enum {CUTOFF=TOriginalSwitchingFunction::CUTOFF};$/;" e enum:ProtoMol::RangeSwitchingFunction:: CUTOFF framework/topology/ShiftSwitchingFunction.h /^ enum {CUTOFF=1};$/;" e enum:ProtoMol::ShiftSwitchingFunction:: CUTOFF framework/topology/UniversalSwitchingFunction.h /^ enum {CUTOFF=0};$/;" e enum:ProtoMol::UniversalSwitchingFunction:: CUTOFFSWITCHINGFUNCTIONBASE_H framework/topology/CutoffSwitchingFunctionBase.h 3;" d CUTOFFSWITCHINGFUNCTION_H framework/topology/CutoffSwitchingFunction.h 3;" d CYCLES_H framework/base/Cycles.h 3;" d Cell framework/topology/CubicCellManager.h /^ typedef CubicCellLocation Cell;$/;" t class:ProtoMol::CubicCellManager CellListEnumerator framework/topology/CellListEnumerator.h /^ class CellListEnumerator {};$/;" c namespace:ProtoMol CellListEnumerator framework/topology/CellListEnumerator_periodicBoundaries.h /^ CellListEnumerator():myCutoff(-1.0),$/;" f class:ProtoMol::CellListEnumerator CellListEnumerator framework/topology/CellListEnumerator_periodicBoundaries.h /^ class CellListEnumerator {$/;" c namespace:ProtoMol CellListEnumerator framework/topology/CellListEnumerator_standard.h /^ CellListEnumerator():myCutoff(-1.0),$/;" f class:ProtoMol::CellListEnumerator CellListEnumerator framework/topology/CellListEnumerator_standard.h /^ class CellListEnumerator {$/;" c namespace:ProtoMol CellListStructure framework/topology/CubicCellManager.h /^ typedef ArrayCellListStructure CellListStructure;$/;" t class:ProtoMol::CubicCellManager CellManager framework/topology/Topology.h /^ typedef TCellManager CellManager;$/;" t class:ProtoMol::Topology CellPair framework/topology/CellListEnumerator_periodicBoundaries.h /^ struct CellPair {int first; int second;};$/;" s class:ProtoMol::CellListEnumerator CellPair framework/topology/CellListEnumerator_standard.h /^ struct CellPair {int first; int second;};$/;" s class:ProtoMol::CellListEnumerator CellPairType framework/forces/NonbondedCutoffForce.h /^ typedef typename RealTopologyType::Enumerator::CellPair CellPairType;$/;" t class:ProtoMol::NonbondedCutoffForce CellPairType framework/forces/NonbondedCutoffMollyForce.h /^ typedef typename RealTopologyType::Enumerator::CellPair CellPairType;$/;" t class:ProtoMol::NonbondedCutoffMollyForce CellPairType framework/forces/NonbondedCutoffSystemForce.h /^ typedef typename RealTopologyType::Enumerator::CellPair CellPairType;$/;" t class:ProtoMol::NonbondedCutoffSystemForce CellPairType framework/forces/NonbondedFullEwaldSystemForce.h /^ typedef typename RealTopologyType::Enumerator::CellPair CellPairType;$/;" t class:ProtoMol::NonbondedFullEwaldSystemForce CellPairType framework/forces/NonbondedMultiGridSystemForce.h /^ typedef typename RealTopologyType::Enumerator::CellPair CellPairType;$/;" t class:ProtoMol::NonbondedMultiGridSystemForce CellPairType framework/forces/NonbondedPMEwaldSystemForce.h /^ typedef typename RealTopologyType::Enumerator::CellPair CellPairType;$/;" t class:ProtoMol::NonbondedPMEwaldSystemForce CharmmTypeEnum framework/base/PAR.h /^ enum CharmmTypeEnum {$/;" g class:ProtoMol::PAR CmpCnCnSwitchingFunction framework/topology/CmpCnCnSwitchingFunction.cpp /^ CmpCnCnSwitchingFunction::CmpCnCnSwitchingFunction():mySwitchon(-1.0),myCutoff(0.0),myCompoff(0.0),myOrder(0.0){}$/;" f class:ProtoMol::CmpCnCnSwitchingFunction CmpCnCnSwitchingFunction framework/topology/CmpCnCnSwitchingFunction.cpp /^ CmpCnCnSwitchingFunction::CmpCnCnSwitchingFunction(Real switchon,Real cutoff,Real switchoff,Real order):$/;" f class:ProtoMol::CmpCnCnSwitchingFunction CmpCnCnSwitchingFunction framework/topology/CmpCnCnSwitchingFunction.h /^ class CmpCnCnSwitchingFunction : private CmpCnCnSwitchingFunctionBase {$/;" c namespace:ProtoMol CmpCnCnSwitchingFunctionBase framework/topology/CmpCnCnSwitchingFunctionBase.h /^ class CmpCnCnSwitchingFunctionBase {$/;" c namespace:ProtoMol CnSWITCHINGFUNCTIONBASE_H framework/topology/CnSwitchingFunctionBase.h 3;" d CnSWITCHINGFUNCTION_H framework/topology/CnSwitchingFunction.h 3;" d CnSwitchingFunction framework/topology/CnSwitchingFunction.cpp /^ CnSwitchingFunction::CnSwitchingFunction( Real switchon,Real cutoff,Real$/;" f class:ProtoMol::CnSwitchingFunction CnSwitchingFunction framework/topology/CnSwitchingFunction.cpp /^ CnSwitchingFunction::CnSwitchingFunction():mySwitchon(-1.0),myCutoff(0.0),myOrder(0.0),mySwitchoff(0.0){}$/;" f class:ProtoMol::CnSwitchingFunction CnSwitchingFunction framework/topology/CnSwitchingFunction.h /^ class CnSwitchingFunction : private CnSwitchingFunctionBase {$/;" c namespace:ProtoMol CnSwitchingFunctionBase framework/topology/CnSwitchingFunctionBase.h /^ class CnSwitchingFunctionBase {$/;" c namespace:ProtoMol CompareError framework/forces/CompareForce.h /^ CompareError():absF2(0.0),rFavg(0.0),rFmax(0.0),rPE(0.0){}$/;" f struct:ProtoMol::CompareForce::CompareError CompareError framework/forces/CompareForce.h /^ CompareError(Real a,Real b,Real c,Real d):absF2(a),rFavg(b),rFmax(c),rPE(d){}$/;" f struct:ProtoMol::CompareForce::CompareError CompareError framework/forces/CompareForce.h /^ struct CompareError {$/;" s class:ProtoMol::CompareForce CompareForce framework/forces/CompareForce.cpp /^ CompareForce::CompareForce(Force* actualForce, CompareForce* compareForce):myForces(new Vector3DBlock),$/;" f class:ProtoMol::CompareForce CompareForce framework/forces/CompareForce.h /^ class CompareForce : virtual public Force {$/;" c namespace:ProtoMol ComplementSwitchingFunction framework/topology/ComplementSwitchingFunction.h /^ ComplementSwitchingFunction(){}$/;" f class:ProtoMol::ComplementSwitchingFunction ComplementSwitchingFunction framework/topology/ComplementSwitchingFunction.h /^ ComplementSwitchingFunction(const TOriginalSwitchingFunction sw) : myOrigFunc(sw){};$/;" f class:ProtoMol::ComplementSwitchingFunction ComplementSwitchingFunction framework/topology/ComplementSwitchingFunction.h /^ class ComplementSwitchingFunction : private ComplementSwitchingFunctionBase {$/;" c namespace:ProtoMol ComplementSwitchingFunctionBase framework/topology/ComplementSwitchingFunctionBase.h /^ class ComplementSwitchingFunctionBase {$/;" c namespace:ProtoMol Configuration framework/base/Configuration.h /^ class Configuration {$/;" c namespace:ProtoMol ConfigurationReader framework/io/ConfigurationReader.cpp /^ ConfigurationReader::ConfigurationReader():Reader(),myConfig(NULL){}$/;" f class:ProtoMol::ConfigurationReader ConfigurationReader framework/io/ConfigurationReader.cpp /^ ConfigurationReader::ConfigurationReader(const std::string& filename):Reader(filename),myConfig(NULL){}$/;" f class:ProtoMol::ConfigurationReader ConfigurationReader framework/io/ConfigurationReader.h /^ class ConfigurationReader : public Reader {$/;" c namespace:ProtoMol Constant framework/base/pmconstants.cpp /^ namespace Constant {$/;" n namespace:ProtoMol file: Constant framework/base/pmconstants.h /^ namespace Constant {$/;" n namespace:ProtoMol Constraint framework/frontend/InputValue.h /^ typedef typename ConstraintValueEnum::Enum2Type Constraint;$/;" t class:ProtoMol::InputValue Constraint framework/topology/Bond.h /^ Constraint():atom1(-1),atom2(-1),restLength(0.0){}$/;" f struct:ProtoMol::Bond::Constraint Constraint framework/topology/Bond.h /^ Constraint(int a, int b, Real c):atom1(a),atom2(b),restLength(c){}$/;" f struct:ProtoMol::Bond::Constraint Constraint framework/topology/Bond.h /^ struct Constraint {$/;" s class:ProtoMol::Bond ConstraintValueEnum framework/base/ConstraintValueType.h /^ class ConstraintValueEnum {$/;" c namespace:ProtoMol ConstraintValueType framework/base/ConstraintValueType.h /^ typedef AbstractEnumType ConstraintValueType;$/;" t namespace:ProtoMol Container framework/frontend/OutputCollection.h /^ typedef std::list Container;$/;" t class:ProtoMol::OutputCollection Conv framework/base/LookUpTableBase.h /^ typedef union { TReal f; TInt i; } Conv;$/;" t class:ProtoMol::LookUpTableBase CoulombEwaldRealForce framework/forces/CoulombEwaldRealForce.cpp /^ CoulombEwaldRealForce::CoulombEwaldRealForce():myAlpha(-1.0){}$/;" f class:ProtoMol::CoulombEwaldRealForce CoulombEwaldRealForce framework/forces/CoulombEwaldRealForce.cpp /^ CoulombEwaldRealForce::CoulombEwaldRealForce(Real a):myAlpha(a),$/;" f class:ProtoMol::CoulombEwaldRealForce CoulombEwaldRealForce framework/forces/CoulombEwaldRealForce.h /^ class CoulombEwaldRealForce {$/;" c namespace:ProtoMol CoulombEwaldRealTableForce framework/forces/CoulombEwaldRealTableForce.h /^ CoulombEwaldRealTableForce():LookUpTableBase, $/;" c namespace:ProtoMol CoulombEwaldRealTableForceBase framework/forces/CoulombEwaldRealTableForceBase.h /^ class CoulombEwaldRealTableForceBase {$/;" c namespace:ProtoMol CoulombForce framework/forces/CoulombForce.h /^ class CoulombForce {$/;" c namespace:ProtoMol CoulombMultiGridDirectForce framework/forces/CoulombMultiGridDirectForce.h /^ CoulombMultiGridDirectForce():myS(0.0){}$/;" f class:ProtoMol::CoulombMultiGridDirectForce CoulombMultiGridDirectForce framework/forces/CoulombMultiGridDirectForce.h /^ CoulombMultiGridDirectForce(Real s):myS(s),myRS(1.0\/s){}$/;" f class:ProtoMol::CoulombMultiGridDirectForce CoulombMultiGridDirectForce framework/forces/CoulombMultiGridDirectForce.h /^ class CoulombMultiGridDirectForce : private CoulombMultiGridDirectForceBase {$/;" c namespace:ProtoMol CoulombMultiGridDirectForceBase framework/forces/CoulombMultiGridDirectForceBase.h /^ class CoulombMultiGridDirectForceBase {$/;" c namespace:ProtoMol CoulombMultiGridDirectTableForce framework/forces/CoulombMultiGridDirectTableForce.h /^ CoulombMultiGridDirectTableForce():LookUpTableBase,$/;" f class:ProtoMol::CoulombMultiGridDirectTableForce CoulombMultiGridDirectTableForce framework/forces/CoulombMultiGridDirectTableForce.h /^ CoulombMultiGridDirectTableForce(Real rc, $/;" f class:ProtoMol::CoulombMultiGridDirectTableForce CoulombMultiGridDirectTableForce framework/forces/CoulombMultiGridDirectTableForce.h /^ class CoulombMultiGridDirectTableForce : public LookUpTableBase,PRE,TReal>, $/;" c namespace:ProtoMol CoulombMultiGridDirectTableForceBase framework/forces/CoulombMultiGridDirectTableForceBase.h /^ class CoulombMultiGridDirectTableForceBase {$/;" c namespace:ProtoMol CoulombTableForce framework/forces/CoulombTableForce.h /^ CoulombTableForce():LookUpTableBase, $/;" c namespace:ProtoMol CoulombTableForceBase framework/forces/CoulombTableForceBase.h /^ class CoulombTableForceBase {$/;" c namespace:ProtoMol CubicCellLocation framework/topology/CubicCellLocation.h /^ CubicCellLocation(int a, int b, int c) : x(a),y(b),z(c){}$/;" f class:ProtoMol::CubicCellLocation CubicCellLocation framework/topology/CubicCellLocation.h /^ CubicCellLocation(void):x(0),y(0),z(0){}$/;" f class:ProtoMol::CubicCellLocation CubicCellLocation framework/topology/CubicCellLocation.h /^ class CubicCellLocation {$/;" c namespace:ProtoMol CubicCellManager framework/topology/CubicCellManager.cpp /^ CubicCellManager::CubicCellManager(Real r):myCellSize(r),$/;" f class:ProtoMol::CubicCellManager CubicCellManager framework/topology/CubicCellManager.h /^ CubicCellManager():myCellSize(0.0){}$/;" f class:ProtoMol::CubicCellManager CubicCellManager framework/topology/CubicCellManager.h /^ class CubicCellManager {$/;" c namespace:ProtoMol Cutoff framework/forces/oneAtomContraints.h /^ template<> struct Cutoff {$/;" s namespace:ProtoMol Cutoff framework/forces/oneAtomContraints.h /^ template struct Cutoff {$/;" s namespace:ProtoMol CutoffSwitchingFunction framework/topology/CutoffSwitchingFunction.cpp /^ CutoffSwitchingFunction::CutoffSwitchingFunction():myCutoff(0.0),myCutoff2(0.0){}$/;" f class:ProtoMol::CutoffSwitchingFunction CutoffSwitchingFunction framework/topology/CutoffSwitchingFunction.cpp /^ CutoffSwitchingFunction::CutoffSwitchingFunction(Real cutoff):myCutoff(cutoff),myCutoff2(cutoff*cutoff){}$/;" f class:ProtoMol::CutoffSwitchingFunction CutoffSwitchingFunction framework/topology/CutoffSwitchingFunction.h /^ class CutoffSwitchingFunction : private CutoffSwitchingFunctionBase {$/;" c namespace:ProtoMol CutoffSwitchingFunctionBase framework/topology/CutoffSwitchingFunctionBase.h /^ class CutoffSwitchingFunctionBase {$/;" c namespace:ProtoMol Cycles framework/base/Cycles.h /^ Cycles():myRunningFlag(false){}$/;" f class:ProtoMol::Cycles Cycles framework/base/Cycles.h /^ class Cycles {$/;" c namespace:ProtoMol DCD tools/bccAnalyzer.cpp /^ DCD,$/;" e enum:Format::Type file: DCDTRAJECTORYREADER_H framework/io/DCDTrajectoryReader.h 3;" d DCDTRAJECTORYWRITER_H framework/io/DCDTrajectoryWriter.h 3;" d DCDTrajectoryReader framework/io/DCDTrajectoryReader.cpp /^ DCDTrajectoryReader::DCDTrajectoryReader():Reader(std::ios::binary),myCoords(NULL),mySwapEndian(false),myFirst(true){}$/;" f class:ProtoMol::DCDTrajectoryReader DCDTrajectoryReader framework/io/DCDTrajectoryReader.cpp /^ DCDTrajectoryReader::DCDTrajectoryReader(const std::string& filename):Reader(std::ios::binary,filename),myCoords(NULL),mySwapEndian(false),myFirst(true){}$/;" f class:ProtoMol::DCDTrajectoryReader DCDTrajectoryReader framework/io/DCDTrajectoryReader.h /^ class DCDTrajectoryReader : public Reader {$/;" c namespace:ProtoMol DCDTrajectoryWriter framework/io/DCDTrajectoryWriter.cpp /^ DCDTrajectoryWriter::DCDTrajectoryWriter(Real timestep, unsigned int firststep, bool isLittleEndian):$/;" f class:ProtoMol::DCDTrajectoryWriter DCDTrajectoryWriter framework/io/DCDTrajectoryWriter.cpp /^ DCDTrajectoryWriter::DCDTrajectoryWriter(const char* filename, Real timestep, unsigned int firststep, bool isLittleEndian):$/;" f class:ProtoMol::DCDTrajectoryWriter DCDTrajectoryWriter framework/io/DCDTrajectoryWriter.cpp /^ DCDTrajectoryWriter::DCDTrajectoryWriter(const string& filename, Real timestep, unsigned int firststep, bool isLittleEndian):$/;" f class:ProtoMol::DCDTrajectoryWriter DCDTrajectoryWriter framework/io/DCDTrajectoryWriter.h /^ class DCDTrajectoryWriter : public Writer {$/;" c namespace:ProtoMol DEBUG tools/rem/sequential/main.cc 20;" d file: DEBUG_OUTPUTDIHEDRALS framework/frontend/OutputDihedrals.cpp 26;" d file: DEBUG_OUTPUTDIHEDRALS framework/frontend/OutputState.cpp 26;" d file: DELTATIME framework/base/ScalarStructure.h /^ DELTATIME, \/\/\/< needed for iSG and oSG simulations$/;" e enum:ProtoMol::ScalarStructure::Index DIHEDRAL framework/base/ScalarStructure.h /^ DIHEDRAL,$/;" e enum:ProtoMol::ScalarStructure::Index DIHEDRAL framework/io/PARReader.h /^ DIHEDRAL,$/;" e enum:ProtoMol::PARReader::PARRecordTypeEnum DIHEDRALHMCINTEGRATOR_H framework/integrators/DihedralHMCIntegrator.h 3;" d DIHEDRALSYSTEMFORCEBASE_H framework/forces/DihedralSystemForceBase.h 3;" d DIHEDRALSYSTEMFORCE_H framework/forces/DihedralSystemForce.h 3;" d DIHEDRAL_DELTAMU framework/base/ScalarStructure.h /^ DIHEDRAL_DELTAMU, \/\/\/< needed for iSG and oSG simulations$/;" e enum:ProtoMol::ScalarStructure::Index DIST_R2 framework/forces/CoulombEwaldRealForce.h /^ enum {DIST_R2=1};$/;" e enum:ProtoMol::CoulombEwaldRealForce:: DIST_R2 framework/forces/CoulombEwaldRealTableForce.h /^ enum {DIST_R2=0};$/;" e enum:ProtoMol::CoulombEwaldRealTableForce:: DIST_R2 framework/forces/CoulombForce.h /^ enum {DIST_R2=1};$/;" e enum:ProtoMol::CoulombForce:: DIST_R2 framework/forces/CoulombMultiGridDirectForce.h /^ enum {DIST_R2=0};$/;" e enum:ProtoMol::CoulombMultiGridDirectForce:: DIST_R2 framework/forces/CoulombMultiGridDirectTableForce.h /^ enum {DIST_R2=0};$/;" e enum:ProtoMol::CoulombMultiGridDirectTableForce:: DIST_R2 framework/forces/CoulombTableForce.h /^ enum {DIST_R2=0};$/;" e enum:ProtoMol::CoulombTableForce:: DIST_R2 framework/forces/GravitationForce.h /^ enum {DIST_R2=1};$/;" e enum:ProtoMol::GravitationForce:: DIST_R2 framework/forces/LennardJonesForce.h /^ enum {DIST_R2=1};$/;" e enum:ProtoMol::LennardJonesForce:: DIST_R2 framework/forces/LennardJonesTableForce.h /^ enum {DIST_R2=0};$/;" e enum:ProtoMol::LennardJonesTableForce:: DIST_R2 framework/forces/MagneticDipoleForce.h /^ enum {DIST_R2=1};$/;" e enum:ProtoMol::MagneticDipoleForce:: DLMCINTEGRATOR_H framework/integrators/DLMCIntegrator.h 3;" d DLMCIntegrator framework/integrators/DLMCIntegrator.cpp /^ DLMCIntegrator::DLMCIntegrator() $/;" f class:ProtoMol::DLMCIntegrator DLMCIntegrator framework/integrators/DLMCIntegrator.cpp /^ DLMCIntegrator::DLMCIntegrator(int cycles,$/;" f class:ProtoMol::DLMCIntegrator DLMCIntegrator framework/integrators/DLMCIntegrator.h /^ class DLMCIntegrator: public MCIntegrator {$/;" c namespace:ProtoMol DMDLEAPFROGINTEGRATOR_H framework/integrators/DMDLeapfrogIntegrator.h 3;" d DMDLeapfrogIntegrator framework/integrators/DMDLeapfrogIntegrator.cpp /^ DMDLeapfrogIntegrator::DMDLeapfrogIntegrator()$/;" f class:ProtoMol::DMDLeapfrogIntegrator DMDLeapfrogIntegrator framework/integrators/DMDLeapfrogIntegrator.cpp /^ DMDLeapfrogIntegrator::DMDLeapfrogIntegrator(Real timestep,$/;" f class:ProtoMol::DMDLeapfrogIntegrator DMDLeapfrogIntegrator framework/integrators/DMDLeapfrogIntegrator.h /^ class DMDLeapfrogIntegrator: public STSIntegrator {$/;" c namespace:ProtoMol DONE framework/parallel/Parallel.h /^ DONE, \/\/\/< next() always false, when slave has nothing more to compute$/;" e enum:ProtoMol::Parallel::WorkState DYNAMIC framework/parallel/ParallelType.h /^ DYNAMIC, \/\/\/< Dynamic load balancing, similar to master-slave but with working master$/;" e enum:ProtoMol::ParallelEnum::Enum DebugPostConstraint framework/forces/oneAtomContraints.h /^ struct DebugPostConstraint {$/;" s namespace:ProtoMol DebugPreConstraint framework/forces/oneAtomContraints.h /^ struct DebugPreConstraint {$/;" s namespace:ProtoMol DeltaK framework/topology/Angle.h /^ Real DeltaK, DeltaTheta0, Delta_ubK, Delta_ubR0;$/;" m class:ProtoMol::Angle DeltaK framework/topology/Bond.h /^ Real DeltaK, DeltaR0;$/;" m class:ProtoMol::Bond DeltaK framework/topology/Torsion.h /^ std::vector< Real > DeltaK, DeltaPhase;$/;" m class:ProtoMol::Torsion DeltaPhase framework/topology/Torsion.h /^ std::vector< Real > DeltaK, DeltaPhase;$/;" m class:ProtoMol::Torsion DeltaR0 framework/topology/Bond.h /^ Real DeltaK, DeltaR0;$/;" m class:ProtoMol::Bond DeltaTheta0 framework/topology/Angle.h /^ Real DeltaK, DeltaTheta0, Delta_ubK, Delta_ubR0;$/;" m class:ProtoMol::Angle Delta_ubK framework/topology/Angle.h /^ Real DeltaK, DeltaTheta0, Delta_ubK, Delta_ubR0;$/;" m class:ProtoMol::Angle Delta_ubR0 framework/topology/Angle.h /^ Real DeltaK, DeltaTheta0, Delta_ubK, Delta_ubR0;$/;" m class:ProtoMol::Angle Details framework/frontend/ForceFactoryDetails.h /^ typedef ForceFactoryDetails Details;$/;" t class:ProtoMol::FactoryTraits Details framework/frontend/IntegratorFactoryDetails.h /^ typedef IntegratorFactoryDetails Details;$/;" t class:ProtoMol::FactoryTraits Details framework/frontend/OutputFactoryDetails.h /^ typedef OutputFactoryDetails Details;$/;" t class:ProtoMol::FactoryTraits Details framework/frontend/TopologyFactoryDetails.h /^ typedef TopologyFactoryDetails Details;$/;" t class:ProtoMol::FactoryTraits Dihedral framework/base/PAR.h /^ Dihedral(){}$/;" f struct:ProtoMol::PAR::Dihedral Dihedral framework/base/PAR.h /^ Dihedral(int a, std::string b, std::string c, std::string d, std::string e, $/;" f struct:ProtoMol::PAR::Dihedral Dihedral framework/base/PAR.h /^ Dihedral(int a, std::string b, std::string c, std::string d, std::string e, Real f, int g, Real h):$/;" f struct:ProtoMol::PAR::Dihedral Dihedral framework/base/PAR.h /^ struct Dihedral{$/;" s class:ProtoMol::PAR Dihedral framework/base/PSF.h /^ Dihedral():number(0),atom1(0),atom2(0),atom3(0),atom4(0){}$/;" f struct:ProtoMol::PSF::Dihedral Dihedral framework/base/PSF.h /^ Dihedral(int a, int b, int c, int d, int e):number(a),atom1(b),atom2(c),atom3(d),atom4(e){}$/;" f struct:ProtoMol::PSF::Dihedral Dihedral framework/base/PSF.h /^ struct Dihedral {$/;" s class:ProtoMol::PSF DihedralHMCIntegrator framework/integrators/DihedralHMCIntegrator.cpp /^ DihedralHMCIntegrator::DihedralHMCIntegrator() $/;" f class:ProtoMol::DihedralHMCIntegrator DihedralHMCIntegrator framework/integrators/DihedralHMCIntegrator.cpp /^ DihedralHMCIntegrator::DihedralHMCIntegrator(int cycles,$/;" f class:ProtoMol::DihedralHMCIntegrator DihedralHMCIntegrator framework/integrators/DihedralHMCIntegrator.h /^ class DihedralHMCIntegrator: public MTSIntegrator {$/;" c namespace:ProtoMol DihedralSystemForce framework/forces/DihedralSystemForce.h /^ class DihedralSystemForce: public MTorsionSystemForce, private DihedralSystemForceBase{$/;" c namespace:ProtoMol DihedralSystemForceBase framework/forces/DihedralSystemForceBase.h /^ class DihedralSystemForceBase {$/;" c namespace:ProtoMol Donor framework/base/PSF.h /^ Donor():number(0),atom1(0),atom2(0){}$/;" f struct:ProtoMol::PSF::Donor Donor framework/base/PSF.h /^ Donor(int a, int b, int c):number(a),atom1(b),atom2(c){}$/;" f struct:ProtoMol::PSF::Donor Donor framework/base/PSF.h /^ struct Donor {$/;" s class:ProtoMol::PSF E framework/base/LookUpTableBase.h /^ enum{E=BinaryExponent::max_exponent-std::numeric_limits::min_exponent>::N};$/;" e enum:ProtoMol::LookUpTableBase:: E1 framework/base/mathutilities.cpp /^ const Real E1 = 0.254829592; \/\/ Polynomial Constants used in $/;" v E2 framework/base/mathutilities.cpp /^ const Real E2 =-0.284496736; \/\/ Evaluation of the complementary $/;" v E3 framework/base/mathutilities.cpp /^ const Real E3 = 1.421413741; \/\/ Error function. $/;" v E4 framework/base/mathutilities.cpp /^ const Real E4 =-1.453152027; \/\/ Approximation used is that of $/;" v E5 framework/base/mathutilities.cpp /^ const Real E5 = 1.061405429; \/\/ Abramowitz & Stegun p299. $/;" v ELECTRICFIELDFORCEBASE_H framework/forces/ElectricFieldSystemForceBase.h 3;" d ELECTRICFIELDFORCE_H framework/forces/ElectricFieldSystemForce.h 3;" d ELECTRON_CHARGE framework/base/pmconstants.cpp /^ const Real ELECTRON_CHARGE = 1.6021892e-19; \/\/ [C]$/;" v EMPTY framework/base/ConstraintValueType.h /^ EMPTY,$/;" e enum:ProtoMol::ConstraintValueEnum::Enum ENERGYSTRUCTURE_H framework/base/ScalarStructure.h 3;" d ENTRIES framework/forces/CoulombEwaldRealTableForceBase.h /^ enum {ENTRIES=1};$/;" e enum:ProtoMol::CoulombEwaldRealTableForceBase::LookUpValues:: ENTRIES framework/forces/CoulombMultiGridDirectTableForceBase.h /^ enum {ENTRIES=1};$/;" e enum:ProtoMol::CoulombMultiGridDirectTableForceBase::LookUpValues:: ENTRIES framework/forces/CoulombTableForceBase.h /^ enum {ENTRIES=1};$/;" e enum:ProtoMol::CoulombTableForceBase::LookUpValues:: ENTRIES framework/forces/LennardJonesTableForceBase.h /^ enum {ENTRIES=2};$/;" e enum:ProtoMol::LennardJonesTableForceBase::LookUpValues:: EPOCHFILETIME framework/base/Timer.cpp 233;" d file: EPOCHFILETIME framework/base/Timer.cpp 235;" d file: EPSILON framework/base/pmconstants.cpp /^ const Real EPSILON = 1.0e-14;$/;" v EPS_GOURAUD_THRESHOLD framework/base/pmconstants.cpp /^ const Real EPS_GOURAUD_THRESHOLD = 0.1;$/;" v EPS_SMOOTH_LINE_FACTOR framework/base/pmconstants.cpp /^ const Real EPS_SMOOTH_LINE_FACTOR = 0.06;$/;" v EQUILIBRIUMMOLLYINTEGRATOR_H framework/integrators/EquilibriumMOLLYIntegrator.h 3;" d EXCLUSIONTABLE_H framework/topology/ExclusionTable.h 3;" d EXCLUSIONTYPE_H framework/topology/ExclusionType.h 3;" d EXCLUSION_FULL framework/topology/ExclusionTable.h /^ EXCLUSION_FULL=2 \/\/\/< do exclude$/;" e enum:ProtoMol::ExclusionClass EXCLUSION_MODIFIED framework/topology/ExclusionTable.h /^ EXCLUSION_MODIFIED=1, \/\/\/< do not exlcude, but modify$/;" e enum:ProtoMol::ExclusionClass EXCLUSION_NONE framework/topology/ExclusionTable.h /^ EXCLUSION_NONE=0, \/\/\/< do not exclude$/;" e enum:ProtoMol::ExclusionClass EXTENDEDCOMPAREFORCE_H framework/forces/ExtendedCompareForce.h 3;" d EXTENDEDFORCE_H framework/forces/ExtendedForce.h 3;" d EXTENDEDTIMEFORCE_H framework/forces/ExtendedTimeForce.h 3;" d EXTERNALGRAVITATIONSYSTEMFORCE_H framework/forces/ExternalGravitationSystemForce.h 3;" d EXTERNALMAGNETICFIELDEXTENDEDFORCE_H framework/forces/ExternalMagneticFieldExtendedForce.h 3;" d Eangle framework/imd/imd.h /^ float Eangle;$/;" m struct:ProtoMol::IMD:: Ebond framework/imd/imd.h /^ float Ebond;$/;" m struct:ProtoMol::IMD:: Edihe framework/imd/imd.h /^ float Edihe;$/;" m struct:ProtoMol::IMD:: Eelec framework/imd/imd.h /^ float Eelec;$/;" m struct:ProtoMol::IMD:: Eimpr framework/imd/imd.h /^ float Eimpr;$/;" m struct:ProtoMol::IMD:: ElectricFieldSystemForce framework/forces/ElectricFieldSystemForce.h /^ ElectricFieldSystemForce::ElectricFieldSystemForce():SystemForce(),myOrigin(Vector3D(0.0,0.0,0.0)),myE(0.0),myA(0.0),myC(0.0){}$/;" f class:ProtoMol::ElectricFieldSystemForce ElectricFieldSystemForce framework/forces/ElectricFieldSystemForce.h /^ ElectricFieldSystemForce::ElectricFieldSystemForce(TSwitchingFunction sF, Vector3D origin, Real e, Real a):SystemForce(),switchingFunction(sF),myOrigin(origin),myE(e),myA(a),myC(Constant::SQRTCOULOMBCONSTANT*e),mySquaredCutoff(sF.cutoffSquared()){}$/;" f class:ProtoMol::ElectricFieldSystemForce ElectricFieldSystemForce framework/forces/ElectricFieldSystemForce.h /^ class ElectricFieldSystemForce : public SystemForce, private ElectricFieldSystemForceBase {$/;" c namespace:ProtoMol ElectricFieldSystemForceBase framework/forces/ElectricFieldSystemForceBase.h /^ class ElectricFieldSystemForceBase {$/;" c namespace:ProtoMol Empty framework/base/ConstraintValueType.h /^ typedef Enum2Type Empty;$/;" t class:ProtoMol::ConstraintValueEnum Endian framework/base/systemutilities.cpp /^ struct Endian {$/;" s namespace:ProtoMol file: Enum framework/base/AbstractEnumType.h /^ typedef typename T::Enum Enum;$/;" t class:ProtoMol::AbstractEnumType Enum framework/base/BSplineType.h /^ enum Enum {$/;" g class:ProtoMol::BSplineEnum Enum framework/base/ConstraintValueType.h /^ enum Enum {$/;" g class:ProtoMol::ConstraintValueEnum Enum framework/base/TimerStatistic.h /^ enum Enum {$/;" g class:ProtoMol::TimerStatistic Enum framework/base/ValueType.h /^ enum Enum {$/;" g class:ProtoMol::ValueEnum Enum framework/frontend/InputPosVelType.h /^ enum Enum {$/;" g class:ProtoMol::InputPosVelEnum Enum framework/integrators/PaulTrapIntegrator.h /^ enum Enum {$/;" g class:ProtoMol::ThermostatEnum Enum framework/parallel/ParallelType.h /^ enum Enum {$/;" g class:ProtoMol::ParallelEnum Enum framework/topology/ExclusionType.h /^ enum Enum {$/;" g class:ProtoMol::ExclusionEnum Enum2Type framework/base/ConstraintValueType.h /^ struct Enum2Type{$/;" s class:ProtoMol::ConstraintValueEnum Enum2ValueTraits framework/base/ValueType.h /^ struct Enum2ValueTraits{$/;" s namespace:ProtoMol Enum2ValueTraits framework/base/ValueType.h /^ struct Enum2ValueTraits{$/;" s namespace:ProtoMol Enum2ValueTraits framework/base/ValueType.h /^ struct Enum2ValueTraits{$/;" s namespace:ProtoMol Enum2ValueTraits framework/base/ValueType.h /^ struct Enum2ValueTraits{$/;" s namespace:ProtoMol Enum2ValueTraits framework/base/ValueType.h /^ struct Enum2ValueTraits{$/;" s namespace:ProtoMol Enum2ValueTraits framework/base/ValueType.h /^ struct Enum2ValueTraits{$/;" s namespace:ProtoMol Enum2ValueTraits framework/base/ValueType.h /^ struct Enum2ValueTraits{$/;" s namespace:ProtoMol Enum2ValueTraits framework/base/ValueType.h /^ struct Enum2ValueTraits{$/;" s namespace:ProtoMol Enum2ValueTraits framework/base/ValueType.h /^ struct Enum2ValueTraits{$/;" s namespace:ProtoMol Enum2ValueType framework/base/ValueType.h /^ explicit Enum2ValueType(char const* c):str(std::string(c)){} $/;" f struct:ProtoMol::ValueEnum::Enum2ValueType Enum2ValueType framework/base/ValueType.h /^ explicit Enum2ValueType(std::string s):str(s){}$/;" f struct:ProtoMol::ValueEnum::Enum2ValueType Enum2ValueType framework/base/ValueType.h /^ struct Enum2ValueType{$/;" s class:ProtoMol::ValueEnum Enumerator framework/topology/Topology.h /^ typedef CellListEnumerator Enumerator;$/;" t class:ProtoMol::Topology EnumeratorType framework/forces/NonbondedCutoffForce.h /^ typedef typename RealTopologyType::Enumerator EnumeratorType;$/;" t class:ProtoMol::NonbondedCutoffForce EnumeratorType framework/forces/NonbondedCutoffMollyForce.h /^ typedef typename RealTopologyType::Enumerator EnumeratorType;$/;" t class:ProtoMol::NonbondedCutoffMollyForce EnumeratorType framework/forces/NonbondedCutoffSystemForce.h /^ typedef typename RealTopologyType::Enumerator EnumeratorType;$/;" t class:ProtoMol::NonbondedCutoffSystemForce EnumeratorType framework/forces/NonbondedFullEwaldSystemForce.h /^ typedef typename RealTopologyType::Enumerator EnumeratorType;$/;" t class:ProtoMol::NonbondedFullEwaldSystemForce EnumeratorType framework/forces/NonbondedMultiGridSystemForce.h /^ typedef typename RealTopologyType::Enumerator EnumeratorType;$/;" t class:ProtoMol::NonbondedMultiGridSystemForce EnumeratorType framework/forces/NonbondedPMEwaldSystemForce.h /^ typedef typename RealTopologyType::Enumerator EnumeratorType;$/;" t class:ProtoMol::NonbondedPMEwaldSystemForce Epot framework/imd/imd.h /^ float Epot;$/;" m struct:ProtoMol::IMD:: Epsilon_vel framework/base/XSC.h /^ Real Vol, Epsilon_vel;$/;" m struct:ProtoMol::XSC EquilibriumMOLLYIntegrator framework/integrators/EquilibriumMOLLYIntegrator.cpp /^ EquilibriumMOLLYIntegrator::EquilibriumMOLLYIntegrator (int cycles,$/;" f class:ProtoMol::EquilibriumMOLLYIntegrator EquilibriumMOLLYIntegrator framework/integrators/EquilibriumMOLLYIntegrator.cpp /^ EquilibriumMOLLYIntegrator::EquilibriumMOLLYIntegrator():MOLLYIntegrator(),myAveragedPositions(NULL){}$/;" f class:ProtoMol::EquilibriumMOLLYIntegrator EquilibriumMOLLYIntegrator framework/integrators/EquilibriumMOLLYIntegrator.h /^ class EquilibriumMOLLYIntegrator: public MOLLYIntegrator {$/;" c namespace:ProtoMol Eta framework/base/XSC.h /^ Real Eta, EtaVol, Eta_vel, EtaVol_vel, EtaLambda, EtaLambda_vel;$/;" m struct:ProtoMol::XSC EtaLambda framework/base/XSC.h /^ Real Eta, EtaVol, Eta_vel, EtaVol_vel, EtaLambda, EtaLambda_vel;$/;" m struct:ProtoMol::XSC EtaLambda_vel framework/base/XSC.h /^ Real Eta, EtaVol, Eta_vel, EtaVol_vel, EtaLambda, EtaLambda_vel;$/;" m struct:ProtoMol::XSC EtaVol framework/base/XSC.h /^ Real Eta, EtaVol, Eta_vel, EtaVol_vel, EtaLambda, EtaLambda_vel;$/;" m struct:ProtoMol::XSC EtaVol_vel framework/base/XSC.h /^ Real Eta, EtaVol, Eta_vel, EtaVol_vel, EtaLambda, EtaLambda_vel;$/;" m struct:ProtoMol::XSC Eta_vel framework/base/XSC.h /^ Real Eta, EtaVol, Eta_vel, EtaVol_vel, EtaLambda, EtaLambda_vel;$/;" m struct:ProtoMol::XSC Etot framework/imd/imd.h /^ float Etot;$/;" m struct:ProtoMol::IMD:: Evdw framework/imd/imd.h /^ float Evdw;$/;" m struct:ProtoMol::IMD:: ExclusionClass framework/topology/ExclusionTable.h /^ enum ExclusionClass {$/;" g namespace:ProtoMol ExclusionEnum framework/topology/ExclusionType.h /^ class ExclusionEnum {$/;" c namespace:ProtoMol ExclusionPair framework/topology/ExclusionTable.cpp /^ ExclusionPair::ExclusionPair():a1(-1),a2(-1),excl(EXCLUSION_NONE){}$/;" f class:ProtoMol::ExclusionPair ExclusionPair framework/topology/ExclusionTable.cpp /^ ExclusionPair::ExclusionPair(int a,int b):a1(a),a2(b),excl(EXCLUSION_NONE){}$/;" f class:ProtoMol::ExclusionPair ExclusionPair framework/topology/ExclusionTable.cpp /^ ExclusionPair::ExclusionPair(int a,int b, ExclusionClass c):a1(a),a2(b),excl(c){}$/;" f class:ProtoMol::ExclusionPair ExclusionPair framework/topology/ExclusionTable.h /^ struct ExclusionPair {$/;" s namespace:ProtoMol ExclusionTable framework/topology/ExclusionTable.cpp /^ ExclusionTable::ExclusionTable():lowDeltas(NULL),anyExclsForThisDelta(NULL),myMaxDelta(0),myCurrentSize(0),myFastDeltaMax(0){}$/;" f class:ProtoMol::ExclusionTable ExclusionTable framework/topology/ExclusionTable.h /^ class ExclusionTable {$/;" c namespace:ProtoMol ExclusionType framework/topology/ExclusionType.h /^ typedef AbstractEnumType ExclusionType;$/;" t namespace:ProtoMol ExtendedCompareForce framework/forces/ExtendedCompareForce.cpp /^ ExtendedCompareForce::ExtendedCompareForce(Force* actualForce, CompareForce* compareForce):CompareForce(actualForce,compareForce){}$/;" f class:ProtoMol::ExtendedCompareForce ExtendedCompareForce framework/forces/ExtendedCompareForce.h /^ class ExtendedCompareForce : public CompareForce, public ExtendedForce {$/;" c namespace:ProtoMol ExtendedForce framework/forces/ExtendedForce.h /^ ExtendedForce():Force(){}$/;" f class:ProtoMol::ExtendedForce ExtendedForce framework/forces/ExtendedForce.h /^ class ExtendedForce : virtual public Force {$/;" c namespace:ProtoMol ExtendedTimeForce framework/forces/ExtendedTimeForce.cpp /^ ExtendedTimeForce::ExtendedTimeForce(Force* actualForce):TimeForce(actualForce){}$/;" f class:ProtoMol::ExtendedTimeForce ExtendedTimeForce framework/forces/ExtendedTimeForce.h /^ class ExtendedTimeForce : public TimeForce, public ExtendedForce {$/;" c namespace:ProtoMol ExternalGravitationSystemForce framework/forces/ExternalGravitationSystemForce.cpp /^ ExternalGravitationSystemForce::ExternalGravitationSystemForce():SystemForce(),myG(Vector3D(0.0,0.0,0.0)){}$/;" f class:ProtoMol::ExternalGravitationSystemForce ExternalGravitationSystemForce framework/forces/ExternalGravitationSystemForce.cpp /^ ExternalGravitationSystemForce::ExternalGravitationSystemForce(const Vector3D& g):SystemForce(),myG(g){}$/;" f class:ProtoMol::ExternalGravitationSystemForce ExternalGravitationSystemForce framework/forces/ExternalGravitationSystemForce.h /^ class ExternalGravitationSystemForce : public SystemForce {$/;" c namespace:ProtoMol ExternalMagneticFieldExtendedForce framework/forces/ExternalMagneticFieldExtendedForce.cpp /^ ExternalMagneticFieldExtendedForce::ExternalMagneticFieldExtendedForce():ExtendedForce(),myB(Vector3D(0.0,0.0,0.0)){}$/;" f class:ProtoMol::ExternalMagneticFieldExtendedForce ExternalMagneticFieldExtendedForce framework/forces/ExternalMagneticFieldExtendedForce.cpp /^ ExternalMagneticFieldExtendedForce::ExternalMagneticFieldExtendedForce(const Vector3D& b ):ExtendedForce(),myB(b){}$/;" f class:ProtoMol::ExternalMagneticFieldExtendedForce ExternalMagneticFieldExtendedForce framework/forces/ExternalMagneticFieldExtendedForce.h /^ class ExternalMagneticFieldExtendedForce : public ExtendedForce {$/;" c namespace:ProtoMol FACTORY_H framework/frontend/Factory.h 3;" d FASTDELTAMAX framework/base/pmconstants.cpp /^ const int FASTDELTAMAX=32;$/;" v FFTCOMPLEX_H framework/base/FFTComplex.h 3;" d FFTComplex framework/base/FFTComplex.cpp /^ FFTComplex::FFTComplex():myFFTInternal(NULL){$/;" f class:ProtoMol::FFTComplex FFTComplex framework/base/FFTComplex.h /^ class FFTComplex {$/;" c namespace:ProtoMol FFTComplexMPIFinalize framework/base/FFTComplex.cpp /^ void FFTComplex::FFTComplexMPIFinalize(){$/;" f class:ProtoMol::FFTComplex FFTComplexMPIFinalize framework/base/FFTComplex.cpp /^ void FFTComplex::FFTComplexMPIFinalize(){} $/;" f class:ProtoMol::FFTComplex FFTComplexMPIInit framework/base/FFTComplex.cpp /^ void FFTComplex::FFTComplexMPIInit(int master){$/;" f class:ProtoMol::FFTComplex FFTComplexMPIInit framework/base/FFTComplex.cpp /^ void FFTComplex::FFTComplexMPIInit(int){}$/;" f class:ProtoMol::FFTComplex FFTInternal framework/base/FFTComplex.cpp /^ FFTInternal():myNX(0),myNY(0),myNZ(0),myArray(NULL),myFFTCoeff(NULL){}$/;" f class:ProtoMol::FFTInternal FFTInternal framework/base/FFTComplex.cpp /^ class FFTInternal {$/;" c namespace:ProtoMol file: FILE_H framework/io/File.h 3;" d FIRST framework/base/BSplineType.h /^ FIRST = 0, \/\/ Only internal purpose$/;" e enum:ProtoMol::BSplineEnum::Enum FIRST framework/base/ConstraintValueType.h /^ FIRST = 0, \/\/ Used internally only$/;" e enum:ProtoMol::ConstraintValueEnum::Enum FIRST framework/base/ScalarStructure.h /^ FIRST = 0, \/\/ Only internal purpose$/;" e enum:ProtoMol::ScalarStructure::Index FIRST framework/base/TimerStatistic.h /^ FIRST = 0, \/\/ Only internal purpose$/;" e enum:ProtoMol::TimerStatistic::Enum FIRST framework/base/ValueType.h /^ FIRST = 0, \/\/ Used internally only$/;" e enum:ProtoMol::ValueEnum::Enum FIRST framework/frontend/InputPosVelType.h /^ FIRST = 0, \/\/ Used internally only$/;" e enum:ProtoMol::InputPosVelEnum::Enum FIRST framework/integrators/PaulTrapIntegrator.h /^ FIRST = 0, \/\/ Only internal purpose$/;" e enum:ProtoMol::ThermostatEnum::Enum FIRST framework/parallel/ParallelType.h /^ FIRST = 0, \/\/ Only internal purpose$/;" e enum:ProtoMol::ParallelEnum::Enum FIRST framework/topology/ExclusionType.h /^ FIRST = 0, \/\/ Used internally only$/;" e enum:ProtoMol::ExclusionEnum::Enum FORCE framework/base/ValueType.h /^ FORCE,$/;" e enum:ProtoMol::ValueEnum::Enum FORCEFACTORYDETAILS_H framework/frontend/ForceFactoryDetails.h 3;" d FORCEFACTORY_H framework/frontend/ForceFactory.h 3;" d FORCEGROUP_H framework/forces/ForceGroup.h 3;" d FORCES framework/base/TimerStatistic.h /^ FORCES,$/;" e enum:ProtoMol::TimerStatistic::Enum FORCE_H framework/forces/Force.h 3;" d FRICTIONEXTENDEDFORCE_H framework/forces/FrictionExtendedForce.h 3;" d FSTREAM_READ_1BY1 framework/io/File.cpp 7;" d file: F_OK framework/base/systemutilities.cpp 15;" d file: Factory framework/frontend/Factory.h /^ Factory():FactoryTraits::Details(){$/;" f class:ProtoMol::Factory Factory framework/frontend/Factory.h /^ Factory(const Factory&){}$/;" f class:ProtoMol::Factory Factory framework/frontend/Factory.h /^ class Factory : public FactoryTraits::Details{ $/;" c namespace:ProtoMol FactoryBase framework/frontend/Factory.h /^ FactoryBase():myCache(false){$/;" f class:ProtoMol::FactoryBase FactoryBase framework/frontend/Factory.h /^ FactoryBase(const FactoryBase&){}$/;" f class:ProtoMol::FactoryBase FactoryBase framework/frontend/Factory.h /^ class FactoryBase {$/;" c namespace:ProtoMol FactoryTraits framework/frontend/ForceFactoryDetails.h /^ class FactoryTraits {$/;" c namespace:ProtoMol FactoryTraits framework/frontend/IntegratorFactoryDetails.h /^ class FactoryTraits {$/;" c namespace:ProtoMol FactoryTraits framework/frontend/OutputFactoryDetails.h /^ class FactoryTraits {$/;" c namespace:ProtoMol FactoryTraits framework/frontend/TopologyFactoryDetails.h /^ class FactoryTraits {$/;" c namespace:ProtoMol File framework/io/File.cpp /^ File::File(std::ios::openmode mode):myMode(mode),myFilename(""),myComment(""){}$/;" f class:ProtoMol::File File framework/io/File.cpp /^ File::File(std::ios::openmode mode,const string& filename):myMode(mode),myFilename(filename),myComment(""){}$/;" f class:ProtoMol::File File framework/io/File.h /^ File(){} \/\/ Force to use one of the constructors below$/;" f class:ProtoMol::File File framework/io/File.h /^ class File {$/;" c namespace:ProtoMol Float framework/base/typeSelection.h /^ template struct Float {$/;" s namespace:ProtoMol::TypeSelection Force framework/base/ValueType.h /^ typedef Enum2ValueType Force;$/;" t class:ProtoMol::ValueEnum Force framework/forces/Force.h /^ Force(){}$/;" f class:ProtoMol::Force Force framework/forces/Force.h /^ class Force : public Makeable{$/;" c namespace:ProtoMol ForceFactory framework/frontend/ForceFactory.h /^ typedef Factory ForceFactory;$/;" t namespace:ProtoMol ForceFactoryDetails framework/frontend/ForceFactoryDetails.cpp /^ ForceFactoryDetails::ForceFactoryDetails():FactoryBase(),myLastCompareForce(NULL){$/;" f class:ProtoMol::ForceFactoryDetails ForceFactoryDetails framework/frontend/ForceFactoryDetails.cpp /^ ForceFactoryDetails::ForceFactoryDetails(const ForceFactoryDetails&){}$/;" f class:ProtoMol::ForceFactoryDetails ForceFactoryDetails framework/frontend/ForceFactoryDetails.h /^ class ForceFactoryDetails : public FactoryBase {$/;" c namespace:ProtoMol ForceGroup framework/forces/ForceGroup.cpp /^ ForceGroup::ForceGroup() {}$/;" f class:ProtoMol::ForceGroup ForceGroup framework/forces/ForceGroup.h /^ class ForceGroup {$/;" c namespace:ProtoMol ForceType framework/frontend/ForceFactoryDetails.h /^ struct ForceType {$/;" s class:ProtoMol::ForceFactoryDetails Format tools/bccAnalyzer.cpp /^struct Format{$/;" s file: FrictionExtendedForce framework/forces/FrictionExtendedForce.cpp /^ FrictionExtendedForce::FrictionExtendedForce():ExtendedForce(),myF(0.0), myRnd(Vector3D(0.0,0.0,0.0)){}$/;" f class:ProtoMol::FrictionExtendedForce FrictionExtendedForce framework/forces/FrictionExtendedForce.cpp /^ FrictionExtendedForce::FrictionExtendedForce(Real f, const Vector3D& random):ExtendedForce(),myF(f), myRnd(random){}$/;" f class:ProtoMol::FrictionExtendedForce FrictionExtendedForce framework/forces/FrictionExtendedForce.h /^ class FrictionExtendedForce : public ExtendedForce {$/;" c namespace:ProtoMol GENERICTOPOLOGY_H framework/topology/GenericTopology.h 3;" d GRAVITATIONFORCE_H framework/forces/GravitationForce.h 3;" d GRID_H framework/base/Grid.h 3;" d GenericTopology framework/topology/GenericTopology.cpp /^ GenericTopology::GenericTopology():Makeable(),$/;" f class:ProtoMol::GenericTopology GenericTopology framework/topology/GenericTopology.cpp /^ GenericTopology::GenericTopology(Real c, const ExclusionType& e):Makeable(),$/;" f class:ProtoMol::GenericTopology GenericTopology framework/topology/GenericTopology.h /^ class GenericTopology : public Makeable{$/;" c namespace:ProtoMol GetRefArray framework/base/Array_Fastest.h /^ RefArray GetRefArray() $/;" f class:ProtoMol::Array GetRefArray framework/base/Array_Fastest.h /^ const RefArray GetRefArray() const $/;" f class:ProtoMol::Array GetRefArray framework/base/Array_NoPartialSpecialization.h /^ RefArray GetRefArray() $/;" f class:ProtoMol::Array GetRefArray framework/base/Array_NoPartialSpecialization.h /^ const RefArray GetRefArray() const $/;" f class:ProtoMol::Array GravitationForce framework/forces/GravitationForce.h /^ GravitationForce():myG(0.0){}$/;" f class:ProtoMol::GravitationForce GravitationForce framework/forces/GravitationForce.h /^ GravitationForce(Real g):myG(g){}$/;" f class:ProtoMol::GravitationForce GravitationForce framework/forces/GravitationForce.h /^ class GravitationForce {$/;" c namespace:ProtoMol Grid framework/base/Grid.h /^ Grid::Grid(): $/;" f class:ProtoMol::Grid Grid framework/base/Grid.h /^ class Grid {$/;" c namespace:ProtoMol H framework/base/ReducedHessAngle.h /^ Matrix3by3 H[3][3];$/;" m class:ProtoMol::ReducedHessAngle HAPTICSYSTEMFORCEBASE_H framework/imd/HapticSystemForceBase.h 3;" d HAPTICSYSTEMFORCE_H framework/imd/HapticSystemForce.h 3;" d HARMDIHEDRALSYSTEMFORCEBASE_H framework/forces/HarmDihedralSystemForceBase.h 3;" d HARMDIHEDRALSYSTEMFORCE_H framework/forces/HarmDihedralSystemForce.h 3;" d HAVE_INTTYPES_H protomol_config.h 20;" d HAVE_LIBICE protomol_config.h 48;" d HAVE_LIBPNG protomol_config.h 51;" d HAVE_LIBSM protomol_config.h 54;" d HAVE_LIBX11 protomol_config.h 60;" d HAVE_LIBXEXT protomol_config.h 63;" d HAVE_LIBXI protomol_config.h 66;" d HAVE_LIBXMU protomol_config.h 69;" d HAVE_LIBXT protomol_config.h 72;" d HAVE_MEMORY_H protomol_config.h 75;" d HAVE_STDINT_H protomol_config.h 81;" d HAVE_STDLIB_H protomol_config.h 84;" d HAVE_STRINGS_H protomol_config.h 87;" d HAVE_STRING_H protomol_config.h 90;" d HAVE_SYS_STAT_H protomol_config.h 93;" d HAVE_SYS_TIME_H protomol_config.h 96;" d HAVE_SYS_TYPES_H protomol_config.h 99;" d HAVE_TICK_COUNTER framework/base/Cycles.h 118;" d HAVE_TICK_COUNTER framework/base/Cycles.h 140;" d HAVE_TICK_COUNTER framework/base/Cycles.h 165;" d HAVE_TICK_COUNTER framework/base/Cycles.h 185;" d HAVE_TICK_COUNTER framework/base/Cycles.h 211;" d HAVE_TICK_COUNTER framework/base/Cycles.h 230;" d HAVE_TICK_COUNTER framework/base/Cycles.h 241;" d HAVE_TICK_COUNTER framework/base/Cycles.h 261;" d HAVE_TICK_COUNTER framework/base/Cycles.h 279;" d HAVE_TICK_COUNTER framework/base/Cycles.h 294;" d HAVE_TICK_COUNTER framework/base/Cycles.h 325;" d HAVE_TICK_COUNTER framework/base/Cycles.h 342;" d HAVE_TICK_COUNTER framework/base/Cycles.h 361;" d HAVE_TICK_COUNTER framework/base/Cycles.h 377;" d HAVE_TICK_COUNTER framework/base/Cycles.h 394;" d HAVE_TICK_COUNTER framework/base/Cycles.h 413;" d HAVE_TICK_COUNTER framework/base/Cycles.h 429;" d HAVE_UNISTD_H protomol_config.h 105;" d HBOND framework/io/PARReader.h /^ HBOND$/;" e enum:ProtoMol::PARReader::PARRecordTypeEnum HBondConstraint framework/forces/oneAtomContraints.h /^ struct HBondConstraint {$/;" s namespace:ProtoMol HEADERSIZE framework/imd/imd.cpp 15;" d file: HELPTEXTFACTORY_H framework/frontend/HelpTextFactory.h 3;" d HERMITE_H framework/base/Hermite.h 3;" d HIBITI framework/base/Real.h 17;" d HMCINTEGRATOR_H framework/integrators/HMCIntegrator.h 3;" d HMCIntegrator framework/integrators/HMCIntegrator.cpp /^ HMCIntegrator::HMCIntegrator() $/;" f class:ProtoMol::HMCIntegrator HMCIntegrator framework/integrators/HMCIntegrator.cpp /^ HMCIntegrator::HMCIntegrator(int cycles,$/;" f class:ProtoMol::HMCIntegrator HMCIntegrator framework/integrators/HMCIntegrator.h /^ class HMCIntegrator: public MCIntegrator {$/;" c namespace:ProtoMol HapticSystemForce framework/imd/HapticSystemForce.cpp /^ HapticSystemForce::HapticSystemForce():SystemForce(),$/;" f class:ProtoMol::HapticSystemForce HapticSystemForce framework/imd/HapticSystemForce.cpp /^ HapticSystemForce::HapticSystemForce(int port, int trate, int timeout, $/;" f class:ProtoMol::HapticSystemForce HapticSystemForce framework/imd/HapticSystemForce.h /^ class HapticSystemForce : public SystemForce {$/;" c namespace:ProtoMol HapticSystemForceBase framework/imd/HapticSystemForceBase.h /^class HapticSystemForceBase {$/;" c HarmDihedralSystemForce framework/forces/HarmDihedralSystemForce.h /^ HarmDihedralSystemForce( Real kbias, int dihedral, Real dihedralReference, bool other) : k(kbias),myDihedral(dihedral),$/;" f class:ProtoMol::HarmDihedralSystemForce HarmDihedralSystemForce framework/forces/HarmDihedralSystemForce.h /^ HarmDihedralSystemForce(): k(1), myDihedral(0), myDihedralReference(0.0),$/;" f class:ProtoMol::HarmDihedralSystemForce HarmDihedralSystemForce framework/forces/HarmDihedralSystemForce.h /^ class HarmDihedralSystemForce: public MTorsionSystemForce, private HarmDihedralSystemForceBase {$/;" c namespace:ProtoMol HarmDihedralSystemForceBase framework/forces/HarmDihedralSystemForceBase.h /^ class HarmDihedralSystemForceBase {$/;" c namespace:ProtoMol Hbond framework/base/PAR.h /^ Hbond(){}$/;" f struct:ProtoMol::PAR::Hbond Hbond framework/base/PAR.h /^ Hbond(int a, std::string b, std::string c, Real d, Real e):number(a),atom1(b),atom2(c),emin(d),rmin(e){}$/;" f struct:ProtoMol::PAR::Hbond Hbond framework/base/PAR.h /^ struct Hbond{$/;" s class:ProtoMol::PAR HelpText framework/frontend/HelpTextFactory.h /^ struct HelpText {$/;" s namespace:ProtoMol HelpTextFactory framework/frontend/HelpTextFactory.cpp /^ HelpTextFactory::HelpTextFactory(){}$/;" f class:ProtoMol::HelpTextFactory HelpTextFactory framework/frontend/HelpTextFactory.cpp /^ HelpTextFactory::HelpTextFactory(const HelpTextFactory&){}$/;" f class:ProtoMol::HelpTextFactory HelpTextFactory framework/frontend/HelpTextFactory.h /^ class HelpTextFactory { $/;" c namespace:ProtoMol HelpTextMapType framework/frontend/HelpTextFactory.h /^ typedef std::map HelpTextMapType;$/;" t class:ProtoMol::HelpTextFactory Hermite framework/base/Hermite.cpp /^ Hermite::Hermite():myInterOrder(0),$/;" f class:ProtoMol::Hermite Hermite framework/base/Hermite.cpp /^ Hermite::Hermite(const Hermite& Hermite){$/;" f class:ProtoMol::Hermite Hermite framework/base/Hermite.cpp /^ Hermite::Hermite(unsigned int order):myInterOrder(order),$/;" f class:ProtoMol::Hermite Hermite framework/base/Hermite.cpp /^ Hermite::Hermite(unsigned int order, Real w):myInterOrder(order),$/;" f class:ProtoMol::Hermite Hermite framework/base/Hermite.h /^ class Hermite {$/;" c namespace:ProtoMol Hessian framework/forces/ReducedHessTraits.h /^ typedef ReducedHessCoulomb Hessian;$/;" t struct:ProtoMol::ReducedHessTraits Hessian framework/forces/ReducedHessTraits.h /^ typedef ReducedHessLennardJones Hessian;$/;" t struct:ProtoMol::ReducedHessTraits Holder framework/base/Value.h /^ Holder(const Holder& rhs):holder(rhs.holder),ok(rhs.ok){}$/;" f class:ProtoMol::Value::Holder Holder framework/base/Value.h /^ Holder(const typename ValueTrait::RepType& v, bool def=true):holder(def?v:ValueTrait::init()),ok(ValueTrait::check(Constraint(),v) && def){}$/;" f class:ProtoMol::Value::Holder Holder framework/base/Value.h /^ class Holder : public PlaceHolder {$/;" c class:ProtoMol::Value HydrogenBond framework/integrators/EquilibriumMOLLYIntegrator.h /^ struct HydrogenBond {$/;" s class:ProtoMol::EquilibriumMOLLYIntegrator IDLE framework/base/TimerStatistic.h /^ IDLE,$/;" e enum:ProtoMol::TimerStatistic::Enum IGNORE_WATER framework/topology/topologyutilities.h /^ enum waterOption {IGNORE_WATER, ONLY_WATER, ALL};$/;" e enum:ProtoMol::waterOption IMD framework/imd/imd.cpp /^ namespace IMD {$/;" n namespace:ProtoMol file: IMD framework/imd/imd.h /^ namespace IMD {$/;" n namespace:ProtoMol IMD framework/imd/vmdsock.cpp /^ namespace IMD {$/;" n namespace:ProtoMol file: IMD framework/imd/vmdsock.h /^ namespace IMD {$/;" n namespace:ProtoMol IMDELF framework/imd/IMDElf.h 3;" d IMDElf framework/imd/IMDElf.cpp /^ IMDElf::IMDElf():trate(1),timeout(1000),wait_imd(0),sock(NULL),clientsock(NULL){}$/;" f class:ProtoMol::IMDElf IMDElf framework/imd/IMDElf.h /^ class IMDElf {$/;" c namespace:ProtoMol IMDEnergies framework/imd/imd.h /^ } IMDEnergies;$/;" t namespace:ProtoMol::IMD IMDType framework/imd/imd.h /^ enum IMDType {$/;" g namespace:ProtoMol::IMD IMDVERSION framework/imd/imd.cpp 16;" d file: IMD_DISCONNECT framework/imd/imd.h /^ IMD_DISCONNECT,$/;" e enum:ProtoMol::IMD::IMDType IMD_ENERGIES framework/imd/imd.h /^ IMD_ENERGIES, $/;" e enum:ProtoMol::IMD::IMDType IMD_FCOORDS framework/imd/imd.h /^ IMD_FCOORDS, $/;" e enum:ProtoMol::IMD::IMDType IMD_GO framework/imd/imd.h /^ IMD_GO,$/;" e enum:ProtoMol::IMD::IMDType IMD_H framework/imd/imd.h 3;" d IMD_HANDSHAKE framework/imd/imd.h /^ IMD_HANDSHAKE, $/;" e enum:ProtoMol::IMD::IMDType IMD_IOERROR framework/imd/imd.h /^ IMD_IOERROR$/;" e enum:ProtoMol::IMD::IMDType IMD_KILL framework/imd/imd.h /^ IMD_KILL, $/;" e enum:ProtoMol::IMD::IMDType IMD_MDCOMM framework/imd/imd.h /^ IMD_MDCOMM, $/;" e enum:ProtoMol::IMD::IMDType IMD_PAUSE framework/imd/imd.h /^ IMD_PAUSE,$/;" e enum:ProtoMol::IMD::IMDType IMD_TRATE framework/imd/imd.h /^ IMD_TRATE,$/;" e enum:ProtoMol::IMD::IMDType IMDheader framework/imd/imd.cpp /^ } IMDheader;$/;" t namespace:ProtoMol::IMD file: IMPROPER framework/base/ScalarStructure.h /^ IMPROPER,$/;" e enum:ProtoMol::ScalarStructure::Index IMPROPER framework/io/PARReader.h /^ IMPROPER,$/;" e enum:ProtoMol::PARReader::PARRecordTypeEnum IMPROPERSYSTEMFORCEBASE_H framework/forces/ImproperSystemForceBase.h 3;" d IMPROPERSYSTEMFORCE_H framework/forces/ImproperSystemForce.h 3;" d IMPROPER_DELTAMU framework/base/ScalarStructure.h /^ IMPROPER_DELTAMU, \/\/\/< needed for iSG and oSG simulations$/;" e enum:ProtoMol::ScalarStructure::Index IMPULSEINTEGRATOR_H framework/integrators/ImpulseIntegrator.h 3;" d INCR_SIZE framework/base/Stack.h /^ static const unsigned int INCR_SIZE=50;$/;" m class:ProtoMol::Stack INLINE_ELAPSED framework/base/Cycles.h 104;" d INPUTPOSVELTYPE_H framework/frontend/InputPosVelType.h 3;" d INPUTPOSVEL_H framework/frontend/InputPosVel.h 3;" d INPUTVALUEDEFINITIONS_H framework/frontend/inputValueDefinitions.h 3;" d INPUTVALUE_H framework/frontend/InputValue.h 3;" d INT framework/base/ValueType.h /^ INT,$/;" e enum:ProtoMol::ValueEnum::Enum INT32_TYPE protomol_config.h 111;" d INT32_TYPE protomol_config_windows.h 4;" d INT32_TYPE protomol_config_windows.h 6;" d INTEGRATOR framework/base/ScalarStructure.h /^ INTEGRATOR,$/;" e enum:ProtoMol::ScalarStructure::Index INTEGRATOR framework/base/TimerStatistic.h /^ INTEGRATOR,$/;" e enum:ProtoMol::TimerStatistic::Enum INTEGRATOR framework/base/ValueType.h /^ INTEGRATOR, \/\/ Extended types start here, which act like a STRING $/;" e enum:ProtoMol::ValueEnum::Enum INTEGRATORDEFINITION_H framework/integrators/IntegratorDefinition.h 3;" d INTEGRATORFACTORYDETAILS_H framework/frontend/IntegratorFactoryDetails.h 3;" d INTEGRATORFACTORY_H framework/frontend/IntegratorFactory.h 3;" d INTEGRATOR_H framework/integrators/Integrator.h 3;" d INV_TIMEFACTOR framework/base/pmconstants.cpp /^ const Real INV_TIMEFACTOR = 0.02045482828087295; \/\/ 1 \/ TIMEFACTOR$/;" v ISLITTLEENDIAN framework/base/systemutilities.cpp /^ const bool ISLITTLEENDIAN = Endian::isLittleEndian();$/;" v IVMDSOCK_H framework/imd/vmdsock.h 3;" d Improper framework/base/PAR.h /^ Improper(){}$/;" f struct:ProtoMol::PAR::Improper Improper framework/base/PAR.h /^ Improper(int a, std::string b, std::string c, std::string d, std::string e, Real f, int g, Real h):$/;" f struct:ProtoMol::PAR::Improper Improper framework/base/PAR.h /^ struct Improper{$/;" s class:ProtoMol::PAR Improper framework/base/PSF.h /^ Improper():number(0),atom1(0),atom2(0),atom3(0),atom4(0){}$/;" f struct:ProtoMol::PSF::Improper Improper framework/base/PSF.h /^ Improper(int a, int b, int c, int d, int e):number(a),atom1(b),atom2(c),atom3(d),atom4(e){}$/;" f struct:ProtoMol::PSF::Improper Improper framework/base/PSF.h /^ struct Improper {$/;" s class:ProtoMol::PSF ImproperSystemForce framework/forces/ImproperSystemForce.h /^ class ImproperSystemForce: public MTorsionSystemForce, private ImproperSystemForceBase {$/;" c namespace:ProtoMol ImproperSystemForceBase framework/forces/ImproperSystemForceBase.h /^ class ImproperSystemForceBase {$/;" c namespace:ProtoMol ImpulseIntegrator framework/integrators/ImpulseIntegrator.cpp /^ ImpulseIntegrator::ImpulseIntegrator():MTSIntegrator(){}$/;" f class:ProtoMol::ImpulseIntegrator ImpulseIntegrator framework/integrators/ImpulseIntegrator.cpp /^ ImpulseIntegrator::ImpulseIntegrator(int cycles, $/;" f class:ProtoMol::ImpulseIntegrator ImpulseIntegrator framework/integrators/ImpulseIntegrator.h /^ class ImpulseIntegrator : public MTSIntegrator {$/;" c namespace:ProtoMol Index framework/base/ScalarStructure.h /^ enum Index {$/;" g class:ProtoMol::ScalarStructure Init framework/base/Array_Fastest.h /^ bool resize(const size_t (&Dimensions)[N], const T & Init=T(), bool PreserveElems=false)$/;" m class:ProtoMol::Array Init framework/base/Array_Fastest.h /^ explicit Array(const size_t (&Dimensions)[N], const T & Init=T())$/;" m class:ProtoMol::Array InputPosVel framework/frontend/InputPosVel.cpp /^ InputPosVel::InputPosVel():myFilename(""),myOk(true),myType(InputPosVelType::UNDEFINED){}$/;" f class:ProtoMol::InputPosVel InputPosVel framework/frontend/InputPosVel.cpp /^ InputPosVel::InputPosVel(const string& filename):myFilename(filename),myOk(isAccessible(filename)),myType(InputPosVelType::UNDEFINED){}$/;" f class:ProtoMol::InputPosVel InputPosVel framework/frontend/InputPosVel.h /^ class InputPosVel {$/;" c namespace:ProtoMol InputPosVelEnum framework/frontend/InputPosVelType.h /^ class InputPosVelEnum {$/;" c namespace:ProtoMol InputPosVelType framework/frontend/InputPosVelType.h /^ typedef AbstractEnumType InputPosVelType;$/;" t namespace:ProtoMol InputValue framework/frontend/InputValue.h /^ InputValue():myValue(typename Type::Type(),Constraint(),Value::undefined){}$/;" f class:ProtoMol::InputValue InputValue framework/frontend/InputValue.h /^ explicit InputValue(const T& v):myValue(Type(),Constraint(),v,true){}$/;" f class:ProtoMol::InputValue InputValue framework/frontend/InputValue.h /^ explicit InputValue(const char* v):myValue(Type(),Constraint(),std::string(v),true){}$/;" f class:ProtoMol::InputValue InputValue framework/frontend/InputValue.h /^ class InputValue : public TBase {$/;" c namespace:ProtoMol Int framework/base/typeSelection.h /^ template struct Int {$/;" s namespace:ProtoMol::TypeSelection Int3D framework/base/Grid.h /^ struct Int3D {int x; int y; int z;};$/;" s class:ProtoMol::Grid Int3D framework/base/MultiGrid.h /^ struct Int3D {int x, y, z;};$/;" s class:ProtoMol::MultiGrid Integrator framework/base/ValueType.h /^ typedef Enum2ValueType Integrator;$/;" t class:ProtoMol::ValueEnum Integrator framework/integrators/Integrator.cpp /^ Integrator::Integrator():$/;" f class:ProtoMol::Integrator Integrator framework/integrators/Integrator.cpp /^ Integrator::Integrator(ForceGroup* forceGroup):$/;" f class:ProtoMol::Integrator Integrator framework/integrators/Integrator.h /^ class Integrator : public Makeable {$/;" c namespace:ProtoMol IntegratorDefinition framework/integrators/IntegratorDefinition.h /^ IntegratorDefinition(){}$/;" f struct:ProtoMol::IntegratorDefinition IntegratorDefinition framework/integrators/IntegratorDefinition.h /^ IntegratorDefinition(const MakeableDefinition& i,const std::vector& f):$/;" f struct:ProtoMol::IntegratorDefinition IntegratorDefinition framework/integrators/IntegratorDefinition.h /^ struct IntegratorDefinition {$/;" s namespace:ProtoMol IntegratorFactory framework/frontend/IntegratorFactory.h /^ typedef Factory IntegratorFactory;$/;" t namespace:ProtoMol IntegratorFactoryDetails framework/frontend/IntegratorFactoryDetails.cpp /^ IntegratorFactoryDetails::IntegratorFactoryDetails():FactoryBase(){$/;" f class:ProtoMol::IntegratorFactoryDetails IntegratorFactoryDetails framework/frontend/IntegratorFactoryDetails.cpp /^ IntegratorFactoryDetails::IntegratorFactoryDetails(const IntegratorFactoryDetails&){}$/;" f class:ProtoMol::IntegratorFactoryDetails IntegratorFactoryDetails framework/frontend/IntegratorFactoryDetails.h /^ class IntegratorFactoryDetails : public FactoryBase {$/;" c namespace:ProtoMol IntegratorInput framework/frontend/IntegratorFactoryDetails.h /^ IntegratorInput():prototype(NULL){}$/;" f struct:ProtoMol::IntegratorFactoryDetails::IntegratorInput IntegratorInput framework/frontend/IntegratorFactoryDetails.h /^ struct IntegratorInput {$/;" s class:ProtoMol::IntegratorFactoryDetails Interpolation3D framework/base/Grid.h /^ Interpolation3D(){};$/;" f struct:ProtoMol::Grid::Interpolation3D Interpolation3D framework/base/Grid.h /^ Interpolation3D(unsigned int order):x(order),y(order),z(order){}$/;" f struct:ProtoMol::Grid::Interpolation3D Interpolation3D framework/base/Grid.h /^ struct Interpolation3D {$/;" s class:ProtoMol::Grid Interpolation3D framework/base/MultiGrid.h /^ Interpolation3D(){};$/;" f struct:ProtoMol::MultiGrid::Interpolation3D Interpolation3D framework/base/MultiGrid.h /^ Interpolation3D(unsigned int order):x(order),y(order),z(order){};$/;" f struct:ProtoMol::MultiGrid::Interpolation3D Interpolation3D framework/base/MultiGrid.h /^ struct Interpolation3D {$/;" s class:ProtoMol::MultiGrid KCAL framework/base/pmconstants.cpp /^ const Real KCAL = 1.0\/4184.0; \/\/ [J]$/;" v LAGRANGE_H framework/base/Lagrange.h 3;" d LAMBDA_TEMPERATURE framework/base/ScalarStructure.h /^ LAMBDA_TEMPERATURE, \/\/\/< needed for iSG and oSG simulations$/;" e enum:ProtoMol::ScalarStructure::Index LANGEVINIMPULSEINTEGRATOR_H framework/integrators/LangevinImpulseIntegrator.h 3;" d LAST framework/base/BSplineType.h /^ LAST \/\/ Only internal purpose$/;" e enum:ProtoMol::BSplineEnum::Enum LAST framework/base/ConstraintValueType.h /^ LAST \/\/ Used internally only$/;" e enum:ProtoMol::ConstraintValueEnum::Enum LAST framework/base/ScalarStructure.h /^ LAST \/\/ Only internal purpose $/;" e enum:ProtoMol::ScalarStructure::Index LAST framework/base/TimerStatistic.h /^ LAST \/\/ Only internal purpose$/;" e enum:ProtoMol::TimerStatistic::Enum LAST framework/base/ValueType.h /^ LAST \/\/ Used internally only$/;" e enum:ProtoMol::ValueEnum::Enum LAST framework/frontend/InputPosVelType.h /^ LAST \/\/ Used internally only$/;" e enum:ProtoMol::InputPosVelEnum::Enum LAST framework/integrators/PaulTrapIntegrator.h /^ LAST \/\/ Only internal purpose$/;" e enum:ProtoMol::ThermostatEnum::Enum LAST framework/parallel/ParallelType.h /^ LAST \/\/ Only internal purpose$/;" e enum:ProtoMol::ParallelEnum::Enum LAST framework/topology/ExclusionType.h /^ LAST \/\/ Used internally only$/;" e enum:ProtoMol::ExclusionEnum::Enum LASTREDUCE framework/base/ScalarStructure.h /^ LASTREDUCE, \/\/\/< Last value to be reduced in parallel environment, only internal purpose$/;" e enum:ProtoMol::ScalarStructure::Index LEAPFROGINTEGRATOR_H framework/integrators/LeapfrogIntegrator.h 3;" d LENGTH_AA framework/base/pmconstants.cpp /^ const Real LENGTH_AA = 1e+10; \/\/ [AA]$/;" v LENNARDJONES framework/base/ScalarStructure.h /^ LENNARDJONES,$/;" e enum:ProtoMol::ScalarStructure::Index LENNARDJONESFORCE_H framework/forces/LennardJonesForce.h 3;" d LENNARDJONESPARAMETERS_H framework/topology/LennardJonesParameters.h 3;" d LENNARDJONESPARAMETERTABLE_H framework/topology/LennardJonesParameterTable.h 3;" d LENNARDJONESTABLEFORCEBASE_H framework/forces/LennardJonesTableForceBase.h 3;" d LENNARDJONESTABLEFORCE_H framework/forces/LennardJonesTableForce.h 3;" d LENNARDJONES_DELTAMU framework/base/ScalarStructure.h /^ LENNARDJONES_DELTAMU, \/\/\/< needed for iSG and oSG simulations$/;" e enum:ProtoMol::ScalarStructure::Index LIMIT framework/base/Vector3DBlock.h /^ enum {LIMIT = 30};$/;" e enum:ProtoMol::Vector3DBlock:: LONG framework/base/BSplineType.h /^ LONG,$/;" e enum:ProtoMol::BSplineEnum::Enum LOOKUPTABLEBASE_H framework/base/LookUpTableBase.h 3;" d L_ALT_LOC framework/base/PDB.h /^ L_ALT_LOC = 1-(17 - 17),$/;" e enum:ProtoMol::PDB::Atom::Length L_ATOM_NAME framework/base/PDB.h /^ L_ATOM_NAME = 1-(13 - 16),$/;" e enum:ProtoMol::PDB::Atom::Length L_CHAIN_ID framework/base/PDB.h /^ L_CHAIN_ID = 1-(22 - 22),$/;" e enum:ProtoMol::PDB::Atom::Length L_CHAIN_ID framework/base/PDB.h /^ L_CHAIN_ID = 1-(22 - 22),$/;" e enum:ProtoMol::PDB::Ter::Length L_CHARGE framework/base/PDB.h /^ L_CHARGE = 1-(79 - 80)$/;" e enum:ProtoMol::PDB::Atom::Length L_ELEMENT_SYMBOL framework/base/PDB.h /^ L_ELEMENT_SYMBOL = 1-(77 - 78),$/;" e enum:ProtoMol::PDB::Atom::Length L_I_CODE framework/base/PDB.h /^ L_I_CODE = 1-(27 - 27)$/;" e enum:ProtoMol::PDB::Ter::Length L_I_CODE framework/base/PDB.h /^ L_I_CODE = 1-(27 - 27),$/;" e enum:ProtoMol::PDB::Atom::Length L_OCCUP framework/base/PDB.h /^ L_OCCUP = 1-(55 - 60),$/;" e enum:ProtoMol::PDB::Atom::Length L_RECORD_NAME framework/base/PDB.h /^ L_RECORD_NAME = 1-( 1 - 6),$/;" e enum:ProtoMol::PDB::Atom::Length L_RECORD_NAME framework/base/PDB.h /^ L_RECORD_NAME = 1-( 1 - 6),$/;" e enum:ProtoMol::PDB::Ter::Length L_RES_NAME framework/base/PDB.h /^ L_RES_NAME = 1-(18 - 20),$/;" e enum:ProtoMol::PDB::Atom::Length L_RES_NAME framework/base/PDB.h /^ L_RES_NAME = 1-(18 - 20),$/;" e enum:ProtoMol::PDB::Ter::Length L_RES_SEQ framework/base/PDB.h /^ L_RES_SEQ = 1-(23 - 26),$/;" e enum:ProtoMol::PDB::Atom::Length L_RES_SEQ framework/base/PDB.h /^ L_RES_SEQ = 1-(23 - 26),$/;" e enum:ProtoMol::PDB::Ter::Length L_SEG_ID framework/base/PDB.h /^ L_SEG_ID = 1-(73 - 76),$/;" e enum:ProtoMol::PDB::Atom::Length L_SERIAL framework/base/PDB.h /^ L_SERIAL = 1-( 7 - 11),$/;" e enum:ProtoMol::PDB::Atom::Length L_SERIAL framework/base/PDB.h /^ L_SERIAL = 1-( 7 - 11),$/;" e enum:ProtoMol::PDB::Ter::Length L_TEMP_FACT framework/base/PDB.h /^ L_TEMP_FACT = 1-(61 - 66),$/;" e enum:ProtoMol::PDB::Atom::Length L_X framework/base/PDB.h /^ L_X = 1-(31 - 38),$/;" e enum:ProtoMol::PDB::Atom::Length L_Y framework/base/PDB.h /^ L_Y = 1-(39 - 46),$/;" e enum:ProtoMol::PDB::Atom::Length L_Z framework/base/PDB.h /^ L_Z = 1-(47 - 54),$/;" e enum:ProtoMol::PDB::Atom::Length Lagrange framework/base/Lagrange.cpp /^ Lagrange::Lagrange():myInterOrder(0),$/;" f class:ProtoMol::Lagrange Lagrange framework/base/Lagrange.cpp /^ Lagrange::Lagrange(const Lagrange& Lagrange){$/;" f class:ProtoMol::Lagrange Lagrange framework/base/Lagrange.cpp /^ Lagrange::Lagrange(unsigned int order):myInterOrder(order),$/;" f class:ProtoMol::Lagrange Lagrange framework/base/Lagrange.cpp /^ Lagrange::Lagrange(unsigned int order, Real w):myInterOrder(order),$/;" f class:ProtoMol::Lagrange Lagrange framework/base/Lagrange.h /^ class Lagrange {$/;" c namespace:ProtoMol Lambda framework/base/XSC.h /^ Real Lambda, Lambda_vel;$/;" m struct:ProtoMol::XSC Lambda_vel framework/base/XSC.h /^ Real Lambda, Lambda_vel;$/;" m struct:ProtoMol::XSC LangevinImpulseIntegrator framework/integrators/LangevinImpulseIntegrator.cpp /^ LangevinImpulseIntegrator::LangevinImpulseIntegrator():$/;" f class:ProtoMol::LangevinImpulseIntegrator LangevinImpulseIntegrator framework/integrators/LangevinImpulseIntegrator.cpp /^ LangevinImpulseIntegrator::LangevinImpulseIntegrator(Real timestep,$/;" f class:ProtoMol::LangevinImpulseIntegrator LangevinImpulseIntegrator framework/integrators/LangevinImpulseIntegrator.h /^ class LangevinImpulseIntegrator: public STSIntegrator {$/;" c namespace:ProtoMol LeapfrogIntegrator framework/integrators/LeapfrogIntegrator.cpp /^ LeapfrogIntegrator::LeapfrogIntegrator() : STSIntegrator() {}$/;" f class:ProtoMol::LeapfrogIntegrator LeapfrogIntegrator framework/integrators/LeapfrogIntegrator.cpp /^ LeapfrogIntegrator::LeapfrogIntegrator(Real timestep,$/;" f class:ProtoMol::LeapfrogIntegrator LeapfrogIntegrator framework/integrators/LeapfrogIntegrator.h /^ class LeapfrogIntegrator : public STSIntegrator {$/;" c namespace:ProtoMol Length framework/base/PDB.h /^ enum Length{$/;" g struct:ProtoMol::PDB::Atom Length framework/base/PDB.h /^ enum Length{$/;" g struct:ProtoMol::PDB::Ter LennardJonesForce framework/forces/LennardJonesForce.h /^ class LennardJonesForce {$/;" c namespace:ProtoMol LennardJonesParameterTable framework/topology/LennardJonesParameterTable.cpp /^ LennardJonesParameterTable::LennardJonesParameterTable():myCurrentSize(0),myData(NULL){}$/;" f class:ProtoMol::LennardJonesParameterTable LennardJonesParameterTable framework/topology/LennardJonesParameterTable.h /^ class LennardJonesParameterTable {$/;" c namespace:ProtoMol LennardJonesParameters framework/topology/LennardJonesParameters.h /^ LennardJonesParameters():A(0.0),B(0.0),A14(0.0),B14(0.0){};$/;" f struct:ProtoMol::LennardJonesParameters LennardJonesParameters framework/topology/LennardJonesParameters.h /^ LennardJonesParameters(Real a, Real b):A(a),B(b),A14(0.0),B14(0.0){};$/;" f struct:ProtoMol::LennardJonesParameters LennardJonesParameters framework/topology/LennardJonesParameters.h /^ LennardJonesParameters(Real a, Real b, Real a14, Real b14):A(a),B(b),A14(a14),B14(b14){};$/;" f struct:ProtoMol::LennardJonesParameters LennardJonesParameters framework/topology/LennardJonesParameters.h /^ struct LennardJonesParameters {$/;" s namespace:ProtoMol LennardJonesTableForce framework/forces/LennardJonesTableForce.h /^ LennardJonesTableForce():LookUpTableBase, $/;" c namespace:ProtoMol LennardJonesTableForceBase framework/forces/LennardJonesTableForceBase.h /^ class LennardJonesTableForceBase {$/;" c namespace:ProtoMol LookUpTableBase framework/base/LookUpTableBase.h /^ LookUpTableBase():myTable(NULL),$/;" f class:ProtoMol::LookUpTableBase LookUpTableBase framework/base/LookUpTableBase.h /^ LookUpTableBase(TReal from, $/;" f class:ProtoMol::LookUpTableBase LookUpTableBase framework/base/LookUpTableBase.h /^ LookUpTableBase(const LookUpTableBase& rhs){$/;" f class:ProtoMol::LookUpTableBase LookUpTableBase framework/base/LookUpTableBase.h /^ class LookUpTableBase {$/;" c namespace:ProtoMol LookUpValues framework/forces/CoulombEwaldRealTableForceBase.h /^ LookUpValues(Real a):myAlpha(a){}$/;" f class:ProtoMol::CoulombEwaldRealTableForceBase::LookUpValues LookUpValues framework/forces/CoulombEwaldRealTableForceBase.h /^ class LookUpValues {$/;" c class:ProtoMol::CoulombEwaldRealTableForceBase LookUpValues framework/forces/CoulombMultiGridDirectTableForceBase.h /^ LookUpValues(Real a):myS(a){}$/;" f class:ProtoMol::CoulombMultiGridDirectTableForceBase::LookUpValues LookUpValues framework/forces/CoulombMultiGridDirectTableForceBase.h /^ class LookUpValues {$/;" c class:ProtoMol::CoulombMultiGridDirectTableForceBase LookUpValues framework/forces/CoulombTableForceBase.h /^ class LookUpValues {$/;" c class:ProtoMol::CoulombTableForceBase LookUpValues framework/forces/LennardJonesTableForceBase.h /^ class LookUpValues {$/;" c class:ProtoMol::LennardJonesTableForceBase M framework/base/LookUpTableBase.h /^ enum{M=(sizeof(TReal)*8-1-E)};$/;" e enum:ProtoMol::LookUpTableBase:: MAGNETICDIPOLEFORCE_H framework/forces/MagneticDipoleForce.h 3;" d MAKABLEDEFINITION_H framework/base/MakeableDefinition.h 3;" d MAKEABLE_H framework/base/Makeable.h 3;" d MASTER framework/parallel/Parallel.h /^ MASTER \/\/\/< master$/;" e enum:ProtoMol::Parallel::WorkState MASTERSLAVE framework/parallel/ParallelType.h /^ MASTERSLAVE, \/\/\/< Master-slave$/;" e enum:ProtoMol::ParallelEnum::Enum MATHUTILITIES_H framework/base/mathutilities.h 3;" d MATRIX3by3_H framework/base/Matrix3by3.h 3;" d MAXDOUBLE framework/base/Real.h 19;" d MAXEQNCM framework/topology/CmpCnCnSwitchingFunction.h 20;" d MAXEQNN framework/topology/CnSwitchingFunction.h 20;" d MAXINT framework/base/Real.h 18;" d MAXREAL framework/base/pmconstants.cpp /^ const Real MAXREAL = MAXDOUBLE; $/;" v MAXREAL framework/base/pmconstants.cpp /^ const Real MAXREAL = MAXFLOAT; $/;" v MAX_INT framework/base/pmconstants.cpp /^ const int MAX_INT = MAXINT;$/;" v MAX_INT_2 framework/base/pmconstants.cpp /^ const int MAX_INT_2 = MAXINT\/2;$/;" v MCINTEGRATOR_H framework/integrators/MCIntegrator.h 3;" d MCIntegrator framework/integrators/MCIntegrator.cpp /^ MCIntegrator::MCIntegrator() $/;" f class:ProtoMol::MCIntegrator MCIntegrator framework/integrators/MCIntegrator.cpp /^ MCIntegrator::MCIntegrator(int cycles,$/;" f class:ProtoMol::MCIntegrator MCIntegrator framework/integrators/MCIntegrator.h /^ class MCIntegrator: public MTSIntegrator {$/;" c namespace:ProtoMol METAFORCE_H framework/forces/MetaForce.h 3;" d MINDOUBLE framework/base/Real.h 20;" d MINREAL framework/base/pmconstants.cpp /^ const Real MINREAL = MINDOUBLE;$/;" v MINREAL framework/base/pmconstants.cpp /^ const Real MINREAL = MINFLOAT;$/;" v MODIFIERAVERAGING_H framework/integrators/ModifierAveraging.h 3;" d MODIFIERFRICTION_H framework/integrators/ModifierFriction.h 3;" d MODIFIERINCREMENTTIMESTEP_H framework/integrators/ModifierIncrementTimestep.h 3;" d MODIFIERMETARATTLESHAKE_H framework/integrators/ModifierMetaRattleShake.h 3;" d MODIFIERMETARATTLE_H framework/integrators/ModifierMetaRattle.h 3;" d MODIFIERMETASHAKE_H framework/integrators/ModifierMetaShake.h 3;" d MODIFIERMOLLIFICATION_H framework/integrators/ModifierMollification.h 3;" d MODIFIERNPTRATTLE_H framework/integrators/ModifierNPTRattle.h 3;" d MODIFIERNPTSHAKE_H framework/integrators/ModifierNPTShake.h 3;" d MODIFIERNVTRATTLE_H framework/integrators/ModifierNVTRattle.h 3;" d MODIFIERNVTSHAKE_H framework/integrators/ModifierNVTShake.h 3;" d MODIFIERPOSTFORCEBAROSTAT_H framework/integrators/ModifierPostForceBarostat.h 3;" d MODIFIERPOSTFORCETHERMOSTAT_H framework/integrators/ModifierPostForceThermostat.h 3;" d MODIFIERPREFORCEBAROSTAT_H framework/integrators/ModifierPreForceBarostat.h 3;" d MODIFIERPREFORCETHERMOSTAT_H framework/integrators/ModifierPreForceThermostat.h 3;" d MODIFIERRATTLE_H framework/integrators/ModifierRattle.h 3;" d MODIFIERREMOVEANGULARMOMENTUM_H framework/integrators/ModifierRemoveAngularMomentum.h 3;" d MODIFIERREMOVELINEARMOMENTUM_H framework/integrators/ModifierRemoveLinearMomentum.h 3;" d MODIFIERSHADOW_H framework/integrators/ModifierShadow.h 2;" d MODIFIERSHAKE_H framework/integrators/ModifierShake.h 3;" d MODIFIER_H framework/integrators/Modifier.h 3;" d MODIFY framework/topology/C1SwitchingFunction.h /^ enum {MODIFY=1};$/;" e enum:ProtoMol::C1SwitchingFunction:: MODIFY framework/topology/C2SwitchingFunction.h /^ enum {MODIFY=1};$/;" e enum:ProtoMol::C2SwitchingFunction:: MODIFY framework/topology/CmpCnCnSwitchingFunction.h /^ enum {MODIFY=1};$/;" e enum:ProtoMol::CmpCnCnSwitchingFunction:: MODIFY framework/topology/CnSwitchingFunction.h /^ enum {MODIFY=1};$/;" e enum:ProtoMol::CnSwitchingFunction:: MODIFY framework/topology/ComplementSwitchingFunction.h /^ enum {MODIFY=1};$/;" e enum:ProtoMol::ComplementSwitchingFunction:: MODIFY framework/topology/CutoffSwitchingFunction.h /^ enum {MODIFY=0};$/;" e enum:ProtoMol::CutoffSwitchingFunction:: MODIFY framework/topology/RangeSwitchingFunction.h /^ enum {MODIFY=1};$/;" e enum:ProtoMol::RangeSwitchingFunction:: MODIFY framework/topology/ShiftSwitchingFunction.h /^ enum {MODIFY=1};$/;" e enum:ProtoMol::ShiftSwitchingFunction:: MODIFY framework/topology/UniversalSwitchingFunction.h /^ enum {MODIFY=0};$/;" e enum:ProtoMol::UniversalSwitchingFunction:: MOLECULE_H framework/base/Molecule.h 3;" d MOLLYFORCE_H framework/forces/MollyForce.h 3;" d MOLLYINTEGRATOR_H framework/integrators/MOLLYIntegrator.h 3;" d MOLLYIntegrator framework/integrators/MOLLYIntegrator.cpp /^ MOLLYIntegrator::MOLLYIntegrator (int cycles,$/;" f class:ProtoMol::MOLLYIntegrator MOLLYIntegrator framework/integrators/MOLLYIntegrator.cpp /^ MOLLYIntegrator::MOLLYIntegrator():MTSIntegrator(),mySwapPositions(NULL){}$/;" f class:ProtoMol::MOLLYIntegrator MOLLYIntegrator framework/integrators/MOLLYIntegrator.h /^ class MOLLYIntegrator : public MTSIntegrator {$/;" c namespace:ProtoMol MOLVIRIALXX framework/base/ScalarStructure.h /^ MOLVIRIALXX,$/;" e enum:ProtoMol::ScalarStructure::Index MOLVIRIALXY framework/base/ScalarStructure.h /^ MOLVIRIALXY,$/;" e enum:ProtoMol::ScalarStructure::Index MOLVIRIALXZ framework/base/ScalarStructure.h /^ MOLVIRIALXZ,$/;" e enum:ProtoMol::ScalarStructure::Index MOLVIRIALYX framework/base/ScalarStructure.h /^ MOLVIRIALYX,$/;" e enum:ProtoMol::ScalarStructure::Index MOLVIRIALYY framework/base/ScalarStructure.h /^ MOLVIRIALYY,$/;" e enum:ProtoMol::ScalarStructure::Index MOLVIRIALYZ framework/base/ScalarStructure.h /^ MOLVIRIALYZ,$/;" e enum:ProtoMol::ScalarStructure::Index MOLVIRIALZX framework/base/ScalarStructure.h /^ MOLVIRIALZX,$/;" e enum:ProtoMol::ScalarStructure::Index MOLVIRIALZY framework/base/ScalarStructure.h /^ MOLVIRIALZY,$/;" e enum:ProtoMol::ScalarStructure::Index MOLVIRIALZZ framework/base/ScalarStructure.h /^ MOLVIRIALZZ,$/;" e enum:ProtoMol::ScalarStructure::Index MPITypeTraits framework/parallel/Parallel-FD.cpp /^ struct MPITypeTraits$/;" s namespace:ProtoMol file: MPITypeTraits framework/parallel/Parallel-FD.cpp /^ struct MPITypeTraits$/;" s namespace:ProtoMol file: MPITypeTraits framework/parallel/Parallel.cpp /^ struct MPITypeTraits$/;" s namespace:ProtoMol file: MPITypeTraits framework/parallel/Parallel.cpp /^ struct MPITypeTraits$/;" s namespace:ProtoMol file: MTORSIONSYSTEMFORCE_H framework/forces/MTorsionSystemForce.h 3;" d MTSINTEGRATOR_H framework/integrators/MTSIntegrator.h 3;" d MTSIntegrator framework/integrators/MTSIntegrator.cpp /^ MTSIntegrator::MTSIntegrator (int cycles,$/;" f class:ProtoMol::MTSIntegrator MTSIntegrator framework/integrators/MTSIntegrator.cpp /^ MTSIntegrator::MTSIntegrator():StandardIntegrator(),myNextIntegrator(NULL),myCycleLength(0){}$/;" f class:ProtoMol::MTSIntegrator MTSIntegrator framework/integrators/MTSIntegrator.h /^ class MTSIntegrator: public StandardIntegrator {$/;" c namespace:ProtoMol MTorsionSystemForce framework/forces/MTorsionSystemForce.h /^ class MTorsionSystemForce: public SystemForce {$/;" c namespace:ProtoMol MULTIGRID_H framework/base/MultiGrid.h 3;" d MY_MPI_REAL framework/base/FFTComplex.cpp 285;" d file: MY_MPI_REAL framework/base/FFTComplex.cpp 289;" d file: MY_MPI_REAL framework/parallel/Parallel-FD.cpp 33;" d file: MY_MPI_REAL framework/parallel/Parallel-FD.cpp 37;" d file: MY_MPI_REAL framework/parallel/Parallel.cpp 29;" d file: MY_MPI_REAL framework/parallel/Parallel.cpp 33;" d file: M_2PI framework/base/Real.h 25;" d M_PI framework/base/Real.h 23;" d M_PI_2 framework/base/Real.h 24;" d MagneticDipoleForce framework/forces/MagneticDipoleForce.cpp /^ MagneticDipoleForce::MagneticDipoleForce():myChi(0.0),myR(0.0),myOmega(0.0),myPhi(0.0),myHx(0.0),myHy(0.0),myHz(0.0),myD(0.0){}$/;" f class:ProtoMol::MagneticDipoleForce MagneticDipoleForce framework/forces/MagneticDipoleForce.cpp /^ MagneticDipoleForce::MagneticDipoleForce(Real chi, Real radius, Real omega, Real phi, Real Hx,Real Hy, Real Hz, Real D):$/;" f class:ProtoMol::MagneticDipoleForce MagneticDipoleForce framework/forces/MagneticDipoleForce.h /^ class MagneticDipoleForce {$/;" c namespace:ProtoMol MagneticDipoleMirrorSystemForce framework/forces/MagneticDipoleMirrorSystemForce.h /^ MagneticDipoleMirrorSystemForce():myChi(0.0), myR(0.0), myD(0.0), myHx(0.0), myHy(0.0), myHz(0.0){}$/;" f class:ProtoMol::MagneticDipoleMirrorSystemForce MagneticDipoleMirrorSystemForce framework/forces/MagneticDipoleMirrorSystemForce.h /^ MagneticDipoleMirrorSystemForce(Real chi, Real r, Real Hx, Real Hy, Real Hz, Real d):$/;" f class:ProtoMol::MagneticDipoleMirrorSystemForce MagneticDipoleMirrorSystemForce framework/forces/MagneticDipoleMirrorSystemForce.h /^ class MagneticDipoleMirrorSystemForce : public SystemForce, private MagneticDipoleMirrorSystemForceBase {$/;" c namespace:ProtoMol MagneticDipoleMirrorSystemForceBASE_H framework/forces/MagneticDipoleMirrorSystemForceBase.h 3;" d MagneticDipoleMirrorSystemForceBase framework/forces/MagneticDipoleMirrorSystemForceBase.h /^ class MagneticDipoleMirrorSystemForceBase {$/;" c namespace:ProtoMol MagneticDipoleMirrorSystemForce_H framework/forces/MagneticDipoleMirrorSystemForce.h 3;" d Makeable framework/base/Makeable.h /^ class Makeable{$/;" c namespace:ProtoMol MakeableDefinition framework/base/MakeableDefinition.h /^ MakeableDefinition(){}$/;" f struct:ProtoMol::MakeableDefinition MakeableDefinition framework/base/MakeableDefinition.h /^ MakeableDefinition(const std::string& i,const std::vector& p):id(i),parameters(p){}$/;" f struct:ProtoMol::MakeableDefinition MakeableDefinition framework/base/MakeableDefinition.h /^ struct MakeableDefinition {$/;" s namespace:ProtoMol Matrix3by3 framework/base/Matrix3by3.cpp /^ Matrix3by3::Matrix3by3()$/;" f class:ProtoMol::Matrix3by3 Matrix3by3 framework/base/Matrix3by3.cpp /^ Matrix3by3::Matrix3by3(Real x00, Real x01, Real x02,$/;" f class:ProtoMol::Matrix3by3 Matrix3by3 framework/base/Matrix3by3.cpp /^ Matrix3by3::Matrix3by3(const Vector3D &a, const Vector3D &b)$/;" f class:ProtoMol::Matrix3by3 Matrix3by3 framework/base/Matrix3by3.cpp /^ Matrix3by3::Matrix3by3(const Vector3D& v1, const Vector3D& v2, $/;" f class:ProtoMol::Matrix3by3 Matrix3by3 framework/base/Matrix3by3.cpp /^ Matrix3by3::Matrix3by3(double mat[9])$/;" f class:ProtoMol::Matrix3by3 Matrix3by3 framework/base/Matrix3by3.cpp /^ Matrix3by3::Matrix3by3(float mat[9])$/;" f class:ProtoMol::Matrix3by3 Matrix3by3 framework/base/Matrix3by3.h /^ class Matrix3by3 {$/;" c namespace:ProtoMol MetaForce framework/forces/MetaForce.h /^ MetaForce():Force(){}$/;" f class:ProtoMol::MetaForce MetaForce framework/forces/MetaForce.h /^ class MetaForce : public Force {$/;" c namespace:ProtoMol Modifier framework/integrators/Modifier.h /^ Modifier(int order=0):myOrder(order),$/;" f class:ProtoMol::Modifier Modifier framework/integrators/Modifier.h /^ class Modifier {$/;" c namespace:ProtoMol ModifierAveraging framework/integrators/ModifierAveraging.h /^ ModifierAveraging(MOLLYIntegrator* i):Modifier(),myTheIntegrator(i){}$/;" f class:ProtoMol::ModifierAveraging ModifierAveraging framework/integrators/ModifierAveraging.h /^ class ModifierAveraging : public Modifier {$/;" c namespace:ProtoMol ModifierFriction framework/integrators/ModifierFriction.h /^ ModifierFriction(NoseNVTLeapfrogIntegrator* i):Modifier(Constant::MAX_INT-400),myTheIntegrator(i){}$/;" f class:ProtoMol::ModifierFriction ModifierFriction framework/integrators/ModifierFriction.h /^ class ModifierFriction : public Modifier {$/;" c namespace:ProtoMol ModifierIncrementTimestep framework/integrators/ModifierIncrementTimestep.h /^ ModifierIncrementTimestep(STSIntegrator* i):Modifier(Constant::MAX_INT),myTheIntegrator(i){}$/;" f class:ProtoMol::ModifierIncrementTimestep ModifierIncrementTimestep framework/integrators/ModifierIncrementTimestep.h /^ class ModifierIncrementTimestep : public Modifier {$/;" c namespace:ProtoMol ModifierMetaRattle framework/integrators/ModifierMetaRattle.cpp /^ ModifierMetaRattle::ModifierMetaRattle(Real eps, int maxIter, int order):ModifierMetaRattleShake(eps,maxIter,order){}$/;" f class:ProtoMol::ModifierMetaRattle ModifierMetaRattle framework/integrators/ModifierMetaRattle.h /^ class ModifierMetaRattle : public ModifierMetaRattleShake {$/;" c namespace:ProtoMol ModifierMetaRattleShake framework/integrators/ModifierMetaRattleShake.cpp /^ ModifierMetaRattleShake::ModifierMetaRattleShake(Real eps, int maxIter,int order):Modifier(order),$/;" f class:ProtoMol::ModifierMetaRattleShake ModifierMetaRattleShake framework/integrators/ModifierMetaRattleShake.h /^ class ModifierMetaRattleShake : public Modifier {$/;" c namespace:ProtoMol ModifierMetaShake framework/integrators/ModifierMetaShake.cpp /^ ModifierMetaShake::ModifierMetaShake(Real eps, int maxIter, int order):ModifierMetaRattleShake(eps,maxIter,order){}$/;" f class:ProtoMol::ModifierMetaShake ModifierMetaShake framework/integrators/ModifierMetaShake.h /^ class ModifierMetaShake : public ModifierMetaRattleShake {$/;" c namespace:ProtoMol ModifierMollification framework/integrators/ModifierMollification.h /^ ModifierMollification(MOLLYIntegrator* i):Modifier(),myTheIntegrator(i){}$/;" f class:ProtoMol::ModifierMollification ModifierMollification framework/integrators/ModifierMollification.h /^ class ModifierMollification : public Modifier {$/;" c namespace:ProtoMol ModifierNPTRattle framework/integrators/ModifierNPTRattle.h /^ ModifierNPTRattle(Real eps, $/;" f class:ProtoMol::ModifierNPTRattle ModifierNPTRattle framework/integrators/ModifierNPTRattle.h /^ class ModifierNPTRattle : public ModifierNPTRattleDetails {$/;" c namespace:ProtoMol ModifierNPTRattleDetails framework/integrators/ModifierNPTRattle.cpp /^ ModifierNPTRattleDetails::ModifierNPTRattleDetails(Real eps, int maxIter, int order):ModifierMetaRattle(eps,maxIter,order){}$/;" f class:ProtoMol::ModifierNPTRattleDetails ModifierNPTRattleDetails framework/integrators/ModifierNPTRattle.h /^ class ModifierNPTRattleDetails : public ModifierMetaRattle {$/;" c namespace:ProtoMol ModifierNPTShake framework/integrators/ModifierNPTShake.h /^ ModifierNPTShake(Real eps, $/;" f class:ProtoMol::ModifierNPTShake ModifierNPTShake framework/integrators/ModifierNPTShake.h /^ class ModifierNPTShake : public ModifierNPTShakeDetails {$/;" c namespace:ProtoMol ModifierNPTShakeDetails framework/integrators/ModifierNPTShake.cpp /^ ModifierNPTShakeDetails::ModifierNPTShakeDetails(Real eps, int maxIter, int order):ModifierMetaShake(eps,maxIter,order){}$/;" f class:ProtoMol::ModifierNPTShakeDetails ModifierNPTShakeDetails framework/integrators/ModifierNPTShake.h /^ class ModifierNPTShakeDetails : public ModifierMetaShake {$/;" c namespace:ProtoMol ModifierNVTRattle framework/integrators/ModifierNVTRattle.h /^ ModifierNVTRattle(Real eps,$/;" f class:ProtoMol::ModifierNVTRattle ModifierNVTRattle framework/integrators/ModifierNVTRattle.h /^ class ModifierNVTRattle : public ModifierNVTRattleDetails {$/;" c namespace:ProtoMol ModifierNVTRattleDetails framework/integrators/ModifierNVTRattle.cpp /^ ModifierNVTRattleDetails::ModifierNVTRattleDetails(Real eps, int maxIter, int order):ModifierMetaRattle(eps,maxIter,order){}$/;" f class:ProtoMol::ModifierNVTRattleDetails ModifierNVTRattleDetails framework/integrators/ModifierNVTRattle.h /^ class ModifierNVTRattleDetails : public ModifierMetaRattle {$/;" c namespace:ProtoMol ModifierNVTShake framework/integrators/ModifierNVTShake.h /^ ModifierNVTShake(Real eps,$/;" f class:ProtoMol::ModifierNVTShake ModifierNVTShake framework/integrators/ModifierNVTShake.h /^ class ModifierNVTShake : public ModifierNVTShakeDetails {$/;" c namespace:ProtoMol ModifierNVTShakeDetails framework/integrators/ModifierNVTShake.cpp /^ ModifierNVTShakeDetails::ModifierNVTShakeDetails(Real eps, int maxIter, int order):ModifierMetaShake(eps,maxIter,order){}$/;" f class:ProtoMol::ModifierNVTShakeDetails ModifierNVTShakeDetails framework/integrators/ModifierNVTShake.h /^ class ModifierNVTShakeDetails : public ModifierMetaShake {$/;" c namespace:ProtoMol ModifierPostForceBarostat framework/integrators/ModifierPostForceBarostat.h /^ ModifierPostForceBarostat(TIntegrator* i):Modifier(Constant::MAX_INT-400),myTheIntegrator(i){}$/;" f class:ProtoMol::ModifierPostForceBarostat ModifierPostForceBarostat framework/integrators/ModifierPostForceBarostat.h /^ ModifierPostForceBarostat(TIntegrator* i, int order):Modifier(order),myTheIntegrator(i){}$/;" f class:ProtoMol::ModifierPostForceBarostat ModifierPostForceBarostat framework/integrators/ModifierPostForceBarostat.h /^ class ModifierPostForceBarostat : public Modifier {$/;" c namespace:ProtoMol ModifierPostForceThermostat framework/integrators/ModifierPostForceThermostat.h /^ ModifierPostForceThermostat(TIntegrator* i):Modifier(Constant::MAX_INT-400),myTheIntegrator(i){}$/;" f class:ProtoMol::ModifierPostForceThermostat ModifierPostForceThermostat framework/integrators/ModifierPostForceThermostat.h /^ ModifierPostForceThermostat(TIntegrator* i, int order):Modifier(order),myTheIntegrator(i){}$/;" f class:ProtoMol::ModifierPostForceThermostat ModifierPostForceThermostat framework/integrators/ModifierPostForceThermostat.h /^ class ModifierPostForceThermostat : public Modifier {$/;" c namespace:ProtoMol ModifierPreForceBarostat framework/integrators/ModifierPreForceBarostat.h /^ ModifierPreForceBarostat(TIntegrator* i):Modifier(Constant::MAX_INT-400),myTheIntegrator(i){}$/;" f class:ProtoMol::ModifierPreForceBarostat ModifierPreForceBarostat framework/integrators/ModifierPreForceBarostat.h /^ ModifierPreForceBarostat(TIntegrator* i, int order):Modifier(order),myTheIntegrator(i){}$/;" f class:ProtoMol::ModifierPreForceBarostat ModifierPreForceBarostat framework/integrators/ModifierPreForceBarostat.h /^ class ModifierPreForceBarostat : public Modifier {$/;" c namespace:ProtoMol ModifierPreForceThermostat framework/integrators/ModifierPreForceThermostat.h /^ ModifierPreForceThermostat(TIntegrator* i):Modifier(Constant::MAX_INT-400),myTheIntegrator(i){}$/;" f class:ProtoMol::ModifierPreForceThermostat ModifierPreForceThermostat framework/integrators/ModifierPreForceThermostat.h /^ ModifierPreForceThermostat(TIntegrator* i, int order):Modifier(order),myTheIntegrator(i){}$/;" f class:ProtoMol::ModifierPreForceThermostat ModifierPreForceThermostat framework/integrators/ModifierPreForceThermostat.h /^ class ModifierPreForceThermostat : public Modifier {$/;" c namespace:ProtoMol ModifierRattle framework/integrators/ModifierRattle.cpp /^ ModifierRattle::ModifierRattle(Real eps, int maxIter,const Integrator* i, int order):ModifierMetaRattle(eps,maxIter,order),myTheIntegrator(i){}$/;" f class:ProtoMol::ModifierRattle ModifierRattle framework/integrators/ModifierRattle.h /^ class ModifierRattle : public ModifierMetaRattle {$/;" c namespace:ProtoMol ModifierRemoveAngularMomentum framework/integrators/ModifierRemoveAngularMomentum.h /^ ModifierRemoveAngularMomentum(int freq):Modifier(Constant::MAX_INT-200),myStep(0),myFreq(freq){}$/;" f class:ProtoMol::ModifierRemoveAngularMomentum ModifierRemoveAngularMomentum framework/integrators/ModifierRemoveAngularMomentum.h /^ class ModifierRemoveAngularMomentum : public Modifier {$/;" c namespace:ProtoMol ModifierRemoveLinearMomentum framework/integrators/ModifierRemoveLinearMomentum.h /^ ModifierRemoveLinearMomentum(int freq):Modifier(Constant::MAX_INT-100),myStep(0),myFreq(freq){}$/;" f class:ProtoMol::ModifierRemoveLinearMomentum ModifierRemoveLinearMomentum framework/integrators/ModifierRemoveLinearMomentum.h /^ class ModifierRemoveLinearMomentum : public Modifier {$/;" c namespace:ProtoMol ModifierShadow framework/integrators/ModifierShadow.cpp /^ ModifierShadow::ModifierShadow( int order2k, int freq,$/;" f class:ProtoMol::ModifierShadow ModifierShadow framework/integrators/ModifierShadow.h /^ class ModifierShadow : public Modifier {$/;" c namespace:ProtoMol ModifierShake framework/integrators/ModifierShake.cpp /^ ModifierShake::ModifierShake(Real eps, int maxIter,const Integrator* i, int order):ModifierMetaShake(eps,maxIter,order),myTheIntegrator(i){}$/;" f class:ProtoMol::ModifierShake ModifierShake framework/integrators/ModifierShake.h /^ class ModifierShake : public ModifierMetaShake {$/;" c namespace:ProtoMol Molecule framework/base/Molecule.h /^ Molecule():mass(0.0),position(0.0,0.0,0.0),momentum(0.0,0.0,0.0),water(false),$/;" f struct:ProtoMol::Molecule Molecule framework/base/Molecule.h /^ struct Molecule {$/;" s namespace:ProtoMol MollyForce framework/forces/MollyForce.h /^ MollyForce():Force(){}$/;" f class:ProtoMol::MollyForce MollyForce framework/forces/MollyForce.h /^ class MollyForce : public Force {$/;" c namespace:ProtoMol MultiGrid framework/base/MultiGrid.h /^ MultiGrid::MultiGrid(): $/;" f class:ProtoMol::MultiGrid MultiGrid framework/base/MultiGrid.h /^ class MultiGrid {$/;" c namespace:ProtoMol MyStreamer framework/base/Report.cpp /^ MyStreamer::MyStreamer(ostream* a) {$/;" f class:ProtoMol::Report::MyStreamer MyStreamer framework/base/Report.h /^ class MyStreamer {$/;" c namespace:ProtoMol::Report N framework/base/LookUpTableBase.h /^ enum{N=(1< N framework/base/mathutilities.h /^ enum {N = 1+BinaryExponentHelper::N};$/;" e class:ProtoMol::Private::BinaryExponentHelper::::A N framework/base/mathutilities.h /^ enum {N = 1+BinaryExponentHelper::N};$/;" e enum:ProtoMol::Private::BinaryExponentHelper:: N framework/base/mathutilities.h /^ enum {N=1};$/;" e enum:ProtoMol::Private::BinaryExponentHelper:: N framework/base/mathutilities.h /^ enum {N=Private::BinaryExponentHelper

::N};$/;" e class:ProtoMol::BinaryExponent::::P N framework/base/mathutilities.h /^ enum {N=Private::BinaryExponentHelper

::N};$/;" e enum:ProtoMol::BinaryExponent:: NBFIX framework/io/PARReader.h /^ NBFIX,$/;" e enum:ProtoMol::PARReader::PARRecordTypeEnum NEED_RANGE framework/parallel/Parallel-FD.cpp /^ const int NEED_RANGE = 1;$/;" v NEED_RANGE framework/parallel/Parallel.cpp /^ const int NEED_RANGE = 1;$/;" v NEGATIVE framework/base/ConstraintValueType.h /^ NEGATIVE,$/;" e enum:ProtoMol::ConstraintValueEnum::Enum NOCONSTRAINTS framework/base/ConstraintValueType.h /^ NOCONSTRAINTS,$/;" e enum:ProtoMol::ConstraintValueEnum::Enum NONBONDED framework/io/PARReader.h /^ NONBONDED,$/;" e enum:ProtoMol::PARReader::PARRecordTypeEnum NONBONDEDCUTOFFFORCEBASE_H framework/forces/NonbondedCutoffForceBase.h 3;" d NONBONDEDCUTOFFFORCE_H framework/forces/NonbondedCutoffForce.h 3;" d NONBONDEDCUTOFFMOLLYFORCE_H framework/forces/NonbondedCutoffMollyForce.h 3;" d NONBONDEDCUTOFFSYSTEMFORCE_H framework/forces/NonbondedCutoffSystemForce.h 3;" d NONBONDEDFULLEWALDSYSTEMFORCEBASE_H framework/forces/NonbondedFullEwaldSystemForceBase.h 3;" d NONBONDEDFULLEWALDSYSTEMFORCE_H framework/forces/NonbondedFullEwaldSystemForce.h 3;" d NONBONDEDFULLSYSTEMFORCEBASE_H framework/forces/NonbondedFullSystemForceBase.h 3;" d NONBONDEDFULLSYSTEMFORCE_H framework/forces/NonbondedFullSystemForce.h 3;" d NONBONDEDMULTIGRIDSYSTEMFORCEBASE_H framework/forces/NonbondedMultiGridSystemForceBase.h 3;" d NONBONDEDMULTIGRIDSYSTEMFORCE_H framework/forces/NonbondedMultiGridSystemForce.h 3;" d NONBONDEDPMEWALDSYSTEMFORCEBASE_H framework/forces/NonbondedPMEwaldSystemForceBase.h 3;" d NONBONDEDPMEWALDSYSTEMFORCE_H framework/forces/NonbondedPMEwaldSystemForce.h 3;" d NONBONDEDSIMPLEFULLSYSTEMFORCEBASE_H framework/forces/NonbondedSimpleFullSystemForceBase.h 3;" d NONBONDEDSIMPLEFULLSYSTEMFORCE_H framework/forces/NonbondedSimpleFullSystemForce.h 3;" d NONE framework/topology/ExclusionType.h /^ NONE, \/\/\/< no exclusions at all$/;" e enum:ProtoMol::ExclusionEnum::Enum NONSTANDARDINTEGRATOR_H framework/integrators/NonStandardIntegrator.h 3;" d NOSENVTLEAPFROGINTEGRATOR_H framework/integrators/NoseNVTLeapfrogIntegrator.h 3;" d NOTEMPTY framework/base/ConstraintValueType.h /^ NOTEMPTY,$/;" e enum:ProtoMol::ConstraintValueEnum::Enum NOTNEGATIVE framework/base/ConstraintValueType.h /^ NOTNEGATIVE,$/;" e enum:ProtoMol::ConstraintValueEnum::Enum NOTPOSITIVE framework/base/ConstraintValueType.h /^ NOTPOSITIVE,$/;" e enum:ProtoMol::ConstraintValueEnum::Enum NOTZERO framework/base/ConstraintValueType.h /^ NOTZERO,$/;" e enum:ProtoMol::ConstraintValueEnum::Enum NOT_VISITED framework/topology/AngleInfo.h /^ NOT_VISITED = 10002};$/;" e enum:ProtoMol::AngleInfo::AngleType NPTVERLETINTEGRATOR_H framework/integrators/NPTVerletIntegrator.h 3;" d NPTVerletIntegrator framework/integrators/NPTVerletIntegrator.cpp /^ NPTVerletIntegrator::NPTVerletIntegrator(): STSIntegrator(),$/;" f class:ProtoMol::NPTVerletIntegrator NPTVerletIntegrator framework/integrators/NPTVerletIntegrator.cpp /^ NPTVerletIntegrator::NPTVerletIntegrator(Real timestep,$/;" f class:ProtoMol::NPTVerletIntegrator NPTVerletIntegrator framework/integrators/NPTVerletIntegrator.h /^ class NPTVerletIntegrator: public STSIntegrator {$/;" c namespace:ProtoMol NUMSW framework/topology/CnSwitchingFunction.h 21;" d NUMSWCM framework/topology/CmpCnCnSwitchingFunction.h 21;" d NV framework/base/LookUpTableBase.h /^ enum{NV=4};$/;" e enum:ProtoMol::LookUpTableBase:: NVT framework/integrators/PaulTrapIntegrator.h /^ NVT,$/;" e enum:ProtoMol::ThermostatEnum::Enum NVTVERLETINTEGRATOR_H framework/integrators/NVTVerletIntegrator.h 3;" d NVTVerletIntegrator framework/integrators/NVTVerletIntegrator.cpp /^ NVTVerletIntegrator::NVTVerletIntegrator(): STSIntegrator(),$/;" f class:ProtoMol::NVTVerletIntegrator NVTVerletIntegrator framework/integrators/NVTVerletIntegrator.cpp /^ NVTVerletIntegrator::NVTVerletIntegrator(Real timestep,$/;" f class:ProtoMol::NVTVerletIntegrator NVTVerletIntegrator framework/integrators/NVTVerletIntegrator.h /^ class NVTVerletIntegrator: public STSIntegrator {$/;" c namespace:ProtoMol NVT_GLOBAL framework/integrators/PaulTrapIntegrator.h /^ NVT_GLOBAL,$/;" e enum:ProtoMol::ThermostatEnum::Enum NVT_IND framework/integrators/PaulTrapIntegrator.h /^ NVT_IND,$/;" e enum:ProtoMol::ThermostatEnum::Enum NVT_SHELL framework/integrators/PaulTrapIntegrator.h /^ NVT_SHELL,$/;" e enum:ProtoMol::ThermostatEnum::Enum NVT_ZERO framework/integrators/PaulTrapIntegrator.h /^ NVT_ZERO,$/;" e enum:ProtoMol::ThermostatEnum::Enum Nbfix framework/base/PAR.h /^ Nbfix(){}$/;" f struct:ProtoMol::PAR::Nbfix Nbfix framework/base/PAR.h /^ Nbfix(int a_, std::string b_, std::string c, Real d, Real e, Real f, Real g):number(a_),atom1(b_),atom2(c),a(d),b(e),a14(f),b14(g){}$/;" f struct:ProtoMol::PAR::Nbfix Nbfix framework/base/PAR.h /^ struct Nbfix{$/;" s class:ProtoMol::PAR Negative framework/base/ConstraintValueType.h /^ typedef Enum2Type Negative;$/;" t class:ProtoMol::ConstraintValueEnum Ngrp framework/base/PSF.h /^ Ngrp():number(0),atom1(0),atom2(0),atom3(0){}$/;" f struct:ProtoMol::PSF::Ngrp Ngrp framework/base/PSF.h /^ Ngrp(int a, int b, int c, int d):number(a),atom1(b),atom2(c),atom3(d){}$/;" f struct:ProtoMol::PSF::Ngrp Ngrp framework/base/PSF.h /^ struct Ngrp {$/;" s class:ProtoMol::PSF NoConstraint framework/forces/oneAtomContraints.h /^ struct NoConstraint {$/;" s namespace:ProtoMol NoConstraints framework/base/ConstraintValueType.h /^ typedef Enum2Type NoConstraints;$/;" t class:ProtoMol::ConstraintValueEnum NonStandardIntegrator framework/integrators/NonStandardIntegrator.h /^ NonStandardIntegrator(){};$/;" f class:ProtoMol::NonStandardIntegrator NonStandardIntegrator framework/integrators/NonStandardIntegrator.h /^ NonStandardIntegrator(ForceGroup* forceGroup):Integrator(forceGroup){};$/;" f class:ProtoMol::NonStandardIntegrator NonStandardIntegrator framework/integrators/NonStandardIntegrator.h /^ class NonStandardIntegrator: public Integrator {$/;" c namespace:ProtoMol Nonbonded framework/base/PAR.h /^ Nonbonded(){}$/;" f struct:ProtoMol::PAR::Nonbonded Nonbonded framework/base/PAR.h /^ Nonbonded(int a, std::string b, Real c, Real d, Real e, bool f, bool g, Real h, Real i, Real j, bool k):$/;" f struct:ProtoMol::PAR::Nonbonded Nonbonded framework/base/PAR.h /^ struct Nonbonded{$/;" s class:ProtoMol::PAR Nonbonded framework/base/PSF.h /^ Nonbonded():number(0),atom1(0){}$/;" f struct:ProtoMol::PSF::Nonbonded Nonbonded framework/base/PSF.h /^ Nonbonded(int a, int b):number(a),atom1(b){}$/;" f struct:ProtoMol::PSF::Nonbonded Nonbonded framework/base/PSF.h /^ struct Nonbonded {$/;" s class:ProtoMol::PSF NonbondedCutoffForce framework/forces/NonbondedCutoffForce.h /^ NonbondedCutoffForce():myCutoff(0.0){}$/;" f class:ProtoMol::NonbondedCutoffForce NonbondedCutoffForce framework/forces/NonbondedCutoffForce.h /^ NonbondedCutoffForce(Real cutoff, TOneAtomPair oneAtomPair) : $/;" f class:ProtoMol::NonbondedCutoffForce NonbondedCutoffForce framework/forces/NonbondedCutoffForce.h /^ class NonbondedCutoffForce: public TForce, private NonbondedCutoffForceBase {$/;" c namespace:ProtoMol NonbondedCutoffForceBase framework/forces/NonbondedCutoffForceBase.h /^ class NonbondedCutoffForceBase {$/;" c namespace:ProtoMol NonbondedCutoffMollyForce framework/forces/NonbondedCutoffMollyForce.h /^ NonbondedCutoffMollyForce():NonbondedCutoffForce(){}$/;" f class:ProtoMol::NonbondedCutoffMollyForce NonbondedCutoffMollyForce framework/forces/NonbondedCutoffMollyForce.h /^ NonbondedCutoffMollyForce(Real cutoff, TOneAtomPair oneAtomPair) : NonbondedCutoffForce(cutoff,oneAtomPair) {}$/;" f class:ProtoMol::NonbondedCutoffMollyForce NonbondedCutoffMollyForce framework/forces/NonbondedCutoffMollyForce.h /^ class NonbondedCutoffMollyForce: public NonbondedCutoffForce > {$/;" c namespace:ProtoMol NonbondedCutoffSystemForce framework/forces/NonbondedCutoffSystemForce.h /^ NonbondedCutoffSystemForce() : $/;" f class:ProtoMol::NonbondedCutoffSystemForce NonbondedCutoffSystemForce framework/forces/NonbondedCutoffSystemForce.h /^ NonbondedCutoffSystemForce(Real cutoff, TOneAtomPair oneAtomPair) : $/;" f class:ProtoMol::NonbondedCutoffSystemForce NonbondedCutoffSystemForce framework/forces/NonbondedCutoffSystemForce.h /^ class NonbondedCutoffSystemForce: public NonbondedCutoffForce > {$/;" c namespace:ProtoMol NonbondedFullEwaldSystemForce framework/forces/NonbondedFullEwaldSystemForce.h /^ TSwitchingFunction>::NonbondedFullEwaldSystemForce() $/;" f class:ProtoMol::NonbondedFullEwaldSystemForce NonbondedFullEwaldSystemForce framework/forces/NonbondedFullEwaldSystemForce.h /^ TSwitchingFunction>::NonbondedFullEwaldSystemForce(Real alpha, Real accuracy, Real expansionFactor)$/;" f class:ProtoMol::NonbondedFullEwaldSystemForce NonbondedFullEwaldSystemForce framework/forces/NonbondedFullEwaldSystemForce.h /^ class NonbondedFullEwaldSystemForce: public SystemForce, private NonbondedFullEwaldSystemForceBase {$/;" c namespace:ProtoMol NonbondedFullEwaldSystemForceBase framework/forces/NonbondedFullEwaldSystemForceBase.h /^ class NonbondedFullEwaldSystemForceBase {$/;" c namespace:ProtoMol NonbondedFullSystemForce framework/forces/NonbondedFullSystemForce.h /^ NonbondedFullSystemForce(): SystemForce(),myCutoff(0.0),myBlockSize(0){};$/;" f class:ProtoMol::NonbondedFullSystemForce NonbondedFullSystemForce framework/forces/NonbondedFullSystemForce.h /^ NonbondedFullSystemForce(Real cutoff, TOneAtomPair oneAtomPair, unsigned int blockSize = defaultBlockSize) :$/;" f class:ProtoMol::NonbondedFullSystemForce NonbondedFullSystemForce framework/forces/NonbondedFullSystemForce.h /^ class NonbondedFullSystemForce: public SystemForce, private NonbondedFullSystemForceBase {$/;" c namespace:ProtoMol NonbondedFullSystemForceBase framework/forces/NonbondedFullSystemForceBase.h /^ class NonbondedFullSystemForceBase {$/;" c namespace:ProtoMol NonbondedMultiGridSystemForce framework/forces/NonbondedMultiGridSystemForce.h /^ smooth>::NonbondedMultiGridSystemForce() : $/;" f class:ProtoMol::NonbondedMultiGridSystemForce NonbondedMultiGridSystemForce framework/forces/NonbondedMultiGridSystemForce.h /^ smooth>::NonbondedMultiGridSystemForce(unsigned int nx, $/;" f class:ProtoMol::NonbondedMultiGridSystemForce NonbondedMultiGridSystemForce framework/forces/NonbondedMultiGridSystemForce.h /^ class NonbondedMultiGridSystemForce: public SystemForce, private NonbondedMultiGridSystemForceBase {$/;" c namespace:ProtoMol NonbondedMultiGridSystemForceBase framework/forces/NonbondedMultiGridSystemForceBase.h /^ class NonbondedMultiGridSystemForceBase {$/;" c namespace:ProtoMol NonbondedPMEwaldSystemForce framework/forces/NonbondedPMEwaldSystemForce.h /^ TSwitchingFunction>::NonbondedPMEwaldSystemForce() : SystemForce(),myCached(false),myExpansionFactor(3.0),myTRate(0.0),myAccuracy(0.0),myAlpha(-1.0),myAlphaDefault(true),myRc(0.0),myKc(0.0),myV(-1.0),myNX(0),myNY(0),myNZ(0),myInterOrder(0) {$/;" f class:ProtoMol::NonbondedPMEwaldSystemForce NonbondedPMEwaldSystemForce framework/forces/NonbondedPMEwaldSystemForce.h /^ TSwitchingFunction>::NonbondedPMEwaldSystemForce(unsigned int nx, unsigned int ny, unsigned int nz, unsigned int order, Real cutoff, Real accuracy, Real alpha, Real expansionFactor) : SystemForce(),myCached(false),myExpansionFactor(expansionFactor),myTRate(0.0),myAccuracy(accuracy),myAlpha(alpha),myAlphaDefault(alpha<= 0.0),myRc(cutoff),myKc(0.0),myV(-1.0),myNX(nx),myNY(ny),myNZ(nz),myInterOrder(order){$/;" f class:ProtoMol::NonbondedPMEwaldSystemForce NonbondedPMEwaldSystemForce framework/forces/NonbondedPMEwaldSystemForce.h /^ class NonbondedPMEwaldSystemForce: public SystemForce, private NonbondedPMEwaldSystemForceBase {$/;" c namespace:ProtoMol NonbondedPMEwaldSystemForceBase framework/forces/NonbondedPMEwaldSystemForceBase.h /^ class NonbondedPMEwaldSystemForceBase {$/;" c namespace:ProtoMol NonbondedSimpleFullSystemForce framework/forces/NonbondedSimpleFullSystemForce.h /^ NonbondedSimpleFullSystemForce(): SystemForce(),myBlockSize(0),myCached(false){}; $/;" f class:ProtoMol::NonbondedSimpleFullSystemForce NonbondedSimpleFullSystemForce framework/forces/NonbondedSimpleFullSystemForce.h /^ NonbondedSimpleFullSystemForce(TOneAtomPair oneAtomPair, unsigned int blockSize = defaultBlockSize) : $/;" f class:ProtoMol::NonbondedSimpleFullSystemForce NonbondedSimpleFullSystemForce framework/forces/NonbondedSimpleFullSystemForce.h /^ class NonbondedSimpleFullSystemForce: public SystemForce, private NonbondedSimpleFullSystemForceBase {$/;" c namespace:ProtoMol NonbondedSimpleFullSystemForceBase framework/forces/NonbondedSimpleFullSystemForceBase.h /^ class NonbondedSimpleFullSystemForceBase {$/;" c namespace:ProtoMol NoseNVTLeapfrogIntegrator framework/integrators/NoseNVTLeapfrogIntegrator.cpp /^ NoseNVTLeapfrogIntegrator::NoseNVTLeapfrogIntegrator(): STSIntegrator(),$/;" f class:ProtoMol::NoseNVTLeapfrogIntegrator NoseNVTLeapfrogIntegrator framework/integrators/NoseNVTLeapfrogIntegrator.cpp /^ NoseNVTLeapfrogIntegrator::NoseNVTLeapfrogIntegrator(Real timestep,$/;" f class:ProtoMol::NoseNVTLeapfrogIntegrator NoseNVTLeapfrogIntegrator framework/integrators/NoseNVTLeapfrogIntegrator.h /^ class NoseNVTLeapfrogIntegrator : public STSIntegrator {$/;" c namespace:ProtoMol NotEmpty framework/base/ConstraintValueType.h /^ typedef Enum2Type NotEmpty;$/;" t class:ProtoMol::ConstraintValueEnum NotNegative framework/base/ConstraintValueType.h /^ typedef Enum2Type NotNegative;$/;" t class:ProtoMol::ConstraintValueEnum NotPositive framework/base/ConstraintValueType.h /^ typedef Enum2Type NotPositive;$/;" t class:ProtoMol::ConstraintValueEnum NotSameMoleculeConstraint framework/forces/oneAtomContraints.h /^ struct NotSameMoleculeConstraint {$/;" s namespace:ProtoMol NotZero framework/base/ConstraintValueType.h /^ typedef Enum2Type NotZero;$/;" t class:ProtoMol::ConstraintValueEnum NumAtoms framework/integrators/NPTVerletIntegrator.h /^ unsigned int NumAtoms; \/\/ Total # of atoms in the system.$/;" m class:ProtoMol::NPTVerletIntegrator NumAtoms framework/integrators/NVTVerletIntegrator.h /^ unsigned int NumAtoms; \/\/ Total # of atoms in the system.$/;" m class:ProtoMol::NVTVerletIntegrator OBJECTDEFINITION_H framework/base/ObjectDefinition.h 3;" d ONE2 framework/topology/ExclusionType.h /^ ONE2, \/\/\/< exclude 1. neighbors$/;" e enum:ProtoMol::ExclusionEnum::Enum ONE3 framework/topology/ExclusionType.h /^ ONE3, \/\/\/< exclude 1. and 2. neighbors$/;" e enum:ProtoMol::ExclusionEnum::Enum ONE4 framework/topology/ExclusionType.h /^ ONE4, \/\/\/< exclude 1., 2. and 3. neighbors$/;" e enum:ProtoMol::ExclusionEnum::Enum ONE4MODIFIED framework/topology/ExclusionType.h /^ ONE4MODIFIED, \/\/\/< exclude 1. and 2. and modify 3. neighbors$/;" e enum:ProtoMol::ExclusionEnum::Enum ONEATOMCONSTRAINTS_H framework/forces/oneAtomContraints.h 3;" d ONEATOMPAIRFULL_H framework/forces/OneAtomPairFull.h 3;" d ONEATOMPAIRTWOFULL_H framework/forces/OneAtomPairTwoFull.h 3;" d ONEATOMPAIRTWO_H framework/forces/OneAtomPairTwo.h 3;" d ONEATOMPAIR_H framework/forces/OneAtomPair.h 3;" d ONEMOLLYPAIRTWO_H framework/forces/OneMollyPairTwo.h 3;" d ONEMOLLYPAIR_H framework/forces/OneMollyPair.h 3;" d ONLY_WATER framework/topology/topologyutilities.h /^ enum waterOption {IGNORE_WATER, ONLY_WATER, ALL};$/;" e enum:ProtoMol::waterOption OTHER framework/base/ScalarStructure.h /^ OTHER,$/;" e enum:ProtoMol::ScalarStructure::Index OUTPUTBSDL_H framework/frontend/OutputBSDL.h 3;" d OUTPUTCACHE_H framework/frontend/OutputCache.h 3;" d OUTPUTCOLLECTION_H framework/frontend/OutputCollection.h 3;" d OUTPUTDCDTRAJECTORY_H framework/frontend/OutputDCDTrajectory.h 3;" d OUTPUTDIFFUSION_H framework/frontend/OutputDiffusion.h 3;" d OUTPUTDIHEDRALS_H framework/frontend/OutputDihedrals.h 3;" d OUTPUTENERGIES_H framework/frontend/OutputEnergies.h 3;" d OUTPUTFACTORYDETAILS_H framework/frontend/OutputFactoryDetails.h 3;" d OUTPUTFACTORY_H framework/frontend/OutputFactory.h 3;" d OUTPUTFILE_H framework/frontend/OutputFile.h 3;" d OUTPUTFINALPDBPOS_H framework/frontend/OutputFinalPDBPos.h 3;" d OUTPUTFINALXYZBINPOS_H framework/frontend/OutputFinalXYZBinPos.h 3;" d OUTPUTFINALXYZBINVEL_H framework/frontend/OutputFinalXYZBinVel.h 3;" d OUTPUTFINALXYZPOS_H framework/frontend/OutputFinalXYZPos.h 3;" d OUTPUTFINALXYZVEL_H framework/frontend/OutputFinalXYZVel.h 3;" d OUTPUTMOMENTUM_H framework/frontend/OutputMomentum.h 3;" d OUTPUTPAULTRAP_H framework/frontend/OutputPaulTrap.h 3;" d OUTPUTPDBFRAMEPOS_H framework/frontend/OutputPDBFramePos.h 3;" d OUTPUTREMEXCHANGERATE_H framework/frontend/OutputREMExchangeRate.h 3;" d OUTPUTREMHISTORY_H framework/frontend/OutputREMHistory.h 3;" d OUTPUTSCREEN_H framework/frontend/OutputScreen.h 3;" d OUTPUTSTATE_H framework/frontend/OutputState.h 3;" d OUTPUTTEMPERATURES_H framework/frontend/OutputTemperatures.h 3;" d OUTPUTXYZBINTRAJECTORYPOS_H framework/frontend/OutputXYZBinTrajectoryPos.h 3;" d OUTPUTXYZBINTRAJECTORYVEL_H framework/frontend/OutputXYZBinTrajectoryVel.h 3;" d OUTPUTXYZTRAJECTORYFORCE_H framework/frontend/OutputXYZTrajectoryForce.h 3;" d OUTPUTXYZTRAJECTORYPOS_H framework/frontend/OutputXYZTrajectoryPos.h 3;" d OUTPUTXYZTRAJECTORYVEL_H framework/frontend/OutputXYZTrajectoryVel.h 3;" d OUTPUT_H framework/frontend/Output.h 3;" d ObjectDefinition framework/base/ObjectDefinition.h /^ ObjectDefinition(){}$/;" f struct:ProtoMol::ObjectDefinition ObjectDefinition framework/base/ObjectDefinition.h /^ ObjectDefinition(const std::string& i,const std::vector& p):id(i),parameters(p){}$/;" f struct:ProtoMol::ObjectDefinition ObjectDefinition framework/base/ObjectDefinition.h /^ struct ObjectDefinition {$/;" s namespace:ProtoMol OneAtomPair framework/forces/OneAtomPair.h /^ OneAtomPair(): switchingFunction(), nonbondedForceFunction(){};$/;" f class:ProtoMol::OneAtomPair OneAtomPair framework/forces/OneAtomPair.h /^ OneAtomPair(TNonbondedForce nF,$/;" f class:ProtoMol::OneAtomPair OneAtomPair framework/forces/OneAtomPair.h /^ class OneAtomPair {$/;" c namespace:ProtoMol OneAtomPairFull framework/forces/OneAtomPairFull.h /^ OneAtomPairFull(): switchingFunction(), nonbondedForceFunction(){};$/;" f class:ProtoMol::OneAtomPairFull OneAtomPairFull framework/forces/OneAtomPairFull.h /^ OneAtomPairFull(TNonbondedForce nF,$/;" f class:ProtoMol::OneAtomPairFull OneAtomPairFull framework/forces/OneAtomPairFull.h /^ class OneAtomPairFull {$/;" c namespace:ProtoMol OneAtomPairTwo framework/forces/OneAtomPairTwo.h /^ OneAtomPairTwo(){}$/;" f class:ProtoMol::OneAtomPairTwo OneAtomPairTwo framework/forces/OneAtomPairTwo.h /^ OneAtomPairTwo(TNonbondedForceFirst f1, $/;" f class:ProtoMol::OneAtomPairTwo OneAtomPairTwo framework/forces/OneAtomPairTwo.h /^ class OneAtomPairTwo {$/;" c namespace:ProtoMol OneAtomPairTwoFull framework/forces/OneAtomPairTwoFull.h /^ OneAtomPairTwoFull(){}$/;" f class:ProtoMol::OneAtomPairTwoFull OneAtomPairTwoFull framework/forces/OneAtomPairTwoFull.h /^ OneAtomPairTwoFull(TNonbondedForceFirst f1, $/;" f class:ProtoMol::OneAtomPairTwoFull OneAtomPairTwoFull framework/forces/OneAtomPairTwoFull.h /^ class OneAtomPairTwoFull {$/;" c namespace:ProtoMol OneMollyPair framework/forces/OneMollyPair.h /^ OneMollyPair(): switchingFunction(), nonbondedForceFunction(){};$/;" f class:ProtoMol::OneMollyPair OneMollyPair framework/forces/OneMollyPair.h /^ OneMollyPair(TNonbondedForce nF,$/;" f class:ProtoMol::OneMollyPair OneMollyPair framework/forces/OneMollyPair.h /^ class OneMollyPair {$/;" c namespace:ProtoMol OneMollyPairTwo framework/forces/OneMollyPairTwo.h /^ OneMollyPairTwo(){}$/;" f class:ProtoMol::OneMollyPairTwo OneMollyPairTwo framework/forces/OneMollyPairTwo.h /^ OneMollyPairTwo(TNonbondedForceFirst f1, $/;" f class:ProtoMol::OneMollyPairTwo OneMollyPairTwo framework/forces/OneMollyPairTwo.h /^ class OneMollyPairTwo {$/;" c namespace:ProtoMol Output framework/frontend/Output.cpp /^ Output::Output(int freq):Makeable(),$/;" f class:ProtoMol::Output Output framework/frontend/Output.cpp /^ Output::Output():Makeable(),$/;" f class:ProtoMol::Output Output framework/frontend/Output.h /^ class Output : public Makeable {$/;" c namespace:ProtoMol OutputBSDL framework/frontend/OutputBSDL.cpp /^ OutputBSDL::OutputBSDL():Output(),myFilename(""),myMinimalImage(false),myIncludeView(true),myWater(true),myCounter(0),myScale(1.0),myMolecularDistance(false){}$/;" f class:ProtoMol::OutputBSDL OutputBSDL framework/frontend/OutputBSDL.cpp /^ OutputBSDL::OutputBSDL(const string& filename, int freq, bool minimal, bool include, bool water):Output(freq),myFilename(filename),myMinimalImage(minimal),myIncludeView(include),myWater(water),myCounter(0),myScale(1.0),myMolecularDistance(false){}$/;" f class:ProtoMol::OutputBSDL OutputBSDL framework/frontend/OutputBSDL.h /^ class OutputBSDL : public Output {$/;" c namespace:ProtoMol OutputCache framework/frontend/OutputCache.cpp /^ OutputCache::OutputCache():myConfig(NULL), $/;" f class:ProtoMol::OutputCache OutputCache framework/frontend/OutputCache.h /^ class OutputCache {$/;" c namespace:ProtoMol OutputCollection framework/frontend/OutputCollection.cpp /^ OutputCollection::OutputCollection():myCache(new OutputCache()),$/;" f class:ProtoMol::OutputCollection OutputCollection framework/frontend/OutputCollection.h /^ class OutputCollection {$/;" c namespace:ProtoMol OutputDCDTrajectory framework/frontend/OutputDCDTrajectory.cpp /^ OutputDCDTrajectory::OutputDCDTrajectory():Output(),myDCD(NULL),myMinimalImage(false){}$/;" f class:ProtoMol::OutputDCDTrajectory OutputDCDTrajectory framework/frontend/OutputDCDTrajectory.cpp /^ OutputDCDTrajectory::OutputDCDTrajectory(const string& filename, int freq, bool minimal):Output(freq),myDCD(new DCDTrajectoryWriter(filename)),myMinimalImage(minimal){}$/;" f class:ProtoMol::OutputDCDTrajectory OutputDCDTrajectory framework/frontend/OutputDCDTrajectory.h /^ class OutputDCDTrajectory : public Output {$/;" c namespace:ProtoMol OutputDiffusion framework/frontend/OutputDiffusion.cpp /^ OutputDiffusion::OutputDiffusion(): OutputFile(){}$/;" f class:ProtoMol::OutputDiffusion OutputDiffusion framework/frontend/OutputDiffusion.cpp /^ OutputDiffusion::OutputDiffusion(const string& filename, $/;" f class:ProtoMol::OutputDiffusion OutputDiffusion framework/frontend/OutputDiffusion.h /^ class OutputDiffusion : public OutputFile {$/;" c namespace:ProtoMol OutputDihedrals framework/frontend/OutputDihedrals.cpp /^ OutputDihedrals::OutputDihedrals(): OutputFile(),$/;" f class:ProtoMol::OutputDihedrals OutputDihedrals framework/frontend/OutputDihedrals.cpp /^ OutputDihedrals::OutputDihedrals(const string& filename, $/;" f class:ProtoMol::OutputDihedrals OutputDihedrals framework/frontend/OutputDihedrals.h /^ class OutputDihedrals : public OutputFile {$/;" c namespace:ProtoMol OutputEnergies framework/frontend/OutputEnergies.cpp /^ OutputEnergies::OutputEnergies():OutputFile(),myDoMolecularTemperature(false),myDoShadow(false){}$/;" f class:ProtoMol::OutputEnergies OutputEnergies framework/frontend/OutputEnergies.cpp /^ OutputEnergies::OutputEnergies(const string& filename, int freq, int cacheFreq, int cacheSize, Real closeTime, bool doMolTemp, bool doShadow):OutputFile(filename,freq,cacheFreq,cacheSize,closeTime),myDoMolecularTemperature(doMolTemp),myDoShadow(doShadow){}$/;" f class:ProtoMol::OutputEnergies OutputEnergies framework/frontend/OutputEnergies.h /^ class OutputEnergies : public OutputFile {$/;" c namespace:ProtoMol OutputFactory framework/frontend/OutputFactory.h /^ typedef Factory OutputFactory;$/;" t namespace:ProtoMol OutputFactoryDetails framework/frontend/OutputFactoryDetails.cpp /^ OutputFactoryDetails::OutputFactoryDetails():FactoryBase(){$/;" f class:ProtoMol::OutputFactoryDetails OutputFactoryDetails framework/frontend/OutputFactoryDetails.cpp /^ OutputFactoryDetails::OutputFactoryDetails(const OutputFactoryDetails&){}$/;" f class:ProtoMol::OutputFactoryDetails OutputFactoryDetails framework/frontend/OutputFactoryDetails.h /^ class OutputFactoryDetails : public FactoryBase {$/;" c namespace:ProtoMol OutputFile framework/frontend/OutputFile.cpp /^ OutputFile::OutputFile():Output(),myFilename(""),myCacheFreq(0),myCount(0),myCacheSize(0),myCloseTime(0.0){}$/;" f class:ProtoMol::OutputFile OutputFile framework/frontend/OutputFile.cpp /^ OutputFile::OutputFile(const string& filename, $/;" f class:ProtoMol::OutputFile OutputFile framework/frontend/OutputFile.h /^ class OutputFile : public Output {$/;" c namespace:ProtoMol OutputFinalPDBPos framework/frontend/OutputFinalPDBPos.cpp /^ OutputFinalPDBPos::OutputFinalPDBPos():Output(1),myFilename(""),myMinimalImage(false){}$/;" f class:ProtoMol::OutputFinalPDBPos OutputFinalPDBPos framework/frontend/OutputFinalPDBPos.cpp /^ OutputFinalPDBPos::OutputFinalPDBPos(const string& filename, bool minimal):Output(1),myFilename(filename),myMinimalImage(minimal){}$/;" f class:ProtoMol::OutputFinalPDBPos OutputFinalPDBPos framework/frontend/OutputFinalPDBPos.h /^ class OutputFinalPDBPos : public Output {$/;" c namespace:ProtoMol OutputFinalXYZBinPos framework/frontend/OutputFinalXYZBinPos.cpp /^ OutputFinalXYZBinPos::OutputFinalXYZBinPos():Output(1),myFilename(""),myMinimalImage(false){}$/;" f class:ProtoMol::OutputFinalXYZBinPos OutputFinalXYZBinPos framework/frontend/OutputFinalXYZBinPos.cpp /^ OutputFinalXYZBinPos::OutputFinalXYZBinPos(const string& filename, bool minimal):Output(1),myFilename(filename),myMinimalImage(minimal){}$/;" f class:ProtoMol::OutputFinalXYZBinPos OutputFinalXYZBinPos framework/frontend/OutputFinalXYZBinPos.h /^ class OutputFinalXYZBinPos : public Output {$/;" c namespace:ProtoMol OutputFinalXYZBinVel framework/frontend/OutputFinalXYZBinVel.cpp /^ OutputFinalXYZBinVel::OutputFinalXYZBinVel():Output(1),myFilename(""){}$/;" f class:ProtoMol::OutputFinalXYZBinVel OutputFinalXYZBinVel framework/frontend/OutputFinalXYZBinVel.cpp /^ OutputFinalXYZBinVel::OutputFinalXYZBinVel(const string& filename):Output(1),myFilename(filename){}$/;" f class:ProtoMol::OutputFinalXYZBinVel OutputFinalXYZBinVel framework/frontend/OutputFinalXYZBinVel.h /^ class OutputFinalXYZBinVel : public Output {$/;" c namespace:ProtoMol OutputFinalXYZPos framework/frontend/OutputFinalXYZPos.cpp /^ OutputFinalXYZPos::OutputFinalXYZPos():Output(1),myFilename(""),myMinimalImage(false){}$/;" f class:ProtoMol::OutputFinalXYZPos OutputFinalXYZPos framework/frontend/OutputFinalXYZPos.cpp /^ OutputFinalXYZPos::OutputFinalXYZPos(const string& filename, bool minimal):Output(1),myFilename(filename),myMinimalImage(minimal){}$/;" f class:ProtoMol::OutputFinalXYZPos OutputFinalXYZPos framework/frontend/OutputFinalXYZPos.h /^ class OutputFinalXYZPos : public Output {$/;" c namespace:ProtoMol OutputFinalXYZVel framework/frontend/OutputFinalXYZVel.cpp /^ OutputFinalXYZVel::OutputFinalXYZVel():Output(1),myFilename(""){}$/;" f class:ProtoMol::OutputFinalXYZVel OutputFinalXYZVel framework/frontend/OutputFinalXYZVel.cpp /^ OutputFinalXYZVel::OutputFinalXYZVel(const string& filename):Output(1),myFilename(filename){}$/;" f class:ProtoMol::OutputFinalXYZVel OutputFinalXYZVel framework/frontend/OutputFinalXYZVel.h /^ class OutputFinalXYZVel : public Output {$/;" c namespace:ProtoMol OutputMomentum framework/frontend/OutputMomentum.cpp /^ OutputMomentum::OutputMomentum(): OutputFile(){}$/;" f class:ProtoMol::OutputMomentum OutputMomentum framework/frontend/OutputMomentum.cpp /^ OutputMomentum::OutputMomentum(const string& filename, $/;" f class:ProtoMol::OutputMomentum OutputMomentum framework/frontend/OutputMomentum.h /^ class OutputMomentum : public OutputFile {$/;" c namespace:ProtoMol OutputPDBFramePos framework/frontend/OutputPDBFramePos.cpp /^ OutputPDBFramePos::OutputPDBFramePos():Output(),myFilename(""),myMinimalImage(false){}$/;" f class:ProtoMol::OutputPDBFramePos OutputPDBFramePos framework/frontend/OutputPDBFramePos.cpp /^ OutputPDBFramePos::OutputPDBFramePos(const string& filename, int freq, bool minimal):Output(freq),myFilename(filename),myMinimalImage(minimal){}$/;" f class:ProtoMol::OutputPDBFramePos OutputPDBFramePos framework/frontend/OutputPDBFramePos.h /^ class OutputPDBFramePos : public Output {$/;" c namespace:ProtoMol OutputPaulTrap framework/frontend/OutputPaulTrap.cpp /^ OutputPaulTrap::OutputPaulTrap()$/;" f class:ProtoMol::OutputPaulTrap OutputPaulTrap framework/frontend/OutputPaulTrap.cpp /^ OutputPaulTrap::OutputPaulTrap(const std::string& filename, int freq, int cacheFreq, int cacheSize, $/;" f class:ProtoMol::OutputPaulTrap OutputPaulTrap framework/frontend/OutputPaulTrap.h /^ class OutputPaulTrap : public OutputFile {$/;" c namespace:ProtoMol OutputREMExchangeRate framework/frontend/OutputREMExchangeRate.cpp /^ OutputREMExchangeRate::OutputREMExchangeRate(): OutputFile() {}$/;" f class:ProtoMol::OutputREMExchangeRate OutputREMExchangeRate framework/frontend/OutputREMExchangeRate.cpp /^ OutputREMExchangeRate::OutputREMExchangeRate(const string &filename, int freq, int cacheFreq, int cacheSize, Real closeTime): OutputFile(filename, freq, cacheFreq, cacheSize, closeTime) {}$/;" f class:ProtoMol::OutputREMExchangeRate OutputREMExchangeRate framework/frontend/OutputREMExchangeRate.h /^ class OutputREMExchangeRate : public OutputFile {$/;" c namespace:ProtoMol OutputREMHistoryFile framework/frontend/OutputREMHistory.cpp /^ OutputREMHistoryFile::OutputREMHistoryFile(): OutputFile() {}$/;" f class:ProtoMol::OutputREMHistoryFile OutputREMHistoryFile framework/frontend/OutputREMHistory.cpp /^ OutputREMHistoryFile::OutputREMHistoryFile(const string &filename, int freq, int cacheFreq, int cacheSize, Real closeTime): OutputFile(filename, freq, cacheFreq, cacheSize, closeTime) {}$/;" f class:ProtoMol::OutputREMHistoryFile OutputREMHistoryFile framework/frontend/OutputREMHistory.h /^ class OutputREMHistoryFile : public OutputFile {$/;" c namespace:ProtoMol OutputScreen framework/frontend/OutputScreen.cpp /^ OutputScreen::OutputScreen():Output(),myUnit("fs"),myFactor(1.0){}$/;" f class:ProtoMol::OutputScreen OutputScreen framework/frontend/OutputScreen.cpp /^ OutputScreen::OutputScreen(int freq):Output(freq),myUnit("fs"),myFactor(1.0){}$/;" f class:ProtoMol::OutputScreen OutputScreen framework/frontend/OutputScreen.h /^ class OutputScreen : public Output {$/;" c namespace:ProtoMol OutputState framework/frontend/OutputState.cpp /^ OutputState::OutputState(): OutputFile(),$/;" f class:ProtoMol::OutputState OutputState framework/frontend/OutputState.cpp /^ OutputState::OutputState(const string& filename, $/;" f class:ProtoMol::OutputState OutputState framework/frontend/OutputState.h /^ class OutputState : public OutputFile {$/;" c namespace:ProtoMol OutputTemperatures framework/frontend/OutputTemperatures.cpp /^ OutputTemperatures::OutputTemperatures():OutputFile(), mySeparateWater(true){}$/;" f class:ProtoMol::OutputTemperatures OutputTemperatures framework/frontend/OutputTemperatures.cpp /^ OutputTemperatures::OutputTemperatures(const string& filename, $/;" f class:ProtoMol::OutputTemperatures OutputTemperatures framework/frontend/OutputTemperatures.h /^ class OutputTemperatures : public OutputFile {$/;" c namespace:ProtoMol OutputXYZBinTrajectoryPos framework/frontend/OutputXYZBinTrajectoryPos.cpp /^ OutputXYZBinTrajectoryPos::OutputXYZBinTrajectoryPos():Output(),myXYZ(NULL),myMinimalImage(false){}$/;" f class:ProtoMol::OutputXYZBinTrajectoryPos OutputXYZBinTrajectoryPos framework/frontend/OutputXYZBinTrajectoryPos.cpp /^ OutputXYZBinTrajectoryPos::OutputXYZBinTrajectoryPos(const string& filename, int freq, bool minimal):Output(freq),myXYZ(new XYZBinWriter(filename)),myMinimalImage(minimal){}$/;" f class:ProtoMol::OutputXYZBinTrajectoryPos OutputXYZBinTrajectoryPos framework/frontend/OutputXYZBinTrajectoryPos.h /^ class OutputXYZBinTrajectoryPos : public Output {$/;" c namespace:ProtoMol OutputXYZBinTrajectoryVel framework/frontend/OutputXYZBinTrajectoryVel.cpp /^ OutputXYZBinTrajectoryVel::OutputXYZBinTrajectoryVel():Output(),myXYZ(){}$/;" f class:ProtoMol::OutputXYZBinTrajectoryVel OutputXYZBinTrajectoryVel framework/frontend/OutputXYZBinTrajectoryVel.cpp /^ OutputXYZBinTrajectoryVel::OutputXYZBinTrajectoryVel(const string& filename, int freq):Output(freq),myXYZ(new XYZBinWriter(filename)){}$/;" f class:ProtoMol::OutputXYZBinTrajectoryVel OutputXYZBinTrajectoryVel framework/frontend/OutputXYZBinTrajectoryVel.h /^ class OutputXYZBinTrajectoryVel : public Output {$/;" c namespace:ProtoMol OutputXYZTrajectoryForce framework/frontend/OutputXYZTrajectoryForce.cpp /^ OutputXYZTrajectoryForce::OutputXYZTrajectoryForce():Output(),myXYZ(){}$/;" f class:ProtoMol::OutputXYZTrajectoryForce OutputXYZTrajectoryForce framework/frontend/OutputXYZTrajectoryForce.cpp /^ OutputXYZTrajectoryForce::OutputXYZTrajectoryForce(const string& filename, int freq):Output(freq),myXYZ(new XYZTrajectoryWriter(filename)){}$/;" f class:ProtoMol::OutputXYZTrajectoryForce OutputXYZTrajectoryForce framework/frontend/OutputXYZTrajectoryForce.h /^ class OutputXYZTrajectoryForce : public Output {$/;" c namespace:ProtoMol OutputXYZTrajectoryPos framework/frontend/OutputXYZTrajectoryPos.cpp /^ OutputXYZTrajectoryPos::OutputXYZTrajectoryPos():Output(),myXYZ(NULL),myMinimalImage(false){}$/;" f class:ProtoMol::OutputXYZTrajectoryPos OutputXYZTrajectoryPos framework/frontend/OutputXYZTrajectoryPos.cpp /^ OutputXYZTrajectoryPos::OutputXYZTrajectoryPos(const string& filename, int freq, bool minimal):Output(freq),myXYZ(new XYZTrajectoryWriter(filename)),myMinimalImage(minimal){}$/;" f class:ProtoMol::OutputXYZTrajectoryPos OutputXYZTrajectoryPos framework/frontend/OutputXYZTrajectoryPos.h /^ class OutputXYZTrajectoryPos : public Output {$/;" c namespace:ProtoMol OutputXYZTrajectoryVel framework/frontend/OutputXYZTrajectoryVel.cpp /^ OutputXYZTrajectoryVel::OutputXYZTrajectoryVel():Output(),myXYZ(){}$/;" f class:ProtoMol::OutputXYZTrajectoryVel OutputXYZTrajectoryVel framework/frontend/OutputXYZTrajectoryVel.cpp /^ OutputXYZTrajectoryVel::OutputXYZTrajectoryVel(const string& filename, int freq):Output(freq),myXYZ(new XYZTrajectoryWriter(filename)){}$/;" f class:ProtoMol::OutputXYZTrajectoryVel OutputXYZTrajectoryVel framework/frontend/OutputXYZTrajectoryVel.h /^ class OutputXYZTrajectoryVel : public Output {$/;" c namespace:ProtoMol P framework/base/mathutilities.h /^ enum {N=Private::BinaryExponentHelper

::N};$/;" e enum:ProtoMol::BinaryExponent:: PACKAGE protomol_config.h 114;" d PACKAGE protomol_config_windows.h 10;" d PACKAGE_BUGREPORT protomol_config.h 117;" d PACKAGE_BUGREPORT protomol_config_windows.h 13;" d PACKAGE_CITE protomol_config.h 120;" d PACKAGE_CITE protomol_config_windows.h 16;" d PACKAGE_COMPILER protomol_config.h 123;" d PACKAGE_COMPILER protomol_config_windows.h 19;" d PACKAGE_COMPILER_VERSION protomol_config.h 126;" d PACKAGE_COMPILER_VERSION protomol_config_windows.h 22;" d PACKAGE_HOMEPAGE protomol_config.h 129;" d PACKAGE_HOMEPAGE protomol_config_windows.h 25;" d PACKAGE_NAME protomol_config.h 132;" d PACKAGE_NAME protomol_config_windows.h 28;" d PACKAGE_STRING protomol_config.h 135;" d PACKAGE_STRING protomol_config_windows.h 31;" d PACKAGE_TARNAME protomol_config.h 138;" d PACKAGE_TARNAME protomol_config_windows.h 34;" d PACKAGE_UNAME protomol_config.h 141;" d PACKAGE_UNAME protomol_config_windows.h 37;" d PACKAGE_VERSION protomol_config.h 144;" d PACKAGE_VERSION protomol_config_windows.h 40;" d PACKAGE_WHOAMI protomol_config.h 147;" d PACKAGE_WHOAMI protomol_config_windows.h 43;" d PAR framework/base/PAR.h /^ class PAR{$/;" c namespace:ProtoMol PARALLELTYPE_H framework/parallel/ParallelType.h 3;" d PARALLEL_H framework/parallel/Parallel.h 3;" d PARAMETER_H framework/base/Parameter.h 3;" d PARREADER_H framework/io/PARReader.h 3;" d PARReader framework/io/PARReader.cpp /^ PARReader::PARReader(PAR::CharmmTypeEnum charmmType):$/;" f class:ProtoMol::PARReader PARReader framework/io/PARReader.cpp /^ PARReader::PARReader(const char* filename, PAR::CharmmTypeEnum charmmType):$/;" f class:ProtoMol::PARReader PARReader framework/io/PARReader.cpp /^ PARReader::PARReader(const std::string& filename, PAR::CharmmTypeEnum charmmType):$/;" f class:ProtoMol::PARReader PARReader framework/io/PARReader.h /^ class PARReader : public Reader {$/;" c namespace:ProtoMol PARRecordTypeEnum framework/io/PARReader.h /^ enum PARRecordTypeEnum {$/;" g class:ProtoMol::PARReader PARSECOMMANDLINE_H framework/frontend/parseCommandLine.h 3;" d PARWRITER_H framework/io/PARWriter.h 3;" d PARWriter framework/io/PARWriter.cpp /^ PARWriter::PARWriter(PAR::CharmmTypeEnum charmmType):$/;" f class:ProtoMol::PARWriter PARWriter framework/io/PARWriter.cpp /^ PARWriter::PARWriter(const char* filename, PAR::CharmmTypeEnum charmmType):$/;" f class:ProtoMol::PARWriter PARWriter framework/io/PARWriter.cpp /^ PARWriter::PARWriter(const string& filename, PAR::CharmmTypeEnum charmmType):$/;" f class:ProtoMol::PARWriter PARWriter framework/io/PARWriter.h /^ class PARWriter : public Writer {$/;" c namespace:ProtoMol PAR_H framework/base/PAR.h 3;" d PATHSEP framework/base/systemutilities.cpp 10;" d file: PATHSEP framework/base/systemutilities.cpp 23;" d file: PATHSEPSTR framework/base/systemutilities.cpp 11;" d file: PATHSEPSTR framework/base/systemutilities.cpp 24;" d file: PAULTRAPEXTENDEDFORCEBASE_H framework/forces/PaulTrapExtendedForceBase.h 3;" d PAULTRAPEXTENDEDFORCE_H framework/forces/PaulTrapExtendedForce.h 3;" d PAULTRAPINTEGRATOR_H framework/integrators/PaulTrapIntegrator.h 3;" d PDB framework/base/PDB.h /^ PDB(){};$/;" f struct:ProtoMol::PDB PDB framework/base/PDB.h /^ PDB(size_t n):coords(n,Vector3D(0.0,0.0,0.0)),atoms(n){}$/;" f struct:ProtoMol::PDB PDB framework/base/PDB.h /^ struct PDB {$/;" s namespace:ProtoMol PDB framework/frontend/InputPosVelType.h /^ PDB,$/;" e enum:ProtoMol::InputPosVelEnum::Enum PDB tools/bccAnalyzer.cpp /^ PDB,$/;" e enum:Format::Type file: PDBREADER_H framework/io/PDBReader.h 3;" d PDBReader framework/io/PDBReader.cpp /^ PDBReader::PDBReader():$/;" f class:ProtoMol::PDBReader PDBReader framework/io/PDBReader.cpp /^ PDBReader::PDBReader(const std::string& filename):$/;" f class:ProtoMol::PDBReader PDBReader framework/io/PDBReader.h /^ class PDBReader : public Reader {$/;" c namespace:ProtoMol PDBVELSCALINGFACTOR framework/base/pmconstants.cpp /^ const Real PDBVELSCALINGFACTOR = 20.45482706;$/;" v PDBWRITER_H framework/io/PDBWriter.h 3;" d PDBWriter framework/io/PDBWriter.cpp /^ PDBWriter::PDBWriter():Writer(){}$/;" f class:ProtoMol::PDBWriter PDBWriter framework/io/PDBWriter.cpp /^ PDBWriter::PDBWriter(const string& filename):Writer(filename){}$/;" f class:ProtoMol::PDBWriter PDBWriter framework/io/PDBWriter.h /^ class PDBWriter : public Writer {$/;" c namespace:ProtoMol PDB_H framework/base/PDB.h 3;" d PERIODIC framework/topology/PeriodicBoundaryConditions.h /^ enum {PERIODIC = 1, VACUUM = 0};$/;" e enum:ProtoMol::PeriodicBoundaryConditions:: PERIODIC framework/topology/VacuumBoundaryConditions.h /^ enum {PERIODIC = 0, VACUUM = 1};$/;" e enum:ProtoMol::VacuumBoundaryConditions:: PERIODIC_BOUNDARY_TOLERANCE framework/base/pmconstants.cpp /^ const Real PERIODIC_BOUNDARY_TOLERANCE = 3.0;$/;" v PERODICBOUNDARYCONDITIONS_H framework/topology/PeriodicBoundaryConditions.h 3;" d PGM framework/base/PGM.cpp /^ PGM::PGM():w(0),h(0),p(NULL){$/;" f class:ProtoMol::PGM PGM framework/base/PGM.cpp /^ PGM::PGM(int x, int y):w(x),h(y),p(new unsigned char[x*y]){$/;" f class:ProtoMol::PGM PGM framework/base/PGM.h /^ class PGM{$/;" c namespace:ProtoMol PGMREADER_H framework/io/PGMReader.h 3;" d PGMReader framework/io/PGMReader.cpp /^ PGMReader::PGMReader():Reader(),myPGM(NULL){}$/;" f class:ProtoMol::PGMReader PGMReader framework/io/PGMReader.cpp /^ PGMReader::PGMReader(const std::string& filename):Reader(filename),myPGM(NULL){}$/;" f class:ProtoMol::PGMReader PGMReader framework/io/PGMReader.h /^ class PGMReader : public Reader {$/;" c namespace:ProtoMol PGMWRITER_H framework/io/PGMWriter.h 3;" d PGMWriter framework/io/PGMWriter.cpp /^ PGMWriter::PGMWriter():Writer(){}$/;" f class:ProtoMol::PGMWriter PGMWriter framework/io/PGMWriter.cpp /^ PGMWriter::PGMWriter(const std::string& filename):Writer(filename){}$/;" f class:ProtoMol::PGMWriter PGMWriter framework/io/PGMWriter.h /^ class PGMWriter : public Writer {$/;" c namespace:ProtoMol PGM_H framework/base/PGM.h 3;" d PLEAPFROGINTEGRATOR_H framework/integrators/PLeapfrogIntegrator.h 3;" d PLeapfrogIntegrator framework/integrators/PLeapfrogIntegrator.cpp /^ PLeapfrogIntegrator::PLeapfrogIntegrator() : STSIntegrator(),myTempForces(NULL) {}$/;" f class:ProtoMol::PLeapfrogIntegrator PLeapfrogIntegrator framework/integrators/PLeapfrogIntegrator.cpp /^ PLeapfrogIntegrator::PLeapfrogIntegrator(Real timestep,$/;" f class:ProtoMol::PLeapfrogIntegrator PLeapfrogIntegrator framework/integrators/PLeapfrogIntegrator.h /^ class PLeapfrogIntegrator : public STSIntegrator {$/;" c namespace:ProtoMol PNGWRITER_H framework/io/PNGWriter.h 3;" d PNGWriter framework/io/PNGWriter.cpp /^ PNGWriter::PNGWriter():Writer(){$/;" f class:ProtoMol::PNGWriter PNGWriter framework/io/PNGWriter.cpp /^ PNGWriter::PNGWriter(const std::string& filename):Writer(filename){$/;" f class:ProtoMol::PNGWriter PNGWriter framework/io/PNGWriter.h /^ class PNGWriter : public Writer {$/;" c namespace:ProtoMol POSITIVE framework/base/ConstraintValueType.h /^ POSITIVE,$/;" e enum:ProtoMol::ConstraintValueEnum::Enum POST_CHECK framework/forces/oneAtomContraints.h /^ enum {PRE_CHECK=0, POST_CHECK=0};$/;" e enum:ProtoMol::NoConstraint:: POST_CHECK framework/forces/oneAtomContraints.h /^ enum {PRE_CHECK=0, POST_CHECK=1};$/;" e enum:ProtoMol::DebugPostConstraint:: POST_CHECK framework/forces/oneAtomContraints.h /^ enum {PRE_CHECK=1, POST_CHECK=0};$/;" e enum:ProtoMol::DebugPreConstraint:: POST_CHECK framework/forces/oneAtomContraints.h /^ enum {PRE_CHECK=1, POST_CHECK=0};$/;" e enum:ProtoMol::HBondConstraint:: POST_CHECK framework/forces/oneAtomContraints.h /^ enum {PRE_CHECK=1, POST_CHECK=0};$/;" e enum:ProtoMol::NotSameMoleculeConstraint:: POST_CHECK framework/forces/oneAtomContraints.h /^ enum {PRE_CHECK=1, POST_CHECK=0};$/;" e enum:ProtoMol::SameMoleculeConstraint:: PP framework/base/mathutilities.cpp /^ const Real PP = 0.3275911;$/;" v PPM compilerTests/pngTest.cpp /^PPM::PPM():w(0),h(0),p(NULL){}$/;" f class:PPM PPM compilerTests/pngTest.cpp /^PPM::PPM(int a, int b):w(a),h(b),p(new unsigned char[3*a*b]){$/;" f class:PPM PPM compilerTests/pngTest.cpp /^class PPM{$/;" c file: PPM framework/base/PPM.cpp /^ PPM::PPM():w(0),h(0),p(NULL){$/;" f class:ProtoMol::PPM PPM framework/base/PPM.cpp /^ PPM::PPM(int x, int y):w(x),h(y),p(new unsigned char[3*x*y]){$/;" f class:ProtoMol::PPM PPM framework/base/PPM.h /^ class PPM{$/;" c namespace:ProtoMol PPMREADER_H framework/io/PPMReader.h 3;" d PPMReader framework/io/PPMReader.cpp /^ PPMReader::PPMReader():Reader(),myPPM(NULL){}$/;" f class:ProtoMol::PPMReader PPMReader framework/io/PPMReader.cpp /^ PPMReader::PPMReader(const std::string& filename):Reader(filename),myPPM(NULL){}$/;" f class:ProtoMol::PPMReader PPMReader framework/io/PPMReader.h /^ class PPMReader : public Reader {$/;" c namespace:ProtoMol PPMWRITER_H framework/io/PPMWriter.h 3;" d PPMWriter framework/io/PPMWriter.cpp /^ PPMWriter::PPMWriter():Writer(){}$/;" f class:ProtoMol::PPMWriter PPMWriter framework/io/PPMWriter.cpp /^ PPMWriter::PPMWriter(const std::string& filename):Writer(filename){}$/;" f class:ProtoMol::PPMWriter PPMWriter framework/io/PPMWriter.h /^ class PPMWriter : public Writer {$/;" c namespace:ProtoMol PPM_H framework/base/PPM.h 3;" d PRECISION framework/base/LookUpTableBase.h /^ enum{PRECISION=PRE};$/;" e enum:ProtoMol::LookUpTableBase:: PRESSUREFACTOR framework/base/pmconstants.cpp /^ const Real PRESSUREFACTOR = 69478.0593635551;\/\/ ENERGY_TO_SI\/(LENGTH_TO_SI*LENGTH_TO_SI*LENGTH_TO_SI)*1e-5; \/\/ bar$/;" v PRE_CHECK framework/forces/oneAtomContraints.h /^ enum {PRE_CHECK=0, POST_CHECK=0};$/;" e enum:ProtoMol::NoConstraint:: PRE_CHECK framework/forces/oneAtomContraints.h /^ enum {PRE_CHECK=0, POST_CHECK=1};$/;" e enum:ProtoMol::DebugPostConstraint:: PRE_CHECK framework/forces/oneAtomContraints.h /^ enum {PRE_CHECK=1, POST_CHECK=0};$/;" e enum:ProtoMol::DebugPreConstraint:: PRE_CHECK framework/forces/oneAtomContraints.h /^ enum {PRE_CHECK=1, POST_CHECK=0};$/;" e enum:ProtoMol::HBondConstraint:: PRE_CHECK framework/forces/oneAtomContraints.h /^ enum {PRE_CHECK=1, POST_CHECK=0};$/;" e enum:ProtoMol::NotSameMoleculeConstraint:: PRE_CHECK framework/forces/oneAtomContraints.h /^ enum {PRE_CHECK=1, POST_CHECK=0};$/;" e enum:ProtoMol::SameMoleculeConstraint:: PRINTMAXWIDTH framework/base/pmconstants.cpp /^ const unsigned int PRINTMAXWIDTH = 30;$/;" v PROTOMOL_H framework/base/protomol.h 3;" d PROXY_H framework/base/Proxy.h 3;" d PSF framework/base/PSF.h /^ class PSF {$/;" c namespace:ProtoMol PSFREADER_H framework/io/PSFReader.h 3;" d PSFReader framework/io/PSFReader.cpp /^ PSFReader::PSFReader():$/;" f class:ProtoMol::PSFReader PSFReader framework/io/PSFReader.cpp /^ PSFReader::PSFReader(const std::string& filename):$/;" f class:ProtoMol::PSFReader PSFReader framework/io/PSFReader.h /^ class PSFReader : public Reader {$/;" c namespace:ProtoMol PSFWRITER_H framework/io/PSFWriter.h 3;" d PSFWriter framework/io/PSFWriter.cpp /^ PSFWriter::PSFWriter():Writer(){}$/;" f class:ProtoMol::PSFWriter PSFWriter framework/io/PSFWriter.cpp /^ PSFWriter::PSFWriter(const std::string& filename):Writer(filename){}$/;" f class:ProtoMol::PSFWriter PSFWriter framework/io/PSFWriter.h /^ class PSFWriter : public Writer {$/;" c namespace:ProtoMol PSF_H framework/base/PSF.h 3;" d PairInt framework/base/simpleTypes.h /^ typedef std::pair PairInt;$/;" t namespace:ProtoMol PairIntSorted framework/base/simpleTypes.h /^ PairIntSorted():first(0),second(0){}$/;" f struct:ProtoMol::PairIntSorted PairIntSorted framework/base/simpleTypes.h /^ PairIntSorted(unsigned int a, unsigned int b):first(std::min(a,b)),second(std::max(a,b)){}$/;" f struct:ProtoMol::PairIntSorted PairIntSorted framework/base/simpleTypes.h /^ struct PairIntSorted {$/;" s namespace:ProtoMol PairString framework/base/simpleTypes.h /^ typedef std::pair PairString;$/;" t namespace:ProtoMol PairUInt framework/base/simpleTypes.h /^ typedef std::pair PairUInt;$/;" t namespace:ProtoMol PairVector3D tools/bccAnalyzer.cpp /^ PairVector3D(){}$/;" f class:PairVector3D PairVector3D tools/bccAnalyzer.cpp /^ PairVector3D(const Vector3DIdx& a, const Vector3DIdx& b, const Vector3DIdx& c):v0(a),c(b),v1(c){}$/;" f class:PairVector3D PairVector3D tools/bccAnalyzer.cpp /^class PairVector3D {$/;" c file: Parallel framework/parallel/Parallel-FD.cpp /^ Parallel::Parallel(){$/;" f class:ProtoMol::Parallel Parallel framework/parallel/Parallel.cpp /^ Parallel::Parallel(){$/;" f class:ProtoMol::Parallel Parallel framework/parallel/Parallel.h /^ Parallel(const Parallel&){}$/;" f class:ProtoMol::Parallel Parallel framework/parallel/Parallel.h /^ class Parallel {$/;" c namespace:ProtoMol ParallelEnum framework/parallel/ParallelType.h /^ class ParallelEnum {$/;" c namespace:ProtoMol ParallelType framework/parallel/ParallelType.h /^ typedef AbstractEnumType ParallelType;$/;" t namespace:ProtoMol Parameter framework/base/Parameter.cpp /^ Parameter::Parameter():keyword(""),value(Value()),defaultValue(Value()) {}$/;" f class:ProtoMol::Parameter Parameter framework/base/Parameter.cpp /^ Parameter::Parameter(const char* k, const Value& val):keyword(string(k)),value(val),defaultValue(val,Value::undefined) {}$/;" f class:ProtoMol::Parameter Parameter framework/base/Parameter.cpp /^ Parameter::Parameter(const char* k, const Value& val, const Text& t):keyword(string(k)),value(val),defaultValue(val,Value::undefined),text(t.text) {}$/;" f class:ProtoMol::Parameter Parameter framework/base/Parameter.cpp /^ Parameter::Parameter(const char* k, const Value& val, const Value& def):keyword(string(k)),value(val),defaultValue(def) {}$/;" f class:ProtoMol::Parameter Parameter framework/base/Parameter.cpp /^ Parameter::Parameter(const char* k, const Value& val, const Value& def, const Text& t):keyword(string(k)),value(val),defaultValue(def),text(t.text) {} $/;" f class:ProtoMol::Parameter Parameter framework/base/Parameter.cpp /^ Parameter::Parameter(const string& k, const Value& val):keyword(k),value(val),defaultValue(val,Value::undefined) {}$/;" f class:ProtoMol::Parameter Parameter framework/base/Parameter.cpp /^ Parameter::Parameter(const string& k, const Value& val, const Text& t):keyword(k),value(val),defaultValue(val,Value::undefined),text(t.text) {}$/;" f class:ProtoMol::Parameter Parameter framework/base/Parameter.cpp /^ Parameter::Parameter(const string& k, const Value& val, const Value& def):keyword(k),value(val),defaultValue(def) {}$/;" f class:ProtoMol::Parameter Parameter framework/base/Parameter.cpp /^ Parameter::Parameter(const string& k, const Value& val, const Value& def, const Text& t):keyword(k),value(val),defaultValue(def),text(t.text) {}$/;" f class:ProtoMol::Parameter Parameter framework/base/Parameter.h /^ Parameter(const char* k, const Value& val, T def):keyword(std::string(k)),value(val),defaultValue(val) {defaultValue.set(def);}$/;" f struct:ProtoMol::Parameter Parameter framework/base/Parameter.h /^ Parameter(const char* k, const Value& val, T def, const Text& t):keyword(std::string(k)),value(val),defaultValue(val),text(t.text) {defaultValue.set(def);}$/;" f struct:ProtoMol::Parameter Parameter framework/base/Parameter.h /^ Parameter(const std::string& k, const Value& val, T def):keyword(k),value(val),defaultValue(val) {defaultValue.set(def);}$/;" f struct:ProtoMol::Parameter Parameter framework/base/Parameter.h /^ Parameter(const std::string& k, const Value& val, T def, const Text& t):keyword(k),value(val),defaultValue(val),text(t.text) {defaultValue.set(def);}$/;" f struct:ProtoMol::Parameter Parameter framework/base/Parameter.h /^ struct Parameter {$/;" s namespace:ProtoMol ParseCommandLine framework/base/pmconstants.cpp /^ namespace ParseCommandLine {$/;" n namespace:ProtoMol::Constant file: ParseCommandLine framework/base/pmconstants.h /^ namespace ParseCommandLine {$/;" n namespace:ProtoMol::Constant PaulTrapExtendedForce framework/forces/PaulTrapExtendedForce.h /^ PaulTrapExtendedForce::PaulTrapExtendedForce():ExtendedForce(),myOmegaR1(0.0),myOmegaZ1(0.0),myAlpha(0.0),myR0(0.0),myU0(0.0),myK(Vector3D(0.0,0.0,0.0)),myAlphaR04(0.0),myOmega(0.0),myA(0.0),myCached(false){$/;" f class:ProtoMol::PaulTrapExtendedForce PaulTrapExtendedForce framework/forces/PaulTrapExtendedForce.h /^ PaulTrapExtendedForce::PaulTrapExtendedForce(Real omegaR, Real omegaZ, Real alpha, Real r0, Real u0, Vector3D k):ExtendedForce(),myOmegaR1(omegaR),myOmegaZ1(omegaZ),myU0(u0),myK(k),myOmega(0.0),myA(0.0),myCached(false){$/;" f class:ProtoMol::PaulTrapExtendedForce PaulTrapExtendedForce framework/forces/PaulTrapExtendedForce.h /^ class PaulTrapExtendedForce : public ExtendedForce, private PaulTrapExtendedForceBase {$/;" c namespace:ProtoMol PaulTrapExtendedForceBase framework/forces/PaulTrapExtendedForceBase.h /^ class PaulTrapExtendedForceBase {$/;" c namespace:ProtoMol PaulTrapIntegrator framework/integrators/PaulTrapIntegrator.cpp /^ PaulTrapIntegrator::PaulTrapIntegrator(): STSIntegrator(),$/;" f class:ProtoMol::PaulTrapIntegrator PaulTrapIntegrator framework/integrators/PaulTrapIntegrator.cpp /^ PaulTrapIntegrator::PaulTrapIntegrator(Real timestep,$/;" f class:ProtoMol::PaulTrapIntegrator PaulTrapIntegrator framework/integrators/PaulTrapIntegrator.h /^ class PaulTrapIntegrator: public STSIntegrator {$/;" c namespace:ProtoMol PeriodicBoundaryConditions framework/topology/PeriodicBoundaryConditions.cpp /^ PeriodicBoundaryConditions::PeriodicBoundaryConditions():myE1(0,0,0),myE2(0,0,0),myE3(0,0,0),$/;" f class:ProtoMol::PeriodicBoundaryConditions PeriodicBoundaryConditions framework/topology/PeriodicBoundaryConditions.cpp /^ PeriodicBoundaryConditions::PeriodicBoundaryConditions(const Vector3D &e1 ,const Vector3D &e2 ,$/;" f class:ProtoMol::PeriodicBoundaryConditions PeriodicBoundaryConditions framework/topology/PeriodicBoundaryConditions.h /^ class PeriodicBoundaryConditions {$/;" c namespace:ProtoMol PlaceHolder framework/base/Value.h /^ class PlaceHolder {$/;" c class:ProtoMol::Value Positive framework/base/ConstraintValueType.h /^ typedef Enum2Type Positive;$/;" t class:ProtoMol::ConstraintValueEnum PostForceBarostat framework/integrators/NPTVerletIntegrator.cpp /^ void NPTVerletIntegrator::PostForceBarostat() {$/;" f class:ProtoMol::NPTVerletIntegrator PostForceThermostat framework/integrators/NPTVerletIntegrator.cpp /^ void NPTVerletIntegrator::PostForceThermostat() {$/;" f class:ProtoMol::NPTVerletIntegrator PostForceThermostat framework/integrators/NVTVerletIntegrator.cpp /^ void NVTVerletIntegrator::PostForceThermostat() {$/;" f class:ProtoMol::NVTVerletIntegrator Power framework/base/mathutilities.h /^ struct Power {$/;" s namespace:ProtoMol::Private Power framework/base/mathutilities.h /^ struct Power<-1> {$/;" s namespace:ProtoMol::Private Power framework/base/mathutilities.h /^ struct Power<0> {$/;" s namespace:ProtoMol::Private Power framework/base/mathutilities.h /^ struct Power<1> {$/;" s namespace:ProtoMol::Private PreForceBarostat framework/integrators/NPTVerletIntegrator.cpp /^ void NPTVerletIntegrator::PreForceBarostat() {$/;" f class:ProtoMol::NPTVerletIntegrator PreForceThermostat framework/integrators/NPTVerletIntegrator.cpp /^ void NPTVerletIntegrator::PreForceThermostat() {$/;" f class:ProtoMol::NPTVerletIntegrator PreForceThermostat framework/integrators/NVTVerletIntegrator.cpp /^ void NVTVerletIntegrator::PreForceThermostat() {$/;" f class:ProtoMol::NVTVerletIntegrator PreserveElems framework/base/Array_Fastest.h /^ bool resize(const size_t (&Dimensions)[N], const T & Init=T(), bool PreserveElems=false)$/;" m class:ProtoMol::Array Private framework/base/Cycles.h /^ namespace Private {$/;" n namespace:ProtoMol Private framework/base/mathutilities.h /^ namespace Private {$/;" n namespace:ProtoMol Private framework/base/typeSelection.h /^ namespace Private {$/;" n namespace:ProtoMol ProtoMol framework/base/AbstractEnumType.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Array_Fastest.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Array_NoPartialSpecialization.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Atom.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/AtomType.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/BSpline.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/BSpline.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/BSplineType.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/BSplineType.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Configuration.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/Configuration.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/ConstraintValueType.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/ConstraintValueType.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Cycles.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/FFTComplex.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/FFTComplex.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Grid.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Hermite.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/Hermite.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Lagrange.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/Lagrange.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/LookUpTableBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Makeable.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/Makeable.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/MakeableDefinition.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Matrix3by3.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/Matrix3by3.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Molecule.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/MultiGrid.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/ObjectDefinition.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/PAR.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/PAR.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/PDB.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/PDB.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/PGM.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/PGM.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/PPM.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/PPM.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/PSF.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/PSF.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Parameter.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/Parameter.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Proxy.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Real.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/ReducedHessAngle.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/ReducedHessAngle.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Report.cpp /^namespace ProtoMol { $/;" n file: ProtoMol framework/base/Report.h /^namespace ProtoMol { $/;" n ProtoMol framework/base/ScalarStructure.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/ScalarStructure.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Stack.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Timer.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/Timer.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/TimerStatistic.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/TimerStatistic.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Value.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/Value.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/ValueType.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/ValueType.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Vector.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Vector3D.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/Vector3DBlock.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/Vector3DBlock.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/XSC.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/XSC.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/XYZ.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/XYZ.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/mathutilities.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/mathutilities.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/pmconstants.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/pmconstants.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/reducedHessBond.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/reducedHessBond.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/simpleTypes.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/stringutilities.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/stringutilities.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/systemutilities.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/base/systemutilities.h /^namespace ProtoMol {$/;" n ProtoMol framework/base/typeSelection.h /^namespace ProtoMol {$/;" n ProtoMol framework/factories/registerForceExemplars.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/factories/registerForceExemplars.h /^namespace ProtoMol {$/;" n ProtoMol framework/factories/registerForceExemplarsBonded.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/factories/registerForceExemplarsBonded.h /^namespace ProtoMol {$/;" n ProtoMol framework/factories/registerForceExemplarsCutoff.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/factories/registerForceExemplarsCutoff.h /^namespace ProtoMol {$/;" n ProtoMol framework/factories/registerForceExemplarsFastElectrostatic.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/factories/registerForceExemplarsFastElectrostatic.h /^namespace ProtoMol {$/;" n ProtoMol framework/factories/registerForceExemplarsFull.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/factories/registerForceExemplarsFull.h /^namespace ProtoMol {$/;" n ProtoMol framework/factories/registerForceExemplarsOther.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/factories/registerForceExemplarsOther.h /^namespace ProtoMol {$/;" n ProtoMol framework/factories/registerForceExemplarsSimpleFull.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/factories/registerForceExemplarsSimpleFull.h /^namespace ProtoMol {$/;" n ProtoMol framework/factories/registerIntegratorExemplars.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/factories/registerIntegratorExemplars.h /^namespace ProtoMol {$/;" n ProtoMol framework/factories/registerOutputExemplars.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/factories/registerOutputExemplars.h /^namespace ProtoMol {$/;" n ProtoMol framework/factories/registerTopologyExemplars.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/factories/registerTopologyExemplars.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/AngleSystemForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/AngleSystemForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/AngleSystemForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/BondSystemForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/BondSystemForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/BondSystemForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/CompareForce.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/CompareForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/CoulombEwaldRealForce.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/CoulombEwaldRealForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/CoulombEwaldRealTableForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/CoulombEwaldRealTableForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/CoulombEwaldRealTableForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/CoulombForce.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/CoulombForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/CoulombMultiGridDirectForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/CoulombMultiGridDirectForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/CoulombMultiGridDirectForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/CoulombMultiGridDirectTableForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/CoulombMultiGridDirectTableForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/CoulombMultiGridDirectTableForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/CoulombTableForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/CoulombTableForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/CoulombTableForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/DihedralSystemForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/DihedralSystemForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/DihedralSystemForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/ElectricFieldSystemForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/ElectricFieldSystemForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/ElectricFieldSystemForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/ExtendedCompareForce.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/ExtendedCompareForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/ExtendedForce.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/ExtendedForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/ExtendedTimeForce.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/ExtendedTimeForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/ExternalGravitationSystemForce.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/ExternalGravitationSystemForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/ExternalMagneticFieldExtendedForce.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/ExternalMagneticFieldExtendedForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/Force.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/Force.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/ForceGroup.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/ForceGroup.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/FrictionExtendedForce.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/FrictionExtendedForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/GravitationForce.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/GravitationForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/HarmDihedralSystemForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/HarmDihedralSystemForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/HarmDihedralSystemForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/ImproperSystemForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/ImproperSystemForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/ImproperSystemForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/LennardJonesForce.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/LennardJonesForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/LennardJonesTableForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/LennardJonesTableForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/LennardJonesTableForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/MTorsionSystemForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/MagneticDipoleForce.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/MagneticDipoleForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/MagneticDipoleMirrorSystemForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/MagneticDipoleMirrorSystemForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/MagneticDipoleMirrorSystemForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/MetaForce.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/MetaForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/MollyForce.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/MollyForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/NonbondedCutoffForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/NonbondedCutoffForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/NonbondedCutoffForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/NonbondedCutoffMollyForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/NonbondedCutoffSystemForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/NonbondedFullEwaldSystemForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/NonbondedFullEwaldSystemForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/NonbondedFullEwaldSystemForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/NonbondedFullSystemForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/NonbondedFullSystemForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/NonbondedFullSystemForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/NonbondedMultiGridSystemForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/NonbondedMultiGridSystemForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/NonbondedMultiGridSystemForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/NonbondedPMEwaldSystemForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/NonbondedPMEwaldSystemForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/NonbondedPMEwaldSystemForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/NonbondedSimpleFullSystemForce.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/NonbondedSimpleFullSystemForceBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/forces/NonbondedSimpleFullSystemForceBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/forces/OneAtomPair.h /^namespace ProtoMol {$/;" n ProtoMol 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framework/topology/PeriodicBoundaryConditions.h /^namespace ProtoMol {$/;" n ProtoMol framework/topology/RangeSwitchingFunction.h /^namespace ProtoMol {$/;" n ProtoMol framework/topology/RangeSwitchingFunctionBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/topology/RangeSwitchingFunctionBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/topology/SemiGenericTopology.h /^namespace ProtoMol {$/;" n ProtoMol framework/topology/ShiftSwitchingFunction.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/topology/ShiftSwitchingFunction.h /^namespace ProtoMol {$/;" n ProtoMol framework/topology/ShiftSwitchingFunctionBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/topology/ShiftSwitchingFunctionBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/topology/Topology.h /^namespace ProtoMol {$/;" n ProtoMol framework/topology/Torsion.h /^namespace ProtoMol {$/;" n ProtoMol framework/topology/UniversalSwitchingFunction.h /^namespace ProtoMol {$/;" n ProtoMol framework/topology/UniversalSwitchingFunctionBase.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/topology/UniversalSwitchingFunctionBase.h /^namespace ProtoMol {$/;" n ProtoMol framework/topology/VacuumBoundaryConditions.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/topology/VacuumBoundaryConditions.h /^namespace ProtoMol {$/;" n ProtoMol framework/topology/buildCellLists.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/topology/buildCellLists.h /^namespace ProtoMol {$/;" n ProtoMol framework/topology/topologyutilities.cpp /^namespace ProtoMol {$/;" n file: ProtoMol framework/topology/topologyutilities.h /^namespace ProtoMol {$/;" n Proxy framework/base/Proxy.h /^ Proxy(): myCount(0){}$/;" f class:ProtoMol::Proxy Proxy framework/base/Proxy.h /^ class Proxy {$/;" c namespace:ProtoMol Qnew framework/base/Atom.h /^ Real Qold, Qnew;$/;" m struct:ProtoMol::Atom Qo framework/integrators/NPTVerletIntegrator.h /^ Real Qo; \/\/ Particle thermostat mass. Units: (kcal fs^2 \/ mol)$/;" m class:ProtoMol::NPTVerletIntegrator Qo framework/integrators/NVTVerletIntegrator.h /^ Real Qo; \/\/ Particle thermostat mass. Units: (kcal fs^2 \/ mol)$/;" m class:ProtoMol::NVTVerletIntegrator Qold framework/base/Atom.h /^ Real Qold, Qnew;$/;" m struct:ProtoMol::Atom Qv framework/integrators/NPTVerletIntegrator.h /^ Real Qv; \/\/ Volume thermostat mass. Units: (kcal fs^2 \/ mol)$/;" m class:ProtoMol::NPTVerletIntegrator RANGESWITCHINGFUNCTIONBASE_H framework/topology/RangeSwitchingFunctionBase.h 3;" d RANGESWITCHINGFUNCTION_H framework/topology/RangeSwitchingFunction.h 3;" d RDTSC framework/base/Cycles.h 192;" d READER_H framework/io/Reader.h 3;" d REAL framework/base/ValueType.h /^ REAL,$/;" e enum:ProtoMol::ValueEnum::Enum REAL_H framework/base/Real.h 3;" d REAL_INFINITY framework/base/pmconstants.cpp /^ const Real REAL_INFINITY = 2.0*MAXREAL;$/;" v REAL_NAN framework/base/pmconstants.cpp /^ const Real REAL_NAN = REAL_INFINITY;$/;" v REDUCEDHESSANGLE_H framework/base/ReducedHessAngle.h 3;" d REDUCEDHESSBOND_H framework/base/reducedHessBond.h 3;" d REDUCEDHESSCOULOMB_H framework/forces/ReducedHessCoulomb.h 3;" d REDUCEDHESSLENNARDJONES_H framework/forces/ReducedHessLennardJones.h 3;" d REDUCEDHESSTRAITS_H framework/forces/ReducedHessTraits.h 3;" d REGISTERFORCEEXEMPLARSBONDED_H framework/factories/registerForceExemplarsBonded.h 3;" d REGISTERFORCEEXEMPLARSCUTOFF_H framework/factories/registerForceExemplarsCutoff.h 3;" d REGISTERFORCEEXEMPLARSFASTELECTROSTATIC_H framework/factories/registerForceExemplarsFastElectrostatic.h 3;" d REGISTERFORCEEXEMPLARSFULL_H framework/factories/registerForceExemplarsFull.h 3;" d REGISTERFORCEEXEMPLARSOTHER_H framework/factories/registerForceExemplarsOther.h 3;" d REGISTERFORCEEXEMPLARSSIMPLEFULL_H framework/factories/registerForceExemplarsSimpleFull.h 3;" d REGISTERFORCEEXEMPLARS_H framework/factories/registerForceExemplars.h 3;" d REGISTERINTEGRATOREXEMPLARS_H framework/factories/registerIntegratorExemplars.h 3;" d REGISTEROUTPUTEXEMPLARS_H framework/factories/registerOutputExemplars.h 3;" d REGISTERTOPOLOGYEXEMPLARS_H framework/factories/registerTopologyExemplars.h 3;" d REMCONFIGURATIONREADER_H framework/io/REMConfigurationReader.h 3;" d REMConfigurationReader framework/io/REMConfigurationReader.cpp /^ REMConfigurationReader::REMConfigurationReader(Real temp):Reader(),myConfig(NULL),myTemp(temp){}$/;" f class:ProtoMol::REMConfigurationReader REMConfigurationReader framework/io/REMConfigurationReader.cpp /^ REMConfigurationReader::REMConfigurationReader(const std::string& filename):Reader(filename),myConfig(NULL){}$/;" f class:ProtoMol::REMConfigurationReader REMConfigurationReader framework/io/REMConfigurationReader.h /^ class REMConfigurationReader : public Reader {$/;" c namespace:ProtoMol REMRates framework/frontend/OutputCache.h /^ const std::vector &REMRates() const {return myREMRates;}$/;" f class:ProtoMol::OutputCache REPLICA_h tools/rem/sequential/replica.h 2;" d REPORT_H framework/base/Report.h 3;" d RUN framework/base/TimerStatistic.h /^ RUN,$/;" e enum:ProtoMol::TimerStatistic::Enum R_OK framework/base/systemutilities.cpp 17;" d file: RangeSwitchingFunction framework/topology/RangeSwitchingFunction.h /^ RangeSwitchingFunction():myR0(0.0),myR1(0.0){}$/;" f class:ProtoMol::RangeSwitchingFunction RangeSwitchingFunction framework/topology/RangeSwitchingFunction.h /^ RangeSwitchingFunction(const TOriginalSwitchingFunction sw, Real r0, Real r1):myOrigFunc(sw),$/;" f class:ProtoMol::RangeSwitchingFunction RangeSwitchingFunction framework/topology/RangeSwitchingFunction.h /^ class RangeSwitchingFunction : private RangeSwitchingFunctionBase {$/;" c namespace:ProtoMol RangeSwitchingFunctionBase framework/topology/RangeSwitchingFunctionBase.h /^ class RangeSwitchingFunctionBase {$/;" c namespace:ProtoMol Reader framework/io/Reader.cpp /^ Reader::Reader():File(std::ios::in){}$/;" f class:ProtoMol::Reader Reader framework/io/Reader.cpp /^ Reader::Reader(const string& filename):File(std::ios::in,filename){$/;" f class:ProtoMol::Reader Reader framework/io/Reader.cpp /^ Reader::Reader(std::ios::openmode mode):File(std::ios::in|mode){}$/;" f class:ProtoMol::Reader Reader framework/io/Reader.cpp /^ Reader::Reader(std::ios::openmode mode,const string& filename):File(std::ios::in|mode,filename){$/;" f class:ProtoMol::Reader Reader framework/io/Reader.h /^ class Reader : public File {$/;" c namespace:ProtoMol Real framework/base/Real.h /^ typedef double Real;$/;" t namespace:ProtoMol Real framework/base/Real.h /^ typedef float Real;$/;" t namespace:ProtoMol Real framework/integrators/EquilibriumMOLLYIntegrator.cpp /^ void EquilibriumMOLLYIntegrator::luBksb(Real (&m)[maxGDim][maxGDim], $/;" m class:ProtoMol::EquilibriumMOLLYIntegrator file: Real framework/integrators/EquilibriumMOLLYIntegrator.cpp /^ void EquilibriumMOLLYIntegrator::luDcmp(Real (&m)[maxGDim][maxGDim], $/;" m class:ProtoMol::EquilibriumMOLLYIntegrator file: Real framework/integrators/EquilibriumMOLLYIntegrator.h /^ void luBksb(Real (&m)[maxGDim][maxGDim], int dim, const int (&index)[maxGDim], Real (&b)[maxGDim]) const;$/;" m class:ProtoMol::EquilibriumMOLLYIntegrator Real framework/integrators/EquilibriumMOLLYIntegrator.h /^ void luDcmp(Real (&m)[maxGDim][maxGDim], int dim, int (&index)[maxGDim], Real& d) const;$/;" m class:ProtoMol::EquilibriumMOLLYIntegrator RealTopologyType framework/forces/NonbondedCutoffForce.h /^ typedef Topology RealTopologyType;$/;" t class:ProtoMol::NonbondedCutoffForce RealTopologyType framework/forces/NonbondedCutoffMollyForce.h /^ typedef Topology RealTopologyType;$/;" t class:ProtoMol::NonbondedCutoffMollyForce RealTopologyType framework/forces/NonbondedCutoffSystemForce.h /^ typedef Topology RealTopologyType;$/;" t class:ProtoMol::NonbondedCutoffSystemForce RealTopologyType framework/forces/NonbondedFullEwaldSystemForce.h /^ typedef Topology RealTopologyType;$/;" t class:ProtoMol::NonbondedFullEwaldSystemForce RealTopologyType framework/forces/NonbondedFullSystemForce.h /^ typedef SemiGenericTopology RealTopologyType;$/;" t class:ProtoMol::NonbondedFullSystemForce RealTopologyType framework/forces/NonbondedMultiGridSystemForce.h /^ typedef Topology RealTopologyType;$/;" t class:ProtoMol::NonbondedMultiGridSystemForce RealTopologyType framework/forces/NonbondedPMEwaldSystemForce.h /^ typedef Topology RealTopologyType;$/;" t class:ProtoMol::NonbondedPMEwaldSystemForce RealTopologyType framework/forces/NonbondedSimpleFullSystemForce.h /^ typedef SemiGenericTopology RealTopologyType;$/;" t class:ProtoMol::NonbondedSimpleFullSystemForce ReducedHessAngle framework/base/ReducedHessAngle.cpp /^ ReducedHessAngle::ReducedHessAngle(){$/;" f class:ProtoMol::ReducedHessAngle ReducedHessAngle framework/base/ReducedHessAngle.cpp /^ ReducedHessAngle::ReducedHessAngle(const Vector3D& atom_i, \/\/position of atom i$/;" f class:ProtoMol::ReducedHessAngle ReducedHessAngle framework/base/ReducedHessAngle.h /^ class ReducedHessAngle{$/;" c namespace:ProtoMol ReducedHessCoulomb framework/forces/ReducedHessCoulomb.h /^ class ReducedHessCoulomb {$/;" c namespace:ProtoMol ReducedHessLennardJones framework/forces/ReducedHessLennardJones.h /^ class ReducedHessLennardJones {$/;" c namespace:ProtoMol ReducedHessTraits framework/forces/ReducedHessTraits.h /^ struct ReducedHessTraits{$/;" s namespace:ProtoMol ReducedHessTraits framework/forces/ReducedHessTraits.h /^ struct ReducedHessTraits{$/;" s namespace:ProtoMol RefArray framework/base/Array_Fastest.h /^ RefArray()$/;" f class:ProtoMol::RefArray RefArray framework/base/Array_Fastest.h /^ RefArray()$/;" f class:ProtoMol::RefArray RefArray framework/base/Array_Fastest.h /^ class RefArray : public RefArray$/;" c namespace:ProtoMol RefArray framework/base/Array_Fastest.h /^ class RefArray$/;" c namespace:ProtoMol RefArray framework/base/Array_NoPartialSpecialization.h /^ RefArray<1>(T * pElements, const size_type * pNDimensions, $/;" f class:ProtoMol::Array::RefArray RefArray framework/base/Array_NoPartialSpecialization.h /^ RefArray(T * pElements, const size_type * pNDimensions, $/;" f class:ProtoMol::Array::RefArray RefArray framework/base/Array_NoPartialSpecialization.h /^ class RefArray$/;" c class:ProtoMol::Array RefArray framework/base/Array_NoPartialSpecialization.h /^ class RefArray<1>$/;" c class:ProtoMol::Array RepType framework/base/ValueType.h /^ typedef Real RepType;$/;" t struct:ProtoMol::ValueTraits RepType framework/base/ValueType.h /^ typedef Vector3D RepType;$/;" t struct:ProtoMol::ValueTraits RepType framework/base/ValueType.h /^ typedef bool RepType;$/;" t struct:ProtoMol::ValueTraits RepType framework/base/ValueType.h /^ typedef int RepType;$/;" t struct:ProtoMol::ValueTraits RepType framework/base/ValueType.h /^ typedef std::string RepType; \/\/ Representation type of the value$/;" t struct:ProtoMol::ValueTraits RepType framework/base/ValueType.h /^ typedef std::string RepType;$/;" t struct:ProtoMol::ValueTraits RepType framework/base/ValueType.h /^ typedef std::vector RepType;$/;" t struct:ProtoMol::ValueTraits RepType framework/base/ValueType.h /^ typedef unsigned int RepType;$/;" t struct:ProtoMol::ValueTraits Replica tools/rem/sequential/replica.cc /^Replica::Replica( string name, string parentDir, string pdbFile, string psfFile,$/;" f class:Replica Replica tools/rem/sequential/replica.h /^class Replica {$/;" c Report framework/base/Report.cpp /^ namespace Report { $/;" n namespace:ProtoMol file: Report framework/base/Report.h /^ namespace Report { $/;" n namespace:ProtoMol ResetDimensions framework/base/Array_Fastest.h /^ void ResetDimensions()$/;" f class:ProtoMol::RefArray SEMIGENERICTOPOLOGY_H framework/topology/SemiGenericTopology.h 3;" d SEND_RANGE framework/parallel/Parallel-FD.cpp /^ const int SEND_RANGE = 2;$/;" v SEND_RANGE framework/parallel/Parallel.cpp /^ const int SEND_RANGE = 2;$/;" v SEQUENTIAL framework/parallel/Parallel.h /^ SEQUENTIAL, \/\/\/< next() always true, traps calls of next() when running with 1 node (should not happen!)$/;" e enum:ProtoMol::Parallel::WorkState SHADOW framework/base/ScalarStructure.h /^ SHADOW=LASTREDUCE,$/;" e enum:ProtoMol::ScalarStructure::Index SHADOWHMCINTEGRATOR_H framework/integrators/ShadowHMCIntegrator.h 2;" d SHIFT framework/base/LookUpTableBase.h /^ enum{SHIFT=(sizeof(TReal)*8-1-E-PRE)};$/;" e enum:ProtoMol::LookUpTableBase:: SHIFTSWITCHINGFUNCTIONBASE_H framework/topology/ShiftSwitchingFunctionBase.h 3;" d SHIFTSWITCHINGFUNCTION_H framework/topology/ShiftSwitchingFunction.h 3;" d SHORT framework/base/BSplineType.h /^ SHORT,$/;" e enum:ProtoMol::BSplineEnum::Enum SI framework/base/pmconstants.cpp /^ namespace SI {$/;" n namespace:ProtoMol::Constant file: SI framework/base/pmconstants.h /^ namespace SI {$/;" n namespace:ProtoMol::Constant SIGMA_CHARMM19_TO_CHARMM28 framework/base/PAR.h /^ static const Real SIGMA_CHARMM19_TO_CHARMM28;$/;" m struct:ProtoMol::PAR::Nonbonded SIGMA_CHARMM28_TO_CHARMM19 framework/base/PAR.h /^ static const Real SIGMA_CHARMM28_TO_CHARMM19;$/;" m struct:ProtoMol::PAR::Nonbonded SIMPLETYPES_H framework/base/simpleTypes.h 3;" d SIZEOF_CHAR protomol_config.h 150;" d SIZEOF_INT protomol_config.h 153;" d SIZEOF_LONG protomol_config.h 156;" d SIZEOF_SHORT protomol_config.h 159;" d SIZEOF_SIZE_T protomol_config.h 162;" d SIZEOF_VOIDP protomol_config.h 165;" d SI_FACTOR framework/forces/ExternalGravitationSystemForce.cpp /^ static const Real SI_FACTOR = 1e-3*Constant::SI::KCAL\/Constant::SI::LENGTH_AA;$/;" v file: SI_FORCE_FACTOR framework/forces/ExternalMagneticFieldExtendedForce.cpp /^ static const Real SI_FORCE_FACTOR = Constant::SI::ELECTRON_CHARGE*Constant::SI::AVOGADRO*Constant::SI::KCAL\/Constant::SI::LENGTH_AA*(1e8\/sqrt(4184.0));$/;" v file: SLAVE framework/parallel/Parallel.h /^ SLAVE, \/\/\/< slave$/;" e enum:ProtoMol::Parallel::WorkState SOCKLEN_TYPE protomol_config.h 168;" d SOCKLEN_TYPE protomol_config_windows.h 46;" d SPHERICALSYSTEMFORCE_H framework/forces/SphericalSystemForce.h 3;" d SQRTCOULOMBCONSTANT framework/base/pmconstants.cpp /^ const Real SQRTCOULOMBCONSTANT = 18.2226123264;$/;" v STACK_H framework/base/Stack.h 3;" d STANDARDINTEGRATOR_H framework/integrators/StandardIntegrator.h 3;" d STATIC framework/parallel/Parallel.h /^ STATIC, \/\/\/< next() based on modulo, simple load balancing$/;" e enum:ProtoMol::Parallel::WorkState STATIC framework/parallel/ParallelType.h /^ STATIC, \/\/\/< Static load balancing$/;" e enum:ProtoMol::ParallelEnum::Enum STDC_HEADERS protomol_config.h 171;" d STEP framework/base/LookUpTableBase.h /^ enum{STEP=TLookUpValue::ENTRIES*NV};$/;" e enum:ProtoMol::LookUpTableBase:: STRING framework/base/ValueType.h /^ STRING,$/;" e enum:ProtoMol::ValueEnum::Enum STRINGUTILITIES_H framework/base/stringutilities.h 3;" d STSINTEGRATOR_H framework/integrators/STSIntegrator.h 3;" d STSIntegrator framework/integrators/STSIntegrator.cpp /^ STSIntegrator::STSIntegrator() : StandardIntegrator(),myTimestep(0.0){}$/;" f class:ProtoMol::STSIntegrator STSIntegrator framework/integrators/STSIntegrator.cpp /^ STSIntegrator::STSIntegrator(Real timestep, ForceGroup *overloadedForces) :$/;" f class:ProtoMol::STSIntegrator STSIntegrator framework/integrators/STSIntegrator.h /^ class STSIntegrator: public StandardIntegrator {$/;" c namespace:ProtoMol SYSTEMCOMPAREFORCE_H framework/forces/SystemCompareForce.h 3;" d SYSTEMFORCE_H framework/forces/SystemForce.h 3;" d SYSTEMTIMEFORCE_H framework/forces/SystemTimeForce.h 3;" d SYSTEMUTILITIES_H framework/base/systemutilities.h 3;" d S_ALT_LOC framework/base/PDB.h /^ S_ALT_LOC = 17 - 1,$/;" e enum:ProtoMol::PDB::Atom::Start S_ATOM_NAME framework/base/PDB.h /^ S_ATOM_NAME = 13 - 1,$/;" e enum:ProtoMol::PDB::Atom::Start S_CHAIN_ID framework/base/PDB.h /^ S_CHAIN_ID = 22 - 1,$/;" e enum:ProtoMol::PDB::Atom::Start S_CHAIN_ID framework/base/PDB.h /^ S_CHAIN_ID = 22 - 1,$/;" e enum:ProtoMol::PDB::Ter::Start S_CHARGE framework/base/PDB.h /^ S_CHARGE = 79 - 1$/;" e enum:ProtoMol::PDB::Atom::Start S_ELEMENT_SYMBOL framework/base/PDB.h /^ S_ELEMENT_SYMBOL = 77 - 1,$/;" e enum:ProtoMol::PDB::Atom::Start S_I_CODE framework/base/PDB.h /^ S_I_CODE = 27 - 1$/;" e enum:ProtoMol::PDB::Ter::Start S_I_CODE framework/base/PDB.h /^ S_I_CODE = 27 - 1,$/;" e enum:ProtoMol::PDB::Atom::Start S_OCCUP framework/base/PDB.h /^ S_OCCUP = 55 - 1,$/;" e enum:ProtoMol::PDB::Atom::Start S_RECORD_NAME framework/base/PDB.h /^ S_RECORD_NAME = 1 - 1,$/;" e enum:ProtoMol::PDB::Atom::Start S_RECORD_NAME framework/base/PDB.h /^ S_RECORD_NAME = 1 - 1,$/;" e enum:ProtoMol::PDB::Ter::Start S_RES_NAME framework/base/PDB.h /^ S_RES_NAME = 18 - 1,$/;" e enum:ProtoMol::PDB::Atom::Start S_RES_NAME framework/base/PDB.h /^ S_RES_NAME = 18 - 1,$/;" e enum:ProtoMol::PDB::Ter::Start S_RES_SEQ framework/base/PDB.h /^ S_RES_SEQ = 23 - 1,$/;" e enum:ProtoMol::PDB::Atom::Start S_RES_SEQ framework/base/PDB.h /^ S_RES_SEQ = 23 - 1,$/;" e enum:ProtoMol::PDB::Ter::Start S_SEG_ID framework/base/PDB.h /^ S_SEG_ID = 73 - 1,$/;" e enum:ProtoMol::PDB::Atom::Start S_SERIAL framework/base/PDB.h /^ S_SERIAL = 7 - 1,$/;" e enum:ProtoMol::PDB::Atom::Start S_SERIAL framework/base/PDB.h /^ S_SERIAL = 7 - 1,$/;" e enum:ProtoMol::PDB::Ter::Start S_TEMP_FACT framework/base/PDB.h /^ S_TEMP_FACT = 61 - 1,$/;" e enum:ProtoMol::PDB::Atom::Start S_X framework/base/PDB.h /^ S_X = 31 - 1,$/;" e enum:ProtoMol::PDB::Atom::Start S_Y framework/base/PDB.h /^ S_Y = 39 - 1,$/;" e enum:ProtoMol::PDB::Atom::Start S_Z framework/base/PDB.h /^ S_Z = 47 - 1,$/;" e enum:ProtoMol::PDB::Atom::Start SameMoleculeConstraint framework/forces/oneAtomContraints.h /^ struct SameMoleculeConstraint {$/;" s namespace:ProtoMol ScalarStructure framework/base/ScalarStructure.cpp /^ ScalarStructure::ScalarStructure() : Proxy(),$/;" f class:ProtoMol::ScalarStructure ScalarStructure framework/base/ScalarStructure.h /^ class ScalarStructure : public Proxy {$/;" c namespace:ProtoMol SelectType framework/base/typeSelection.h /^ template struct SelectType {$/;" s namespace:ProtoMol::Private SelectTypeCheck framework/base/typeSelection.h /^ template struct SelectTypeCheck {$/;" s namespace:ProtoMol::Private SelectTypeCheckHelper framework/base/typeSelection.h /^ template struct SelectTypeCheckHelper {};$/;" s namespace:ProtoMol::Private SelectTypeCheckHelper framework/base/typeSelection.h /^ template struct SelectTypeCheckHelper {$/;" s namespace:ProtoMol::Private SelectTypeHelper framework/base/typeSelection.h /^ template struct SelectTypeHelper {$/;" s namespace:ProtoMol::Private SelectTypeHelper framework/base/typeSelection.h /^ template struct SelectTypeHelper {$/;" s namespace:ProtoMol::Private SemiGenericTopology framework/topology/SemiGenericTopology.h /^ SemiGenericTopology():GenericTopology(){}$/;" f class:ProtoMol::SemiGenericTopology SemiGenericTopology framework/topology/SemiGenericTopology.h /^ SemiGenericTopology(Real csf, $/;" f class:ProtoMol::SemiGenericTopology SemiGenericTopology framework/topology/SemiGenericTopology.h /^ class SemiGenericTopology: public GenericTopology {$/;" c namespace:ProtoMol SetupDimensions framework/base/Array_Fastest.h /^ void SetupDimensions(const size_type * pNDimensions, $/;" f class:ProtoMol::RefArray ShadowHMCIntegrator framework/integrators/ShadowHMCIntegrator.cpp /^ ShadowHMCIntegrator::ShadowHMCIntegrator( int cycleLen, Real initTemp,$/;" f class:ProtoMol::ShadowHMCIntegrator ShadowHMCIntegrator framework/integrators/ShadowHMCIntegrator.cpp /^ ShadowHMCIntegrator::ShadowHMCIntegrator() : MCIntegrator(), myOrder(0),$/;" f class:ProtoMol::ShadowHMCIntegrator ShadowHMCIntegrator framework/integrators/ShadowHMCIntegrator.h /^ class ShadowHMCIntegrator : public MCIntegrator {$/;" c namespace:ProtoMol ShiftSwitchingFunction framework/topology/ShiftSwitchingFunction.cpp /^ ShiftSwitchingFunction::ShiftSwitchingFunction():myCutoff(0.0),$/;" f class:ProtoMol::ShiftSwitchingFunction ShiftSwitchingFunction framework/topology/ShiftSwitchingFunction.cpp /^ ShiftSwitchingFunction::ShiftSwitchingFunction(Real cutoff):myCutoff(cutoff),$/;" f class:ProtoMol::ShiftSwitchingFunction ShiftSwitchingFunction framework/topology/ShiftSwitchingFunction.h /^ class ShiftSwitchingFunction : private ShiftSwitchingFunctionBase {$/;" c namespace:ProtoMol ShiftSwitchingFunctionBase framework/topology/ShiftSwitchingFunctionBase.h /^ class ShiftSwitchingFunctionBase {$/;" c namespace:ProtoMol SphericalSystemForce framework/forces/SphericalSystemForce.cpp /^ SphericalSystemForce::SphericalSystemForce():SystemForce(),$/;" f class:ProtoMol::SphericalSystemForce SphericalSystemForce framework/forces/SphericalSystemForce.cpp /^ SphericalSystemForce::SphericalSystemForce(Vector3D center, Real radius, Real k, int j \/*, Real u*\/):SystemForce(),$/;" f class:ProtoMol::SphericalSystemForce SphericalSystemForce framework/forces/SphericalSystemForce.h /^ class SphericalSystemForce : public SystemForce {$/;" c namespace:ProtoMol Stack framework/base/Stack.h /^ Stack::Stack() {$/;" f class:ProtoMol::Stack Stack framework/base/Stack.h /^ class Stack {$/;" c namespace:ProtoMol StandardIntegrator framework/integrators/StandardIntegrator.cpp /^ StandardIntegrator::StandardIntegrator() :$/;" f class:ProtoMol::StandardIntegrator StandardIntegrator framework/integrators/StandardIntegrator.cpp /^ StandardIntegrator::StandardIntegrator(ForceGroup* forceGroup)$/;" f class:ProtoMol::StandardIntegrator StandardIntegrator framework/integrators/StandardIntegrator.h /^ class StandardIntegrator: public Integrator {$/;" c namespace:ProtoMol Start framework/base/PDB.h /^ enum Start{$/;" g struct:ProtoMol::PDB::Atom Start framework/base/PDB.h /^ enum Start{$/;" g struct:ProtoMol::PDB::Ter SystemCompareForce framework/forces/SystemCompareForce.cpp /^ SystemCompareForce::SystemCompareForce(Force* actualForce, CompareForce* compareForce):CompareForce(actualForce,compareForce){}$/;" f class:ProtoMol::SystemCompareForce SystemCompareForce framework/forces/SystemCompareForce.h /^ class SystemCompareForce : public CompareForce, public SystemForce {$/;" c namespace:ProtoMol SystemForce framework/forces/SystemForce.h /^ SystemForce():Force(){}$/;" f class:ProtoMol::SystemForce SystemForce framework/forces/SystemForce.h /^ class SystemForce : virtual public Force {$/;" c namespace:ProtoMol SystemTimeForce framework/forces/SystemTimeForce.cpp /^ SystemTimeForce::SystemTimeForce(Force* actualForce):TimeForce(actualForce){}$/;" f class:ProtoMol::SystemTimeForce SystemTimeForce framework/forces/SystemTimeForce.h /^ class SystemTimeForce : public TimeForce, public SystemForce {$/;" c namespace:ProtoMol T framework/imd/imd.h /^ float T;$/;" m struct:ProtoMol::IMD:: T framework/topology/ArrayCellListStructure.h /^ typedef std::pair T;$/;" t class:ProtoMol::ArrayCellListStructure T1 framework/topology/ArrayCellListStructure.h /^ typedef CubicCellLocation T1;$/;" t class:ProtoMol::ArrayCellListStructure T2 framework/topology/ArrayCellListStructure.h /^ typedef int T2;$/;" t class:ProtoMol::ArrayCellListStructure TContainer framework/topology/ArrayCellListStructure.h /^ typedef Array TContainer;$/;" t class:ProtoMol::ArrayCellListStructure TEMPFILEREADER_H framework/io/TempFileReader.h 3;" d TFactory framework/frontend/ForceFactoryDetails.h /^ typedef Factory TFactory;$/;" t class:ProtoMol::ForceFactoryDetails TFactory framework/frontend/IntegratorFactoryDetails.h /^ typedef Factory TFactory;$/;" t class:ProtoMol::IntegratorFactoryDetails TFactory framework/frontend/OutputFactoryDetails.h /^ typedef Factory TFactory;$/;" t class:ProtoMol::OutputFactoryDetails TFactory framework/frontend/TopologyFactoryDetails.h /^ typedef Factory TFactory;$/;" t class:ProtoMol::TopologyFactoryDetails TIMEFACTOR framework/base/pmconstants.cpp /^ const Real TIMEFACTOR = 48.88821290839616; \/\/ TIMEUNIT is 1 \/ sqrt(4.184e-4)$/;" v TIMEFORCE_H framework/forces/TimeForce.h 3;" d TIMERSTATISTIC_H framework/base/TimerStatistic.h 3;" d TIME_FS framework/base/pmconstants.cpp /^ const Real TIME_FS = 1e+15; \/\/ [fs]$/;" v TIME_WITH_SYS_TIME protomol_config.h 174;" d TINY framework/base/pmconstants.cpp /^ const Real TINY = 1.0e-20;$/;" v TInt framework/base/LookUpTableBase.h /^ typedef typename TypeSelection::Int::type TInt;$/;" t class:ProtoMol::LookUpTableBase TOPOLOGYFACTORYDETAILS_H framework/frontend/TopologyFactoryDetails.h 3;" d TOPOLOGYFACTORY_H framework/frontend/TopologyFactory.h 3;" d TOPOLOGYUTILITIES_H framework/topology/topologyutilities.h 3;" d TOPOLOGY_H framework/topology/Topology.h 3;" d TORSION_H framework/topology/Torsion.h 3;" d TYPESELECTION_H framework/base/typeSelection.h 3;" d TempFileReader framework/io/TempFileReader.h /^ explicit TempFileReader(const std::string& filename) : Reader(filename), myTemp(0), node(0) {}$/;" f class:ProtoMol::TempFileReader TempFileReader framework/io/TempFileReader.h /^ class TempFileReader : public Reader {$/;" c namespace:ProtoMol Ter framework/base/PDB.cpp /^ PDB::Ter::Ter():elementType(""), $/;" f class:ProtoMol::PDB::Ter Ter framework/base/PDB.cpp /^ PDB::Ter::Ter(std::string etype, $/;" f class:ProtoMol::PDB::Ter Ter framework/base/PDB.h /^ struct Ter{$/;" s struct:ProtoMol::PDB Text framework/base/simpleTypes.h /^ Text():text(""){}$/;" f struct:ProtoMol::Text Text framework/base/simpleTypes.h /^ Text(const char* t):text(t){}$/;" f struct:ProtoMol::Text Text framework/base/simpleTypes.h /^ Text(const std::string& t):text(t){}$/;" f struct:ProtoMol::Text Text framework/base/simpleTypes.h /^ struct Text {$/;" s namespace:ProtoMol TextMapType framework/base/Configuration.h /^ typedef std::map TextMapType;$/;" t class:ProtoMol::Configuration ThermostatEnum framework/integrators/PaulTrapIntegrator.h /^ class ThermostatEnum {$/;" c namespace:ProtoMol ThermostatType framework/integrators/PaulTrapIntegrator.h /^ typedef AbstractEnumType ThermostatType;$/;" t namespace:ProtoMol TimeForce framework/forces/TimeForce.cpp /^ TimeForce::TimeForce(Force* actualForce){$/;" f class:ProtoMol::TimeForce TimeForce framework/forces/TimeForce.h /^ class TimeForce : virtual public Force {$/;" c namespace:ProtoMol TimeRep framework/base/Timer.cpp /^ TimeRep::TimeRep()$/;" f class:ProtoMol::TimeRep TimeRep framework/base/Timer.cpp /^ TimeRep::TimeRep(double realTime, double userTime, double sysTime)$/;" f class:ProtoMol::TimeRep TimeRep framework/base/Timer.h /^ class TimeRep {$/;" c namespace:ProtoMol Timer framework/base/Timer.cpp /^ Timer::Timer()$/;" f class:ProtoMol::Timer Timer framework/base/Timer.h /^ class Timer {$/;" c namespace:ProtoMol TimerStatistic framework/base/TimerStatistic.h /^ class TimerStatistic {$/;" c namespace:ProtoMol Topology framework/topology/Topology.h /^ Topology():SemiGenericTopology(){}$/;" f class:ProtoMol::Topology Topology framework/topology/Topology.h /^ Topology(Real csf, $/;" f class:ProtoMol::Topology Topology framework/topology/Topology.h /^ class Topology: public SemiGenericTopology {$/;" c namespace:ProtoMol TopologyFactory framework/frontend/TopologyFactory.h /^ typedef Factory TopologyFactory;$/;" t namespace:ProtoMol TopologyFactoryDetails framework/frontend/TopologyFactoryDetails.cpp /^ TopologyFactoryDetails::TopologyFactoryDetails():FactoryBase(){$/;" f class:ProtoMol::TopologyFactoryDetails TopologyFactoryDetails framework/frontend/TopologyFactoryDetails.cpp /^ TopologyFactoryDetails::TopologyFactoryDetails(const TopologyFactoryDetails&){}$/;" f class:ProtoMol::TopologyFactoryDetails TopologyFactoryDetails framework/frontend/TopologyFactoryDetails.h /^ class TopologyFactoryDetails : public FactoryBase {$/;" c namespace:ProtoMol Torsion framework/topology/Torsion.h /^ Torsion():atom1(-1), atom2(-1), atom3(-1), atom4(-1) {$/;" f class:ProtoMol::Torsion Torsion framework/topology/Torsion.h /^ class Torsion {$/;" c namespace:ProtoMol TripleInt framework/base/simpleTypes.h /^ TripleInt():h(0),k(0),l(0){}$/;" f struct:ProtoMol::TripleInt TripleInt framework/base/simpleTypes.h /^ TripleInt(int a, int b,int c):h(a),k(b),l(c){}$/;" f struct:ProtoMol::TripleInt TripleInt framework/base/simpleTypes.h /^ struct TripleInt {$/;" s namespace:ProtoMol Type framework/base/ValueType.h /^ typedef Real Type;$/;" t struct:ProtoMol::ValueTraits Type framework/base/ValueType.h /^ typedef ValueTraits Type;$/;" t struct:ProtoMol::Enum2ValueTraits Type framework/base/ValueType.h /^ typedef ValueTraits Type;$/;" t struct:ProtoMol::Enum2ValueTraits Type framework/base/ValueType.h /^ typedef ValueTraits Type;$/;" t struct:ProtoMol::Enum2ValueTraits Type framework/base/ValueType.h /^ typedef ValueTraits Type;$/;" t struct:ProtoMol::Enum2ValueTraits Type framework/base/ValueType.h /^ typedef ValueTraits Type;$/;" t struct:ProtoMol::Enum2ValueTraits Type framework/base/ValueType.h /^ typedef ValueTraits Type;$/;" t struct:ProtoMol::Enum2ValueTraits Type framework/base/ValueType.h /^ typedef ValueTraits Type;$/;" t struct:ProtoMol::Enum2ValueTraits Type framework/base/ValueType.h /^ typedef ValueTraits > Type;$/;" t struct:ProtoMol::Enum2ValueTraits Type framework/base/ValueType.h /^ typedef ValueTraits Type;$/;" t struct:ProtoMol::Enum2ValueTraits Type framework/base/ValueType.h /^ typedef ValueType::Force Type;$/;" t struct:ProtoMol::ValueTraits Type framework/base/ValueType.h /^ typedef ValueType::Integrator Type;$/;" t struct:ProtoMol::ValueTraits Type framework/base/ValueType.h /^ typedef Vector3D Type;$/;" t struct:ProtoMol::ValueTraits Type framework/base/ValueType.h /^ typedef bool Type;$/;" t struct:ProtoMol::ValueTraits Type framework/base/ValueType.h /^ typedef int Type;$/;" t struct:ProtoMol::ValueTraits Type framework/base/ValueType.h /^ typedef std::string Type; \/\/ Type, template parameter$/;" t struct:ProtoMol::ValueTraits Type framework/base/ValueType.h /^ typedef std::vector Type;$/;" t struct:ProtoMol::ValueTraits Type framework/base/ValueType.h /^ typedef unsigned int Type;$/;" t struct:ProtoMol::ValueTraits Type framework/frontend/InputValue.h /^ typedef typename Enum2ValueTraits::Type Type;$/;" t class:ProtoMol::InputValue Type tools/bccAnalyzer.cpp /^ enum Type {UNDEF,$/;" g struct:Format file: TypeSelection framework/base/typeSelection.h /^ namespace TypeSelection {$/;" n namespace:ProtoMol UINT framework/base/ValueType.h /^ UINT,$/;" e enum:ProtoMol::ValueEnum::Enum UIntArrayN framework/base/Array_Fastest.h /^ typedef const size_t (&UIntArrayN)[N];$/;" t class:ProtoMol::ArraySize UNDEF tools/bccAnalyzer.cpp /^ enum Type {UNDEF,$/;" e enum:Format::Type file: UNDEFINED framework/base/BSplineType.h /^ UNDEFINED = 0, \/\/ Value returned when no string matches$/;" e enum:ProtoMol::BSplineEnum::Enum UNDEFINED framework/base/ConstraintValueType.h /^ UNDEFINED = 0, \/\/ ConstraintValue returned when no string matches$/;" e enum:ProtoMol::ConstraintValueEnum::Enum UNDEFINED framework/base/PAR.h /^ UNDEFINED,$/;" e enum:ProtoMol::PAR::CharmmTypeEnum UNDEFINED framework/base/ValueType.h /^ UNDEFINED = 0, \/\/ Value returned when no string matches$/;" e enum:ProtoMol::ValueEnum::Enum UNDEFINED framework/frontend/InputPosVelType.h /^ UNDEFINED = 0, \/\/ InputPosVel returned when no string matches$/;" e enum:ProtoMol::InputPosVelEnum::Enum UNDEFINED framework/integrators/PaulTrapIntegrator.h /^ UNDEFINED = 0, \/\/ Value returned when no string matches$/;" e enum:ProtoMol::ThermostatEnum::Enum UNDEFINED framework/io/PARReader.h /^ UNDEFINED,$/;" e enum:ProtoMol::PARReader::PARRecordTypeEnum UNDEFINED framework/parallel/ParallelType.h /^ UNDEFINED = 0, \/\/ Value returned when no string matches$/;" e enum:ProtoMol::ParallelEnum::Enum UNDEFINED framework/topology/ExclusionType.h /^ UNDEFINED = 0, \/\/ Value returned when no string matches$/;" e enum:ProtoMol::ExclusionEnum::Enum UNIVERSALSWITCHINGFUNCTIONBASE_H framework/topology/UniversalSwitchingFunctionBase.h 3;" d UNIVERSALSWITCHINGFUNCTION_H framework/topology/UniversalSwitchingFunction.h 3;" d USE framework/topology/C1SwitchingFunction.h /^ enum {USE=1};$/;" e enum:ProtoMol::C1SwitchingFunction:: USE framework/topology/C2SwitchingFunction.h /^ enum {USE=1};$/;" e enum:ProtoMol::C2SwitchingFunction:: USE framework/topology/CmpCnCnSwitchingFunction.h /^ enum {USE=1};$/;" e enum:ProtoMol::CmpCnCnSwitchingFunction:: USE framework/topology/CnSwitchingFunction.h /^ enum {USE=1};$/;" e enum:ProtoMol::CnSwitchingFunction:: USE framework/topology/ComplementSwitchingFunction.h /^ enum {USE=1};$/;" e enum:ProtoMol::ComplementSwitchingFunction:: USE framework/topology/CutoffSwitchingFunction.h /^ enum {USE=1};$/;" e enum:ProtoMol::CutoffSwitchingFunction:: USE framework/topology/RangeSwitchingFunction.h /^ enum {USE=1};$/;" e enum:ProtoMol::RangeSwitchingFunction:: USE framework/topology/ShiftSwitchingFunction.h /^ enum {USE=1};$/;" e enum:ProtoMol::ShiftSwitchingFunction:: USE framework/topology/UniversalSwitchingFunction.h /^ enum {USE=0};$/;" e enum:ProtoMol::UniversalSwitchingFunction:: USE_REAL_IS_DOUBLE framework/base/Real.h 9;" d Undefined framework/base/Value.h /^ struct Undefined{};$/;" s class:ProtoMol::Value UniversalSwitchingFunction framework/topology/UniversalSwitchingFunction.h /^ class UniversalSwitchingFunction : private UniversalSwitchingFunctionBase {$/;" c namespace:ProtoMol UniversalSwitchingFunctionBase framework/topology/UniversalSwitchingFunctionBase.h /^ class UniversalSwitchingFunctionBase {$/;" c namespace:ProtoMol VACUUM framework/topology/PeriodicBoundaryConditions.h /^ enum {PERIODIC = 1, VACUUM = 0};$/;" e enum:ProtoMol::PeriodicBoundaryConditions:: VACUUM framework/topology/VacuumBoundaryConditions.h /^ enum {PERIODIC = 0, VACUUM = 1};$/;" e enum:ProtoMol::VacuumBoundaryConditions:: VACUUMBOUNDARYCONDITIONS_H framework/topology/VacuumBoundaryConditions.h 3;" d VALUETYPE_H framework/base/ValueType.h 3;" d VALUE_H framework/base/Value.h 3;" d VECTOR framework/base/ValueType.h /^ VECTOR,$/;" e enum:ProtoMol::ValueEnum::Enum VECTOR3D framework/base/ValueType.h /^ VECTOR3D,$/;" e enum:ProtoMol::ValueEnum::Enum VECTOR3DBLOCK_H framework/base/Vector3DBlock.h 3;" d VECTOR3D_H framework/base/Vector3D.h 3;" d VECTOR_H framework/base/Vector.h 3;" d VERSION protomol_config.h 177;" d VIRIALXX framework/base/ScalarStructure.h /^ VIRIALXX,$/;" e enum:ProtoMol::ScalarStructure::Index VIRIALXY framework/base/ScalarStructure.h /^ VIRIALXY,$/;" e enum:ProtoMol::ScalarStructure::Index VIRIALXZ framework/base/ScalarStructure.h /^ VIRIALXZ,$/;" e enum:ProtoMol::ScalarStructure::Index VIRIALYX framework/base/ScalarStructure.h /^ VIRIALYX,$/;" e enum:ProtoMol::ScalarStructure::Index VIRIALYY framework/base/ScalarStructure.h /^ VIRIALYY,$/;" e enum:ProtoMol::ScalarStructure::Index VIRIALYZ framework/base/ScalarStructure.h /^ VIRIALYZ,$/;" e enum:ProtoMol::ScalarStructure::Index VIRIALZX framework/base/ScalarStructure.h /^ VIRIALZX,$/;" e enum:ProtoMol::ScalarStructure::Index VIRIALZY framework/base/ScalarStructure.h /^ VIRIALZY,$/;" e enum:ProtoMol::ScalarStructure::Index VIRIALZZ framework/base/ScalarStructure.h /^ VIRIALZZ,$/;" e enum:ProtoMol::ScalarStructure::Index VISITED framework/topology/AngleInfo.h /^ VISITED = 10001,$/;" e enum:ProtoMol::AngleInfo::AngleType VMDSOCKINTERNAL framework/imd/vmdsock.cpp 29;" d file: VacuumBoundaryConditions framework/topology/VacuumBoundaryConditions.h /^ class VacuumBoundaryConditions {$/;" c namespace:ProtoMol Value framework/base/Value.cpp /^ Value::Value():myValue(NULL){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(Real value ):myValue(new Holder > (value)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(Real value, const Undefined*):myValue(new Holder > (value,false)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(bool value ):myValue(new Holder > (value)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(bool value, const Undefined*):myValue(new Holder > (value,false)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(const Value& other):myValue(other.myValue ? other.myValue->clone() : NULL){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(const Value& value, const Undefined*):myValue(value.myValue ? value.myValue->clone() : NULL){clear();}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(const ValueType::Force& value ):myValue(new Holder > (value)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(const ValueType::Force& value, const Undefined*):myValue(new Holder > (value,false)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(const ValueType::Integrator& value):myValue(new Holder >(value)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(const ValueType::Integrator& value, const Undefined*):myValue(new Holder >(value,false)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(const Vector3D& value ):myValue(new Holder > (value)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(const Vector3D& value, const Undefined*):myValue(new Holder > (value,false)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(const char* value ):myValue(new Holder > (value)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(const char* value, const Undefined*):myValue(new Holder > (value,false)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(const std::string& value ):myValue(new Holder > (value)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(const std::string& value, const Undefined*):myValue(new Holder > (value,false)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(const vector& value ):myValue(new Holder > > (value)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(const vector& value, const Undefined*):myValue(new Holder > > (value,false)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(int value ):myValue(new Holder > (value)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(int value, const Undefined*):myValue(new Holder > (value,false)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(unsigned int value ):myValue(new Holder > (value)){}$/;" f class:ProtoMol::Value Value framework/base/Value.cpp /^ Value::Value(unsigned int value, const Undefined*):myValue(new Holder > (value,false)){}$/;" f class:ProtoMol::Value Value framework/base/Value.h /^ Value(const T&, const C&, const Value& value):myValue(new Holder, C>(ValueTraits::init())){$/;" f class:ProtoMol::Value Value framework/base/Value.h /^ Value(const T& value, const C&):myValue(new Holder, C>(value)){}$/;" f class:ProtoMol::Value Value framework/base/Value.h /^ Value(const T& value, const C&, const Undefined*):myValue(new Holder, C>(value,false)){}$/;" f class:ProtoMol::Value Value framework/base/Value.h /^ class Value{$/;" c namespace:ProtoMol ValueEnum framework/base/ValueType.h /^ class ValueEnum {$/;" c namespace:ProtoMol ValueMapType framework/base/Configuration.h /^ typedef std::map ValueMapType;$/;" t class:ProtoMol::Configuration ValueTraits framework/base/ValueType.h /^ struct ValueTraits{$/;" s namespace:ProtoMol ValueTraits framework/base/ValueType.h /^ struct ValueTraits{$/;" s namespace:ProtoMol ValueTraits framework/base/ValueType.h /^ struct ValueTraits{$/;" s namespace:ProtoMol ValueTraits framework/base/ValueType.h /^ struct ValueTraits{$/;" s namespace:ProtoMol ValueTraits framework/base/ValueType.h /^ struct ValueTraits{$/;" s namespace:ProtoMol ValueTraits framework/base/ValueType.h /^ struct ValueTraits : public ValueTraits {}; $/;" s namespace:ProtoMol ValueTraits framework/base/ValueType.h /^ struct ValueTraits : public ValueTraits {}; $/;" s namespace:ProtoMol ValueTraits framework/base/ValueType.h /^ struct ValueTraits{$/;" s namespace:ProtoMol ValueTraits framework/base/ValueType.h /^ struct ValueTraits{$/;" s namespace:ProtoMol ValueTraits framework/base/ValueType.h /^ struct ValueTraits >{$/;" s namespace:ProtoMol ValueTraits framework/base/ValueType.h /^ struct ValueTraits{$/;" s namespace:ProtoMol ValueType framework/base/ValueType.h /^ typedef AbstractEnumType ValueType;$/;" t namespace:ProtoMol Vect framework/base/Array_NoPartialSpecialization.h /^ const std::vector & Vect() const $/;" f class:ProtoMol::ArraySize Vector framework/base/Array_NoPartialSpecialization.h /^ std::vector & Vector;$/;" m class:ProtoMol::ArraySize Vector framework/base/Array_NoPartialSpecialization.h /^ std::vector Vector;$/;" m class:ProtoMol::ArraySizes Vector framework/base/Vector.h /^ Vector(void){}$/;" f class:ProtoMol::Vector Vector framework/base/Vector.h /^ explicit Vector(T elm) { $/;" f class:ProtoMol::Vector Vector framework/base/Vector.h /^ class Vector {$/;" c namespace:ProtoMol Vector3D framework/base/Vector3D.h /^ Vector3D():x(0.0),y(0.0),z(0.0) {}$/;" f struct:ProtoMol::Vector3D Vector3D framework/base/Vector3D.h /^ Vector3D(Real X, Real Y, Real Z):x(X),y(Y),z(Z) {}$/;" f struct:ProtoMol::Vector3D Vector3D framework/base/Vector3D.h /^ Vector3D(const Vector3D &c) {$/;" f struct:ProtoMol::Vector3D Vector3D framework/base/Vector3D.h /^ struct Vector3D {$/;" s namespace:ProtoMol Vector3DBlock framework/base/Vector3DBlock.h /^ Vector3DBlock() : Proxy(),vec() {} $/;" f class:ProtoMol::Vector3DBlock Vector3DBlock framework/base/Vector3DBlock.h /^ Vector3DBlock(size_type n, const Vector3D& t): Proxy(),vec(n,t) {} $/;" f class:ProtoMol::Vector3DBlock Vector3DBlock framework/base/Vector3DBlock.h /^ explicit Vector3DBlock(size_type n) : Proxy(),vec(n) {} $/;" f class:ProtoMol::Vector3DBlock Vector3DBlock framework/base/Vector3DBlock.h /^ class Vector3DBlock: public Proxy{$/;" c namespace:ProtoMol Vector3DIdx tools/bccAnalyzer.cpp /^ Vector3DIdx():v(Vector3D(0.0,0.0,0.0)),i(-1){}$/;" f class:Vector3DIdx Vector3DIdx tools/bccAnalyzer.cpp /^ Vector3DIdx(const Vector3D& a):v(a),i(-1){}$/;" f class:Vector3DIdx Vector3DIdx tools/bccAnalyzer.cpp /^ Vector3DIdx(const Vector3D& a, int b):v(a),i(b){}$/;" f class:Vector3DIdx Vector3DIdx tools/bccAnalyzer.cpp /^class Vector3DIdx {$/;" c file: VectorPacker framework/base/Vector.h /^ VectorPacker(std::vector & v):myVector(v){}$/;" f class:ProtoMol::VectorPacker VectorPacker framework/base/Vector.h /^ class VectorPacker{$/;" c namespace:ProtoMol Vol framework/base/XSC.h /^ Real Vol, Epsilon_vel;$/;" m struct:ProtoMol::XSC W framework/integrators/NPTVerletIntegrator.h /^ Real W; \/\/ Barostat mass. Units: (kcal fs^2 \/ mol)$/;" m class:ProtoMol::NPTVerletIntegrator WALL framework/base/TimerStatistic.h /^ WALL = 0, $/;" e enum:ProtoMol::TimerStatistic::Enum WRAPPERMETAFORCE_H framework/forces/WrapperMetaForce.h 3;" d WRITER_H framework/io/Writer.h 3;" d W_OK framework/base/systemutilities.cpp 16;" d file: WindowAve framework/base/mathutilities.h /^ WindowAve(unsigned int max = 25 ) : maxItems(max), sumItems(0.0) {}$/;" f class:ProtoMol::WindowAve WindowAve framework/base/mathutilities.h /^ class WindowAve {$/;" c namespace:ProtoMol WorkState framework/parallel/Parallel.h /^ enum WorkState {$/;" g class:ProtoMol::Parallel WrapperMetaForce framework/forces/WrapperMetaForce.cpp /^ WrapperMetaForce::WrapperMetaForce(string id, bool minimal, Force* force, string forceAlias):MetaForce(),keyword(id),myMinimal(minimal){$/;" f class:ProtoMol::WrapperMetaForce WrapperMetaForce framework/forces/WrapperMetaForce.cpp /^ WrapperMetaForce::WrapperMetaForce(string id, bool minimal, Force* force1, string forceAlias1, Force* force2, string forceAlias2):MetaForce(),keyword(id),myMinimal(minimal){$/;" f class:ProtoMol::WrapperMetaForce WrapperMetaForce framework/forces/WrapperMetaForce.h /^ class WrapperMetaForce : public MetaForce {$/;" c namespace:ProtoMol Writer framework/io/Writer.cpp /^ Writer::Writer():File(std::ios::out|std::ios::trunc){}$/;" f class:ProtoMol::Writer Writer framework/io/Writer.cpp /^ Writer::Writer(const string& filename):File(std::ios::out|std::ios::trunc,filename){$/;" f class:ProtoMol::Writer Writer framework/io/Writer.cpp /^ Writer::Writer(std::ios::openmode mode):File(std::ios::out|mode){}$/;" f class:ProtoMol::Writer Writer framework/io/Writer.cpp /^ Writer::Writer(std::ios::openmode mode,const string& filename):File(std::ios::out|mode,filename){$/;" f class:ProtoMol::Writer Writer framework/io/Writer.h /^ class Writer : public File {$/;" c namespace:ProtoMol XFIGWRITER_H framework/io/XFigWriter.h 3;" d XFigWriter framework/io/XFigWriter.cpp /^ XFigWriter::XFigWriter():Writer(),$/;" f class:ProtoMol::XFigWriter XFigWriter framework/io/XFigWriter.cpp /^ XFigWriter::XFigWriter(const std::string& filename):Writer(filename),$/;" f class:ProtoMol::XFigWriter XFigWriter framework/io/XFigWriter.h /^ class XFigWriter : public Writer {$/;" c namespace:ProtoMol XSC framework/base/XSC.h /^ struct XSC{$/;" s namespace:ProtoMol XSC_H framework/base/XSC.h 3;" d XYZ framework/base/XYZ.h /^ XYZ(){};$/;" f struct:ProtoMol::XYZ XYZ framework/base/XYZ.h /^ XYZ(size_t n):coords(n,Vector3D(0.0,0.0,0.0)),names(n,std::string("")){}$/;" f struct:ProtoMol::XYZ XYZ framework/base/XYZ.h /^ struct XYZ{$/;" s namespace:ProtoMol XYZ framework/frontend/InputPosVelType.h /^ XYZ,$/;" e enum:ProtoMol::InputPosVelEnum::Enum XYZ tools/bccAnalyzer.cpp /^ XYZ,$/;" e enum:Format::Type file: XYZBIN framework/frontend/InputPosVelType.h /^ XYZBIN,$/;" e enum:ProtoMol::InputPosVelEnum::Enum XYZBIN tools/bccAnalyzer.cpp /^ XYZBIN,$/;" e enum:Format::Type file: XYZBINREADER_H framework/io/XYZBinReader.h 3;" d XYZBINWRITER_H framework/io/XYZBinWriter.h 3;" d XYZBinReader framework/io/XYZBinReader.cpp /^ XYZBinReader::XYZBinReader():Reader(std::ios::binary),myCoords(NULL){}$/;" f class:ProtoMol::XYZBinReader XYZBinReader framework/io/XYZBinReader.cpp /^ XYZBinReader::XYZBinReader(const std::string& filename):Reader(std::ios::binary,filename),myCoords(NULL){}$/;" f class:ProtoMol::XYZBinReader XYZBinReader framework/io/XYZBinReader.h /^ class XYZBinReader : public Reader {$/;" c namespace:ProtoMol XYZBinWriter framework/io/XYZBinWriter.cpp /^ XYZBinWriter::XYZBinWriter(bool isLittleEndian, unsigned int size):$/;" f class:ProtoMol::XYZBinWriter XYZBinWriter framework/io/XYZBinWriter.cpp /^ XYZBinWriter::XYZBinWriter(const char* filename, bool isLittleEndian, unsigned int size):$/;" f class:ProtoMol::XYZBinWriter XYZBinWriter framework/io/XYZBinWriter.cpp /^ XYZBinWriter::XYZBinWriter(const std::string& filename, bool isLittleEndian, unsigned int size):$/;" f class:ProtoMol::XYZBinWriter XYZBinWriter framework/io/XYZBinWriter.h /^ class XYZBinWriter : public Writer {$/;" c namespace:ProtoMol XYZREADER_H framework/io/XYZReader.h 3;" d XYZReader framework/io/XYZReader.cpp /^ XYZReader::XYZReader():Reader(),myCoords(NULL),myNames(NULL){}$/;" f class:ProtoMol::XYZReader XYZReader framework/io/XYZReader.cpp /^ XYZReader::XYZReader(const std::string& filename):Reader(filename),myCoords(NULL),myNames(NULL){}$/;" f class:ProtoMol::XYZReader XYZReader framework/io/XYZReader.h /^ class XYZReader : public Reader {$/;" c namespace:ProtoMol XYZTRA tools/bccAnalyzer.cpp /^ XYZTRA};$/;" e enum:Format::Type file: XYZTRAJECTORYREADER_H framework/io/XYZTrajectoryReader.h 3;" d XYZTRAJECTORYWRITER_H framework/io/XYZTrajectoryWriter.h 3;" d XYZTrajectoryReader framework/io/XYZTrajectoryReader.cpp /^ XYZTrajectoryReader::XYZTrajectoryReader():Reader(),myCoords(NULL),myNames(NULL),myFirst(true){}$/;" f class:ProtoMol::XYZTrajectoryReader XYZTrajectoryReader framework/io/XYZTrajectoryReader.cpp /^ XYZTrajectoryReader::XYZTrajectoryReader(const std::string& filename):Reader(filename),myCoords(NULL),myNames(NULL),myFirst(true){}$/;" f class:ProtoMol::XYZTrajectoryReader XYZTrajectoryReader framework/io/XYZTrajectoryReader.h /^ class XYZTrajectoryReader : public Reader {$/;" c namespace:ProtoMol XYZTrajectoryWriter framework/io/XYZTrajectoryWriter.cpp /^ XYZTrajectoryWriter::XYZTrajectoryWriter():$/;" f class:ProtoMol::XYZTrajectoryWriter XYZTrajectoryWriter framework/io/XYZTrajectoryWriter.cpp /^ XYZTrajectoryWriter::XYZTrajectoryWriter(const std::string& filename):$/;" f class:ProtoMol::XYZTrajectoryWriter XYZTrajectoryWriter framework/io/XYZTrajectoryWriter.h /^ class XYZTrajectoryWriter : public Writer {$/;" c namespace:ProtoMol XYZWRITER_H framework/io/XYZWriter.h 3;" d XYZWriter framework/io/XYZWriter.cpp /^ XYZWriter::XYZWriter():Writer(){}$/;" f class:ProtoMol::XYZWriter XYZWriter framework/io/XYZWriter.cpp /^ XYZWriter::XYZWriter(const std::string& filename):Writer(filename){}$/;" f class:ProtoMol::XYZWriter XYZWriter framework/io/XYZWriter.h /^ class XYZWriter : public Writer {$/;" c namespace:ProtoMol XYZ_H framework/base/XYZ.h 3;" d X_AXIS framework/topology/topologyutilities.h /^ enum {X_AXIS,Y_AXIS,Z_AXIS};$/;" e enum:ProtoMol:: Y_AXIS framework/topology/topologyutilities.h /^ enum {X_AXIS,Y_AXIS,Z_AXIS};$/;" e enum:ProtoMol:: ZERO framework/base/ConstraintValueType.h /^ ZERO,$/;" e enum:ProtoMol::ConstraintValueEnum::Enum Z_AXIS framework/topology/topologyutilities.h /^ enum {X_AXIS,Y_AXIS,Z_AXIS};$/;" e enum:ProtoMol:: Zero framework/base/ConstraintValueType.h /^ typedef Enum2Type Zero;$/;" t class:ProtoMol::ConstraintValueEnum _ESV_COMPLEX_ framework/base/FFTComplex.cpp 12;" d file: _TIMER_H framework/base/Timer.h 38;" d __SSTREAM__ framework/base/sstream_local.h 29;" d __my_sb framework/base/sstream_local.h /^ stringbuf __my_sb;$/;" m class:std::stringstreambase a framework/base/PAR.h /^ Real a; \/\/\/< epsilon$/;" m struct:ProtoMol::PAR::Nbfix a1 framework/integrators/EquilibriumMOLLYIntegrator.h /^ int a1; \/\/ Global index of atom 1, GenericTopology)$/;" m struct:ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond a1 framework/topology/ExclusionTable.h /^ int a1,a2;$/;" m struct:ProtoMol::ExclusionPair a14 framework/base/PAR.h /^ Real a14; \/\/\/< epsilon 14$/;" m struct:ProtoMol::PAR::Nbfix a2 framework/integrators/EquilibriumMOLLYIntegrator.h /^ int a2; \/\/ Global index of atom 1, GenericTopology)$/;" m struct:ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond a2 framework/topology/ExclusionTable.h /^ int a1,a2;$/;" m struct:ProtoMol::ExclusionPair aborting framework/base/Report.cpp /^ MyStreamer& aborting(MyStreamer& stream){$/;" f namespace:ProtoMol::Report absF2 framework/forces/CompareForce.h /^ Real absF2,rFavg,rFmax,rPE; $/;" m struct:ProtoMol::CompareForce::CompareError absindex framework/base/LookUpTableBase.h /^ static int absindex(Real r){$/;" f class:ProtoMol::LookUpTableBase acceptors framework/base/PSF.h /^ std::vector acceptors;$/;" m class:ProtoMol::PSF access framework/base/systemutilities.cpp 12;" d file: accumulateEnergy framework/forces/CoulombEwaldRealForce.h /^ static void accumulateEnergy(ScalarStructure* energies, Real energy) {$/;" f class:ProtoMol::CoulombEwaldRealForce accumulateEnergy framework/forces/CoulombEwaldRealTableForce.h /^ static void accumulateEnergy(ScalarStructure* energies, Real energy) {$/;" f class:ProtoMol::CoulombEwaldRealTableForce accumulateEnergy framework/forces/CoulombForce.h /^ static void accumulateEnergy(ScalarStructure* energies, Real energy) {$/;" f class:ProtoMol::CoulombForce accumulateEnergy framework/forces/CoulombMultiGridDirectForce.h /^ static void accumulateEnergy(ScalarStructure* energies, Real energy) {$/;" f class:ProtoMol::CoulombMultiGridDirectForce accumulateEnergy framework/forces/CoulombMultiGridDirectTableForce.h /^ static void accumulateEnergy(ScalarStructure* energies, Real energy) {$/;" f class:ProtoMol::CoulombMultiGridDirectTableForce accumulateEnergy framework/forces/CoulombTableForce.h /^ static void accumulateEnergy(ScalarStructure* energies, Real energy) {$/;" f class:ProtoMol::CoulombTableForce accumulateEnergy framework/forces/GravitationForce.h /^ static void accumulateEnergy(ScalarStructure* energies, Real energy) {(*energies)[ScalarStructure::OTHER] += energy;}$/;" f class:ProtoMol::GravitationForce accumulateEnergy framework/forces/LennardJonesForce.h /^ static void accumulateEnergy(ScalarStructure* energies, Real energy) {$/;" f class:ProtoMol::LennardJonesForce accumulateEnergy framework/forces/LennardJonesTableForce.h /^ static void accumulateEnergy(ScalarStructure* energies, Real energy) {$/;" f class:ProtoMol::LennardJonesTableForce accumulateEnergy framework/forces/MagneticDipoleForce.h /^ static void accumulateEnergy(ScalarStructure* energies, Real energy) {$/;" f class:ProtoMol::MagneticDipoleForce accumulateNegTo framework/base/ReducedHessAngle.cpp /^ void ReducedHessAngle::accumulateNegTo(int i, int j, Matrix3by3 x)$/;" f class:ProtoMol::ReducedHessAngle accumulateTo framework/base/ReducedHessAngle.cpp /^ void ReducedHessAngle::accumulateTo(int i, int j, Matrix3by3 x)$/;" f class:ProtoMol::ReducedHessAngle add framework/base/Vector3D.h /^ Vector3D add(const Vector3D& b) const {return (*this)+b;}$/;" f struct:ProtoMol::Vector3D add framework/base/mathutilities.h /^ inline void WindowAve::add( Real newValue ) {$/;" f class:ProtoMol::WindowAve add framework/frontend/OutputCache.h /^ void add(const PAR& par){myPAR = par;}$/;" f class:ProtoMol::OutputCache add framework/frontend/OutputCache.h /^ void add(const PSF& psf){myPSF = psf;}$/;" f class:ProtoMol::OutputCache add framework/frontend/OutputCache.h /^ void add(const Real *replicaHistory) {myReplicaHistory = replicaHistory;}$/;" f class:ProtoMol::OutputCache add framework/frontend/OutputCache.h /^ void add(const iSGPAR& par){myiSGPAR = par;}$/;" f class:ProtoMol::OutputCache add framework/frontend/OutputCache.h /^ void add(const std::vector& pdbAtoms){myAtoms = pdbAtoms;}$/;" f class:ProtoMol::OutputCache add framework/frontend/OutputCache.h /^ void add(const std::vector &REMExchangeRate) {myREMRates = REMExchangeRate;}$/;" f class:ProtoMol::OutputCache add framework/topology/ExclusionTable.cpp /^ void ExclusionTable::add(int atom1, int atom2, ExclusionClass type) {$/;" f class:ProtoMol::ExclusionTable addBond framework/topology/AngleInfo.cpp /^ void AngleInfo::addBond(int atom) {$/;" f class:ProtoMol::AngleInfo addDoKeyword framework/frontend/Output.h /^ virtual bool addDoKeyword() const{return true;}$/;" f class:ProtoMol::Output addDoKeyword framework/frontend/OutputScreen.h /^ virtual bool addDoKeyword() const {return false;}$/;" f class:ProtoMol::OutputScreen addElement framework/base/Stack.h /^ void Stack::addElement(T newElement) {$/;" f class:ProtoMol::Stack addExtendedForce framework/forces/ForceGroup.cpp /^ void ForceGroup::addExtendedForce(ExtendedForce *force) {$/;" f class:ProtoMol::ForceGroup addForce framework/forces/ForceGroup.cpp /^ void ForceGroup::addForce(Force *force){$/;" f class:ProtoMol::ForceGroup addForce framework/forces/WrapperMetaForce.cpp /^ void WrapperMetaForce::addForce(Force* force, string forceAlias){$/;" f class:ProtoMol::WrapperMetaForce addMetaForce framework/forces/ForceGroup.cpp /^ void ForceGroup::addMetaForce(MetaForce *force) {$/;" f class:ProtoMol::ForceGroup addModifier framework/integrators/Integrator.cpp /^ void Integrator::addModifier(Modifier* modifier){$/;" f class:ProtoMol::Integrator addModifierAfterInitialize framework/integrators/Integrator.h /^ virtual void addModifierAfterInitialize(){}$/;" f class:ProtoMol::Integrator addModifierAfterInitialize framework/integrators/NPTVerletIntegrator.cpp /^ void NPTVerletIntegrator::addModifierAfterInitialize() {$/;" f class:ProtoMol::NPTVerletIntegrator addModifierAfterInitialize framework/integrators/NVTVerletIntegrator.cpp /^ void NVTVerletIntegrator::addModifierAfterInitialize() {$/;" f class:ProtoMol::NVTVerletIntegrator addModifierAfterInitialize framework/integrators/NoseNVTLeapfrogIntegrator.cpp /^ void NoseNVTLeapfrogIntegrator::addModifierAfterInitialize(){$/;" f class:ProtoMol::NoseNVTLeapfrogIntegrator addModifierAfterInitialize framework/integrators/STSIntegrator.cpp /^ void STSIntegrator::addModifierAfterInitialize(){$/;" f class:ProtoMol::STSIntegrator addModifierBeforeInitialize framework/integrators/Integrator.h /^ virtual void addModifierBeforeInitialize(){}$/;" f class:ProtoMol::Integrator addModifierBeforeInitialize framework/integrators/MOLLYIntegrator.cpp /^ void MOLLYIntegrator::addModifierBeforeInitialize(){$/;" f class:ProtoMol::MOLLYIntegrator addMolVirial framework/base/ScalarStructure.cpp /^ void ScalarStructure::addMolVirial(const Vector3D &force12,$/;" f class:ProtoMol::ScalarStructure addMollyForce framework/forces/ForceGroup.cpp /^ void ForceGroup::addMollyForce(MollyForce *force) {$/;" f class:ProtoMol::ForceGroup addRandomForceToMyForce framework/integrators/BBKIntegrator.cpp /^ void BBKIntegrator::addRandomForceToMyForce() {$/;" f class:ProtoMol::BBKIntegrator addSystemForce framework/forces/ForceGroup.cpp /^ void ForceGroup::addSystemForce(SystemForce *force) {$/;" f class:ProtoMol::ForceGroup addToCache framework/frontend/OutputCollection.h /^ void addToCache(const T& obj){myCache->add(obj);}$/;" f class:ProtoMol::OutputCollection addToForceGroup framework/forces/ExtendedForce.cpp /^ void ExtendedForce::addToForceGroup(ForceGroup* forceGroup){$/;" f class:ProtoMol::ExtendedForce addToForceGroup framework/forces/MetaForce.cpp /^ void MetaForce::addToForceGroup(ForceGroup* forceGroup){$/;" f class:ProtoMol::MetaForce addToForceGroup framework/forces/MollyForce.cpp /^ void MollyForce::addToForceGroup(ForceGroup* forceGroup){$/;" f class:ProtoMol::MollyForce addToForceGroup framework/forces/SystemForce.cpp /^ void SystemForce::addToForceGroup(ForceGroup* forceGroup){$/;" f class:ProtoMol::SystemForce addVelocityVirial framework/topology/topologyutilities.cpp /^ void addVelocityVirial(ScalarStructure* energies, $/;" f namespace:ProtoMol addVirial framework/base/ScalarStructure.cpp /^ void ScalarStructure::addVirial(const Vector3D & force12, const Vector3D &diff){$/;" f class:ProtoMol::ScalarStructure addVirial framework/base/ScalarStructure.cpp /^ void ScalarStructure::addVirial(const Vector3D & force12, const Vector3D &diff,$/;" f class:ProtoMol::ScalarStructure addr framework/imd/vmdsock.h /^ struct sockaddr_in addr; \/\/< address of socket provided by bind() $/;" m struct:ProtoMol::IMD:: addrlen framework/imd/vmdsock.h /^ int addrlen; \/\/< size of the addr struct $/;" m struct:ProtoMol::IMD:: adjustAlias framework/base/Makeable.h /^ T* adjustAlias(T* obj) const{$/;" f class:ProtoMol::Makeable adjustWithDefaultParameters framework/base/Makeable.h /^ virtual bool adjustWithDefaultParameters(std::vector& values, const Configuration* \/*config*\/) const{ return checkParameterTypes(values);}$/;" f class:ProtoMol::Makeable adjustWithDefaultParameters framework/frontend/OutputBSDL.cpp /^ bool OutputBSDL::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputBSDL adjustWithDefaultParameters framework/frontend/OutputDCDTrajectory.cpp /^ bool OutputDCDTrajectory::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputDCDTrajectory adjustWithDefaultParameters framework/frontend/OutputDihedrals.cpp /^ bool OutputDihedrals::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputDihedrals adjustWithDefaultParameters framework/frontend/OutputFile.cpp /^ bool OutputFile::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputFile adjustWithDefaultParameters framework/frontend/OutputFinalPDBPos.cpp /^ bool OutputFinalPDBPos::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputFinalPDBPos adjustWithDefaultParameters framework/frontend/OutputFinalXYZBinPos.cpp /^ bool OutputFinalXYZBinPos::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputFinalXYZBinPos adjustWithDefaultParameters framework/frontend/OutputFinalXYZPos.cpp /^ bool OutputFinalXYZPos::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputFinalXYZPos adjustWithDefaultParameters framework/frontend/OutputPDBFramePos.cpp /^ bool OutputPDBFramePos::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputPDBFramePos adjustWithDefaultParameters framework/frontend/OutputPaulTrap.cpp /^ bool OutputPaulTrap::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputPaulTrap adjustWithDefaultParameters framework/frontend/OutputREMExchangeRate.cpp /^ bool OutputREMExchangeRate::adjustWithDefaultParameters(vector &values, const Configuration *config) const {$/;" f class:ProtoMol::OutputREMExchangeRate adjustWithDefaultParameters framework/frontend/OutputREMHistory.cpp /^ bool OutputREMHistoryFile::adjustWithDefaultParameters(vector &values, const Configuration *config) const {$/;" f class:ProtoMol::OutputREMHistoryFile adjustWithDefaultParameters framework/frontend/OutputScreen.cpp /^ bool OutputScreen::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputScreen adjustWithDefaultParameters framework/frontend/OutputState.cpp /^ bool OutputState::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputState adjustWithDefaultParameters framework/frontend/OutputXYZBinTrajectoryPos.cpp /^ bool OutputXYZBinTrajectoryPos::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputXYZBinTrajectoryPos adjustWithDefaultParameters framework/frontend/OutputXYZBinTrajectoryVel.cpp /^ bool OutputXYZBinTrajectoryVel::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputXYZBinTrajectoryVel adjustWithDefaultParameters framework/frontend/OutputXYZTrajectoryForce.cpp /^ bool OutputXYZTrajectoryForce::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputXYZTrajectoryForce adjustWithDefaultParameters framework/frontend/OutputXYZTrajectoryPos.cpp /^ bool OutputXYZTrajectoryPos::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputXYZTrajectoryPos adjustWithDefaultParameters framework/frontend/OutputXYZTrajectoryVel.cpp /^ bool OutputXYZTrajectoryVel::adjustWithDefaultParameters(vector& values, const Configuration* config) const{$/;" f class:ProtoMol::OutputXYZTrajectoryVel adoptMediForceModifier framework/integrators/Integrator.cpp /^ void Integrator::adoptMediForceModifier(Modifier* modifier){$/;" f class:ProtoMol::Integrator adoptOutput framework/frontend/OutputCollection.cpp /^ void OutputCollection::adoptOutput(Output* output){$/;" f class:ProtoMol::OutputCollection adoptPostDriftOrNextModifier framework/integrators/Integrator.cpp /^ void Integrator::adoptPostDriftOrNextModifier(Modifier* modifier){$/;" f class:ProtoMol::Integrator adoptPostForceModifier framework/integrators/Integrator.cpp /^ void Integrator::adoptPostForceModifier(Modifier* modifier){$/;" f class:ProtoMol::Integrator adoptPostStepModifier framework/integrators/Integrator.cpp /^ void Integrator::adoptPostStepModifier(Modifier* modifier){$/;" f class:ProtoMol::Integrator adoptPreDriftOrNextModifier framework/integrators/Integrator.cpp /^ void Integrator::adoptPreDriftOrNextModifier(Modifier* modifier){$/;" f class:ProtoMol::Integrator adoptPreForceModifier framework/integrators/Integrator.cpp /^ void Integrator::adoptPreForceModifier(Modifier* modifier){$/;" f class:ProtoMol::Integrator adoptPreStepModifier framework/integrators/Integrator.cpp /^ void Integrator::adoptPreStepModifier(Modifier* modifier){$/;" f class:ProtoMol::Integrator allReduce framework/parallel/Parallel-FD.cpp /^ void allReduce(ScalarStructure* energies){$/;" f namespace:ProtoMol allReduce framework/parallel/Parallel-FD.cpp /^ void allReduce(T* begin, T* end){$/;" f namespace:ProtoMol allReduce framework/parallel/Parallel-FD.cpp /^ void allReduce(Vector3DBlock* coords){$/;" f namespace:ProtoMol allReduce framework/parallel/Parallel.cpp /^ void allReduce(ScalarStructure* energies){$/;" f namespace:ProtoMol allReduce framework/parallel/Parallel.cpp /^ void allReduce(T* begin, T* end){$/;" f namespace:ProtoMol allReduce framework/parallel/Parallel.cpp /^ void allReduce(Vector3DBlock* coords){$/;" f namespace:ProtoMol allReduceScalar framework/parallel/Parallel-FD.cpp /^ void allReduceScalar(T& begin){$/;" f namespace:ProtoMol allReduceScalar framework/parallel/Parallel.cpp /^ void allReduceScalar(T& begin){$/;" f namespace:ProtoMol allgather framework/parallel/Parallel-FD.cpp /^ void Parallel::allgather(Real *, int, Real *) {}$/;" f class:ProtoMol::Parallel allgather framework/parallel/Parallel-FD.cpp /^ void Parallel::allgather(Real *data, int num, Real *data_array) {$/;" f class:ProtoMol::Parallel allgather framework/parallel/Parallel.cpp /^ void Parallel::allgather(Real *, int, Real *) {}$/;" f class:ProtoMol::Parallel allgather framework/parallel/Parallel.cpp /^ void Parallel::allgather(Real *data, int num, Real *data_array) {$/;" f class:ProtoMol::Parallel allnodes framework/base/Report.cpp /^ MyStreamer& allnodes(MyStreamer& stream){$/;" f namespace:ProtoMol::Report allnodesserial framework/base/Report.cpp /^ MyStreamer& allnodesserial(MyStreamer& stream){$/;" f namespace:ProtoMol::Report allslavesserial framework/base/Report.cpp /^ MyStreamer& allslavesserial(MyStreamer& stream){$/;" f namespace:ProtoMol::Report alphaLJ framework/base/Atom.h /^ Real alphaLJ;$/;" m struct:ProtoMol::Atom altLoc framework/base/PDB.h /^ std::string altLoc; \/\/\/< alternate_location $/;" m struct:ProtoMol::PDB::Atom angle framework/integrators/BSplineMOLLYIntegrator.h /^ int angle,bond1,bond2;$/;" m struct:ProtoMol::BSplineMOLLYIntegrator::AngleIndex angleList framework/base/Molecule.h /^ std::vector angleList;$/;" m struct:ProtoMol::Molecule angles framework/base/PAR.h /^ std::vector angles;$/;" m class:ProtoMol::PAR angles framework/base/PSF.h /^ std::vector angles;$/;" m class:ProtoMol::PSF angles framework/topology/GenericTopology.h /^ std::vector angles;$/;" m class:ProtoMol::GenericTopology angleval framework/base/PAR.h /^ Real angleval; \/\/\/< angle value$/;" m struct:ProtoMol::PAR::Angle angularMomentum framework/frontend/OutputCache.cpp /^ Vector3D OutputCache::angularMomentum() const{$/;" f class:ProtoMol::OutputCache angularMomentum framework/topology/topologyutilities.cpp /^ Vector3D angularMomentum(const Vector3DBlock *positions, $/;" f namespace:ProtoMol anterpolateCharge framework/base/Grid.h /^ inline void Grid::anterpolateCharge(Real q, const Vector3D& coord, unsigned int index) {$/;" f class:ProtoMol::Grid anterpolateCharge framework/base/MultiGrid.h /^ inline void MultiGrid::anterpolateCharge(Real q, const Vector3D& coord, unsigned int index) {$/;" f class:ProtoMol::MultiGrid anyExclsForThisDelta framework/topology/ExclusionTable.h /^ char* anyExclsForThisDelta;$/;" m class:ProtoMol::ExclusionTable anyExtendedForces framework/forces/ForceGroup.h /^ inline bool ForceGroup::anyExtendedForces(void) const {$/;" f class:ProtoMol::ForceGroup anyForces framework/forces/ForceGroup.h /^ inline bool ForceGroup::anyForces(void) const {$/;" f class:ProtoMol::ForceGroup anyMediForceModify framework/integrators/Integrator.h /^ bool anyMediForceModify() const {return !myMediForceModifiers.empty();};$/;" f class:ProtoMol::Integrator anyMetaForces framework/forces/ForceGroup.h /^ inline bool ForceGroup::anyMetaForces(void) const {$/;" f class:ProtoMol::ForceGroup anyMollyForces framework/forces/ForceGroup.h /^ inline bool ForceGroup::anyMollyForces(void) const {$/;" f class:ProtoMol::ForceGroup anyPostDriftOrNextModify framework/integrators/Integrator.h /^ bool anyPostDriftOrNextModify() const {return !myPostDriftOrNextModifiers.empty();};$/;" f class:ProtoMol::Integrator anyPostForceModify framework/integrators/Integrator.h /^ bool anyPostForceModify() const {return !myPostForceModifiers.empty();};$/;" f class:ProtoMol::Integrator anyPostStepModify framework/integrators/Integrator.h /^ bool anyPostStepModify() const {return !myPostStepModifiers.empty();};$/;" f class:ProtoMol::Integrator anyPreDriftOrNextModify framework/integrators/Integrator.h /^ bool anyPreDriftOrNextModify() const {return !myPreDriftOrNextModifiers.empty();};$/;" f class:ProtoMol::Integrator anyPreForceModify framework/integrators/Integrator.h /^ bool anyPreForceModify() const {return !myPreForceModifiers.empty();};$/;" f class:ProtoMol::Integrator anyPreStepModify framework/integrators/Integrator.h /^ bool anyPreStepModify() const {return !myPreStepModifiers.empty();};$/;" f class:ProtoMol::Integrator anySystemForces framework/forces/ForceGroup.h /^ inline bool ForceGroup::anySystemForces(void) const {$/;" f class:ProtoMol::ForceGroup array_dims framework/base/Array_Fastest.h /^ enum { array_dims = 1 };$/;" e enum:ProtoMol::RefArray:: array_dims framework/base/Array_Fastest.h /^ enum { array_dims = N };$/;" e enum:ProtoMol::Array:: array_dims framework/base/Array_Fastest.h /^ enum { array_dims = N };$/;" e enum:ProtoMol::RefArray:: array_dims framework/base/Array_NoPartialSpecialization.h /^ enum { array_dims = 1 };$/;" e enum:ProtoMol::Array::RefArray:: array_dims framework/base/Array_NoPartialSpecialization.h /^ enum { array_dims = N };$/;" e enum:ProtoMol::Array::RefArray:: array_dims framework/base/Array_NoPartialSpecialization.h /^ enum { array_dims = N };$/;" e enum:ProtoMol::Array:: assign framework/forces/CoulombEwaldRealTableForceBase.h /^ void assign(Real r, Real r1, int ex, Real v, Real d, TReal* val) const{$/;" f class:ProtoMol::CoulombEwaldRealTableForceBase::LookUpValues assign framework/forces/CoulombMultiGridDirectTableForceBase.h /^ void assign(Real , Real r1, int, Real v, Real d, TReal* val) const{$/;" f class:ProtoMol::CoulombMultiGridDirectTableForceBase::LookUpValues assign framework/forces/CoulombTableForceBase.h /^ void assign(Real r, Real r1, int ex, Real v, Real d, TReal* val) const{$/;" f class:ProtoMol::CoulombTableForceBase::LookUpValues assign framework/forces/LennardJonesTableForceBase.h /^ void assign(Real r, Real r1, int ex, Real v, Real d, TReal* val) const{$/;" f class:ProtoMol::LennardJonesTableForceBase::LookUpValues atom framework/base/PAR.h /^ std::string atom; \/\/\/< atom number$/;" m struct:ProtoMol::PAR::Nonbonded atom1 framework/base/PAR.h /^ std::string atom1; \/\/\/< atom 1 number$/;" m struct:ProtoMol::PAR::Angle atom1 framework/base/PAR.h /^ std::string atom1; \/\/\/< atom 1 number$/;" m struct:ProtoMol::PAR::Bond atom1 framework/base/PAR.h /^ std::string atom1; \/\/\/< atom 1 number$/;" m struct:ProtoMol::PAR::Dihedral atom1 framework/base/PAR.h /^ std::string atom1; \/\/\/< atom 1 number$/;" m struct:ProtoMol::PAR::Improper atom1 framework/base/PAR.h /^ std::string atom1; \/\/\/< atom 1 number$/;" m struct:ProtoMol::PAR::Nbfix atom1 framework/base/PAR.h /^ std::string atom1; \/\/\/< atom 1 number$/;" m struct:ProtoMol::PAR::Hbond atom1 framework/base/PSF.h /^ int atom1; \/\/\/< acceptor atom 1 number$/;" m struct:ProtoMol::PSF::Acceptor atom1 framework/base/PSF.h /^ int atom1; \/\/\/< angle atom 1 number$/;" m struct:ProtoMol::PSF::Angle atom1 framework/base/PSF.h /^ int atom1; \/\/\/< bonded atom 1 number$/;" m struct:ProtoMol::PSF::Bond atom1 framework/base/PSF.h /^ int atom1; \/\/\/< dihedral atom 1 number$/;" m struct:ProtoMol::PSF::Dihedral atom1 framework/base/PSF.h /^ int atom1; \/\/\/< donor atom 1 number$/;" m struct:ProtoMol::PSF::Donor atom1 framework/base/PSF.h /^ int atom1; \/\/\/< improper atom 1 number$/;" m struct:ProtoMol::PSF::Improper atom1 framework/base/PSF.h /^ int atom1; \/\/\/< ngrp atom 1 number$/;" m struct:ProtoMol::PSF::Ngrp atom1 framework/base/PSF.h /^ int atom1; \/\/\/< nonbonded atom number$/;" m struct:ProtoMol::PSF::Nonbonded atom1 framework/topology/Angle.h /^ int atom1;$/;" m class:ProtoMol::Angle atom1 framework/topology/Bond.h /^ int atom1;$/;" m struct:ProtoMol::Bond::Constraint atom1 framework/topology/Bond.h /^ int atom1;$/;" m class:ProtoMol::Bond atom1 framework/topology/Torsion.h /^ int atom1; \/\/\/< The first atom in this interaction. $/;" m class:ProtoMol::Torsion atom2 framework/base/PAR.h /^ std::string atom2; \/\/\/< atom 2 number$/;" m struct:ProtoMol::PAR::Angle atom2 framework/base/PAR.h /^ std::string atom2; \/\/\/< atom 2 number$/;" m struct:ProtoMol::PAR::Bond atom2 framework/base/PAR.h /^ std::string atom2; \/\/\/< atom 2 number$/;" m struct:ProtoMol::PAR::Dihedral atom2 framework/base/PAR.h /^ std::string atom2; \/\/\/< atom 2 number$/;" m struct:ProtoMol::PAR::Improper atom2 framework/base/PAR.h /^ std::string atom2; \/\/\/< atom 2 number$/;" m struct:ProtoMol::PAR::Nbfix atom2 framework/base/PAR.h /^ std::string atom2; \/\/\/< atom 2 number$/;" m struct:ProtoMol::PAR::Hbond atom2 framework/base/PSF.h /^ int atom2; \/\/\/< acceptor atom 2 number$/;" m struct:ProtoMol::PSF::Acceptor atom2 framework/base/PSF.h /^ int atom2; \/\/\/< angle atom 2 number$/;" m struct:ProtoMol::PSF::Angle atom2 framework/base/PSF.h /^ int atom2; \/\/\/< bonded atom 2 number$/;" m struct:ProtoMol::PSF::Bond atom2 framework/base/PSF.h /^ int atom2; \/\/\/< dihedral atom 2 number$/;" m struct:ProtoMol::PSF::Dihedral atom2 framework/base/PSF.h /^ int atom2; \/\/\/< donor atom 2 number$/;" m struct:ProtoMol::PSF::Donor atom2 framework/base/PSF.h /^ int atom2; \/\/\/< improper atom 2 number$/;" m struct:ProtoMol::PSF::Improper atom2 framework/base/PSF.h /^ int atom2; \/\/\/< ngrp atom 2 number$/;" m struct:ProtoMol::PSF::Ngrp atom2 framework/topology/Angle.h /^ int atom2;$/;" m class:ProtoMol::Angle atom2 framework/topology/Bond.h /^ int atom2;$/;" m struct:ProtoMol::Bond::Constraint atom2 framework/topology/Bond.h /^ int atom2;$/;" m class:ProtoMol::Bond atom2 framework/topology/Torsion.h /^ int atom2; \/\/\/< The second atom in this interaction. $/;" m class:ProtoMol::Torsion atom3 framework/base/PAR.h /^ std::string atom3; \/\/\/< atom 3 number$/;" m struct:ProtoMol::PAR::Angle atom3 framework/base/PAR.h /^ std::string atom3; \/\/\/< atom 3 number$/;" m struct:ProtoMol::PAR::Dihedral atom3 framework/base/PAR.h /^ std::string atom3; \/\/\/< atom 3 number$/;" m struct:ProtoMol::PAR::Improper atom3 framework/base/PSF.h /^ int atom3; \/\/\/< angle atom 3 number$/;" m struct:ProtoMol::PSF::Angle atom3 framework/base/PSF.h /^ int atom3; \/\/\/< dihedral atom 3 number$/;" m struct:ProtoMol::PSF::Dihedral atom3 framework/base/PSF.h /^ int atom3; \/\/\/< improper atom 3 number$/;" m struct:ProtoMol::PSF::Improper atom3 framework/base/PSF.h /^ int atom3; \/\/\/< ngrp atom 3 number$/;" m struct:ProtoMol::PSF::Ngrp atom3 framework/topology/Angle.h /^ int atom3;$/;" m class:ProtoMol::Angle atom3 framework/topology/Torsion.h /^ int atom3; \/\/\/< The third atom in this interaction. $/;" m class:ProtoMol::Torsion atom4 framework/base/PAR.h /^ std::string atom4; \/\/\/< atom 4 number$/;" m struct:ProtoMol::PAR::Dihedral atom4 framework/base/PAR.h /^ std::string atom4; \/\/\/< atom 4 number$/;" m struct:ProtoMol::PAR::Improper atom4 framework/base/PSF.h /^ int atom4; \/\/\/< dihedral atom 4 number$/;" m struct:ProtoMol::PSF::Dihedral atom4 framework/base/PSF.h /^ int atom4; \/\/\/< improper atom 4 number$/;" m struct:ProtoMol::PSF::Improper atom4 framework/topology/Torsion.h /^ int atom4; \/\/\/< The fourth atom in this interaction.$/;" m class:ProtoMol::Torsion atomNum framework/base/Atom.h /^ int atomNum;$/;" m struct:ProtoMol::Atom atomTypeToSymbolName framework/topology/topologyutilities.cpp /^ string atomTypeToSymbolName(const string& type) {$/;" f namespace:ProtoMol atomTypes framework/topology/GenericTopology.h /^ std::vector atomTypes; $/;" m class:ProtoMol::GenericTopology atom_name framework/base/PSF.h /^ std::string atom_name; \/\/\/< atom name$/;" m struct:ProtoMol::PSF::Atom atom_type framework/base/PSF.h /^ std::string atom_type; \/\/\/< atom type$/;" m struct:ProtoMol::PSF::Atom atoms framework/base/Molecule.h /^ std::vector atoms;$/;" m struct:ProtoMol::Molecule atoms framework/base/PDB.h /^ std::vector atoms;$/;" m struct:ProtoMol::PDB atoms framework/base/PSF.h /^ std::vector atoms;$/;" m class:ProtoMol::PSF atoms framework/topology/GenericTopology.h /^ std::vector atoms; $/;" m class:ProtoMol::GenericTopology averagingPositions framework/integrators/MOLLYIntegrator.cpp /^ void MOLLYIntegrator::averagingPositions(){$/;" f class:ProtoMol::MOLLYIntegrator b framework/base/PAR.h /^ Real b; \/\/\/< sigma$/;" m struct:ProtoMol::PAR::Nbfix b1 framework/integrators/BSplineMOLLYIntegrator.h /^ int b1,b2;$/;" m struct:ProtoMol::BSplineMOLLYIntegrator::BondIndex b14 framework/base/PAR.h /^ Real b14; \/\/\/< sigma 14$/;" m struct:ProtoMol::PAR::Nbfix b2 framework/integrators/BSplineMOLLYIntegrator.h /^ int b1,b2;$/;" m struct:ProtoMol::BSplineMOLLYIntegrator::BondIndex back framework/base/Vector3DBlock.h /^ const_reference back() const {return vec.back();} $/;" f class:ProtoMol::Vector3DBlock back framework/base/Vector3DBlock.h /^ reference back() {return vec.back();} $/;" f class:ProtoMol::Vector3DBlock backward framework/base/FFTComplex.cpp /^ void backward(){zfft3d(-1,myNZ,myNY,myNX,myArray,myNZ,myNY,myFFTCoeff);}$/;" f class:ProtoMol::FFTInternal backward framework/base/FFTComplex.cpp /^ void FFTComplex::backward(){$/;" f class:ProtoMol::FFTComplex backward framework/integrators/Integrator.cpp /^ void Integrator::backward(){$/;" f class:ProtoMol::Integrator basisCell framework/topology/ArrayCellListStructure.h /^ T1 basisCell(const T1& t1) const{$/;" f class:ProtoMol::ArrayCellListStructure bcast framework/parallel/Parallel-FD.cpp /^ void Parallel::bcast(Vector3DBlock* coords) {$/;" f class:ProtoMol::Parallel bcast framework/parallel/Parallel-FD.cpp /^ void Parallel::bcast(Vector3DBlock*) {}$/;" f class:ProtoMol::Parallel bcast framework/parallel/Parallel-FD.cpp /^ void Parallel::bcast(int& n) {$/;" f class:ProtoMol::Parallel bcast framework/parallel/Parallel-FD.cpp /^ void Parallel::bcast(int&) {}$/;" f class:ProtoMol::Parallel bcast framework/parallel/Parallel.cpp /^ void Parallel::bcast(Vector3DBlock* coords) {$/;" f class:ProtoMol::Parallel bcast framework/parallel/Parallel.cpp /^ void Parallel::bcast(Vector3DBlock*) {}$/;" f class:ProtoMol::Parallel bcast framework/parallel/Parallel.cpp /^ void Parallel::bcast(int& n) {$/;" f class:ProtoMol::Parallel bcast framework/parallel/Parallel.cpp /^ void Parallel::bcast(int&) {}$/;" f class:ProtoMol::Parallel bcastSlaves framework/parallel/Parallel-FD.cpp /^ void Parallel::bcastSlaves(Real* begin, Real* end) {$/;" f class:ProtoMol::Parallel bcastSlaves framework/parallel/Parallel-FD.cpp /^ void Parallel::bcastSlaves(Real*, Real*){}$/;" f class:ProtoMol::Parallel bcastSlaves framework/parallel/Parallel.cpp /^ void Parallel::bcastSlaves(Real* begin, Real* end) {$/;" f class:ProtoMol::Parallel bcastSlaves framework/parallel/Parallel.cpp /^ void Parallel::bcastSlaves(Real*, Real*){}$/;" f class:ProtoMol::Parallel begin compilerTests/pngTest.cpp /^ unsigned char* begin() const{return &p[0];}$/;" f class:PPM begin framework/base/Array_Fastest.h /^ const_iterator begin() const { return m_pArrayElements; }$/;" f class:ProtoMol::Array begin framework/base/Array_Fastest.h /^ const_iterator begin() const { return m_pElements; }$/;" f class:ProtoMol::RefArray begin framework/base/Array_Fastest.h /^ iterator begin() { return m_pArrayElements; }$/;" f class:ProtoMol::Array begin framework/base/Array_Fastest.h /^ iterator begin() { return m_pElements; }$/;" f class:ProtoMol::RefArray begin framework/base/Array_NoPartialSpecialization.h /^ const_iterator begin() const { return m_pElements; }$/;" f class:ProtoMol::Array::RefArray begin framework/base/Array_NoPartialSpecialization.h /^ iterator begin() { return m_pElements; }$/;" f class:ProtoMol::Array::RefArray begin framework/base/Array_NoPartialSpecialization.h /^ const_iterator begin() const { return m_pArrayElements; }$/;" f class:ProtoMol::Array begin framework/base/Array_NoPartialSpecialization.h /^ iterator begin() { return m_pArrayElements; }$/;" f class:ProtoMol::Array begin framework/base/Configuration.h /^ const_iterator begin() const {return myValues.begin();}$/;" f class:ProtoMol::Configuration begin framework/base/Configuration.h /^ iterator begin() {return myValues.begin();}$/;" f class:ProtoMol::Configuration begin framework/base/PGM.h /^ unsigned char* begin() const{return &p[0];}$/;" f class:ProtoMol::PGM begin framework/base/PPM.h /^ unsigned char* begin() const{return &p[0];}$/;" f class:ProtoMol::PPM begin framework/base/Vector3DBlock.h /^ const_iterator begin() const {return vec.begin();} $/;" f class:ProtoMol::Vector3DBlock begin framework/base/Vector3DBlock.h /^ iterator begin() {return vec.begin();} $/;" f class:ProtoMol::Vector3DBlock begin framework/frontend/Factory.h /^ static const_iterator begin(){$/;" f class:ProtoMol::Factory begin framework/frontend/OutputCollection.h /^ const_iterator begin() const {return myOutputList.begin();}$/;" f class:ProtoMol::OutputCollection begin framework/frontend/OutputCollection.h /^ iterator begin() {return myOutputList.begin();}$/;" f class:ProtoMol::OutputCollection begin framework/topology/ArrayCellListStructure.h /^ const_iterator begin() const { return myBeginConst;}$/;" f class:ProtoMol::ArrayCellListStructure begin framework/topology/ArrayCellListStructure.h /^ iterator begin() { return myBegin;}$/;" f class:ProtoMol::ArrayCellListStructure blocksCorrection framework/base/MultiGrid.h /^ inline void MultiGrid::blocksCorrection(unsigned int nBlocks){$/;" f class:ProtoMol::MultiGrid bond1 framework/integrators/BSplineMOLLYIntegrator.h /^ int angle,bond1,bond2;$/;" m struct:ProtoMol::BSplineMOLLYIntegrator::AngleIndex bond2 framework/integrators/BSplineMOLLYIntegrator.h /^ int angle,bond1,bond2;$/;" m struct:ProtoMol::BSplineMOLLYIntegrator::AngleIndex bondList framework/base/Molecule.h /^ std::vector bondList;$/;" m struct:ProtoMol::Molecule bondRattleShakeConstraints framework/topology/GenericTopology.h /^ std::vector bondRattleShakeConstraints; $/;" m class:ProtoMol::GenericTopology bonds framework/base/PAR.h /^ std::vector bonds;$/;" m class:ProtoMol::PAR bonds framework/base/PSF.h /^ std::vector bonds;$/;" m class:ProtoMol::PSF bonds framework/topology/GenericTopology.h /^ std::vector bonds; $/;" m class:ProtoMol::GenericTopology bottom framework/integrators/Integrator.cpp /^ Integrator* Integrator::bottom(){$/;" f class:ProtoMol::Integrator bottom framework/integrators/Integrator.cpp /^ const Integrator* Integrator::bottom() const{$/;" f class:ProtoMol::Integrator boundaryConditions framework/forces/NonbondedFullEwaldSystemForce.h /^ PeriodicBoundaryConditions boundaryConditions;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce boundaryConditions framework/forces/NonbondedPMEwaldSystemForce.h /^ PeriodicBoundaryConditions boundaryConditions;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce boundaryConditions framework/topology/SemiGenericTopology.h /^ BoundaryConditions boundaryConditions;$/;" m class:ProtoMol::SemiGenericTopology boundingbox framework/base/Vector3DBlock.cpp /^ void Vector3DBlock::boundingbox(Vector3D& minbb, Vector3D& maxbb) const{$/;" f class:ProtoMol::Vector3DBlock brent framework/frontend/OutputCache.cpp /^ Real OutputCache::brent(Real ax, Real bx, Real cx, Real tol, Real &xmin, int dihindex, bool max) const{$/;" f class:ProtoMol::OutputCache brentMaxima framework/frontend/OutputCache.cpp /^ vector< vector< Real > > OutputCache::brentMaxima(vector dihedralset, bool max) const{$/;" f class:ProtoMol::OutputCache broadcast framework/parallel/Parallel-FD.cpp /^ void broadcast(ScalarStructure* energies){$/;" f namespace:ProtoMol broadcast framework/parallel/Parallel-FD.cpp /^ void broadcast(T* begin, T* end){$/;" f namespace:ProtoMol broadcast framework/parallel/Parallel-FD.cpp /^ void broadcast(Vector3DBlock* coords){$/;" f namespace:ProtoMol broadcast framework/parallel/Parallel.cpp /^ void broadcast(ScalarStructure* energies){$/;" f namespace:ProtoMol broadcast framework/parallel/Parallel.cpp /^ void broadcast(T* begin, T* end){$/;" f namespace:ProtoMol broadcast framework/parallel/Parallel.cpp /^ void broadcast(Vector3DBlock* coords){$/;" f namespace:ProtoMol broadcastScalar framework/parallel/Parallel-FD.cpp /^ void broadcastScalar(T& begin){$/;" f namespace:ProtoMol broadcastScalar framework/parallel/Parallel.cpp /^ void broadcastScalar(T& begin){$/;" f namespace:ProtoMol buf framework/base/sstream_local.h /^ std::string buf;$/;" m class:std::stringbuf bufsize framework/base/sstream_local.h /^ streamsize bufsize;$/;" m class:std::stringbuf buildCellLists framework/topology/buildCellLists.cpp /^ void buildCellLists(const Topology* topo,$/;" f namespace:ProtoMol buildCellLists framework/topology/buildCellLists.cpp /^ void buildCellLists(const Topology* topo,$/;" f namespace:ProtoMol buildExclusionTable framework/frontend/buildTopology.cpp /^ void buildExclusionTable(GenericTopology* topo, const ExclusionType& exclusionType) {$/;" f namespace:ProtoMol buildLatticeVectors framework/topology/PeriodicBoundaryConditions.cpp /^ vector PeriodicBoundaryConditions::buildLatticeVectors(Real cutoff) const{$/;" f class:ProtoMol::PeriodicBoundaryConditions buildLatticeVectors framework/topology/VacuumBoundaryConditions.cpp /^ vector VacuumBoundaryConditions::buildLatticeVectors(Real) const{$/;" f class:ProtoMol::VacuumBoundaryConditions buildMolecularCenterOfMass framework/topology/topologyutilities.cpp /^ void buildMolecularCenterOfMass(const Vector3DBlock *positions, $/;" f namespace:ProtoMol buildMolecularMomentum framework/topology/topologyutilities.cpp /^ void buildMolecularMomentum(const Vector3DBlock *velocities, $/;" f namespace:ProtoMol buildMoleculeTable framework/frontend/buildTopology.cpp /^ void buildMoleculeTable(GenericTopology *topo){$/;" f namespace:ProtoMol buildRattleShakeBondConstraintList framework/topology/topologyutilities.cpp /^ void buildRattleShakeBondConstraintList(GenericTopology * topology, vector& bondConstraints){$/;" f namespace:ProtoMol buildTopology framework/frontend/buildTopology.cpp /^ void buildTopology(GenericTopology* topo,const PSF& psf, const PAR& par, bool dihedralMultPSF){$/;" f namespace:ProtoMol build_angle_list framework/topology/topologyutilities.cpp /^ void build_angle_list (const GenericTopology *topo, const unsigned int atomID,const unsigned int inAtomID, const unsigned int outAtomID, const unsigned int exclAtomID, Real rotAngle, vector *angles) {$/;" f namespace:ProtoMol c tools/bccAnalyzer.cpp /^ Vector3DIdx v0,c,v1;$/;" m class:PairVector3D file: c tools/bccAnalyzer.cpp /^ const Vector3D c;$/;" m class:radialCmpVector3D file: calcAngle framework/forces/AngleSystemForce.h /^ inline void AngleSystemForce::calcAngle(const TBoundaryConditions &boundary,$/;" f class:ProtoMol::AngleSystemForce calcAngleEnergy framework/forces/AngleSystemForce.h /^ inline Real AngleSystemForce::calcAngleEnergy(const TBoundaryConditions &boundary,$/;" f class:ProtoMol::AngleSystemForce calcBond framework/forces/BondSystemForce.h /^ inline void BondSystemForce::calcBond(const TBoundaryConditions &boundary,$/;" f class:ProtoMol::BondSystemForce calcBondEnergy framework/forces/BondSystemForce.h /^ inline Real BondSystemForce::calcBondEnergy(const TBoundaryConditions &boundary,$/;" f class:ProtoMol::BondSystemForce calcDelGstats framework/integrators/ShadowHMCIntegrator.cpp /^ void ShadowHMCIntegrator::calcDelGstats( Real muH, Real varH,$/;" f class:ProtoMol::ShadowHMCIntegrator calcError framework/integrators/ModifierMetaRattle.cpp /^ Real ModifierMetaRattle::calcError() const {$/;" f class:ProtoMol::ModifierMetaRattle calcError framework/integrators/ModifierMetaShake.cpp /^ Real ModifierMetaShake::calcError() const {$/;" f class:ProtoMol::ModifierMetaShake calcHessiansBondsAnglesHBonds framework/integrators/BSplineMOLLYIntegrator.cpp /^ void BSplineMOLLYIntegrator::calcHessiansBondsAnglesHBonds() {$/;" f class:ProtoMol::BSplineMOLLYIntegrator calcMGStepVar framework/integrators/ShadowHMCIntegrator.cpp /^ void ShadowHMCIntegrator::calcMGStepVar( Real &mu, Real &var, int numSteps ) {$/;" f class:ProtoMol::ShadowHMCIntegrator calcMOLLYForcesHalfKickOneDrift framework/integrators/BSplineMOLLYIntegrator.cpp /^ void BSplineMOLLYIntegrator::calcMOLLYForcesHalfKickOneDrift(){$/;" f class:ProtoMol::BSplineMOLLYIntegrator calcMOLLYForcesOneKickOneDrift framework/integrators/BSplineMOLLYIntegrator.cpp /^ void BSplineMOLLYIntegrator::calcMOLLYForcesOneKickOneDrift(){$/;" f class:ProtoMol::BSplineMOLLYIntegrator calcShadow framework/integrators/ModifierShadow.cpp /^ Real ModifierShadow::calcShadow() {$/;" f class:ProtoMol::ModifierShadow calcTorsion framework/forces/MTorsionSystemForce.h /^ inline void MTorsionSystemForce::calcTorsion(const TBoundaryConditions &boundary,$/;" f class:ProtoMol::MTorsionSystemForce calcTorsionEnergy framework/forces/MTorsionSystemForce.h /^ inline Real MTorsionSystemForce::calcTorsionEnergy(const TBoundaryConditions &boundary,$/;" f class:ProtoMol::MTorsionSystemForce calculateDissipativeAndRandomForces framework/integrators/DMDLeapfrogIntegrator.cpp /^ void DMDLeapfrogIntegrator::calculateDissipativeAndRandomForces()$/;" f class:ProtoMol::DMDLeapfrogIntegrator calculateDissipativeForces framework/integrators/DMDLeapfrogIntegrator.cpp /^ void DMDLeapfrogIntegrator::calculateDissipativeForces()$/;" f class:ProtoMol::DMDLeapfrogIntegrator calculateForces framework/integrators/STSIntegrator.cpp /^ void STSIntegrator::calculateForces() {$/;" f class:ProtoMol::STSIntegrator calculateForces framework/integrators/StandardIntegrator.cpp /^ void StandardIntegrator::calculateForces(){$/;" f class:ProtoMol::StandardIntegrator calculateMOLLYForcesBonded framework/integrators/BSplineMOLLYIntegrator.cpp /^ void BSplineMOLLYIntegrator::calculateMOLLYForcesBonded() {$/;" f class:ProtoMol::BSplineMOLLYIntegrator calculateMOLLYForcesHBonded framework/integrators/BSplineMOLLYIntegrator.cpp /^ void BSplineMOLLYIntegrator::calculateMOLLYForcesHBonded() {$/;" f class:ProtoMol::BSplineMOLLYIntegrator capacity framework/base/Vector3DBlock.h /^ size_type capacity() const {return vec.capacity();} $/;" f class:ProtoMol::Vector3DBlock cellListNext framework/base/Atom.h /^ mutable int cellListNext;$/;" m struct:ProtoMol::Atom cellLists framework/topology/Topology.h /^ mutable typename CellManager::CellListStructure cellLists;$/;" m class:ProtoMol::Topology cellManager framework/topology/Topology.h /^ CellManager cellManager;$/;" m class:ProtoMol::Topology centerOfMass framework/frontend/OutputCache.cpp /^ Vector3D OutputCache::centerOfMass() const{$/;" f class:ProtoMol::OutputCache centerOfMass framework/topology/topologyutilities.cpp /^ Vector3D centerOfMass(const Vector3DBlock *positions, $/;" f namespace:ProtoMol cerr framework/base/Report.cpp /^ MyStreamer report(&(std::cerr));$/;" v chainID framework/base/PDB.h /^ std::string chainID; \/\/\/< chain_id $/;" m struct:ProtoMol::PDB::Atom chainID framework/base/PDB.h /^ std::string chainID; \/\/\/< chain_id $/;" m struct:ProtoMol::PDB::Ter changeDirectory framework/base/systemutilities.cpp /^ bool changeDirectory(const string& fileName){$/;" f namespace:ProtoMol char_type framework/base/sstream_local.h /^ typedef char char_type;$/;" t class:std::stringbuf charge framework/base/AtomType.h /^ Real charge; \/\/\/< The charge of this atom type.$/;" m struct:ProtoMol::AtomType charge framework/base/PDB.h /^ std::string charge; \/\/\/< charge $/;" m struct:ProtoMol::PDB::Atom charge framework/base/PSF.h /^ Real charge; \/\/\/< charge [e]$/;" m struct:ProtoMol::PSF::Atom check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::Empty&, const RepType& v){return (v.empty());} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::Negative&, RepType v){return (v < 0);} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::Negative&, RepType v){return (v < 0.0);} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::Negative&, const RepType& v){for(unsigned int i=0;i= 0.0) return false; return true;}$/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::NoConstraints&, RepType ){return true;} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::NoConstraints&, RepType){return true;} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::NoConstraints&, const RepType& ){return true;} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::NotEmpty&, const RepType& v){return (v != "");} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::NotEmpty&, const RepType& v){return (v.size() > 0);} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::NotNegative&, RepType v){return (v >= 0);} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::NotNegative&, RepType v){return (v >= 0.0);} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::NotNegative&, const RepType& v){for(unsigned int i=0;i 0.0) return false; return true;}$/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::NotZero&, RepType v){return (0U != v);} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::NotZero&, RepType v){return (v != 0);} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::NotZero&, RepType v){return (v != 0.0);} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::NotZero&, const RepType& v){for(unsigned int i=0;i 0);} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::Positive&, RepType v){return (v > 0.0);} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::Positive&, RepType v){return (v > 0U);} $/;" f struct:ProtoMol::ValueTraits check framework/base/ValueType.h /^ static bool check(const ConstraintValueType::Positive&, const RepType& v){for(unsigned int i=0;iatoms[i].scaledMass,topo->atoms[j].scaledMass));}$/;" f struct:ProtoMol::HBondConstraint check framework/forces/oneAtomContraints.h /^ static bool check(const GenericTopology* topo, int i, int j){return (topo->atoms[i].molecule != topo->atoms[j].molecule);}$/;" f struct:ProtoMol::NotSameMoleculeConstraint check framework/forces/oneAtomContraints.h /^ static bool check(const GenericTopology* topo, int i, int j){return (topo->atoms[i].molecule == topo->atoms[j].molecule);}$/;" f struct:ProtoMol::SameMoleculeConstraint check framework/forces/oneAtomContraints.h /^ static bool check(const GenericTopology*, int i, int j){$/;" f struct:ProtoMol::DebugPreConstraint check framework/forces/oneAtomContraints.h /^ static bool check(const GenericTopology*, int){return true;}$/;" f struct:ProtoMol::DebugPostConstraint check framework/forces/oneAtomContraints.h /^ static bool check(const GenericTopology*, int){return true;}$/;" f struct:ProtoMol::DebugPreConstraint check framework/forces/oneAtomContraints.h /^ static bool check(const GenericTopology*, int){return true;}$/;" f struct:ProtoMol::NoConstraint check framework/forces/oneAtomContraints.h /^ static bool check(const GenericTopology*, int, int){return true;}$/;" f struct:ProtoMol::DebugPostConstraint check framework/forces/oneAtomContraints.h /^ static bool check(const GenericTopology*, int, int){return true;}$/;" f struct:ProtoMol::NoConstraint check framework/forces/oneAtomContraints.h /^ static void check(const GenericTopology*, int i, int j, const Vector3D& diff, Real energy, const Vector3D& force){$/;" f struct:ProtoMol::DebugPostConstraint check framework/forces/oneAtomContraints.h /^ static void check(const GenericTopology*, int, int, const Vector3D&, Real, const Vector3D&){}$/;" f struct:ProtoMol::DebugPreConstraint check framework/forces/oneAtomContraints.h /^ static void check(const GenericTopology*, int, int, const Vector3D&, Real, const Vector3D&){}$/;" f struct:ProtoMol::HBondConstraint check framework/forces/oneAtomContraints.h /^ static void check(const GenericTopology*, int, int, const Vector3D&, Real, const Vector3D&){}$/;" f struct:ProtoMol::NoConstraint check framework/forces/oneAtomContraints.h /^ static void check(const GenericTopology*, int, int, const Vector3D&, Real, const Vector3D&){}$/;" f struct:ProtoMol::NotSameMoleculeConstraint check framework/forces/oneAtomContraints.h /^ static void check(const GenericTopology*, int, int, const Vector3D&, Real, const Vector3D&){}$/;" f struct:ProtoMol::SameMoleculeConstraint check framework/topology/ExclusionTable.h /^ inline ExclusionClass ExclusionTable::check(int atom1, int atom2) const {$/;" f class:ProtoMol::ExclusionTable checkBoundaries framework/topology/ArrayCellListStructure.h /^ bool checkBoundaries(const T1& t1) const{$/;" f class:ProtoMol::ArrayCellListStructure checkMoleculePairDistances framework/topology/SemiGenericTopology.h /^ virtual bool checkMoleculePairDistances(const Vector3DBlock& positions) const{$/;" f class:ProtoMol::SemiGenericTopology checkParameterTypes framework/base/Makeable.cpp /^ bool Makeable::checkParameterTypes(const vector& values) const{$/;" f class:ProtoMol::Makeable checkParameters framework/base/Makeable.cpp /^ bool Makeable::checkParameters(const vector& values) const{$/;" f class:ProtoMol::Makeable checkParameters framework/base/Makeable.cpp /^ bool Makeable::checkParameters(string& errMsg, const vector& values) const{$/;" f class:ProtoMol::Makeable checkReallyFast framework/topology/ExclusionTable.h /^ inline bool ExclusionTable::checkReallyFast(int atom1, int atom2) const {$/;" f class:ProtoMol::ExclusionTable clear compilerTests/pngTest.cpp /^void PPM::clear(){$/;" f class:PPM clear framework/base/Array_NoPartialSpecialization.h /^ void clear()$/;" f class:ProtoMol::Array clear framework/base/Grid.h /^ void Grid::clear(){$/;" f class:ProtoMol::Grid clear framework/base/MultiGrid.h /^ inline void MultiGrid::clear(){$/;" f class:ProtoMol::MultiGrid clear framework/base/PAR.cpp /^ void PAR::clear(){$/;" f class:ProtoMol::PAR clear framework/base/PDB.cpp /^ void PDB::clear(){$/;" f class:ProtoMol::PDB clear framework/base/PGM.cpp /^ void PGM::clear(){$/;" f class:ProtoMol::PGM clear framework/base/PPM.cpp /^ void PPM::clear(){$/;" f class:ProtoMol::PPM clear framework/base/PSF.cpp /^ void PSF::clear(){$/;" f class:ProtoMol::PSF clear framework/base/ReducedHessAngle.cpp /^ void ReducedHessAngle::clear()$/;" f class:ProtoMol::ReducedHessAngle clear framework/base/ScalarStructure.cpp /^ void ScalarStructure::clear() {$/;" f class:ProtoMol::ScalarStructure clear framework/base/Value.h /^ virtual bool clear() { bool tmp = ok; ok = false; return tmp;}$/;" f class:ProtoMol::Value::Holder clear framework/base/Value.h /^ inline bool Value::clear() {$/;" f class:ProtoMol::Value clear framework/base/Vector3DBlock.h /^ void clear() { vec.clear();} $/;" f class:ProtoMol::Vector3DBlock clear framework/base/XSC.cpp /^ void XSC::clear(){$/;" f class:ProtoMol::XSC clear framework/base/XYZ.cpp /^ void XYZ::clear(){$/;" f class:ProtoMol::XYZ clear framework/base/mathutilities.h /^ inline void WindowAve::clear() { while( !data.empty() ) data.pop(); }$/;" f class:ProtoMol::WindowAve clear framework/frontend/Factory.h /^ void clear(){$/;" f class:ProtoMol::FactoryBase clear framework/topology/ExclusionTable.cpp /^ void ExclusionTable::clear(void) {$/;" f class:ProtoMol::ExclusionTable clearCache framework/frontend/OutputFile.cpp /^ void OutputFile::clearCache() {$/;" f class:ProtoMol::OutputFile client_alive framework/imd/IMDElf.cpp /^ bool IMDElf::client_alive() {$/;" f class:ProtoMol::IMDElf clientsock framework/imd/IMDElf.h /^ void *clientsock;$/;" m class:ProtoMol::IMDElf clone framework/base/Value.h /^ virtual PlaceHolder* clone() const { return new Holder(*this);}$/;" f class:ProtoMol::Value::Holder close framework/frontend/OutputFile.cpp /^ bool OutputFile::close(){$/;" f class:ProtoMol::OutputFile close framework/io/File.cpp /^ void File::close(){$/;" f class:ProtoMol::File coarseToFine framework/base/MultiGrid.h /^ void coarseToFine(int level){coarseToFine(level,0,1);}$/;" f class:ProtoMol::MultiGrid coarseToFine framework/base/MultiGrid.h /^ inline void MultiGrid::coarseToFine(int level, unsigned int block, unsigned int nBlocks){$/;" f class:ProtoMol::MultiGrid coeffs framework/integrators/ModifierShadow.h /^ std::vector< Real > coeffs;$/;" m class:ProtoMol::ModifierShadow cohesive framework/forces/PaulTrapExtendedForce.h /^ Real cohesive(Real potentialEnergy){return (potentialEnergy-myPaulUHom)*myPaulF;}$/;" f class:ProtoMol::PaulTrapExtendedForce commX framework/parallel/Parallel-FD.cpp /^ MPI_Comm commX = MPI_COMM_NULL;$/;" v commY framework/parallel/Parallel-FD.cpp /^ MPI_Comm commY = MPI_COMM_NULL;$/;" v computeMolecularPressure framework/topology/topologyutilities.cpp /^ Real computeMolecularPressure(const ScalarStructure* energies, $/;" f namespace:ProtoMol computeOthers framework/forces/HarmDihedralSystemForce.h /^ bool computeOthers;$/;" m class:ProtoMol::HarmDihedralSystemForce computePhiDihedral framework/topology/topologyutilities.cpp /^ Real computePhiDihedral(const GenericTopology *topo, const Vector3DBlock *positions, int index){$/;" f namespace:ProtoMol computePhiDihedralEnergy framework/topology/topologyutilities.cpp /^ Real computePhiDihedralEnergy(const GenericTopology *topo, int index, Real phi){$/;" f namespace:ProtoMol computePressure framework/topology/topologyutilities.cpp /^ Real computePressure(const GenericTopology* topology,$/;" f namespace:ProtoMol computePressure framework/topology/topologyutilities.cpp /^ Real computePressure(const ScalarStructure* energies, $/;" f namespace:ProtoMol confstrings framework/frontend/OutputDihedrals.h /^ std::vector< std::string > confstrings;$/;" m class:ProtoMol::OutputDihedrals confstringsCounter framework/frontend/OutputDihedrals.h /^ std::vector< int > confstringsCounter;$/;" m class:ProtoMol::OutputDihedrals connect framework/imd/IMDElf.cpp /^ int IMDElf::connect(void *s) {$/;" f class:ProtoMol::IMDElf const0 framework/base/fft.c /^static int const0 = 0;$/;" v file: const1 framework/base/fft.c /^static int const1 = 1;$/;" v file: const16384 framework/base/fft.c /^static int const16384 = 16384;$/;" v file: constFalse framework/base/fft.c /^static int constFalse = 0;$/;" v file: constTrue framework/base/fft.c /^static int constTrue = 1;$/;" v file: const_iterator framework/base/Array_Fastest.h /^ typedef const T * const_iterator;$/;" t class:ProtoMol::Array const_iterator framework/base/Array_Fastest.h /^ typedef const T * const_iterator;$/;" t class:ProtoMol::RefArray const_iterator framework/base/Array_NoPartialSpecialization.h /^ typedef const T * const_iterator;$/;" t class:ProtoMol::Array::RefArray const_iterator framework/base/Array_NoPartialSpecialization.h /^ typedef const T * const_iterator;$/;" t class:ProtoMol::Array const_iterator framework/base/Configuration.h /^ typedef ValueMapType::const_iterator const_iterator;$/;" t class:ProtoMol::Configuration const_iterator framework/base/Vector3DBlock.h /^ typedef std::vector::const_iterator const_iterator; $/;" t class:ProtoMol::Vector3DBlock const_iterator framework/frontend/Factory.h /^ typedef typename std::set::const_iterator const_iterator;$/;" t class:ProtoMol::Factory const_iterator framework/frontend/HelpTextFactory.h /^ typedef HelpTextMapType::const_iterator const_iterator;$/;" t class:ProtoMol::HelpTextFactory const_iterator framework/frontend/OutputCollection.h /^ typedef std::list::const_iterator const_iterator;$/;" t class:ProtoMol::OutputCollection const_iterator framework/topology/ArrayCellListStructure.h /^ typedef TContainer::const_iterator const_iterator;$/;" t class:ProtoMol::ArrayCellListStructure const_pointer framework/base/Array_Fastest.h /^ typedef const T * const_pointer;$/;" t class:ProtoMol::Array const_pointer framework/base/Array_Fastest.h /^ typedef const T * const_pointer;$/;" t class:ProtoMol::RefArray const_pointer framework/base/Array_NoPartialSpecialization.h /^ typedef const T * const_pointer;$/;" t class:ProtoMol::Array::RefArray const_pointer framework/base/Array_NoPartialSpecialization.h /^ typedef const T * const_pointer;$/;" t class:ProtoMol::Array const_pointer framework/topology/ArrayCellListStructure.h /^ typedef TContainer::const_pointer const_pointer;$/;" t class:ProtoMol::ArrayCellListStructure const_reference framework/base/Array_Fastest.h /^ typedef const T & const_reference;$/;" t class:ProtoMol::Array const_reference framework/base/Array_Fastest.h /^ typedef const T & const_reference;$/;" t class:ProtoMol::RefArray const_reference framework/base/Array_NoPartialSpecialization.h /^ typedef const T & const_reference;$/;" t class:ProtoMol::Array::RefArray const_reference framework/base/Array_NoPartialSpecialization.h /^ typedef const T & const_reference;$/;" t class:ProtoMol::Array const_reference framework/base/Vector3DBlock.h /^ typedef std::vector::const_reference const_reference; $/;" t class:ProtoMol::Vector3DBlock const_reference framework/topology/ArrayCellListStructure.h /^ typedef TContainer::const_reference const_reference;$/;" t class:ProtoMol::ArrayCellListStructure const_reverse_iterator framework/base/Vector3DBlock.h /^ typedef std::vector::const_reverse_iterator const_reverse_iterator; $/;" t class:ProtoMol::Vector3DBlock convert framework/base/Matrix3by3.cpp /^ void convert(const Matrix3by3& from, double to[16])$/;" f namespace:ProtoMol convert framework/base/Matrix3by3.cpp /^ void convert(const Matrix3by3& from, float to[9])$/;" f namespace:ProtoMol convert framework/base/ValueType.h /^ static bool convert(Real v, RepType& r) { r = (v != 0.0); return true;}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(Real v, RepType& r){ $/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(RepType v, RepType& r){ r=v; return true;}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(RepType v, RepType& r){ r=v; return true;}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(RepType v, RepType& r) { r=v; return true;}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(RepType v, RepType& r) {r=v; return true;}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(RepType v, RepType& r) { r=v; return true;}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(bool v, RepType& r) { r = (v?1:0); return true; }$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(bool v, RepType& r) {r = (v ? 1.0 : 0.0); return true;}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(bool v, RepType& r) { r = (v?1:0); return true;}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(int v, RepType& r) { r = (v != 0); return true;}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(int v, RepType& r) {r = static_cast(v); return true;}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(int v, RepType& r){ $/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(std::string v, RepType& r) { return toInt(v,r);}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(std::string v, RepType& r) {return toBool(v,r);}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(std::string v, RepType& r) {return toReal(v,r);}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(std::string v, RepType& r){ return toUInt(v,r);}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(std::string v, RepType& r){ return toVector(v,r);}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(std::string v, RepType& r){ return toVector3D(v,r);}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(unsigned int v, RepType& r) { r = (v != 0); return true;}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(unsigned int v, RepType& r) {r = static_cast(v); return true;}$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ static bool convert(unsigned int v, RepType& r){ $/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ template static RepType convert(T v) {RepType tmp; convert(v,tmp);return tmp;} $/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ template static RepType convert(T v) {RepType tmp; convert(v,tmp);return tmp;} $/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ template static bool convert(T v, RepType& r){r = toString(v); return true;} \/\/ !NB everything is ok$/;" f struct:ProtoMol::ValueTraits convert framework/base/ValueType.h /^ template static bool convert(T, RepType&){return false;} $/;" f struct:ProtoMol::ValueTraits convertFromJacobian framework/base/ReducedHessAngle.cpp /^ void ReducedHessAngle::convertFromJacobian(Real **jac,int n)$/;" f class:ProtoMol::ReducedHessAngle convertTest framework/base/ValueType.h /^ template static bool convertTest(T v) {RepType tmp; return convert(v,tmp);} $/;" f struct:ProtoMol::ValueTraits convertTest framework/base/ValueType.h /^ template static bool convertTest(T v) {RepType tmp; return convert(v,tmp);} $/;" f struct:ProtoMol::ValueTraits coords framework/base/PDB.h /^ Vector3DBlock coords;$/;" m struct:ProtoMol::PDB coords framework/base/XYZ.h /^ Vector3DBlock coords;$/;" m struct:ProtoMol::XYZ copy framework/base/Array_Fastest.h /^ void copy(const Array & A, const T & Init=T())$/;" f class:ProtoMol::Array copy framework/base/Array_Fastest.h /^ void copy(const RefArray & SA, const T & Init=T())$/;" f class:ProtoMol::RefArray copy framework/base/Array_Fastest.h /^ void copy(const RefArray & SA, const T & Init=T())$/;" f class:ProtoMol::RefArray copy framework/base/Array_NoPartialSpecialization.h /^ void copy(const RefArray<1> & SA, const T & Init=T())$/;" f class:ProtoMol::Array::RefArray copy framework/base/Array_NoPartialSpecialization.h /^ void copy(const RefArray & SA, const T & Init=T())$/;" f class:ProtoMol::Array::RefArray copy framework/base/Array_NoPartialSpecialization.h /^ void copy(const Array & A, const T & Init=T())$/;" f class:ProtoMol::Array copy framework/base/Makeable.h /^ static T* copy(T* obj){$/;" f class:ProtoMol::Makeable correction framework/base/MultiGrid.h /^ void correction(int level){correction(level,0,1);};$/;" f class:ProtoMol::MultiGrid correction framework/base/MultiGrid.h /^ inline void MultiGrid::correction(int level, unsigned int block, unsigned int nBlocks){$/;" f class:ProtoMol::MultiGrid correctionTerm framework/forces/NonbondedFullEwaldSystemForce.h /^ TSwitchingFunction>::correctionTerm(const RealTopologyType* realTopo,$/;" f class:ProtoMol::NonbondedFullEwaldSystemForce correctionTerm framework/forces/NonbondedMultiGridSystemForce.h /^ smooth>::correctionTerm(const RealTopologyType* realTopo,$/;" f class:ProtoMol::NonbondedMultiGridSystemForce correctionTerm framework/forces/NonbondedPMEwaldSystemForce.h /^ TSwitchingFunction>::correctionTerm(const RealTopologyType* realTopo,$/;" f class:ProtoMol::NonbondedPMEwaldSystemForce coulombScalingFactor framework/topology/GenericTopology.h /^ Real coulombScalingFactor;$/;" m class:ProtoMol::GenericTopology createRattleModifier framework/integrators/Integrator.cpp /^ Modifier* Integrator::createRattleModifier(Real eps, int maxIter){$/;" f class:ProtoMol::Integrator createRattleModifier framework/integrators/NPTVerletIntegrator.cpp /^ Modifier* NPTVerletIntegrator::createRattleModifier(Real eps, int maxIter){$/;" f class:ProtoMol::NPTVerletIntegrator createRattleModifier framework/integrators/NVTVerletIntegrator.cpp /^ Modifier* NVTVerletIntegrator::createRattleModifier(Real eps, int maxIter){$/;" f class:ProtoMol::NVTVerletIntegrator createShadowModifier framework/integrators/Integrator.cpp /^ Modifier * Integrator::createShadowModifier( int order2k, int freq ) {$/;" f class:ProtoMol::Integrator createShakeModifier framework/integrators/Integrator.cpp /^ Modifier* Integrator::createShakeModifier(Real eps, int maxIter){$/;" f class:ProtoMol::Integrator createShakeModifier framework/integrators/NPTVerletIntegrator.cpp /^ Modifier* NPTVerletIntegrator::createShakeModifier(Real eps, int maxIter){$/;" f class:ProtoMol::NPTVerletIntegrator createShakeModifier framework/integrators/NVTVerletIntegrator.cpp /^ Modifier* NVTVerletIntegrator::createShakeModifier(Real eps, int maxIter){$/;" f class:ProtoMol::NVTVerletIntegrator createTables framework/topology/BankLennardJonesParameterTable.h /^ void createTables( unsigned int numComp, unsigned int tableSize ) {$/;" f struct:ProtoMol::BankLennardJonesParameterTable cross framework/base/Vector3D.h /^ Vector3D cross(const Vector3D& b) const {return (*this)^b;}$/;" f struct:ProtoMol::Vector3D cutoff framework/forces/oneAtomContraints.h /^ static Real cutoff(const TS& swf, const TF&){return swf.cutoffSquared();}$/;" f struct:ProtoMol::Cutoff cutoff framework/forces/oneAtomContraints.h /^ static Real cutoff(const TS&, const TF& nf){return nf.cutoffSquared();}$/;" f struct:ProtoMol::Cutoff cutoff framework/topology/C1SwitchingFunction.h /^ Real cutoff() const{return myCutoff;}$/;" f class:ProtoMol::C1SwitchingFunction cutoff framework/topology/C2SwitchingFunction.h /^ Real cutoff() const{return myCutoff;}$/;" f class:ProtoMol::C2SwitchingFunction cutoff framework/topology/CmpCnCnSwitchingFunction.h /^ Real cutoff() const{return myCutoff;}$/;" f class:ProtoMol::CmpCnCnSwitchingFunction cutoff framework/topology/CnSwitchingFunction.h /^ Real cutoff() const{return myCutoff;}$/;" f class:ProtoMol::CnSwitchingFunction cutoff framework/topology/ComplementSwitchingFunction.h /^ Real cutoff() const{return Constant::MAXREAL;}$/;" f class:ProtoMol::ComplementSwitchingFunction cutoff framework/topology/CutoffSwitchingFunction.h /^ Real cutoff() const{return myCutoff;}$/;" f class:ProtoMol::CutoffSwitchingFunction cutoff framework/topology/RangeSwitchingFunction.h /^ Real cutoff() const{return std::max(myR1,myOrigFunc.cutoff());}$/;" f class:ProtoMol::RangeSwitchingFunction cutoff framework/topology/ShiftSwitchingFunction.h /^ Real cutoff() const{return myCutoff;}$/;" f class:ProtoMol::ShiftSwitchingFunction cutoff framework/topology/UniversalSwitchingFunction.h /^ Real cutoff() const{return Constant::MAXREAL;}$/;" f class:ProtoMol::UniversalSwitchingFunction cutoffSquared framework/forces/CoulombEwaldRealTableForce.h /^ Real cutoffSquared() const{return myCutoff2;}$/;" f class:ProtoMol::CoulombEwaldRealTableForce cutoffSquared framework/forces/CoulombMultiGridDirectTableForce.h /^ Real cutoffSquared() const{return myCutoff2;}$/;" f class:ProtoMol::CoulombMultiGridDirectTableForce cutoffSquared framework/forces/CoulombTableForce.h /^ Real cutoffSquared() const{return myCutoff2;}$/;" f class:ProtoMol::CoulombTableForce cutoffSquared framework/forces/LennardJonesTableForce.h /^ Real cutoffSquared() const{return myCutoff2;}$/;" f class:ProtoMol::LennardJonesTableForce cutoffSquared framework/topology/C1SwitchingFunction.h /^ Real cutoffSquared() const{return myCutoff2;}$/;" f class:ProtoMol::C1SwitchingFunction cutoffSquared framework/topology/C2SwitchingFunction.h /^ Real cutoffSquared() const{return myCutoff2;}$/;" f class:ProtoMol::C2SwitchingFunction cutoffSquared framework/topology/CmpCnCnSwitchingFunction.h /^ Real cutoffSquared() const{return myCutoff2;}$/;" f class:ProtoMol::CmpCnCnSwitchingFunction cutoffSquared framework/topology/CnSwitchingFunction.h /^ Real cutoffSquared() const{return myCutoff2;}$/;" f class:ProtoMol::CnSwitchingFunction cutoffSquared framework/topology/ComplementSwitchingFunction.h /^ Real cutoffSquared() const{return Constant::MAXREAL;}$/;" f class:ProtoMol::ComplementSwitchingFunction cutoffSquared framework/topology/CutoffSwitchingFunction.h /^ Real cutoffSquared() const{return myCutoff2;}$/;" f class:ProtoMol::CutoffSwitchingFunction cutoffSquared framework/topology/RangeSwitchingFunction.h /^ Real cutoffSquared() const{return std::max(myR1Squared,myOrigFunc.cutoffSquared());}$/;" f class:ProtoMol::RangeSwitchingFunction cutoffSquared framework/topology/ShiftSwitchingFunction.h /^ Real cutoffSquared() const{return myCutoff2;}$/;" f class:ProtoMol::ShiftSwitchingFunction cutoffSquared framework/topology/UniversalSwitchingFunction.h /^ Real cutoffSquared() const{return Constant::MAXREAL;}$/;" f class:ProtoMol::UniversalSwitchingFunction d2swcoef framework/topology/CnSwitchingFunction.cpp /^ Real CnSwitchingFunction::d2swcoef[][MAXEQNN] = {$/;" m class:ProtoMol::CnSwitchingFunction file: d2swcoef framework/topology/CnSwitchingFunction.h /^ d2swcoef[][MAXEQNN];$/;" m class:ProtoMol::CnSwitchingFunction dKernel framework/forces/CoulombForce.h /^ static Real dKernel(Real r) {r=1.0\/r;return (-r*r);}$/;" f class:ProtoMol::CoulombForce::C1 dKernel framework/forces/CoulombForce.h /^ static Real dKernel(Real r) {r=1.0\/r;return (-r*r);}$/;" f class:ProtoMol::CoulombForce::C2 dKernel framework/forces/CoulombForce.h /^ static Real dKernel(Real r) {r=1.0\/r;return (-r*r);}$/;" f class:ProtoMol::CoulombForce::C3 dKernel framework/forces/CoulombForce.h /^ static Real dKernel(Real r) {r=1.0\/r;return (-r*r);}$/;" f class:ProtoMol::CoulombForce::C4 dKernelR framework/forces/CoulombForce.h /^ static Real dKernelR(Real rr) {return (-rr*rr);}$/;" f class:ProtoMol::CoulombForce::C1 dKernelR framework/forces/CoulombForce.h /^ static Real dKernelR(Real rr) {return (-rr*rr);}$/;" f class:ProtoMol::CoulombForce::C2 dKernelR framework/forces/CoulombForce.h /^ static Real dKernelR(Real rr) {return (-rr*rr);}$/;" f class:ProtoMol::CoulombForce::C3 dKernelR framework/forces/CoulombForce.h /^ static Real dKernelR(Real rr) {return (-rr*rr);}$/;" f class:ProtoMol::CoulombForce::C4 dSmooth framework/forces/CoulombForce.h /^ static Real dSmooth(Real r,Real \/*c*\/,Real cr) {return (-r*cr*cr*cr);}$/;" f class:ProtoMol::CoulombForce::C1 dSmooth framework/forces/CoulombForce.h /^ static Real dSmooth(Real r,Real c,Real cr) {c=r*cr*cr;return (cr*c*(1.5*r*c-2.5));}$/;" f class:ProtoMol::CoulombForce::C2 dSmooth framework/forces/CoulombForce.h /^ static Real dSmooth(Real r,Real c,Real cr) {c=r*r*cr*cr;return (r*cr*cr*cr*(-4.375 + c * (5.25 - 1.875 * c)));}$/;" f class:ProtoMol::CoulombForce::C3 dSmooth framework/forces/CoulombForce.h /^ static Real dSmooth(Real r,Real c,Real cr) {c=r*r*cr*cr;return(-r*cr*cr*cr*(6.5625-c*(11.8125-c*(8.4375-c*2.1875))));$/;" f class:ProtoMol::CoulombForce::C4 dSmoothKernel framework/forces/CoulombForce.h /^ static Real dSmoothKernel(Real r,Real c,Real cr){return (r data;$/;" m class:ProtoMol::WindowAve datatype framework/parallel/Parallel-FD.cpp /^ static const MPI_Datatype datatype;$/;" m struct:ProtoMol::MPITypeTraits file: datatype framework/parallel/Parallel-FD.cpp /^ const MPI_Datatype MPITypeTraits::datatype = MY_MPI_REAL; $/;" m class:ProtoMol::MPITypeTraits file: datatype framework/parallel/Parallel-FD.cpp /^ const MPI_Datatype MPITypeTraits::datatype = MPI_INT; $/;" m class:ProtoMol::MPITypeTraits file: datatype framework/parallel/Parallel.cpp /^ static const MPI_Datatype datatype;$/;" m struct:ProtoMol::MPITypeTraits file: datatype framework/parallel/Parallel.cpp /^ const MPI_Datatype MPITypeTraits::datatype = MY_MPI_REAL; $/;" m class:ProtoMol::MPITypeTraits file: datatype framework/parallel/Parallel.cpp /^ const MPI_Datatype MPITypeTraits::datatype = MPI_INT; $/;" m class:ProtoMol::MPITypeTraits file: debug framework/base/Report.h /^ debug() : myLevel(1) {}$/;" f class:ProtoMol::Report::debug debug framework/base/Report.h /^ debug(short l) : myLevel(l) {}$/;" f class:ProtoMol::Report::debug debug framework/base/Report.h /^ class debug{$/;" c namespace:ProtoMol::Report debug framework/base/Value.cpp /^ string Value::debug() const {$/;" f class:ProtoMol::Value declareInputValue framework/frontend/InputValue.h 150;" d defaultBlockSize framework/forces/NonbondedFullSystemForceBase.cpp /^ const unsigned int NonbondedFullSystemForceBase::defaultBlockSize = 64;$/;" m class:ProtoMol::NonbondedFullSystemForceBase file: defaultBlockSize framework/forces/NonbondedFullSystemForceBase.h /^ static const unsigned int defaultBlockSize;$/;" m class:ProtoMol::NonbondedFullSystemForceBase defaultBlockSize framework/forces/NonbondedSimpleFullSystemForceBase.cpp /^ const unsigned int NonbondedSimpleFullSystemForceBase::defaultBlockSize = 64;$/;" m class:ProtoMol::NonbondedSimpleFullSystemForceBase file: defaultBlockSize framework/forces/NonbondedSimpleFullSystemForceBase.h /^ static const unsigned int defaultBlockSize;$/;" m class:ProtoMol::NonbondedSimpleFullSystemForceBase defaultCharmmType framework/io/PARWriter.cpp /^ const PAR::CharmmTypeEnum PARWriter::defaultCharmmType=PAR::CHARMM28;$/;" m class:ProtoMol::PARWriter file: defaultCharmmType framework/io/PARWriter.h /^ static const PAR::CharmmTypeEnum defaultCharmmType;$/;" m class:ProtoMol::PARWriter defaultScale framework/io/XFigWriter.cpp /^ static const Real defaultScale = 1000.0;$/;" v file: defaultValue framework/base/Parameter.h /^ Value defaultValue;$/;" m struct:ProtoMol::Parameter defaultValue framework/frontend/HelpTextFactory.h /^ Value defaultValue;$/;" m struct:ProtoMol::HelpText defbuf framework/base/sstream_local.h /^ char defbuf;$/;" m class:std::stringbuf defineInputValue framework/frontend/InputValue.h 159;" d defineInputValueAndText framework/frontend/InputValue.h 169;" d defineInputValueWithAliases framework/frontend/InputValue.h 164;" d defineInputValueWithAliasesAndText framework/frontend/InputValue.h 174;" d defined framework/base/Configuration.cpp /^ bool Configuration::defined(const string& keyword) const{$/;" f class:ProtoMol::Configuration defined framework/base/Value.h /^ inline bool Value::defined() const {$/;" f class:ProtoMol::Value degreesOfFreedom framework/topology/GenericTopology.h /^ int degreesOfFreedom;$/;" m class:ProtoMol::GenericTopology deleteExternalModifiers framework/integrators/Integrator.cpp /^ void Integrator::deleteExternalModifiers(){$/;" f class:ProtoMol::Integrator deleteInternalModifiers framework/integrators/Integrator.cpp /^ void Integrator::deleteInternalModifiers(){$/;" f class:ProtoMol::Integrator deleteModifier framework/integrators/Integrator.cpp /^ void Integrator::deleteModifier(Modifier* modifier){$/;" f class:ProtoMol::Integrator deltaM framework/base/Atom.h /^ Real deltaM, deltaQ;$/;" m struct:ProtoMol::Atom deltaMu framework/base/ScalarStructure.h /^ inline Real ScalarStructure::deltaMu() const {$/;" f class:ProtoMol::ScalarStructure deltaQ framework/base/Atom.h /^ Real deltaM, deltaQ;$/;" m struct:ProtoMol::Atom density framework/frontend/OutputCache.cpp /^ Real OutputCache::density() const{$/;" f class:ProtoMol::OutputCache det framework/base/Matrix3by3.cpp /^ Real Matrix3by3::det()$/;" f class:ProtoMol::Matrix3by3 dftmod framework/base/Grid.h /^ void Grid::dftmod(unsigned int order, unsigned int n, Real* interpolation, Real* interpolationMod){$/;" f class:ProtoMol::Grid difference_type framework/base/Array_Fastest.h /^ typedef ptrdiff_t difference_type;$/;" t class:ProtoMol::Array difference_type framework/base/Array_Fastest.h /^ typedef ptrdiff_t difference_type;$/;" t class:ProtoMol::RefArray difference_type framework/base/Array_NoPartialSpecialization.h /^ typedef ptrdiff_t difference_type;$/;" t class:ProtoMol::Array::RefArray difference_type framework/base/Array_NoPartialSpecialization.h /^ typedef ptrdiff_t difference_type;$/;" t class:ProtoMol::Array difference_type framework/base/Vector3DBlock.h /^ typedef std::vector::difference_type difference_type; $/;" t class:ProtoMol::Vector3DBlock difference_type framework/topology/ArrayCellListStructure.h /^ typedef TContainer::difference_type difference_type;$/;" t class:ProtoMol::ArrayCellListStructure diffusion framework/frontend/OutputCache.cpp /^ Real OutputCache::diffusion() const{$/;" f class:ProtoMol::OutputCache dihID framework/frontend/OutputState.h /^ int dihID;$/;" m struct:ProtoMol::OutputState::orderParam dihInc framework/frontend/OutputDihedrals.cpp /^ std::vector< std::vector< Real > > OutputDihedrals::dihInc(std::vector dihedralset) {$/;" f class:ProtoMol::OutputDihedrals dihedralList framework/base/Molecule.h /^ std::vector dihedralList;$/;" m struct:ProtoMol::Molecule dihedralPhi framework/frontend/OutputCache.cpp /^ Real OutputCache::dihedralPhi(int index) const{$/;" f class:ProtoMol::OutputCache dihedralPhis framework/frontend/OutputCache.cpp /^ vector OutputCache::dihedralPhis(vector dihedralset) const{$/;" f class:ProtoMol::OutputCache dihedrals framework/base/PAR.h /^ std::vector dihedrals;$/;" m class:ProtoMol::PAR dihedrals framework/base/PSF.h /^ std::vector dihedrals;$/;" m class:ProtoMol::PSF dihedrals framework/topology/GenericTopology.h /^ std::vector dihedrals;$/;" m class:ProtoMol::GenericTopology dim framework/integrators/EquilibriumMOLLYIntegrator.cpp /^ int dim, const int (&index)[maxGDim],$/;" v dim framework/integrators/EquilibriumMOLLYIntegrator.cpp /^ int dim, int (&index)[maxGDim],$/;" v dim framework/integrators/EquilibriumMOLLYIntegrator.h /^ void luBksb(Real (&m)[maxGDim][maxGDim], int dim, const int (&index)[maxGDim], Real (&b)[maxGDim]) const;$/;" m class:ProtoMol::EquilibriumMOLLYIntegrator dim framework/integrators/EquilibriumMOLLYIntegrator.h /^ void luDcmp(Real (&m)[maxGDim][maxGDim], int dim, int (&index)[maxGDim], Real& d) const;$/;" m class:ProtoMol::EquilibriumMOLLYIntegrator dimensions framework/base/Array_Fastest.h /^ size_t dimensions() const { return 1; }$/;" f class:ProtoMol::RefArray dimensions framework/base/Array_Fastest.h /^ size_t dimensions() const { return N; } $/;" f class:ProtoMol::Array dimensions framework/base/Array_Fastest.h /^ size_t dimensions() const { return N; }$/;" f class:ProtoMol::RefArray dimensions framework/base/Array_NoPartialSpecialization.h /^ unsigned int dimensions() const { return 1; }$/;" f class:ProtoMol::Array::RefArray dimensions framework/base/Array_NoPartialSpecialization.h /^ unsigned int dimensions() const { return N; }$/;" f class:ProtoMol::Array::RefArray dimensions framework/base/Array_NoPartialSpecialization.h /^ unsigned int dimensions() const { return N; } $/;" f class:ProtoMol::Array direct framework/base/MultiGrid.h /^ void direct(){direct(0,1);};$/;" f class:ProtoMol::MultiGrid direct framework/base/MultiGrid.h /^ inline void MultiGrid::direct(unsigned int block, unsigned int nBlocks){$/;" f class:ProtoMol::MultiGrid disable framework/integrators/Modifier.h /^ void disable() const{myEnable=false;}$/;" f class:ProtoMol::Modifier display compilerTests/glutTest.cpp /^static void display(){$/;" f file: displs framework/parallel/Parallel-FD.cpp /^ int* displs = NULL;$/;" v distCount framework/base/Proxy.h /^ int distCount() const {return myCount;}$/;" f class:ProtoMol::Proxy distance framework/base/PAR.h /^ Real distance; \/\/\/< distance$/;" m struct:ProtoMol::PAR::Bond distribute framework/base/Proxy.h /^ void distribute() const {myCount++;}$/;" f class:ProtoMol::Proxy distribute framework/parallel/Parallel-FD.cpp /^ void Parallel::distribute(ScalarStructure* energies, Vector3DBlock* coords) {$/;" f class:ProtoMol::Parallel distribute framework/parallel/Parallel-FD.cpp /^ void Parallel::distribute(ScalarStructure*, Vector3DBlock*){}$/;" f class:ProtoMol::Parallel distribute framework/parallel/Parallel.cpp /^ void Parallel::distribute(ScalarStructure* energies, Vector3DBlock* coords) {$/;" f class:ProtoMol::Parallel distribute framework/parallel/Parallel.cpp /^ void Parallel::distribute(ScalarStructure*, Vector3DBlock*){}$/;" f class:ProtoMol::Parallel distributed framework/base/Proxy.h /^ bool distributed() const {return (myCount > 0);}$/;" f class:ProtoMol::Proxy divide framework/base/Vector3D.h /^ Vector3D divide(Real w) const {return (*this)\/w;}$/;" f struct:ProtoMol::Vector3D do2ndHalfKick framework/integrators/NPTVerletIntegrator.cpp /^ void NPTVerletIntegrator::do2ndHalfKick() {$/;" f class:ProtoMol::NPTVerletIntegrator do2ndHalfKick framework/integrators/NVTVerletIntegrator.cpp /^ void NVTVerletIntegrator::do2ndHalfKick() {$/;" f class:ProtoMol::NVTVerletIntegrator doAveragingPositions framework/integrators/BSplineMOLLYIntegrator.cpp /^ Vector3DBlock* BSplineMOLLYIntegrator::doAveragingPositions() {$/;" f class:ProtoMol::BSplineMOLLYIntegrator doAveragingPositions framework/integrators/EquilibriumMOLLYIntegrator.cpp /^ Vector3DBlock* EquilibriumMOLLYIntegrator::doAveragingPositions()$/;" f class:ProtoMol::EquilibriumMOLLYIntegrator doBarrier framework/parallel/Parallel-FD.cpp /^ void doBarrier(){$/;" f namespace:ProtoMol doBarrier framework/parallel/Parallel.cpp /^ void doBarrier(){$/;" f namespace:ProtoMol doDrift framework/integrators/LangevinImpulseIntegrator.cpp /^ void LangevinImpulseIntegrator::doDrift() {$/;" f class:ProtoMol::LangevinImpulseIntegrator doDrift framework/integrators/NPTVerletIntegrator.cpp /^ void NPTVerletIntegrator::doDrift() {$/;" f class:ProtoMol::NPTVerletIntegrator doDrift framework/integrators/NVTVerletIntegrator.cpp /^ void NVTVerletIntegrator::doDrift() {$/;" f class:ProtoMol::NVTVerletIntegrator doDrift framework/integrators/PaulTrapIntegrator.cpp /^ void PaulTrapIntegrator::doDrift(void) {$/;" f class:ProtoMol::PaulTrapIntegrator doDrift framework/integrators/STSIntegrator.cpp /^ void STSIntegrator::doDrift() {$/;" f class:ProtoMol::STSIntegrator doDriftOrNextIntegrator framework/integrators/MTSIntegrator.cpp /^ void MTSIntegrator::doDriftOrNextIntegrator() {$/;" f class:ProtoMol::MTSIntegrator doDriftOrNextIntegrator framework/integrators/STSIntegrator.cpp /^ void STSIntegrator::doDriftOrNextIntegrator() {$/;" f class:ProtoMol::STSIntegrator doEvaluate framework/forces/ElectricFieldSystemForce.h /^ inline void ElectricFieldSystemForce::doEvaluate(const GenericTopology* topo,$/;" f class:ProtoMol::ElectricFieldSystemForce doEvaluate framework/forces/ExternalGravitationSystemForce.cpp /^ void ExternalGravitationSystemForce::doEvaluate(const GenericTopology* topo,$/;" f class:ProtoMol::ExternalGravitationSystemForce doEvaluate framework/forces/ExternalMagneticFieldExtendedForce.cpp /^ void ExternalMagneticFieldExtendedForce::doEvaluate(const GenericTopology* topo,$/;" f class:ProtoMol::ExternalMagneticFieldExtendedForce doEvaluate framework/forces/FrictionExtendedForce.cpp /^ void FrictionExtendedForce::doEvaluate(const GenericTopology*,$/;" f class:ProtoMol::FrictionExtendedForce doEvaluate framework/forces/NonbondedCutoffForce.h /^ void NonbondedCutoffForce::doEvaluate(const GenericTopology* topo, unsigned int n){$/;" f class:ProtoMol::NonbondedCutoffForce doEvaluate framework/forces/NonbondedFullSystemForce.h /^ void NonbondedFullSystemForce::doEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedFullSystemForce doEvaluate framework/forces/NonbondedSimpleFullSystemForce.h /^ void NonbondedSimpleFullSystemForce::doEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedSimpleFullSystemForce doEvaluate framework/forces/PaulTrapExtendedForce.h /^ inline void PaulTrapExtendedForce::doEvaluate(const GenericTopology* topo,$/;" f class:ProtoMol::PaulTrapExtendedForce doEvaluate framework/forces/SphericalSystemForce.cpp /^ void SphericalSystemForce::doEvaluate(const GenericTopology* \/*topo*\/,$/;" f class:ProtoMol::SphericalSystemForce doExecute framework/integrators/ModifierAveraging.h /^ virtual void doExecute(){$/;" f class:ProtoMol::ModifierAveraging doExecute framework/integrators/ModifierFriction.h /^ virtual void doExecute(){$/;" f class:ProtoMol::ModifierFriction doExecute framework/integrators/ModifierIncrementTimestep.h /^ virtual void doExecute(){$/;" f class:ProtoMol::ModifierIncrementTimestep doExecute framework/integrators/ModifierMollification.h /^ virtual void doExecute(){$/;" f class:ProtoMol::ModifierMollification doExecute framework/integrators/ModifierNPTRattle.cpp /^ void ModifierNPTRattleDetails::doExecute(){$/;" f class:ProtoMol::ModifierNPTRattleDetails doExecute framework/integrators/ModifierNPTShake.cpp /^ void ModifierNPTShakeDetails::doExecute(){$/;" f class:ProtoMol::ModifierNPTShakeDetails doExecute framework/integrators/ModifierNVTRattle.cpp /^ void ModifierNVTRattleDetails::doExecute(){$/;" f class:ProtoMol::ModifierNVTRattleDetails doExecute framework/integrators/ModifierNVTShake.cpp /^ void ModifierNVTShakeDetails::doExecute(){$/;" f class:ProtoMol::ModifierNVTShakeDetails doExecute framework/integrators/ModifierPostForceBarostat.h /^ virtual void doExecute(){$/;" f class:ProtoMol::ModifierPostForceBarostat doExecute framework/integrators/ModifierPostForceThermostat.h /^ virtual void doExecute(){$/;" f class:ProtoMol::ModifierPostForceThermostat doExecute framework/integrators/ModifierPreForceBarostat.h /^ virtual void doExecute(){$/;" f class:ProtoMol::ModifierPreForceBarostat doExecute framework/integrators/ModifierPreForceThermostat.h /^ virtual void doExecute(){$/;" f class:ProtoMol::ModifierPreForceThermostat doExecute framework/integrators/ModifierRattle.cpp /^ void ModifierRattle::doExecute(){$/;" f class:ProtoMol::ModifierRattle doExecute framework/integrators/ModifierRemoveAngularMomentum.h /^ virtual void doExecute(){$/;" f class:ProtoMol::ModifierRemoveAngularMomentum doExecute framework/integrators/ModifierRemoveLinearMomentum.h /^ virtual void doExecute(){$/;" f class:ProtoMol::ModifierRemoveLinearMomentum doExecute framework/integrators/ModifierShadow.cpp /^ void ModifierShadow::doExecute() {$/;" f class:ProtoMol::ModifierShadow doExecute framework/integrators/ModifierShake.cpp /^ void ModifierShake::doExecute(){$/;" f class:ProtoMol::ModifierShake doFinalize framework/frontend/OutputBSDL.h /^ virtual void doFinalize(int){};$/;" f class:ProtoMol::OutputBSDL doFinalize framework/frontend/OutputDCDTrajectory.cpp /^ void OutputDCDTrajectory::doFinalize(int){$/;" f class:ProtoMol::OutputDCDTrajectory doFinalize framework/frontend/OutputDihedrals.cpp /^ void OutputDihedrals::doFinalize(int){$/;" f class:ProtoMol::OutputDihedrals doFinalize framework/frontend/OutputFile.cpp /^ void OutputFile::doFinalize(int){$/;" f class:ProtoMol::OutputFile doFinalize framework/frontend/OutputFinalPDBPos.cpp /^ void OutputFinalPDBPos::doFinalize(int step){$/;" f class:ProtoMol::OutputFinalPDBPos doFinalize framework/frontend/OutputFinalXYZBinPos.cpp /^ void OutputFinalXYZBinPos::doFinalize(int){$/;" f class:ProtoMol::OutputFinalXYZBinPos doFinalize framework/frontend/OutputFinalXYZBinVel.cpp /^ void OutputFinalXYZBinVel::doFinalize(int){$/;" f class:ProtoMol::OutputFinalXYZBinVel doFinalize framework/frontend/OutputFinalXYZPos.cpp /^ void OutputFinalXYZPos::doFinalize(int step){$/;" f class:ProtoMol::OutputFinalXYZPos doFinalize framework/frontend/OutputFinalXYZVel.cpp /^ void OutputFinalXYZVel::doFinalize(int step){$/;" f class:ProtoMol::OutputFinalXYZVel doFinalize framework/frontend/OutputPDBFramePos.h /^ virtual void doFinalize(int){};$/;" f class:ProtoMol::OutputPDBFramePos doFinalize framework/frontend/OutputREMExchangeRate.cpp /^ void OutputREMExchangeRate::doFinalize(int \/*step*\/) {$/;" f class:ProtoMol::OutputREMExchangeRate doFinalize framework/frontend/OutputREMHistory.cpp /^ void OutputREMHistoryFile::doFinalize(int \/*step*\/) {$/;" f class:ProtoMol::OutputREMHistoryFile doFinalize framework/frontend/OutputScreen.h /^ virtual void doFinalize(int){}$/;" f class:ProtoMol::OutputScreen doFinalize framework/frontend/OutputState.cpp /^ void OutputState::doFinalize(int){$/;" f class:ProtoMol::OutputState doFinalize framework/frontend/OutputXYZBinTrajectoryPos.cpp /^ void OutputXYZBinTrajectoryPos::doFinalize(int){$/;" f class:ProtoMol::OutputXYZBinTrajectoryPos doFinalize framework/frontend/OutputXYZBinTrajectoryVel.cpp /^ void OutputXYZBinTrajectoryVel::doFinalize(int){$/;" f class:ProtoMol::OutputXYZBinTrajectoryVel doFinalize framework/frontend/OutputXYZTrajectoryForce.cpp /^ void OutputXYZTrajectoryForce::doFinalize(int){$/;" f class:ProtoMol::OutputXYZTrajectoryForce doFinalize framework/frontend/OutputXYZTrajectoryPos.cpp /^ void OutputXYZTrajectoryPos::doFinalize(int){$/;" f class:ProtoMol::OutputXYZTrajectoryPos doFinalize framework/frontend/OutputXYZTrajectoryVel.cpp /^ void OutputXYZTrajectoryVel::doFinalize(int){$/;" f class:ProtoMol::OutputXYZTrajectoryVel doFirstHalfKick framework/integrators/BBKIntegrator.cpp /^ void BBKIntegrator::doFirstHalfKick(){$/;" f class:ProtoMol::BBKIntegrator doFlushCache framework/frontend/OutputFile.h /^ virtual void doFlushCache(){};$/;" f class:ProtoMol::OutputFile doFlushCache framework/frontend/OutputPaulTrap.cpp /^ void OutputPaulTrap::doFlushCache(){$/;" f class:ProtoMol::OutputPaulTrap doHalfDrift framework/integrators/PLeapfrogIntegrator.cpp /^ void PLeapfrogIntegrator::doHalfDrift() {$/;" f class:ProtoMol::PLeapfrogIntegrator doHalfKick framework/integrators/DMDLeapfrogIntegrator.cpp /^ void DMDLeapfrogIntegrator::doHalfKick() $/;" f class:ProtoMol::DMDLeapfrogIntegrator doHalfKick framework/integrators/NPTVerletIntegrator.cpp /^ void NPTVerletIntegrator::doHalfKick() {$/;" f class:ProtoMol::NPTVerletIntegrator doHalfKick framework/integrators/NVTVerletIntegrator.cpp /^ void NVTVerletIntegrator::doHalfKick() {$/;" f class:ProtoMol::NVTVerletIntegrator doHalfKick framework/integrators/StandardIntegrator.cpp /^ void StandardIntegrator::doHalfKick(){$/;" f class:ProtoMol::StandardIntegrator doHalfKickIterate framework/integrators/DMDLeapfrogIntegrator.cpp /^ void DMDLeapfrogIntegrator::doHalfKickIterate() {$/;" f class:ProtoMol::DMDLeapfrogIntegrator doHalfKickVhat framework/integrators/DMDLeapfrogIntegrator.cpp /^ void DMDLeapfrogIntegrator::doHalfKickVhat() $/;" f class:ProtoMol::DMDLeapfrogIntegrator doHalfKickdoDrift framework/integrators/LeapfrogIntegrator.cpp /^ void LeapfrogIntegrator::doHalfKickdoDrift() {$/;" f class:ProtoMol::LeapfrogIntegrator doInitialize framework/frontend/OutputBSDL.cpp /^ void OutputBSDL::doInitialize(){$/;" f class:ProtoMol::OutputBSDL doInitialize framework/frontend/OutputDCDTrajectory.cpp /^ void OutputDCDTrajectory::doInitialize(){$/;" f class:ProtoMol::OutputDCDTrajectory doInitialize framework/frontend/OutputDiffusion.cpp /^ void OutputDiffusion::doInitialize(){$/;" f class:ProtoMol::OutputDiffusion doInitialize framework/frontend/OutputDihedrals.cpp /^ void OutputDihedrals::doInitialize(){$/;" f class:ProtoMol::OutputDihedrals doInitialize framework/frontend/OutputEnergies.cpp /^ void OutputEnergies::doInitialize(){$/;" f class:ProtoMol::OutputEnergies doInitialize framework/frontend/OutputFinalPDBPos.h /^ virtual void doInitialize(){};$/;" f class:ProtoMol::OutputFinalPDBPos doInitialize framework/frontend/OutputFinalXYZBinPos.h /^ virtual void doInitialize(){};$/;" f class:ProtoMol::OutputFinalXYZBinPos doInitialize framework/frontend/OutputFinalXYZBinVel.h /^ virtual void doInitialize(){};$/;" f class:ProtoMol::OutputFinalXYZBinVel doInitialize framework/frontend/OutputFinalXYZPos.h /^ virtual void doInitialize(){};$/;" f class:ProtoMol::OutputFinalXYZPos doInitialize framework/frontend/OutputFinalXYZVel.h /^ virtual void doInitialize(){};$/;" f class:ProtoMol::OutputFinalXYZVel doInitialize framework/frontend/OutputMomentum.cpp /^ void OutputMomentum::doInitialize(){$/;" f class:ProtoMol::OutputMomentum doInitialize framework/frontend/OutputPDBFramePos.h /^ virtual void doInitialize(){};$/;" f class:ProtoMol::OutputPDBFramePos doInitialize framework/frontend/OutputPaulTrap.cpp /^ void OutputPaulTrap::doInitialize(){$/;" f class:ProtoMol::OutputPaulTrap doInitialize framework/frontend/OutputREMExchangeRate.cpp /^ void OutputREMExchangeRate::doInitialize() {$/;" f class:ProtoMol::OutputREMExchangeRate doInitialize framework/frontend/OutputREMHistory.cpp /^ void OutputREMHistoryFile::doInitialize() {$/;" f class:ProtoMol::OutputREMHistoryFile doInitialize framework/frontend/OutputScreen.cpp /^ void OutputScreen::doInitialize(){$/;" f class:ProtoMol::OutputScreen doInitialize framework/frontend/OutputState.cpp /^ void OutputState::doInitialize(){$/;" f class:ProtoMol::OutputState doInitialize framework/frontend/OutputTemperatures.cpp /^ void OutputTemperatures::doInitialize(){$/;" f class:ProtoMol::OutputTemperatures doInitialize framework/frontend/OutputXYZBinTrajectoryPos.cpp /^ void OutputXYZBinTrajectoryPos::doInitialize(){$/;" f class:ProtoMol::OutputXYZBinTrajectoryPos doInitialize framework/frontend/OutputXYZBinTrajectoryVel.cpp /^ void OutputXYZBinTrajectoryVel::doInitialize(){$/;" f class:ProtoMol::OutputXYZBinTrajectoryVel doInitialize framework/frontend/OutputXYZTrajectoryForce.cpp /^ void OutputXYZTrajectoryForce::doInitialize(){$/;" f class:ProtoMol::OutputXYZTrajectoryForce doInitialize framework/frontend/OutputXYZTrajectoryPos.cpp /^ void OutputXYZTrajectoryPos::doInitialize(){$/;" f class:ProtoMol::OutputXYZTrajectoryPos doInitialize framework/frontend/OutputXYZTrajectoryVel.cpp /^ void OutputXYZTrajectoryVel::doInitialize(){$/;" f class:ProtoMol::OutputXYZTrajectoryVel doInitialize framework/integrators/Modifier.h /^ virtual void doInitialize(){}$/;" f class:ProtoMol::Modifier doInitialize framework/integrators/ModifierMetaRattleShake.cpp /^ void ModifierMetaRattleShake::doInitialize(){$/;" f class:ProtoMol::ModifierMetaRattleShake doInitialize framework/integrators/ModifierRemoveAngularMomentum.h /^ virtual void doInitialize(){myStep =0;}$/;" f class:ProtoMol::ModifierRemoveAngularMomentum doInitialize framework/integrators/ModifierRemoveLinearMomentum.h /^ virtual void doInitialize(){myStep =0;}$/;" f class:ProtoMol::ModifierRemoveLinearMomentum doInitialize framework/integrators/ModifierShadow.cpp /^ void ModifierShadow::doInitialize() {$/;" f class:ProtoMol::ModifierShadow doKeywords framework/frontend/HelpTextFactory.cpp /^ string HelpTextFactory::doKeywords() const{$/;" f class:ProtoMol::HelpTextFactory doKick framework/integrators/StandardIntegrator.cpp /^ void StandardIntegrator::doKick(){$/;" f class:ProtoMol::StandardIntegrator doKickdoDrift framework/integrators/LeapfrogIntegrator.cpp /^ void LeapfrogIntegrator::doKickdoDrift() {$/;" f class:ProtoMol::LeapfrogIntegrator doKickdoDrift framework/integrators/PLeapfrogIntegrator.cpp /^ void PLeapfrogIntegrator::doKickdoDrift() {$/;" f class:ProtoMol::PLeapfrogIntegrator doKickdoHalfDrift framework/integrators/PLeapfrogIntegrator.cpp /^ void PLeapfrogIntegrator::doKickdoHalfDrift() {$/;" f class:ProtoMol::PLeapfrogIntegrator doMake framework/forces/AngleSystemForce.h /^ virtual Force* doMake(std::string&, std::vector) const {$/;" f class:ProtoMol::AngleSystemForce doMake framework/forces/BondSystemForce.h /^ virtual Force* doMake(std::string&, std::vector) const {$/;" f class:ProtoMol::BondSystemForce doMake framework/forces/CompareForce.cpp /^ Force* CompareForce::doMake(string& errMsg, vector values) const{$/;" f class:ProtoMol::CompareForce doMake framework/forces/DihedralSystemForce.h /^ virtual Force* doMake(std::string&, std::vector) const { return (new DihedralSystemForce());}$/;" f class:ProtoMol::DihedralSystemForce doMake framework/forces/ElectricFieldSystemForce.h /^ inline Force* ElectricFieldSystemForce::doMake(std::string& errMsg, std::vector values) const {$/;" f class:ProtoMol::ElectricFieldSystemForce doMake framework/forces/ExternalGravitationSystemForce.cpp /^ Force* ExternalGravitationSystemForce::doMake(string&, vector values) const {$/;" f class:ProtoMol::ExternalGravitationSystemForce doMake framework/forces/ExternalMagneticFieldExtendedForce.cpp /^ Force* ExternalMagneticFieldExtendedForce::doMake(string&, vector values) const {$/;" f class:ProtoMol::ExternalMagneticFieldExtendedForce doMake framework/forces/FrictionExtendedForce.cpp /^ Force* FrictionExtendedForce::doMake(string&, vector values) const {$/;" f class:ProtoMol::FrictionExtendedForce doMake framework/forces/HarmDihedralSystemForce.h /^ virtual Force* doMake(std::string&, std::vector values) const { $/;" f class:ProtoMol::HarmDihedralSystemForce doMake framework/forces/ImproperSystemForce.h /^ virtual Force* doMake(std::string&, std::vector) const { return (new ImproperSystemForce()); }$/;" f class:ProtoMol::ImproperSystemForce doMake framework/forces/MagneticDipoleMirrorSystemForce.h /^ inline Force* MagneticDipoleMirrorSystemForce::doMake(std::string&, std::vector values) const {$/;" f class:ProtoMol::MagneticDipoleMirrorSystemForce doMake framework/forces/NonbondedCutoffForce.h /^ Force* NonbondedCutoffForce::doMake(std::string& errMsg, std::vector values) const{$/;" f class:ProtoMol::NonbondedCutoffForce doMake framework/forces/NonbondedFullEwaldSystemForce.h /^ TSwitchingFunction>::doMake(std::string& errMsg, std::vector values) const{$/;" f class:ProtoMol::NonbondedFullEwaldSystemForce doMake framework/forces/NonbondedFullSystemForce.h /^ Force* NonbondedFullSystemForce::doMake(std::string& errMsg, std::vector values) const{$/;" f class:ProtoMol::NonbondedFullSystemForce doMake framework/forces/NonbondedMultiGridSystemForce.h /^ smooth>::doMake(std::string& errMsg, std::vector values) const{$/;" f class:ProtoMol::NonbondedMultiGridSystemForce doMake framework/forces/NonbondedPMEwaldSystemForce.h /^ real,reciprocal,correction,TInterpolation,TSwitchingFunction>::doMake(std::string& errMsg,std::vector values) const{$/;" f class:ProtoMol::NonbondedPMEwaldSystemForce doMake framework/forces/NonbondedSimpleFullSystemForce.h /^ virtual Force* doMake(std::string& errMsg, std::vector values) const{$/;" f class:ProtoMol::NonbondedSimpleFullSystemForce doMake framework/forces/PaulTrapExtendedForce.h /^ inline Force* PaulTrapExtendedForce::doMake(std::string&, std::vector values) const {$/;" f class:ProtoMol::PaulTrapExtendedForce doMake framework/forces/SphericalSystemForce.cpp /^ Force* SphericalSystemForce::doMake(string& errMsg, vector values) const {$/;" f class:ProtoMol::SphericalSystemForce doMake framework/forces/TimeForce.cpp /^ Force* TimeForce::doMake(string& errMsg, vector values) const{$/;" f class:ProtoMol::TimeForce doMake framework/forces/WrapperMetaForce.cpp /^ Force* WrapperMetaForce::doMake(string& errMsg, vector val) const{$/;" f class:ProtoMol::WrapperMetaForce doMake framework/frontend/ForceFactoryDetails.cpp /^ Force* ForceFactoryDetails::doMake(string& errMsg, const string& idInput, vector values) const{$/;" f class:ProtoMol::ForceFactoryDetails doMake framework/frontend/IntegratorFactoryDetails.cpp /^ Integrator* IntegratorFactoryDetails::doMake(string& errMsg, const string& definition) const{$/;" f class:ProtoMol::IntegratorFactoryDetails doMake framework/frontend/OutputBSDL.cpp /^ Output* OutputBSDL::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputBSDL doMake framework/frontend/OutputDCDTrajectory.cpp /^ Output* OutputDCDTrajectory::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputDCDTrajectory doMake framework/frontend/OutputDiffusion.cpp /^ Output* OutputDiffusion::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputDiffusion doMake framework/frontend/OutputDihedrals.cpp /^ Output* OutputDihedrals::doMake(std::string& , const std::vector& values) const{$/;" f class:ProtoMol::OutputDihedrals doMake framework/frontend/OutputEnergies.cpp /^ Output* OutputEnergies::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputEnergies doMake framework/frontend/OutputFactoryDetails.cpp /^ Output* OutputFactoryDetails::doMake(string& errMsg, const string& id, const vector& values) const{$/;" f class:ProtoMol::OutputFactoryDetails doMake framework/frontend/OutputFinalPDBPos.cpp /^ Output* OutputFinalPDBPos::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputFinalPDBPos doMake framework/frontend/OutputFinalXYZBinPos.cpp /^ Output* OutputFinalXYZBinPos::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputFinalXYZBinPos doMake framework/frontend/OutputFinalXYZBinVel.cpp /^ Output* OutputFinalXYZBinVel::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputFinalXYZBinVel doMake framework/frontend/OutputFinalXYZPos.cpp /^ Output* OutputFinalXYZPos::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputFinalXYZPos doMake framework/frontend/OutputFinalXYZVel.cpp /^ Output* OutputFinalXYZVel::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputFinalXYZVel doMake framework/frontend/OutputMomentum.cpp /^ Output* OutputMomentum::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputMomentum doMake framework/frontend/OutputPDBFramePos.cpp /^ Output* OutputPDBFramePos::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputPDBFramePos doMake framework/frontend/OutputPaulTrap.cpp /^ Output* OutputPaulTrap::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputPaulTrap doMake framework/frontend/OutputREMExchangeRate.cpp /^ Output *OutputREMExchangeRate::doMake(string & \/*errMesg*\/, const vector &values) const {$/;" f class:ProtoMol::OutputREMExchangeRate doMake framework/frontend/OutputREMHistory.cpp /^ Output *OutputREMHistoryFile::doMake(string & \/*errMesg*\/, const vector &values) const {$/;" f class:ProtoMol::OutputREMHistoryFile doMake framework/frontend/OutputScreen.cpp /^ Output* OutputScreen::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputScreen doMake framework/frontend/OutputState.cpp /^ Output* OutputState::doMake(std::string& , const std::vector& values) const{$/;" f class:ProtoMol::OutputState doMake framework/frontend/OutputTemperatures.cpp /^ Output* OutputTemperatures::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputTemperatures doMake framework/frontend/OutputXYZBinTrajectoryPos.cpp /^ Output* OutputXYZBinTrajectoryPos::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputXYZBinTrajectoryPos doMake framework/frontend/OutputXYZBinTrajectoryVel.cpp /^ Output* OutputXYZBinTrajectoryVel::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputXYZBinTrajectoryVel doMake framework/frontend/OutputXYZTrajectoryForce.cpp /^ Output* OutputXYZTrajectoryForce::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputXYZTrajectoryForce doMake framework/frontend/OutputXYZTrajectoryPos.cpp /^ Output* OutputXYZTrajectoryPos::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputXYZTrajectoryPos doMake framework/frontend/OutputXYZTrajectoryVel.cpp /^ Output* OutputXYZTrajectoryVel::doMake(string&, const vector& values) const{$/;" f class:ProtoMol::OutputXYZTrajectoryVel doMake framework/frontend/TopologyFactoryDetails.cpp /^ GenericTopology* TopologyFactoryDetails::doMake(string& errMsg, const string& id, const vector& values) const{$/;" f class:ProtoMol::TopologyFactoryDetails doMake framework/imd/HapticSystemForce.cpp /^ Force* HapticSystemForce::doMake(string& , vector values) const {$/;" f class:ProtoMol::HapticSystemForce doMake framework/integrators/BBKIntegrator.cpp /^ STSIntegrator* BBKIntegrator::doMake(string& , const vector& values,ForceGroup* fg)const{$/;" f class:ProtoMol::BBKIntegrator doMake framework/integrators/BSplineMOLLYIntegrator.cpp /^ MTSIntegrator* BSplineMOLLYIntegrator::doMake(std::string& errMsg, const std::vector& values, ForceGroup* fg, StandardIntegrator *nextIntegrator)const{$/;" f class:ProtoMol::BSplineMOLLYIntegrator doMake framework/integrators/DLMCIntegrator.cpp /^ MTSIntegrator* DLMCIntegrator::doMake(string& , const vector& values, $/;" f class:ProtoMol::DLMCIntegrator doMake framework/integrators/DMDLeapfrogIntegrator.cpp /^ STSIntegrator* DMDLeapfrogIntegrator::doMake(string& , const vector& values,ForceGroup* fg)const{$/;" f class:ProtoMol::DMDLeapfrogIntegrator doMake framework/integrators/DihedralHMCIntegrator.cpp /^ MTSIntegrator* DihedralHMCIntegrator::doMake(string& , const vector& values, $/;" f class:ProtoMol::DihedralHMCIntegrator doMake framework/integrators/EquilibriumMOLLYIntegrator.cpp /^ MTSIntegrator* EquilibriumMOLLYIntegrator::doMake(string& , const vector& values,ForceGroup* fg, StandardIntegrator *nextIntegrator)const{$/;" f class:ProtoMol::EquilibriumMOLLYIntegrator doMake framework/integrators/HMCIntegrator.cpp /^ MTSIntegrator* HMCIntegrator::doMake(string& , const vector& values, $/;" f class:ProtoMol::HMCIntegrator doMake framework/integrators/ImpulseIntegrator.cpp /^ MTSIntegrator* ImpulseIntegrator::doMake(string&, const vector& values,ForceGroup* fg, StandardIntegrator *nextIntegrator)const{$/;" f class:ProtoMol::ImpulseIntegrator doMake framework/integrators/LangevinImpulseIntegrator.cpp /^ STSIntegrator* LangevinImpulseIntegrator::doMake(string& , const vector& values,ForceGroup* fg)const{$/;" f class:ProtoMol::LangevinImpulseIntegrator doMake framework/integrators/LeapfrogIntegrator.cpp /^ STSIntegrator* LeapfrogIntegrator::doMake(string& , const vector& values,ForceGroup* fg)const{$/;" f class:ProtoMol::LeapfrogIntegrator doMake framework/integrators/NPTVerletIntegrator.cpp /^ STSIntegrator* NPTVerletIntegrator::doMake(string& , const vector& values,ForceGroup* fg)const{$/;" f class:ProtoMol::NPTVerletIntegrator doMake framework/integrators/NVTVerletIntegrator.cpp /^ STSIntegrator* NVTVerletIntegrator::doMake(string& , const vector& values,ForceGroup* fg)const{$/;" f class:ProtoMol::NVTVerletIntegrator doMake framework/integrators/NoseNVTLeapfrogIntegrator.cpp /^ STSIntegrator* NoseNVTLeapfrogIntegrator::doMake(string&, const vector& values,ForceGroup* fg)const{$/;" f class:ProtoMol::NoseNVTLeapfrogIntegrator doMake framework/integrators/PLeapfrogIntegrator.cpp /^ STSIntegrator* PLeapfrogIntegrator::doMake(string& , const vector& values,ForceGroup* fg)const{$/;" f class:ProtoMol::PLeapfrogIntegrator doMake framework/integrators/PaulTrapIntegrator.cpp /^ STSIntegrator* PaulTrapIntegrator::doMake(string& errMsg, const vector& values,ForceGroup* fg)const{$/;" f class:ProtoMol::PaulTrapIntegrator doMake framework/integrators/ShadowHMCIntegrator.cpp /^ MTSIntegrator * ShadowHMCIntegrator::doMake( string &errMsg,$/;" f class:ProtoMol::ShadowHMCIntegrator doMake framework/topology/Topology.h /^ virtual GenericTopology* doMake(std::string& errMsg, std::vector values)const{$/;" f class:ProtoMol::Topology doMakeCollection framework/frontend/OutputFactoryDetails.cpp /^ OutputCollection* OutputFactoryDetails::doMakeCollection(string& errMsg, const Configuration* config) const{$/;" f class:ProtoMol::OutputFactoryDetails doMollification framework/integrators/BSplineMOLLYIntegrator.cpp /^ void BSplineMOLLYIntegrator::doMollification(Vector3DBlock*){$/;" f class:ProtoMol::BSplineMOLLYIntegrator doMollification framework/integrators/EquilibriumMOLLYIntegrator.cpp /^ void EquilibriumMOLLYIntegrator::doMollification(Vector3DBlock*){$/;" f class:ProtoMol::EquilibriumMOLLYIntegrator doOneAtomPair framework/forces/OneAtomPair.h /^ TConstraint>::doOneAtomPair(const int i, const int j) {$/;" f class:ProtoMol::OneAtomPair doOneAtomPair framework/forces/OneAtomPairFull.h /^ TConstraint>::doOneAtomPair(const int i, const int j) {$/;" f class:ProtoMol::OneAtomPairFull doOneAtomPair framework/forces/OneAtomPairTwo.h /^ TConstraint>::doOneAtomPair(const int i, const int j) {$/;" f class:ProtoMol::OneAtomPairTwo doOneAtomPair framework/forces/OneAtomPairTwoFull.h /^ TConstraint>::doOneAtomPair(const int i, const int j) {$/;" f class:ProtoMol::OneAtomPairTwoFull doOneAtomPair framework/forces/OneMollyPair.h /^ TNonbondedForce>::doOneAtomPair(const int i, const int j) {$/;" f class:ProtoMol::OneMollyPair doOneAtomPair framework/forces/OneMollyPairTwo.h /^ TNonbondedForceSecond>::doOneAtomPair(const int i, const int j) {$/;" f class:ProtoMol::OneMollyPairTwo doPrint framework/frontend/ForceFactoryDetails.cpp /^ string ForceFactoryDetails::doPrint()const{$/;" f class:ProtoMol::ForceFactoryDetails doPrint framework/frontend/IntegratorFactoryDetails.cpp /^ string IntegratorFactoryDetails::doPrint()const{$/;" f class:ProtoMol::IntegratorFactoryDetails doPrint framework/frontend/OutputFactoryDetails.cpp /^ string OutputFactoryDetails::doPrint()const{$/;" f class:ProtoMol::OutputFactoryDetails doPrint framework/frontend/TopologyFactoryDetails.cpp /^ string TopologyFactoryDetails::doPrint()const{$/;" f class:ProtoMol::TopologyFactoryDetails doPrint framework/integrators/ModifierAveraging.h /^ virtual std::string doPrint()const{return std::string("Averaging");};$/;" f class:ProtoMol::ModifierAveraging doPrint framework/integrators/ModifierFriction.h /^ virtual std::string doPrint()const{return std::string("Friction");};$/;" f class:ProtoMol::ModifierFriction doPrint framework/integrators/ModifierIncrementTimestep.h /^ virtual std::string doPrint()const{return std::string("IncrementTimestep");};$/;" f class:ProtoMol::ModifierIncrementTimestep doPrint framework/integrators/ModifierMollification.h /^ virtual std::string doPrint()const{return std::string("Mollification");};$/;" f class:ProtoMol::ModifierMollification doPrint framework/integrators/ModifierNPTRattle.h /^ virtual std::string doPrint()const{return std::string("NPTRattle");};$/;" f class:ProtoMol::ModifierNPTRattleDetails doPrint framework/integrators/ModifierNPTShake.h /^ virtual std::string doPrint()const{return std::string("NPTShake");};$/;" f class:ProtoMol::ModifierNPTShakeDetails doPrint framework/integrators/ModifierNVTRattle.h /^ virtual std::string doPrint()const{return std::string("NPTRattle");};$/;" f class:ProtoMol::ModifierNVTRattleDetails doPrint framework/integrators/ModifierNVTShake.h /^ virtual std::string doPrint()const{return std::string("NVTShake");};$/;" f class:ProtoMol::ModifierNVTShakeDetails doPrint framework/integrators/ModifierPostForceBarostat.h /^ virtual std::string doPrint()const{return std::string("PostForceBarostat");};$/;" f class:ProtoMol::ModifierPostForceBarostat doPrint framework/integrators/ModifierPostForceThermostat.h /^ virtual std::string doPrint()const{return std::string("PostForceThermostat");};$/;" f class:ProtoMol::ModifierPostForceThermostat doPrint framework/integrators/ModifierPreForceBarostat.h /^ virtual std::string doPrint()const{return std::string("PreForceBarostat");};$/;" f class:ProtoMol::ModifierPreForceBarostat doPrint framework/integrators/ModifierPreForceThermostat.h /^ virtual std::string doPrint()const{return std::string("PreForceThermostat");};$/;" f class:ProtoMol::ModifierPreForceThermostat doPrint framework/integrators/ModifierRattle.h /^ virtual std::string doPrint()const{return std::string("Rattle");};$/;" f class:ProtoMol::ModifierRattle doPrint framework/integrators/ModifierRemoveAngularMomentum.h /^ virtual std::string doPrint()const{return std::string("RemoveAngularMomentum");};$/;" f class:ProtoMol::ModifierRemoveAngularMomentum doPrint framework/integrators/ModifierRemoveLinearMomentum.h /^ virtual std::string doPrint()const{return std::string("RemoveLinearMomentum");};$/;" f class:ProtoMol::ModifierRemoveLinearMomentum doPrint framework/integrators/ModifierShadow.h /^ virtual std::string doPrint() const {$/;" f class:ProtoMol::ModifierShadow doPrint framework/integrators/ModifierShake.h /^ virtual std::string doPrint()const{return std::string("Shake");};$/;" f class:ProtoMol::ModifierShake doRegisterAllExemplarsConfiguration framework/frontend/OutputFactoryDetails.cpp /^ void OutputFactoryDetails::doRegisterAllExemplarsConfiguration(Configuration* config) const {$/;" f class:ProtoMol::OutputFactoryDetails doRegisterAllExemplarsConfiguration framework/frontend/TopologyFactoryDetails.cpp /^ void TopologyFactoryDetails::doRegisterAllExemplarsConfiguration(Configuration* config) const {$/;" f class:ProtoMol::TopologyFactoryDetails doRegisterExemplar framework/frontend/Factory.h /^ void doRegisterExemplar(const std::string& id, const Type* exemplar){$/;" f class:ProtoMol::Factory doRegisterExemplar framework/frontend/Factory.h /^ void doRegisterExemplar(const std::string& id, const Type* exemplar,const std::vector& aliases) {$/;" f class:ProtoMol::Factory doRegisterExemplar framework/frontend/HelpTextFactory.cpp /^ void HelpTextFactory::doRegisterExemplar(const string& id, const HelpText& helpText){$/;" f class:ProtoMol::HelpTextFactory doRegisterExemplars framework/frontend/HelpTextFactory.cpp /^ void HelpTextFactory::doRegisterExemplars(const Configuration* config){$/;" f class:ProtoMol::HelpTextFactory doRegisterHelpText framework/frontend/ForceFactoryDetails.cpp /^ void ForceFactoryDetails::doRegisterHelpText() const{$/;" f class:ProtoMol::ForceFactoryDetails doRegisterHelpText framework/frontend/IntegratorFactoryDetails.cpp /^ void IntegratorFactoryDetails::doRegisterHelpText() const{$/;" f class:ProtoMol::IntegratorFactoryDetails doRegisterHelpText framework/frontend/OutputFactoryDetails.cpp /^ void OutputFactoryDetails::doRegisterHelpText() const{$/;" f class:ProtoMol::OutputFactoryDetails doRegisterHelpText framework/frontend/TopologyFactoryDetails.cpp /^ void TopologyFactoryDetails::doRegisterHelpText() const{$/;" f class:ProtoMol::TopologyFactoryDetails doRun framework/frontend/OutputBSDL.cpp /^ void OutputBSDL::doRun(int){$/;" f class:ProtoMol::OutputBSDL doRun framework/frontend/OutputDCDTrajectory.cpp /^ void OutputDCDTrajectory::doRun(int){$/;" f class:ProtoMol::OutputDCDTrajectory doRun framework/frontend/OutputFile.cpp /^ void OutputFile::doRun(int step){$/;" f class:ProtoMol::OutputFile doRun framework/frontend/OutputFinalPDBPos.h /^ virtual void doRun(int){};$/;" f class:ProtoMol::OutputFinalPDBPos doRun framework/frontend/OutputFinalXYZBinPos.h /^ virtual void doRun(int){};$/;" f class:ProtoMol::OutputFinalXYZBinPos doRun framework/frontend/OutputFinalXYZBinVel.h /^ virtual void doRun(int){};$/;" f class:ProtoMol::OutputFinalXYZBinVel doRun framework/frontend/OutputFinalXYZPos.h /^ virtual void doRun(int){};$/;" f class:ProtoMol::OutputFinalXYZPos doRun framework/frontend/OutputFinalXYZVel.h /^ virtual void doRun(int){};$/;" f class:ProtoMol::OutputFinalXYZVel doRun framework/frontend/OutputPDBFramePos.cpp /^ void OutputPDBFramePos::doRun(int step){$/;" f class:ProtoMol::OutputPDBFramePos doRun framework/frontend/OutputScreen.cpp /^ void OutputScreen::doRun(int step){$/;" f class:ProtoMol::OutputScreen doRun framework/frontend/OutputXYZBinTrajectoryPos.cpp /^ void OutputXYZBinTrajectoryPos::doRun(int){$/;" f class:ProtoMol::OutputXYZBinTrajectoryPos doRun framework/frontend/OutputXYZBinTrajectoryVel.cpp /^ void OutputXYZBinTrajectoryVel::doRun(int){$/;" f class:ProtoMol::OutputXYZBinTrajectoryVel doRun framework/frontend/OutputXYZTrajectoryForce.cpp /^ void OutputXYZTrajectoryForce::doRun(int){$/;" f class:ProtoMol::OutputXYZTrajectoryForce doRun framework/frontend/OutputXYZTrajectoryPos.cpp /^ void OutputXYZTrajectoryPos::doRun(int){$/;" f class:ProtoMol::OutputXYZTrajectoryPos doRun framework/frontend/OutputXYZTrajectoryVel.cpp /^ void OutputXYZTrajectoryVel::doRun(int){$/;" f class:ProtoMol::OutputXYZTrajectoryVel doRunCached framework/frontend/OutputDiffusion.cpp /^ void OutputDiffusion::doRunCached(int step){$/;" f class:ProtoMol::OutputDiffusion doRunCached framework/frontend/OutputDihedrals.cpp /^ void OutputDihedrals::doRunCached(int){$/;" f class:ProtoMol::OutputDihedrals doRunCached framework/frontend/OutputEnergies.cpp /^ void OutputEnergies::doRunCached(int){$/;" f class:ProtoMol::OutputEnergies doRunCached framework/frontend/OutputMomentum.cpp /^ void OutputMomentum::doRunCached(int){$/;" f class:ProtoMol::OutputMomentum doRunCached framework/frontend/OutputPaulTrap.cpp /^ void OutputPaulTrap::doRunCached(int step){$/;" f class:ProtoMol::OutputPaulTrap doRunCached framework/frontend/OutputREMExchangeRate.cpp /^ void OutputREMExchangeRate::doRunCached(int \/*step*\/) {$/;" f class:ProtoMol::OutputREMExchangeRate doRunCached framework/frontend/OutputREMHistory.cpp /^ void OutputREMHistoryFile::doRunCached(int \/*step*\/) {$/;" f class:ProtoMol::OutputREMHistoryFile doRunCached framework/frontend/OutputState.cpp /^ void OutputState::doRunCached(int){$/;" f class:ProtoMol::OutputState doRunCached framework/frontend/OutputTemperatures.cpp /^ void OutputTemperatures::doRunCached(int){$/;" f class:ProtoMol::OutputTemperatures doSearch framework/frontend/HelpTextFactory.cpp /^ string HelpTextFactory::doSearch(const string& id) const{$/;" f class:ProtoMol::HelpTextFactory doSecondHalfKick framework/integrators/BBKIntegrator.cpp /^ void BBKIntegrator::doSecondHalfKick(){$/;" f class:ProtoMol::BBKIntegrator doSetParameters framework/forces/AngleSystemForce.h /^ virtual void doSetParameters(std::string&, std::vector){}$/;" f class:ProtoMol::AngleSystemForce doSetParameters framework/forces/BondSystemForce.h /^ virtual void doSetParameters(std::string&, std::vector){}$/;" f class:ProtoMol::BondSystemForce doSetParameters framework/forces/CompareForce.cpp /^ void CompareForce::doSetParameters(std::string& errMsg, std::vector values){$/;" f class:ProtoMol::CompareForce doSetParameters framework/forces/DihedralSystemForce.h /^ virtual void doSetParameters(std::string&, std::vector){}$/;" f class:ProtoMol::DihedralSystemForce doSetParameters framework/forces/Force.h /^ virtual void doSetParameters(std::string& , std::vector ){Report::report << Report::error << "setParameters not implemented for force "<getId()< values){$/;" f class:ProtoMol::HarmDihedralSystemForce doSetParameters framework/forces/ImproperSystemForce.h /^ virtual void doSetParameters(std::string&, std::vector){}$/;" f class:ProtoMol::ImproperSystemForce doSetParameters framework/forces/TimeForce.cpp /^ void TimeForce::doSetParameters(std::string& errMsg, std::vector values){$/;" f class:ProtoMol::TimeForce doUncache framework/integrators/BSplineMOLLYIntegrator.cpp /^ void BSplineMOLLYIntegrator::doUncache(){$/;" f class:ProtoMol::BSplineMOLLYIntegrator doUncache framework/integrators/Integrator.h /^ virtual void doUncache(){}$/;" f class:ProtoMol::Integrator doUncache framework/integrators/PaulTrapIntegrator.cpp /^ void PaulTrapIntegrator::doUncache(){$/;" f class:ProtoMol::PaulTrapIntegrator doUnregisterExemplar framework/frontend/Factory.h /^ bool doUnregisterExemplar(const std::string& id) {$/;" f class:ProtoMol::Factory doUnregisterExemplar framework/frontend/HelpTextFactory.cpp /^ bool HelpTextFactory::doUnregisterExemplar(const string& id){$/;" f class:ProtoMol::HelpTextFactory dohint framework/base/Report.cpp /^ MyStreamer& dohint(MyStreamer& stream){$/;" f namespace:ProtoMol::Report done framework/topology/CellListEnumerator_periodicBoundaries.h /^ bool done() {return (i==the_end);}$/;" f class:ProtoMol::CellListEnumerator done framework/topology/CellListEnumerator_standard.h /^ bool done() {return (i==the_end);}$/;" f class:ProtoMol::CellListEnumerator donors framework/base/PSF.h /^ std::vector donors;$/;" m class:ProtoMol::PSF donthint framework/base/Report.cpp /^ MyStreamer& donthint(MyStreamer& stream){$/;" f namespace:ProtoMol::Report dot framework/base/Vector3D.h /^ Real dot(const Vector3D& b) const { return (*this)*b;}$/;" f struct:ProtoMol::Vector3D drawBox compilerTests/glutTest.cpp /^static void drawBox(){$/;" f file: dswcoef framework/topology/CnSwitchingFunction.cpp /^ Real CnSwitchingFunction::dswcoef[][MAXEQNN] = {$/;" m class:ProtoMol::CnSwitchingFunction file: dswcoef framework/topology/CnSwitchingFunction.h /^ dswcoef[][MAXEQNN],$/;" m class:ProtoMol::CnSwitchingFunction dtor framework/base/mathutilities.cpp /^ vector dtor(const vector& deg){$/;" f namespace:ProtoMol dtor framework/base/mathutilities.h /^ inline Real dtor(Real degree) { $/;" f namespace:ProtoMol e1 framework/topology/PeriodicBoundaryConditions.h /^ const Vector3D& e1() const {return myE1;}$/;" f class:ProtoMol::PeriodicBoundaryConditions e1 framework/topology/VacuumBoundaryConditions.cpp /^ Vector3D VacuumBoundaryConditions::e1() const {return Vector3D(0,0,0);}$/;" f class:ProtoMol::VacuumBoundaryConditions e1r framework/topology/PeriodicBoundaryConditions.h /^ const Vector3D& e1r() const {return myE1r;}$/;" f class:ProtoMol::PeriodicBoundaryConditions e1r framework/topology/VacuumBoundaryConditions.cpp /^ Vector3D VacuumBoundaryConditions::e1r() const {return Vector3D(0,0,0);}$/;" f class:ProtoMol::VacuumBoundaryConditions e2 framework/topology/PeriodicBoundaryConditions.h /^ const Vector3D& e2() const {return myE2;}$/;" f class:ProtoMol::PeriodicBoundaryConditions e2 framework/topology/VacuumBoundaryConditions.cpp /^ Vector3D VacuumBoundaryConditions::e2() const {return Vector3D(0,0,0);}$/;" f class:ProtoMol::VacuumBoundaryConditions e2r framework/topology/PeriodicBoundaryConditions.h /^ const Vector3D& e2r() const {return myE2r;}$/;" f class:ProtoMol::PeriodicBoundaryConditions e2r framework/topology/VacuumBoundaryConditions.cpp /^ Vector3D VacuumBoundaryConditions::e2r() const {return Vector3D(0,0,0);}$/;" f class:ProtoMol::VacuumBoundaryConditions e3 framework/topology/PeriodicBoundaryConditions.h /^ const Vector3D& e3() const {return myE3;}$/;" f class:ProtoMol::PeriodicBoundaryConditions e3 framework/topology/VacuumBoundaryConditions.cpp /^ Vector3D VacuumBoundaryConditions::e3() const {return Vector3D(0,0,0);}$/;" f class:ProtoMol::VacuumBoundaryConditions e3r framework/topology/PeriodicBoundaryConditions.h /^ const Vector3D& e3r() const {return myE3r;}$/;" f class:ProtoMol::PeriodicBoundaryConditions e3r framework/topology/VacuumBoundaryConditions.cpp /^ Vector3D VacuumBoundaryConditions::e3r() const {return Vector3D(0,0,0);}$/;" f class:ProtoMol::VacuumBoundaryConditions elapsed framework/base/Cycles.h /^ static __inline double elapsed(ticks t1, ticks t0)$/;" f namespace:ProtoMol::Private elapsed framework/base/Cycles.h /^ static inline double elapsed(ticks t1, ticks t0) \/* time in nanoseconds *\/$/;" f namespace:ProtoMol::Private elapsed framework/base/Cycles.h /^ static inline double elapsed(ticks t1, ticks t0)$/;" f namespace:ProtoMol::Private elementName framework/base/PDB.h /^ std::string elementName; \/\/\/< atom_name $/;" m struct:ProtoMol::PDB::Atom elementNum framework/base/PDB.h /^ int elementNum; \/\/\/< serial_size $/;" m struct:ProtoMol::PDB::Atom elementNum framework/base/PDB.h /^ int elementNum; \/\/\/< serial_size $/;" m struct:ProtoMol::PDB::Ter elementType framework/base/PDB.h /^ std::string elementType; \/\/\/< record_name $/;" m struct:ProtoMol::PDB::Atom elementType framework/base/PDB.h /^ std::string elementType; \/\/\/< record_name $/;" m struct:ProtoMol::PDB::Ter emin framework/base/PAR.h /^ Real emin; \/\/\/< well depth$/;" m struct:ProtoMol::PAR::Hbond empty framework/base/Array_Fastest.h /^ bool empty() const { return m_nArrayElements==0; }$/;" f class:ProtoMol::Array empty framework/base/Array_NoPartialSpecialization.h /^ bool empty() const { return m_nArrayElements==0; }$/;" f class:ProtoMol::Array empty framework/base/Configuration.cpp /^ bool Configuration::empty(const string& keyword) const{$/;" f class:ProtoMol::Configuration empty framework/base/ValueType.h /^ static Type empty(){return "";}$/;" f struct:ProtoMol::ValueTraits empty framework/base/ValueType.h /^ static Type empty(){return 0.0;}$/;" f struct:ProtoMol::ValueTraits empty framework/base/ValueType.h /^ static Type empty(){return 0;}$/;" f struct:ProtoMol::ValueTraits empty framework/base/ValueType.h /^ static Type empty(){return Type("");}$/;" f struct:ProtoMol::ValueTraits empty framework/base/ValueType.h /^ static Type empty(){return Vector3D(0.0,0.0,0.0);}$/;" f struct:ProtoMol::ValueTraits empty framework/base/ValueType.h /^ static Type empty(){return std::vector();}$/;" f struct:ProtoMol::ValueTraits empty framework/base/ValueType.h /^ static Type empty(){return true;}$/;" f struct:ProtoMol::ValueTraits empty framework/base/Vector3DBlock.h /^ bool empty() const {return vec.empty();} $/;" f class:ProtoMol::Vector3DBlock empty framework/frontend/Factory.h /^ static bool empty(){$/;" f class:ProtoMol::Factory empty framework/frontend/HelpTextFactory.cpp /^ bool HelpTextFactory::empty(){$/;" f class:ProtoMol::HelpTextFactory empty framework/topology/ExclusionTable.h /^ bool empty() const{return (myTable.empty());}$/;" f class:ProtoMol::ExclusionTable enable framework/integrators/Modifier.h /^ void enable() const{myEnable=true;}$/;" f class:ProtoMol::Modifier end compilerTests/pngTest.cpp /^ unsigned char* end() const{return &p[3*w*h];}$/;" f class:PPM end framework/base/Array_Fastest.h /^ const_iterator end() const { return m_pArrayElements+m_nArrayElements; }$/;" f class:ProtoMol::Array end framework/base/Array_Fastest.h /^ const_iterator end() const { return m_pElements+size(); } $/;" f class:ProtoMol::RefArray end framework/base/Array_Fastest.h /^ const_iterator end() const { return m_pElements+size(); }$/;" f class:ProtoMol::RefArray end framework/base/Array_Fastest.h /^ iterator end() { return m_pArrayElements+m_nArrayElements; }$/;" f class:ProtoMol::Array end framework/base/Array_Fastest.h /^ iterator end() { return m_pElements+size(); }$/;" f class:ProtoMol::RefArray end framework/base/Array_NoPartialSpecialization.h /^ const_iterator end() const { return m_pElements+size(); } $/;" f class:ProtoMol::Array::RefArray end framework/base/Array_NoPartialSpecialization.h /^ const_iterator end() const { return m_pElements+size(); }$/;" f class:ProtoMol::Array::RefArray end framework/base/Array_NoPartialSpecialization.h /^ iterator end() { return m_pElements+size(); }$/;" f class:ProtoMol::Array::RefArray end framework/base/Array_NoPartialSpecialization.h /^ const_iterator end() const { return m_pArrayElements+m_nArrayElements; }$/;" f class:ProtoMol::Array end framework/base/Array_NoPartialSpecialization.h /^ iterator end() { return m_pArrayElements+m_nArrayElements; }$/;" f class:ProtoMol::Array end framework/base/Configuration.h /^ const_iterator end() const {return myValues.end();} $/;" f class:ProtoMol::Configuration end framework/base/Configuration.h /^ iterator end() {return myValues.end();}$/;" f class:ProtoMol::Configuration end framework/base/PGM.h /^ unsigned char* end() const{return &p[w*h];}$/;" f class:ProtoMol::PGM end framework/base/PPM.h /^ unsigned char* end() const{return &p[3*w*h];}$/;" f class:ProtoMol::PPM end framework/base/Vector3DBlock.h /^ const_iterator end() const {return vec.end();} $/;" f class:ProtoMol::Vector3DBlock end framework/base/Vector3DBlock.h /^ iterator end() {return vec.end();} $/;" f class:ProtoMol::Vector3DBlock end framework/frontend/Factory.h /^ static const_iterator end(){$/;" f class:ProtoMol::Factory end framework/frontend/OutputCollection.h /^ const_iterator end() const {return myOutputList.end();} $/;" f class:ProtoMol::OutputCollection end framework/frontend/OutputCollection.h /^ iterator end() {return myOutputList.end();}$/;" f class:ProtoMol::OutputCollection end framework/topology/ArrayCellListStructure.h /^ const_iterator end() const { return myEndConst; } $/;" f class:ProtoMol::ArrayCellListStructure end framework/topology/ArrayCellListStructure.h /^ iterator end() { return myEnd; }$/;" f class:ProtoMol::ArrayCellListStructure endr framework/base/Report.cpp /^ MyStreamer& endr(MyStreamer& stream){$/;" f namespace:ProtoMol::Report energies framework/forces/OneAtomPair.h /^ ScalarStructure* energies;$/;" m class:ProtoMol::OneAtomPair energies framework/forces/OneAtomPairFull.h /^ ScalarStructure* energies;$/;" m class:ProtoMol::OneAtomPairFull energies framework/forces/OneAtomPairTwo.h /^ ScalarStructure* energies;$/;" m class:ProtoMol::OneAtomPairTwo energies framework/forces/OneAtomPairTwoFull.h /^ ScalarStructure* energies;$/;" m class:ProtoMol::OneAtomPairTwoFull energy framework/base/MultiGrid.h /^ Real energy(int level){return energy(level,0,1);};$/;" f class:ProtoMol::MultiGrid energy framework/base/MultiGrid.h /^ inline Real MultiGrid::energy(int level, unsigned int block, unsigned int nBlocks){$/;" f class:ProtoMol::MultiGrid enumerator framework/forces/NonbondedCutoffForce.h /^ EnumeratorType enumerator;$/;" m class:ProtoMol::NonbondedCutoffForce enumerator framework/forces/NonbondedFullEwaldSystemForce.h /^ EnumeratorType enumerator;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce enumerator framework/forces/NonbondedMultiGridSystemForce.h /^ EnumeratorType enumerator;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce enumerator framework/forces/NonbondedPMEwaldSystemForce.h /^ EnumeratorType enumerator;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce epsilon framework/base/PAR.h /^ Real epsilon; \/\/\/< well depth or number of effective electrons (see description of negative below)$/;" m struct:ProtoMol::PAR::Nonbonded epsilon14 framework/base/PAR.h /^ Real epsilon14; \/\/\/< VDW parameter well depth or number of effective electrons (see above)$/;" m struct:ProtoMol::PAR::Nonbonded epsilonEnergy framework/forces/PaulTrapExtendedForce.h /^ Real epsilonEnergy(Real potentialEnergy){return potentialEnergy*myPaulF;}$/;" f class:ProtoMol::PaulTrapExtendedForce equal framework/base/Value.cpp /^ inline bool Value::equal(const Value& v1, const Value& v2){$/;" f class:ProtoMol::Value equal framework/base/mathutilities.h /^ inline bool equal(Real x, Real y){$/;" f namespace:ProtoMol equal framework/base/mathutilities.h /^ inline bool equal(Real x, Real y, Real epsilon){ $/;" f namespace:ProtoMol equal framework/base/stringutilities.cpp /^ bool equal(const string& s1, const string& s2){$/;" f namespace:ProtoMol equalBegin framework/base/stringutilities.cpp /^ bool equalBegin(const string& s1, const string& s2){$/;" f namespace:ProtoMol equalBeginNocase framework/base/stringutilities.cpp /^ bool equalBeginNocase(const string& s1, const string& s2){$/;" f namespace:ProtoMol equalConstraint framework/base/Value.h /^ inline bool Value::equalConstraint(const Value& v) const{$/;" f class:ProtoMol::Value equalEnd framework/base/stringutilities.cpp /^ bool equalEnd(const string& s1, const string& s2){$/;" f namespace:ProtoMol equalEndNocase framework/base/stringutilities.cpp /^ bool equalEndNocase(const string& s1, const string& s2){$/;" f namespace:ProtoMol equalNocase framework/base/stringutilities.cpp /^ bool equalNocase(const string& s1, const string& s2){$/;" f namespace:ProtoMol equalStart framework/base/stringutilities.cpp /^ bool equalStart(const string& s1, const string& s2){$/;" f namespace:ProtoMol equalStartNocase framework/base/stringutilities.cpp /^ bool equalStartNocase(const string& s1, const string& s2){$/;" f namespace:ProtoMol equalTerminate framework/base/stringutilities.cpp /^ bool equalTerminate(const string& s1, const string& s2){$/;" f namespace:ProtoMol equalTerminateNocase framework/base/stringutilities.cpp /^ bool equalTerminateNocase(const string& s1, const string& s2){$/;" f namespace:ProtoMol equalType framework/base/Value.cpp /^ inline bool Value::equalType(const Value& v1, const Value& v2){$/;" f class:ProtoMol::Value equalType framework/base/Value.h /^ inline bool Value::equalType(const Value& v) const{$/;" f class:ProtoMol::Value equalTypeAndConstraint framework/base/Value.h /^ inline bool Value::equalTypeAndConstraint(const Value& v) const{$/;" f class:ProtoMol::Value equalWildcard framework/base/stringutilities.cpp /^ int equalWildcard(const string& wildcard, const string& name){$/;" f namespace:ProtoMol erase framework/base/Vector3DBlock.h /^ iterator erase(iterator first, iterator last) {return vec.erase(first,last);}$/;" f class:ProtoMol::Vector3DBlock erase framework/base/Vector3DBlock.h /^ iterator erase(iterator pos) {return vec.erase(pos);}$/;" f class:ProtoMol::Vector3DBlock erf framework/base/mathutilities.h /^ inline Real erf(Real x){return myerf(x);}$/;" f namespace:ProtoMol erfc framework/base/mathutilities.h /^ inline Real erfc(Real x){return (1.0-myerf(x));}$/;" f namespace:ProtoMol error framework/base/Report.cpp /^ MyStreamer& error(MyStreamer& stream){$/;" f namespace:ProtoMol::Report evaluate framework/base/ReducedHessAngle.cpp /^ void ReducedHessAngle::evaluate(const Vector3D& atom_i, \/\/position of atom i$/;" f class:ProtoMol::ReducedHessAngle evaluate framework/forces/AngleSystemForce.h /^ inline void AngleSystemForce::evaluate(const GenericTopology* topo,$/;" f class:ProtoMol::AngleSystemForce evaluate framework/forces/BondSystemForce.h /^ inline void BondSystemForce::evaluate(const GenericTopology* topo,$/;" f class:ProtoMol::BondSystemForce evaluate framework/forces/DihedralSystemForce.h /^ inline void DihedralSystemForce::evaluate(const GenericTopology* topo,$/;" f class:ProtoMol::DihedralSystemForce evaluate framework/forces/ElectricFieldSystemForce.h /^ inline void ElectricFieldSystemForce::evaluate(const GenericTopology* topo,$/;" f class:ProtoMol::ElectricFieldSystemForce evaluate framework/forces/ExtendedCompareForce.cpp /^ void ExtendedCompareForce::evaluate(const GenericTopology* topo, $/;" f class:ProtoMol::ExtendedCompareForce evaluate framework/forces/ExtendedTimeForce.cpp /^ void ExtendedTimeForce::evaluate(const GenericTopology* topo, $/;" f class:ProtoMol::ExtendedTimeForce evaluate framework/forces/ExternalGravitationSystemForce.cpp /^ void ExternalGravitationSystemForce::evaluate(const GenericTopology* topo,$/;" f class:ProtoMol::ExternalGravitationSystemForce evaluate framework/forces/ExternalMagneticFieldExtendedForce.cpp /^ void ExternalMagneticFieldExtendedForce::evaluate(const GenericTopology* topo,$/;" f class:ProtoMol::ExternalMagneticFieldExtendedForce evaluate framework/forces/FrictionExtendedForce.cpp /^ void FrictionExtendedForce::evaluate(const GenericTopology* topo,$/;" f class:ProtoMol::FrictionExtendedForce evaluate framework/forces/HarmDihedralSystemForce.h /^ inline void HarmDihedralSystemForce::evaluate(const GenericTopology* topo,$/;" f class:ProtoMol::HarmDihedralSystemForce evaluate framework/forces/ImproperSystemForce.h /^ inline void ImproperSystemForce::evaluate(const GenericTopology* topo,$/;" f class:ProtoMol::ImproperSystemForce evaluate framework/forces/MagneticDipoleMirrorSystemForce.h /^ inline void MagneticDipoleMirrorSystemForce::evaluate(const GenericTopology* topo,$/;" f class:ProtoMol::MagneticDipoleMirrorSystemForce evaluate framework/forces/NonbondedCutoffMollyForce.h /^ void NonbondedCutoffMollyForce::evaluate(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedCutoffMollyForce evaluate framework/forces/NonbondedCutoffSystemForce.h /^ void NonbondedCutoffSystemForce::evaluate(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedCutoffSystemForce evaluate framework/forces/NonbondedFullEwaldSystemForce.h /^ TSwitchingFunction>::evaluate(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedFullEwaldSystemForce evaluate framework/forces/NonbondedFullSystemForce.h /^ virtual void evaluate(const GenericTopology* to, $/;" f class:ProtoMol::NonbondedFullSystemForce evaluate framework/forces/NonbondedMultiGridSystemForce.h /^ smooth>::evaluate(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedMultiGridSystemForce evaluate framework/forces/NonbondedPMEwaldSystemForce.h /^ TSwitchingFunction>::evaluate(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedPMEwaldSystemForce evaluate framework/forces/NonbondedSimpleFullSystemForce.h /^ virtual void evaluate(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedSimpleFullSystemForce evaluate framework/forces/PaulTrapExtendedForce.h /^ inline void PaulTrapExtendedForce::evaluate(const GenericTopology* topo,$/;" f class:ProtoMol::PaulTrapExtendedForce evaluate framework/forces/SphericalSystemForce.h /^ inline void SphericalSystemForce::evaluate(const GenericTopology* topo,$/;" f class:ProtoMol::SphericalSystemForce evaluate framework/forces/SystemCompareForce.cpp /^ void SystemCompareForce::evaluate(const GenericTopology* topo, $/;" f class:ProtoMol::SystemCompareForce evaluate framework/forces/SystemTimeForce.cpp /^ void SystemTimeForce::evaluate(const GenericTopology* topo, $/;" f class:ProtoMol::SystemTimeForce evaluate framework/imd/HapticSystemForce.cpp /^ void HapticSystemForce::evaluate (const GenericTopology* topo,$/;" f class:ProtoMol::HapticSystemForce evaluateExtendedForces framework/forces/ForceGroup.cpp /^ void ForceGroup::evaluateExtendedForces(GenericTopology* topo, $/;" f class:ProtoMol::ForceGroup evaluateMollyForces framework/forces/ForceGroup.cpp /^ void ForceGroup::evaluateMollyForces(GenericTopology* topo, $/;" f class:ProtoMol::ForceGroup evaluateSystemForces framework/forces/ForceGroup.cpp /^ void ForceGroup::evaluateSystemForces(GenericTopology* topo, $/;" f class:ProtoMol::ForceGroup exchange tools/rem/sequential/replica.cc /^void Replica::exchange(Replica other) {$/;" f class:Replica excl framework/topology/ExclusionTable.h /^ ExclusionClass excl;$/;" m struct:ProtoMol::ExclusionPair exclude framework/topology/GenericTopology.h /^ ExclusionType exclude;$/;" m class:ProtoMol::GenericTopology exclusions framework/topology/GenericTopology.h /^ ExclusionTable exclusions;$/;" m class:ProtoMol::GenericTopology execute framework/integrators/Modifier.h /^ void execute(){$/;" f class:ProtoMol::Modifier expfactor framework/forces/MagneticDipoleForce.h /^ Real volum, expfactor, realChi, kappa;$/;" m class:ProtoMol::MagneticDipoleForce expn framework/base/LookUpTableBase.h /^ static int expn(Real a){$/;" f class:ProtoMol::LookUpTableBase f framework/base/LookUpTableBase.h /^ typedef union { TReal f; TInt i; } Conv;$/;" m union:ProtoMol::LookUpTableBase:: f framework/base/Report.cpp /^ MyStreamer& MyStreamer::operator<< (ostream& (*f)(ostream&)) {$/;" f class:ProtoMol::Report::MyStreamer f framework/base/Report.cpp /^ MyStreamer& MyStreamer::operator<< (std::ios& (*f)(std::ios&)) {$/;" f class:ProtoMol::Report::MyStreamer f framework/base/Report.cpp /^ MyStreamer& MyStreamer::operator<< (MyStreamer& (*f)(MyStreamer&)){$/;" f class:ProtoMol::Report::MyStreamer faces compilerTests/glutTest.cpp /^static GLint faces[6][4] = { \/* Vertex indices for the 6 faces of a cube. *\/$/;" v file: fact framework/base/mathutilities.h /^ inline int fact(int n){$/;" f namespace:ProtoMol fftBack framework/base/Grid.h /^ void fftBack(){myFFT.backward();}$/;" f class:ProtoMol::Grid fftForward framework/base/Grid.h /^ void fftForward(){myFFT.forward();}$/;" f class:ProtoMol::Grid fftcoeff_ framework/base/fft.c /^void fftcoeff_(int *n,zomplex * coeff)$/;" f fftfact_ framework/base/fft.c /^void fftfact_(int *n,int *nf,int *f)$/;" f fill_header framework/imd/imd.cpp /^ static void fill_header(IMDheader *header, IMDType type, int32 length) {$/;" f namespace:ProtoMol::IMD file: finalize framework/frontend/Output.cpp /^ void Output::finalize(int step){$/;" f class:ProtoMol::Output finalize framework/frontend/OutputCollection.cpp /^ void OutputCollection::finalize(int step){$/;" f class:ProtoMol::OutputCollection finalize framework/parallel/Parallel-FD.cpp /^ void Parallel::finalize(){$/;" f class:ProtoMol::Parallel finalize framework/parallel/Parallel.cpp /^ void Parallel::finalize(){$/;" f class:ProtoMol::Parallel finalized framework/parallel/Parallel.h /^ static bool finalized() {return myFinalized;}$/;" f class:ProtoMol::Parallel find framework/base/Configuration.cpp /^ Configuration::const_iterator Configuration::find(const string& keyword) const{$/;" f class:ProtoMol::Configuration find framework/base/Configuration.cpp /^ Configuration::iterator Configuration::find(const string& keyword){$/;" f class:ProtoMol::Configuration find framework/frontend/Factory.h /^ static const Type* find(const std::string& id){$/;" f class:ProtoMol::Factory find framework/topology/ArrayCellListStructure.h /^ const_iterator find(const T1& t1) const {$/;" f class:ProtoMol::ArrayCellListStructure find framework/topology/ArrayCellListStructure.h /^ iterator find(const T1& t1) {$/;" f class:ProtoMol::ArrayCellListStructure findCell framework/topology/CubicCellManager.h /^ Cell findCell(const Vector3D &position) const {$/;" f class:ProtoMol::CubicCellManager findNextNeighbor framework/frontend/buildTopology.cpp /^ void findNextNeighbor(int a, vector& v, vector& p, vector& unused, $/;" f namespace:ProtoMol findPeriodic framework/topology/ArrayCellListStructure.h /^ const_iterator findPeriodic(const T1& t1) const{$/;" f class:ProtoMol::ArrayCellListStructure findPeriodic framework/topology/ArrayCellListStructure.h /^ iterator findPeriodic(const T1& t1) {$/;" f class:ProtoMol::ArrayCellListStructure find_free_port framework/imd/IMDElf.cpp /^ int IMDElf::find_free_port(void *sock, int defport) {$/;" f class:ProtoMol::IMDElf fineToCoarse framework/base/MultiGrid.h /^ void fineToCoarse(int level){fineToCoarse(level,0,1);}$/;" f class:ProtoMol::MultiGrid fineToCoarse framework/base/MultiGrid.h /^ inline void MultiGrid::fineToCoarse(int level, unsigned int block, unsigned int nBlocks){$/;" f class:ProtoMol::MultiGrid first framework/base/simpleTypes.h /^ unsigned int first,second;$/;" m struct:ProtoMol::PairIntSorted first framework/frontend/Output.h /^ bool first() const {return myFirst;}$/;" f class:ProtoMol::Output first framework/parallel/Parallel-FD.cpp /^ bool first = true;$/;" v first framework/topology/CellListEnumerator_periodicBoundaries.h /^ struct CellPair {int first; int second;};$/;" m struct:ProtoMol::CellListEnumerator::CellPair first framework/topology/CellListEnumerator_standard.h /^ struct CellPair {int first; int second;};$/;" m struct:ProtoMol::CellListEnumerator::CellPair first_run tools/rem/sequential/replica.h /^ bool first_run;$/;" m class:Replica fitplane framework/base/Vector3DBlock.cpp /^ bool Vector3DBlock::fitplane(Vector3D& normal, Real& d, Real& err, int limit) const{$/;" f class:ProtoMol::Vector3DBlock fixDiffTable framework/integrators/ModifierShadow.cpp /^ void ModifierShadow::fixDiffTable() {$/;" f class:ProtoMol::ModifierShadow flipcounts framework/frontend/OutputDihedrals.h /^ std::vector< std::vector< int > > flipcounts;$/;" m class:ProtoMol::OutputDihedrals float4 framework/io/DCDTrajectoryReader.h /^ typedef TypeSelection::Float<4>::type float4;$/;" t class:ProtoMol::DCDTrajectoryReader float4 framework/io/DCDTrajectoryWriter.h /^ typedef TypeSelection::Float<4>::type float4;$/;" t class:ProtoMol::DCDTrajectoryWriter fluctuationLI framework/integrators/LangevinImpulseIntegrator.cpp /^ void LangevinImpulseIntegrator::fluctuationLI() {$/;" f class:ProtoMol::LangevinImpulseIntegrator flushCache framework/frontend/OutputFile.cpp /^ void OutputFile::flushCache() {$/;" f class:ProtoMol::OutputFile force framework/parallel/Parallel-FD.cpp /^ bool force = false;$/;" v forceConstant framework/base/PAR.h /^ Real forceConstant; \/\/\/< force constant$/;" m struct:ProtoMol::PAR::Angle forceConstant framework/base/PAR.h /^ Real forceConstant; \/\/\/< force constant$/;" m struct:ProtoMol::PAR::Bond forceConstant framework/base/PAR.h /^ Real forceConstant; \/\/\/< force constant$/;" m struct:ProtoMol::PAR::Improper forceConstant framework/base/PAR.h /^ std::vector< Real > forceConstant; \/\/\/< force constant$/;" m struct:ProtoMol::PAR::Dihedral forceConstant framework/topology/Angle.h /^ Real forceConstant;$/;" m class:ProtoMol::Angle forceConstant framework/topology/Torsion.h /^ std::vector< Real > forceConstant; \/\/\/< The force constant ($k$ value) for this interaction. $/;" m class:ProtoMol::Torsion forces framework/forces/OneAtomPair.h /^ Vector3DBlock* forces;$/;" m class:ProtoMol::OneAtomPair forces framework/forces/OneAtomPairFull.h /^ Vector3DBlock* forces;$/;" m class:ProtoMol::OneAtomPairFull forces framework/forces/OneAtomPairTwo.h /^ Vector3DBlock* forces;$/;" m class:ProtoMol::OneAtomPairTwo forces framework/forces/OneAtomPairTwoFull.h /^ Vector3DBlock* forces;$/;" m class:ProtoMol::OneAtomPairTwoFull forces framework/frontend/IntegratorFactoryDetails.h /^ std::vector forces;$/;" m struct:ProtoMol::IntegratorFactoryDetails::IntegratorInput forces framework/integrators/IntegratorDefinition.h /^ std::vector forces;$/;" m struct:ProtoMol::IntegratorDefinition forward framework/base/FFTComplex.cpp /^ void forward() {zfft3d( 1,myNZ,myNY,myNX,myArray,myNZ,myNY,myFFTCoeff);}$/;" f class:ProtoMol::FFTInternal forward framework/base/FFTComplex.cpp /^ void FFTComplex::forward(){$/;" f class:ProtoMol::FFTComplex forward framework/integrators/Integrator.cpp /^ void Integrator::forward(){$/;" f class:ProtoMol::Integrator friction framework/integrators/NoseNVTLeapfrogIntegrator.cpp /^ void NoseNVTLeapfrogIntegrator::friction() {$/;" f class:ProtoMol::NoseNVTLeapfrogIntegrator front framework/base/Vector3DBlock.h /^ const_reference front() const {return vec.front();} $/;" f class:ProtoMol::Vector3DBlock front framework/base/Vector3DBlock.h /^ reference front() {return vec.front();}$/;" f class:ProtoMol::Vector3DBlock gather framework/parallel/Parallel-FD.cpp /^ void Parallel::gather(Real *data, int num, Real *data_array, int address) {$/;" f class:ProtoMol::Parallel gather framework/parallel/Parallel-FD.cpp /^ void Parallel::gather(Real*, int, Real*, int ) {}$/;" f class:ProtoMol::Parallel gather framework/parallel/Parallel.cpp /^ void Parallel::gather(Real *data, int num, Real *data_array, int address) {$/;" f class:ProtoMol::Parallel gather framework/parallel/Parallel.cpp /^ void Parallel::gather(Real*, int, Real*, int ) {}$/;" f class:ProtoMol::Parallel gcd_ framework/base/fft.c /^int gcd_(int* n1,int* n2)$/;" f general_rotation framework/topology/topologyutilities.cpp /^ void general_rotation(unsigned int innerAtom1, unsigned int innerAtom2, Vector3DBlock *positions, Vector3DBlock *velocities,vector *angles) {$/;" f namespace:ProtoMol general_rotation framework/topology/topologyutilities.cpp /^ void general_rotation(unsigned int innerAtom1, unsigned int innerAtom2, Vector3DBlock *positions, vector *angles) {$/;" f namespace:ProtoMol get compilerTests/pngTest.cpp /^ unsigned char get(unsigned int i, unsigned int j) const {return (p[(h-i-1)*w*3+j*3]+p[(h-i-1)*w*3+j*3+1]+p[(h-i-1)*w*3+j*3+2])\/3;}$/;" f class:PPM get framework/base/Configuration.cpp /^ Value Configuration::get(const string& keyword) const{$/;" f class:ProtoMol::Configuration get framework/base/Configuration.cpp /^ vector Configuration::get(const vector& parameters) const{$/;" f class:ProtoMol::Configuration get framework/base/PGM.h /^ unsigned char get(unsigned int x, unsigned int y) const {return p[(h-y-1)*w+x];}$/;" f class:ProtoMol::PGM get framework/base/PPM.h /^ unsigned char get(unsigned int x, unsigned int y) const {return (p[(h-y-1)*w*3+x*3]+p[(h-y-1)*w*3+x*3+1]+p[(h-y-1)*w*3+x*3+2])\/3;}$/;" f class:ProtoMol::PPM get framework/base/Value.h /^ virtual bool get(Real & v) const { return (ValueTraits::convert(holder,v) && ok);}$/;" f class:ProtoMol::Value::Holder get framework/base/Value.h /^ virtual bool get(Vector3D & v) const { return (ValueTraits::convert(holder,v) && ok);}$/;" f class:ProtoMol::Value::Holder get framework/base/Value.h /^ virtual bool get(bool & v) const { return (ValueTraits::convert(holder,v) && ok);}$/;" f class:ProtoMol::Value::Holder get framework/base/Value.h /^ virtual bool get(int & v) const { return (ValueTraits::convert(holder,v) && ok);}$/;" f class:ProtoMol::Value::Holder get framework/base/Value.h /^ virtual bool get(std::string & v) const { return (ValueTraits::convert(holder,v) && ok);}$/;" f class:ProtoMol::Value::Holder get framework/base/Value.h /^ virtual bool get(std::vector & v) const { return (ValueTraits >::convert(holder,v) && ok);}$/;" f class:ProtoMol::Value::Holder get framework/base/Value.h /^ virtual bool get(unsigned int & v) const { return (ValueTraits::convert(holder,v) && ok);}$/;" f class:ProtoMol::Value::Holder get framework/base/Value.h /^ T get() const{$/;" f class:ProtoMol::Value get framework/base/Value.h /^ bool get(T& value) const{$/;" f class:ProtoMol::Value get framework/frontend/InputValue.h /^ bool get(T& val) const {return myValue.get(val); }$/;" f class:ProtoMol::InputValue get framework/topology/CellListEnumerator_periodicBoundaries.h /^ void get(CellPair &cp) {cp.first=i->second; cp.second=j->second; }$/;" f class:ProtoMol::CellListEnumerator get framework/topology/CellListEnumerator_periodicBoundaries.h /^ void get(int &a,int &b) {a=i->second; b=j->second; }$/;" f class:ProtoMol::CellListEnumerator get framework/topology/CellListEnumerator_standard.h /^ void get(CellPair &cp) {cp.first=i->second; cp.second=j->second; }$/;" f class:ProtoMol::CellListEnumerator get framework/topology/CellListEnumerator_standard.h /^ void get(int &a,int &b) {a=i->second; b=j->second; }$/;" f class:ProtoMol::CellListEnumerator getActualTime framework/base/Timer.cpp /^ TimeRep Timer::getActualTime() const$/;" f class:ProtoMol::Timer getAlias framework/base/Makeable.cpp /^ string Makeable::getAlias() const{$/;" f class:ProtoMol::Makeable getAliases framework/base/Configuration.cpp /^ vector Configuration::getAliases(const string& keyword) const{$/;" f class:ProtoMol::Configuration getAngle framework/topology/AngleInfo.cpp /^ Real AngleInfo::getAngle()const {$/;" f class:ProtoMol::AngleInfo getAngleType framework/topology/AngleInfo.cpp /^ AngleInfo::AngleType AngleInfo::getAngleType()const {$/;" f class:ProtoMol::AngleInfo getAtomID framework/topology/AngleInfo.cpp /^ unsigned int AngleInfo::getAtomID() const{$/;" f class:ProtoMol::AngleInfo getAtomsBondedtoDihedral framework/topology/topologyutilities.cpp /^ void getAtomsBondedtoDihedral(const GenericTopology* topology,$/;" f namespace:ProtoMol getAutofit framework/io/XFigWriter.h /^ bool getAutofit() const {return myAutofit;}$/;" f class:ProtoMol::XFigWriter getAvailableId framework/parallel/Parallel.h /^ static int getAvailableId() {return myAvailableId;}$/;" f class:ProtoMol::Parallel getAvailableNum framework/parallel/Parallel.h /^ static int getAvailableNum() {return myAvailableNum;}$/;" f class:ProtoMol::Parallel getAve framework/base/mathutilities.h /^ inline Real WindowAve::getAve() { return( data.size() > 0 ? sumItems \/$/;" f class:ProtoMol::WindowAve getAxes framework/io/XFigWriter.h /^ bool getAxes() const {return myAxes;}$/;" f class:ProtoMol::XFigWriter getBegin framework/base/stringutilities.cpp /^ string getBegin(const string& s,string::size_type n){$/;" f namespace:ProtoMol getBlue framework/base/PGM.h /^ unsigned char getBlue(unsigned int x, unsigned int y) const {return p[(h-y-1)*w+x];}$/;" f class:ProtoMol::PGM getBlue framework/base/PPM.h /^ unsigned char getBlue(unsigned int x, unsigned int y) const {return p[(h-y-1)*w*3+x*3+2];}$/;" f class:ProtoMol::PPM getBond framework/topology/AngleInfo.cpp /^ unsigned int AngleInfo::getBond(unsigned int index) const{$/;" f class:ProtoMol::AngleInfo getBottomTimestep framework/integrators/Integrator.h /^ inline Real Integrator::getBottomTimestep() const{$/;" f class:ProtoMol::Integrator getBoundaryConditionsBox framework/topology/SemiGenericTopology.h /^ virtual void getBoundaryConditionsBox(Vector3D& minbb, Vector3D& maxbb) const{$/;" f class:ProtoMol::SemiGenericTopology getBoundingbox framework/topology/SemiGenericTopology.h /^ virtual void getBoundingbox(const Vector3DBlock& positions, Vector3D& minbb, Vector3D& maxbb) const{$/;" f class:ProtoMol::SemiGenericTopology getCRD framework/io/CRDReader.cpp /^ Vector3DBlock CRDReader::getCRD() const{$/;" f class:ProtoMol::CRDReader getCellSize framework/topology/CubicCellManager.h /^ Real getCellSize(void) const {return myCellSize;}$/;" f class:ProtoMol::CubicCellManager getCellVolume framework/topology/CubicCellManager.h /^ Real getCellVolume(void) const {return myRealCellSize.x*myRealCellSize.y*myRealCellSize.z;}$/;" f class:ProtoMol::CubicCellManager getCharmmType framework/io/PARWriter.cpp /^ PAR::CharmmTypeEnum PARWriter::getCharmmType() const{$/;" f class:ProtoMol::PARWriter getCharmmTypeDetected framework/io/PARReader.h /^ inline PAR::CharmmTypeEnum PARReader::getCharmmTypeDetected() const{$/;" f class:ProtoMol::PARReader getColor framework/io/XFigWriter.h /^ bool getColor() const {return myColor;}$/;" f class:ProtoMol::XFigWriter getComment framework/io/Reader.cpp /^ const string& Reader::getComment() const{$/;" f class:ProtoMol::Reader getConstraintType framework/base/Value.h /^ virtual ConstraintValueType::Enum getConstraintType()const {return (ConstraintValueType::Enum)Constraint::value;}$/;" f class:ProtoMol::Value::Holder getConstraintType framework/base/Value.h /^ inline ConstraintValueType::Enum Value::getConstraintType() const {$/;" f class:ProtoMol::Value getConstraintTypeString framework/base/Value.h /^ virtual const std::string & getConstraintTypeString() const { return ConstraintValueType::getString((ConstraintValueType::Enum)Constraint::value); }$/;" f class:ProtoMol::Value::Holder getConstraintTypeString framework/base/Value.h /^ inline const std::string & Value::getConstraintTypeString() const {$/;" f class:ProtoMol::Value getCounter framework/base/Cycles.h /^ static ticks getCounter(){return Private::getticks();}$/;" f class:ProtoMol::Cycles getCounter framework/base/MultiGrid.h /^ long getCounter(){return (myCounterDirect + myCounterCorrection);}$/;" f class:ProtoMol::MultiGrid getCurrentTime framework/base/Timer.cpp /^ TimeRep Timer::getCurrentTime()$/;" f class:ProtoMol::Timer getCycles framework/base/Cycles.h /^ double getCycles() const{return elapsed(myEndTime,myStartTime);}$/;" f class:ProtoMol::Cycles getDeepForces framework/forces/WrapperMetaForce.cpp /^ void WrapperMetaForce::getDeepForces(vector& forces) const{$/;" f class:ProtoMol::WrapperMetaForce getDeepMetaForces framework/forces/ForceGroup.cpp /^ vector ForceGroup::getDeepMetaForces() const{$/;" f class:ProtoMol::ForceGroup getDefaults framework/topology/PeriodicBoundaryConditions.cpp /^ vector PeriodicBoundaryConditions::getDefaults(const Vector3DBlock& positions) const{$/;" f class:ProtoMol::PeriodicBoundaryConditions getDefaults framework/topology/SemiGenericTopology.h /^ virtual std::vector getDefaults(const Vector3DBlock& positions) const{ return boundaryConditions.getDefaults(positions);}$/;" f class:ProtoMol::SemiGenericTopology getDefaults framework/topology/VacuumBoundaryConditions.h /^ std::vector getDefaults(const Vector3DBlock&) const{ return std::vector();}$/;" f class:ProtoMol::VacuumBoundaryConditions getDefinition framework/base/Makeable.cpp /^ MakeableDefinition Makeable::getDefinition() const{$/;" f class:ProtoMol::Makeable getDefinition framework/forces/ForceGroup.cpp /^ void ForceGroup::getDefinition(vector& forces) const{$/;" f class:ProtoMol::ForceGroup getDefinitionTypeString framework/base/Value.cpp /^ string Value::getDefinitionTypeString() const{$/;" f class:ProtoMol::Value getDihedral tools/rem/sequential/replica.cc /^double Replica::getDihedral(int dihedralIndex) const {$/;" f class:Replica getDimX framework/topology/ArrayCellListStructure.h /^ int getDimX() const{ return myNX;}$/;" f class:ProtoMol::ArrayCellListStructure getDimY framework/topology/ArrayCellListStructure.h /^ int getDimY() const{ return myNY;}$/;" f class:ProtoMol::ArrayCellListStructure getDimZ framework/topology/ArrayCellListStructure.h /^ int getDimZ() const{ return myNZ;}$/;" f class:ProtoMol::ArrayCellListStructure getDirectory tools/rem/sequential/replica.cc /^string Replica::getDirectory() {$/;" f class:Replica getElement framework/base/Stack.h /^ T Stack::getElement(unsigned int index) {$/;" f class:ProtoMol::Stack getEnd framework/base/stringutilities.cpp /^ string getEnd(const string& s,string::size_type n){$/;" f namespace:ProtoMol getEnergies framework/forces/CompareForce.h /^ const ScalarStructure* getEnergies() const{return myEnergies;}$/;" f class:ProtoMol::CompareForce getEnergy framework/forces/CoulombEwaldRealForce.h /^ static Real getEnergy(const ScalarStructure* energies) {return (*energies)[ScalarStructure::COULOMB];}$/;" f class:ProtoMol::CoulombEwaldRealForce getEnergy framework/forces/CoulombEwaldRealTableForce.h /^ static Real getEnergy(const ScalarStructure* energies) {return (*energies)[ScalarStructure::COULOMB];}$/;" f class:ProtoMol::CoulombEwaldRealTableForce getEnergy framework/forces/CoulombForce.h /^ static Real getEnergy(const ScalarStructure* energies) {return (*energies)[ScalarStructure::COULOMB];}$/;" f class:ProtoMol::CoulombForce getEnergy framework/forces/CoulombMultiGridDirectForce.h /^ static Real getEnergy(const ScalarStructure* energies) {return (*energies)[ScalarStructure::COULOMB];}$/;" f class:ProtoMol::CoulombMultiGridDirectForce getEnergy framework/forces/CoulombMultiGridDirectTableForce.h /^ static Real getEnergy(const ScalarStructure* energies) {return (*energies)[ScalarStructure::COULOMB];}$/;" f class:ProtoMol::CoulombMultiGridDirectTableForce getEnergy framework/forces/CoulombTableForce.h /^ static Real getEnergy(const ScalarStructure* energies) {return (*energies)[ScalarStructure::COULOMB];}$/;" f class:ProtoMol::CoulombTableForce getEnergy framework/forces/GravitationForce.h /^ static Real getEnergy(const ScalarStructure* energies) {return (*energies)[ScalarStructure::OTHER];}$/;" f class:ProtoMol::GravitationForce getEnergy framework/forces/LennardJonesForce.h /^ static Real getEnergy(const ScalarStructure* energies) {return (*energies)[ScalarStructure::LENNARDJONES];} $/;" f class:ProtoMol::LennardJonesForce getEnergy framework/forces/LennardJonesTableForce.h /^ static Real getEnergy(const ScalarStructure* energies) {return (*energies)[ScalarStructure::LENNARDJONES];}$/;" f class:ProtoMol::LennardJonesTableForce getEnergy framework/forces/MagneticDipoleForce.h /^ static Real getEnergy(const ScalarStructure* energies) {return (*energies)[ScalarStructure::OTHER];}$/;" f class:ProtoMol::MagneticDipoleForce getEnum framework/base/AbstractEnumType.h /^ Enum getEnum() const {return myType;}$/;" f class:ProtoMol::AbstractEnumType getEnum framework/base/AbstractEnumType.h /^ typename AbstractEnumType::Enum AbstractEnumType::getEnum(const std::string& s){$/;" f class:ProtoMol::AbstractEnumType getEnum framework/base/AbstractEnumType.h /^ typename AbstractEnumType::Enum AbstractEnumType::getEnum(int n){$/;" f class:ProtoMol::AbstractEnumType getEpsilonVel framework/integrators/ModifierNPTRattle.h /^ virtual Real getEpsilonVel() const{return myTheIntegrator->getEpsilonVel();}$/;" f class:ProtoMol::ModifierNPTRattle getEpsilonVel framework/integrators/ModifierNPTShake.h /^ virtual Real getEpsilonVel() const{return myTheIntegrator->getEpsilonVel();}$/;" f class:ProtoMol::ModifierNPTShake getEpsilonVel framework/integrators/NPTVerletIntegrator.h /^ Real getEpsilonVel() const {return myEpsilonVel;}$/;" f class:ProtoMol::NPTVerletIntegrator getEtaVel framework/integrators/ModifierNPTRattle.h /^ virtual Real getEtaVel() const{return myTheIntegrator->getEtaVel();}$/;" f class:ProtoMol::ModifierNPTRattle getEtaVel framework/integrators/ModifierNPTShake.h /^ virtual Real getEtaVel() const{return myTheIntegrator->getEtaVel();}$/;" f class:ProtoMol::ModifierNPTShake getEtaVel framework/integrators/ModifierNVTRattle.h /^ virtual Real getEtaVel() const{return myTheIntegrator->getEtaVel();}$/;" f class:ProtoMol::ModifierNVTRattle getEtaVel framework/integrators/ModifierNVTShake.h /^ virtual Real getEtaVel() const{return myTheIntegrator->getEtaVel();}$/;" f class:ProtoMol::ModifierNVTShake getEtaVel framework/integrators/NPTVerletIntegrator.h /^ Real getEtaVel() const {return myEtaVel;}$/;" f class:ProtoMol::NPTVerletIntegrator getEtaVel framework/integrators/NVTVerletIntegrator.h /^ Real getEtaVel() const {return myEtaVel;}$/;" f class:ProtoMol::NVTVerletIntegrator getFilename framework/io/File.h /^ inline std::string File::getFilename() const{$/;" f class:ProtoMol::File getFirstStep framework/frontend/Output.h /^ int getFirstStep() const {return myFirstStep;}$/;" f class:ProtoMol::Output getForceGroup framework/integrators/Integrator.h /^ ForceGroup* getForceGroup() const{return myForcesToEvaluate;}$/;" f class:ProtoMol::Integrator getForceKeyword framework/forces/CoulombForce.h /^ static std::string getForceKeyword() {return CoulombForce::keyword;} $/;" f class:ProtoMol::CoulombForce::C1 getForceKeyword framework/forces/CoulombForce.h /^ static std::string getForceKeyword() {return CoulombForce::keyword;} $/;" f class:ProtoMol::CoulombForce::C2 getForceKeyword framework/forces/CoulombForce.h /^ static std::string getForceKeyword() {return CoulombForce::keyword;} $/;" f class:ProtoMol::CoulombForce::C3 getForceKeyword framework/forces/CoulombForce.h /^ static std::string getForceKeyword() {return CoulombForce::keyword;} $/;" f class:ProtoMol::CoulombForce::C4 getForceObject framework/forces/CompareForce.h /^ Force* getForceObject() const{return myActualForce;}$/;" f class:ProtoMol::CompareForce getForces framework/forces/CompareForce.h /^ const Vector3DBlock* getForces() const{return myForces;}$/;" f class:ProtoMol::CompareForce getForces framework/forces/ForceGroup.cpp /^ vector ForceGroup::getForces() const{$/;" f class:ProtoMol::ForceGroup getForces framework/integrators/Integrator.h /^ inline Vector3DBlock* Integrator::getForces() const{$/;" f class:ProtoMol::Integrator getFromZ framework/io/XFigWriter.h /^ Real getFromZ() const{return myFromZ;}$/;" f class:ProtoMol::XFigWriter getGreen framework/base/PGM.h /^ unsigned char getGreen(unsigned int x, unsigned int y) const {return p[(h-y-1)*w+x];}$/;" f class:ProtoMol::PGM getGreen framework/base/PPM.h /^ unsigned char getGreen(unsigned int x, unsigned int y) const {return p[(h-y-1)*w*3+x*3+1];}$/;" f class:ProtoMol::PPM getId framework/base/Makeable.cpp /^ string Makeable::getId() const{$/;" f class:ProtoMol::Makeable getId framework/forces/CoulombEwaldRealForce.h /^ static std::string getId() {return keyword;}$/;" f class:ProtoMol::CoulombEwaldRealForce getId framework/forces/CoulombEwaldRealTableForce.h /^ static std::string getId() {$/;" f class:ProtoMol::CoulombEwaldRealTableForce getId framework/forces/CoulombForce.h /^ static std::string getId() {return keyword;}$/;" f class:ProtoMol::CoulombForce getId framework/forces/CoulombMultiGridDirectForce.h /^ static std::string getId() {return keyword+" -kernel "+TKernel::keyword;}$/;" f class:ProtoMol::CoulombMultiGridDirectForce getId framework/forces/CoulombMultiGridDirectTableForce.h /^ static std::string getId() {$/;" f class:ProtoMol::CoulombMultiGridDirectTableForce getId framework/forces/CoulombTableForce.h /^ static std::string getId() {$/;" f class:ProtoMol::CoulombTableForce getId framework/forces/GravitationForce.h /^ static std::string getId() {return keyword;}$/;" f class:ProtoMol::GravitationForce getId framework/forces/LennardJonesForce.h /^ static std::string getId() {return keyword;}$/;" f class:ProtoMol::LennardJonesForce getId framework/forces/LennardJonesTableForce.h /^ static std::string getId() {$/;" f class:ProtoMol::LennardJonesTableForce getId framework/forces/MagneticDipoleForce.h /^ static std::string getId() {return keyword;}$/;" f class:ProtoMol::MagneticDipoleForce getId framework/forces/OneAtomPair.h /^ static std::string getId() {$/;" f class:ProtoMol::OneAtomPair getId framework/forces/OneAtomPairFull.h /^ static std::string getId() {$/;" f class:ProtoMol::OneAtomPairFull getId framework/forces/OneAtomPairTwo.h /^ static std::string getId() {$/;" f class:ProtoMol::OneAtomPairTwo getId framework/forces/OneAtomPairTwoFull.h /^ static std::string getId() {$/;" f class:ProtoMol::OneAtomPairTwoFull getId framework/forces/OneMollyPair.h /^ static std::string getId() {$/;" f class:ProtoMol::OneMollyPair getId framework/forces/OneMollyPairTwo.h /^ static std::string getId() {$/;" f class:ProtoMol::OneMollyPairTwo getId framework/parallel/Parallel.h /^ static int getId() {return myId;}$/;" f class:ProtoMol::Parallel getId framework/topology/C1SwitchingFunction.h /^ static const std::string& getId() {return keyword;}$/;" f class:ProtoMol::C1SwitchingFunction getId framework/topology/C2SwitchingFunction.h /^ static const std::string& getId() {return keyword;}$/;" f class:ProtoMol::C2SwitchingFunction getId framework/topology/CmpCnCnSwitchingFunction.h /^ static const std::string& getId() {return keyword;}$/;" f class:ProtoMol::CmpCnCnSwitchingFunction getId framework/topology/CnSwitchingFunction.h /^ static const std::string& getId() {return keyword;}$/;" f class:ProtoMol::CnSwitchingFunction getId framework/topology/ComplementSwitchingFunction.h /^ static std::string getId() {return (keyword + TOriginalSwitchingFunction::getId());}$/;" f class:ProtoMol::ComplementSwitchingFunction getId framework/topology/CutoffSwitchingFunction.h /^ static const std::string& getId() {return keyword;}$/;" f class:ProtoMol::CutoffSwitchingFunction getId framework/topology/RangeSwitchingFunction.h /^ static std::string getId() {return (keyword + TOriginalSwitchingFunction::getId());}$/;" f class:ProtoMol::RangeSwitchingFunction getId framework/topology/ShiftSwitchingFunction.h /^ static const std::string& getId() {return keyword;}$/;" f class:ProtoMol::ShiftSwitchingFunction getId framework/topology/UniversalSwitchingFunction.h /^ static const std::string& getId() {return keyword;}$/;" f class:ProtoMol::UniversalSwitchingFunction getIdNoAlias framework/forces/AngleSystemForce.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::AngleSystemForce getIdNoAlias framework/forces/BondSystemForce.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::BondSystemForce getIdNoAlias framework/forces/CompareForce.cpp /^ string CompareForce::getIdNoAlias() const{$/;" f class:ProtoMol::CompareForce getIdNoAlias framework/forces/DihedralSystemForce.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::DihedralSystemForce getIdNoAlias framework/forces/ElectricFieldSystemForce.h /^ virtual std::string getIdNoAlias() const{$/;" f class:ProtoMol::ElectricFieldSystemForce getIdNoAlias framework/forces/ExternalGravitationSystemForce.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::ExternalGravitationSystemForce getIdNoAlias framework/forces/ExternalMagneticFieldExtendedForce.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::ExternalMagneticFieldExtendedForce getIdNoAlias framework/forces/FrictionExtendedForce.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::FrictionExtendedForce getIdNoAlias framework/forces/HarmDihedralSystemForce.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::HarmDihedralSystemForce getIdNoAlias framework/forces/ImproperSystemForce.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::ImproperSystemForce getIdNoAlias framework/forces/MagneticDipoleMirrorSystemForce.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::MagneticDipoleMirrorSystemForce getIdNoAlias framework/forces/NonbondedCutoffForce.h /^ std::string NonbondedCutoffForce::getIdNoAlias() const{$/;" f class:ProtoMol::NonbondedCutoffForce getIdNoAlias framework/forces/NonbondedFullEwaldSystemForce.h /^ TSwitchingFunction>::getIdNoAlias() const{$/;" f class:ProtoMol::NonbondedFullEwaldSystemForce getIdNoAlias framework/forces/NonbondedFullSystemForce.h /^ virtual std::string getIdNoAlias() const {return (TOneAtomPair::getId()+ " -algorithm " + keyword);}$/;" f class:ProtoMol::NonbondedFullSystemForce getIdNoAlias framework/forces/NonbondedMultiGridSystemForce.h /^ smooth>::getIdNoAlias() const{$/;" f class:ProtoMol::NonbondedMultiGridSystemForce getIdNoAlias framework/forces/NonbondedPMEwaldSystemForce.h /^ real,reciprocal,correction,TInterpolation,TSwitchingFunction>::getIdNoAlias() const{$/;" f class:ProtoMol::NonbondedPMEwaldSystemForce getIdNoAlias framework/forces/NonbondedSimpleFullSystemForce.h /^ virtual std::string getIdNoAlias() const {$/;" f class:ProtoMol::NonbondedSimpleFullSystemForce getIdNoAlias framework/forces/PaulTrapExtendedForce.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::PaulTrapExtendedForce getIdNoAlias framework/forces/SphericalSystemForce.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::SphericalSystemForce getIdNoAlias framework/forces/TimeForce.cpp /^ string TimeForce::getIdNoAlias() const{$/;" f class:ProtoMol::TimeForce getIdNoAlias framework/forces/WrapperMetaForce.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::WrapperMetaForce getIdNoAlias framework/frontend/OutputBSDL.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputBSDL getIdNoAlias framework/frontend/OutputDCDTrajectory.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputDCDTrajectory getIdNoAlias framework/frontend/OutputDiffusion.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputDiffusion getIdNoAlias framework/frontend/OutputDihedrals.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputDihedrals getIdNoAlias framework/frontend/OutputEnergies.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputEnergies getIdNoAlias framework/frontend/OutputFinalPDBPos.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputFinalPDBPos getIdNoAlias framework/frontend/OutputFinalXYZBinPos.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputFinalXYZBinPos getIdNoAlias framework/frontend/OutputFinalXYZBinVel.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputFinalXYZBinVel getIdNoAlias framework/frontend/OutputFinalXYZPos.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputFinalXYZPos getIdNoAlias framework/frontend/OutputFinalXYZVel.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputFinalXYZVel getIdNoAlias framework/frontend/OutputMomentum.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputMomentum getIdNoAlias framework/frontend/OutputPDBFramePos.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputPDBFramePos getIdNoAlias framework/frontend/OutputPaulTrap.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputPaulTrap getIdNoAlias framework/frontend/OutputREMExchangeRate.h /^ virtual std::string getIdNoAlias() const { return keyword; }$/;" f class:ProtoMol::OutputREMExchangeRate getIdNoAlias framework/frontend/OutputREMHistory.h /^ virtual std::string getIdNoAlias() const { return keyword; }$/;" f class:ProtoMol::OutputREMHistoryFile getIdNoAlias framework/frontend/OutputScreen.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputScreen getIdNoAlias framework/frontend/OutputState.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputState getIdNoAlias framework/frontend/OutputTemperatures.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputTemperatures getIdNoAlias framework/frontend/OutputXYZBinTrajectoryPos.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputXYZBinTrajectoryPos getIdNoAlias framework/frontend/OutputXYZBinTrajectoryVel.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputXYZBinTrajectoryVel getIdNoAlias framework/frontend/OutputXYZTrajectoryForce.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputXYZTrajectoryForce getIdNoAlias framework/frontend/OutputXYZTrajectoryPos.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputXYZTrajectoryPos getIdNoAlias framework/frontend/OutputXYZTrajectoryVel.h /^ virtual std::string getIdNoAlias() const{ return keyword;}$/;" f class:ProtoMol::OutputXYZTrajectoryVel getIdNoAlias framework/imd/HapticSystemForce.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::HapticSystemForce getIdNoAlias framework/integrators/BBKIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::BBKIntegrator getIdNoAlias framework/integrators/BSplineMOLLYIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::BSplineMOLLYIntegrator getIdNoAlias framework/integrators/DLMCIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::DLMCIntegrator getIdNoAlias framework/integrators/DMDLeapfrogIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::DMDLeapfrogIntegrator getIdNoAlias framework/integrators/DihedralHMCIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::DihedralHMCIntegrator getIdNoAlias framework/integrators/EquilibriumMOLLYIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::EquilibriumMOLLYIntegrator getIdNoAlias framework/integrators/HMCIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::HMCIntegrator getIdNoAlias framework/integrators/ImpulseIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::ImpulseIntegrator getIdNoAlias framework/integrators/LangevinImpulseIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::LangevinImpulseIntegrator getIdNoAlias framework/integrators/LeapfrogIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::LeapfrogIntegrator getIdNoAlias framework/integrators/NPTVerletIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::NPTVerletIntegrator getIdNoAlias framework/integrators/NVTVerletIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::NVTVerletIntegrator getIdNoAlias framework/integrators/NoseNVTLeapfrogIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::NoseNVTLeapfrogIntegrator getIdNoAlias framework/integrators/PLeapfrogIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::PLeapfrogIntegrator getIdNoAlias framework/integrators/PaulTrapIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::PaulTrapIntegrator getIdNoAlias framework/integrators/ShadowHMCIntegrator.h /^ virtual std::string getIdNoAlias() const{return keyword;}$/;" f class:ProtoMol::ShadowHMCIntegrator getIdNoAlias framework/topology/Topology.h /^ virtual std::string getIdNoAlias() const {return std::string(TBoundaryConditions::keyword+TCellManager::keyword);}$/;" f class:ProtoMol::Topology getIdNumber framework/forces/CompareForce.h /^ unsigned int getIdNumber() const{return myIdNumber;}$/;" f class:ProtoMol::CompareForce getIdNumber framework/forces/TimeForce.h /^ unsigned int getIdNumber() const{return myIdNumber;}$/;" f class:ProtoMol::TimeForce getIdentity framework/base/Matrix3by3.h /^ inline const Matrix3by3& Matrix3by3::getIdentity()$/;" f class:ProtoMol::Matrix3by3 getInitialTemperature framework/integrators/MCIntegrator.h /^ Real getInitialTemperature() const { return myInitialTemperature; }$/;" f class:ProtoMol::MCIntegrator getIntegratorDefinition framework/integrators/Integrator.cpp /^ IntegratorDefinition Integrator::getIntegratorDefinition() const{$/;" f class:ProtoMol::Integrator getIntegratorDefinitionAll framework/integrators/Integrator.cpp /^ vector Integrator::getIntegratorDefinitionAll() const{$/;" f class:ProtoMol::Integrator getKeyword framework/base/BSpline.h /^ static const std::string& getKeyword() {return keyword;}$/;" f class:ProtoMol::BSpline getKeyword framework/base/Hermite.h /^ static const std::string& getKeyword() {return keyword;}$/;" f class:ProtoMol::Hermite getKeyword framework/base/Lagrange.h /^ static const std::string& getKeyword() {return keyword;}$/;" f class:ProtoMol::Lagrange getKeyword framework/forces/AngleSystemForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::AngleSystemForce getKeyword framework/forces/BondSystemForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::BondSystemForce getKeyword framework/forces/CompareForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::CompareForce getKeyword framework/forces/CoulombForce.h /^ static std::string getKeyword() {return keyword;}$/;" f class:ProtoMol::CoulombForce::C1 getKeyword framework/forces/CoulombForce.h /^ static std::string getKeyword() {return keyword;}$/;" f class:ProtoMol::CoulombForce::C2 getKeyword framework/forces/CoulombForce.h /^ static std::string getKeyword() {return keyword;}$/;" f class:ProtoMol::CoulombForce::C3 getKeyword framework/forces/CoulombForce.h /^ static std::string getKeyword() {return keyword;}$/;" f class:ProtoMol::CoulombForce::C4 getKeyword framework/forces/DihedralSystemForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::DihedralSystemForce getKeyword framework/forces/ElectricFieldSystemForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::ElectricFieldSystemForce getKeyword framework/forces/ExternalGravitationSystemForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::ExternalGravitationSystemForce getKeyword framework/forces/ExternalMagneticFieldExtendedForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::ExternalMagneticFieldExtendedForce getKeyword framework/forces/FrictionExtendedForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::FrictionExtendedForce getKeyword framework/forces/HarmDihedralSystemForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::HarmDihedralSystemForce getKeyword framework/forces/ImproperSystemForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::ImproperSystemForce getKeyword framework/forces/MagneticDipoleMirrorSystemForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::MagneticDipoleMirrorSystemForce getKeyword framework/forces/NonbondedCutoffForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::NonbondedCutoffForce getKeyword framework/forces/NonbondedFullEwaldSystemForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::NonbondedFullEwaldSystemForce getKeyword framework/forces/NonbondedFullSystemForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::NonbondedFullSystemForce getKeyword framework/forces/NonbondedMultiGridSystemForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::NonbondedMultiGridSystemForce getKeyword framework/forces/NonbondedPMEwaldSystemForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::NonbondedPMEwaldSystemForce getKeyword framework/forces/NonbondedSimpleFullSystemForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::NonbondedSimpleFullSystemForce getKeyword framework/forces/PaulTrapExtendedForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::PaulTrapExtendedForce getKeyword framework/forces/SphericalSystemForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::SphericalSystemForce getKeyword framework/forces/TimeForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::TimeForce getKeyword framework/forces/WrapperMetaForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::WrapperMetaForce getKeyword framework/imd/HapticSystemForce.h /^ virtual std::string getKeyword() const{return keyword;}$/;" f class:ProtoMol::HapticSystemForce getKeyword framework/topology/CubicCellManager.h /^ const std::string& getKeyword() const {return keyword;}$/;" f class:ProtoMol::CubicCellManager getKeyword framework/topology/GenericTopology.h /^ static const std::string& getKeyword(){return keyword;}$/;" f class:ProtoMol::GenericTopology getKeyword framework/topology/PeriodicBoundaryConditions.h /^ const std::string& getKeyword() const {return keyword;}$/;" f class:ProtoMol::PeriodicBoundaryConditions getKeyword framework/topology/VacuumBoundaryConditions.h /^ const std::string& getKeyword() const {return keyword;}$/;" f class:ProtoMol::VacuumBoundaryConditions getLapTime framework/base/Timer.cpp /^ TimeRep Timer::getLapTime() const$/;" f class:ProtoMol::Timer getLastStep framework/frontend/Output.h /^ int getLastStep() const {return myLastStep;}$/;" f class:ProtoMol::Output getLeftFill framework/base/stringutilities.cpp /^ string getLeftFill(const string& s,string::size_type n){$/;" f namespace:ProtoMol getLegend framework/io/XFigWriter.h /^ bool getLegend() const {return myLegend;}$/;" f class:ProtoMol::XFigWriter getMasterId framework/parallel/Parallel.h /^ static int getMasterId() {return myMasterId;}$/;" f class:ProtoMol::Parallel getMax framework/topology/PeriodicBoundaryConditions.h /^ const Vector3D& getMax() const {return myMax;}$/;" f class:ProtoMol::PeriodicBoundaryConditions getMax framework/topology/VacuumBoundaryConditions.cpp /^ Vector3D VacuumBoundaryConditions::getMax() const {$/;" f class:ProtoMol::VacuumBoundaryConditions getMaxDelta framework/topology/ExclusionTable.h /^ int getMaxDelta() const{return myMaxDelta;}$/;" f class:ProtoMol::ExclusionTable getMaxPackages framework/parallel/Parallel.h /^ static int getMaxPackages() {return myMaxPackages;}$/;" f class:ProtoMol::Parallel getMin framework/topology/PeriodicBoundaryConditions.h /^ const Vector3D& getMin() const {return myMin;}$/;" f class:ProtoMol::PeriodicBoundaryConditions getMin framework/topology/VacuumBoundaryConditions.cpp /^ Vector3D VacuumBoundaryConditions::getMin() const {$/;" f class:ProtoMol::VacuumBoundaryConditions getMode framework/parallel/Parallel.h /^ static ParallelType getMode() {return myMode;}$/;" f class:ProtoMol::Parallel getNext framework/frontend/Output.h /^ int getNext() const {return myNextStep;}$/;" f class:ProtoMol::Output getNext framework/frontend/OutputCollection.cpp /^ int OutputCollection::getNext() const{$/;" f class:ProtoMol::OutputCollection getNextStep tools/rem/sequential/replica.cc /^int Replica::getNextStep() const {$/;" f class:Replica getNum framework/parallel/Parallel.h /^ static int getNum() {return myNum;}$/;" f class:ProtoMol::Parallel getNumAtoms framework/integrators/NPTVerletIntegrator.h /^ Real getNumAtoms() const {return NumAtoms;}$/;" f class:ProtoMol::NPTVerletIntegrator getNumAtoms framework/integrators/NVTVerletIntegrator.h /^ Real getNumAtoms() const {return NumAtoms;}$/;" f class:ProtoMol::NVTVerletIntegrator getNumElements framework/base/Stack.h /^ unsigned int Stack::getNumElements() {$/;" f class:ProtoMol::Stack getNumSteps tools/rem/sequential/replica.cc /^int Replica::getNumSteps() const {$/;" f class:Replica getNumberOfPackages framework/parallel/Parallel-FD.cpp /^ unsigned int Parallel::getNumberOfPackages(unsigned int n) {$/;" f class:ProtoMol::Parallel getNumberOfPackages framework/parallel/Parallel.cpp /^ unsigned int Parallel::getNumberOfPackages(unsigned int n) {$/;" f class:ProtoMol::Parallel getOrder framework/base/BSpline.h /^ unsigned int getOrder() const {return myInterOrder;}$/;" f class:ProtoMol::BSpline getOrder framework/base/Hermite.h /^ unsigned int getOrder() const {return myInterOrder;}$/;" f class:ProtoMol::Hermite getOrder framework/base/Lagrange.h /^ unsigned int getOrder() const {return myInterOrder;}$/;" f class:ProtoMol::Lagrange getOutputFreq framework/frontend/Output.h /^ int getOutputFreq() const {return myOutputFreq;}$/;" f class:ProtoMol::Output getPDB framework/io/PDBReader.cpp /^ PDB PDBReader::getPDB() const{$/;" f class:ProtoMol::PDBReader getParameterSize framework/forces/AngleSystemForce.h /^ virtual unsigned int getParameterSize() const{return 0;}$/;" f class:ProtoMol::AngleSystemForce getParameterSize framework/forces/BondSystemForce.h /^ virtual unsigned int getParameterSize() const{return 0;}$/;" f class:ProtoMol::BondSystemForce getParameterSize framework/forces/CompareForce.cpp /^ unsigned int CompareForce::getParameterSize() const{$/;" f class:ProtoMol::CompareForce getParameterSize framework/forces/CoulombEwaldRealForce.h /^ static unsigned int getParameterSize() {return 1;}$/;" f class:ProtoMol::CoulombEwaldRealForce getParameterSize framework/forces/CoulombEwaldRealTableForce.h /^ static unsigned int getParameterSize() {$/;" f class:ProtoMol::CoulombEwaldRealTableForce getParameterSize framework/forces/CoulombForce.h /^ static unsigned int getParameterSize() {return 0;}$/;" f class:ProtoMol::CoulombForce getParameterSize framework/forces/CoulombMultiGridDirectForce.h /^ static unsigned int getParameterSize() {return 1;}$/;" f class:ProtoMol::CoulombMultiGridDirectForce getParameterSize framework/forces/CoulombMultiGridDirectTableForce.h /^ static unsigned int getParameterSize() {$/;" f class:ProtoMol::CoulombMultiGridDirectTableForce getParameterSize framework/forces/CoulombTableForce.h /^ static unsigned int getParameterSize() {$/;" f class:ProtoMol::CoulombTableForce getParameterSize framework/forces/DihedralSystemForce.h /^ virtual unsigned int getParameterSize() const{return 0;}$/;" f class:ProtoMol::DihedralSystemForce getParameterSize framework/forces/ElectricFieldSystemForce.h /^ virtual unsigned int getParameterSize() const{return 3+TSwitchingFunction::getParameterSize();}$/;" f class:ProtoMol::ElectricFieldSystemForce getParameterSize framework/forces/ExternalGravitationSystemForce.h /^ virtual unsigned int getParameterSize() const{return 1;}$/;" f class:ProtoMol::ExternalGravitationSystemForce getParameterSize framework/forces/ExternalMagneticFieldExtendedForce.h /^ virtual unsigned int getParameterSize() const{return 1;}$/;" f class:ProtoMol::ExternalMagneticFieldExtendedForce getParameterSize framework/forces/FrictionExtendedForce.h /^ virtual unsigned int getParameterSize() const{return 2;}$/;" f class:ProtoMol::FrictionExtendedForce getParameterSize framework/forces/GravitationForce.h /^ static unsigned int getParameterSize() {return 1;}$/;" f class:ProtoMol::GravitationForce getParameterSize framework/forces/HarmDihedralSystemForce.h /^ virtual unsigned int getParameterSize() const{return 4;}$/;" f class:ProtoMol::HarmDihedralSystemForce getParameterSize framework/forces/ImproperSystemForce.h /^ virtual unsigned int getParameterSize() const{return 0;}$/;" f class:ProtoMol::ImproperSystemForce getParameterSize framework/forces/LennardJonesForce.h /^ static unsigned int getParameterSize() {return 0;}$/;" f class:ProtoMol::LennardJonesForce getParameterSize framework/forces/LennardJonesTableForce.h /^ static unsigned int getParameterSize() {$/;" f class:ProtoMol::LennardJonesTableForce getParameterSize framework/forces/MagneticDipoleForce.h /^ static unsigned int getParameterSize() {return 8;}$/;" f class:ProtoMol::MagneticDipoleForce getParameterSize framework/forces/MagneticDipoleMirrorSystemForce.h /^ virtual unsigned int getParameterSize() const{return 6;}$/;" f class:ProtoMol::MagneticDipoleMirrorSystemForce getParameterSize framework/forces/NonbondedCutoffForce.h /^ virtual unsigned int getParameterSize() const{return 1+TOneAtomPair::getParameterSize();}$/;" f class:ProtoMol::NonbondedCutoffForce getParameterSize framework/forces/NonbondedFullEwaldSystemForce.h /^ virtual unsigned int getParameterSize() const{return (TBoundaryConditions::PERIODIC ? 2:3);}$/;" f class:ProtoMol::NonbondedFullEwaldSystemForce getParameterSize framework/forces/NonbondedFullSystemForce.h /^ virtual unsigned int getParameterSize() const{return 2+TOneAtomPair::getParameterSize();}$/;" f class:ProtoMol::NonbondedFullSystemForce getParameterSize framework/forces/NonbondedMultiGridSystemForce.h /^ virtual unsigned int getParameterSize() const{return (1 + (TBoundaryConditions::PERIODIC && smooth?3:0) + (smooth?3:0) + (TBoundaryConditions::VACUUM && smooth?2:0));}$/;" f class:ProtoMol::NonbondedMultiGridSystemForce getParameterSize framework/forces/NonbondedPMEwaldSystemForce.h /^ virtual unsigned int getParameterSize() const{return (TBoundaryConditions::PERIODIC ? 7:8);}$/;" f class:ProtoMol::NonbondedPMEwaldSystemForce getParameterSize framework/forces/NonbondedSimpleFullSystemForce.h /^ virtual unsigned int getParameterSize() const{return 1+TOneAtomPair::getParameterSize();}$/;" f class:ProtoMol::NonbondedSimpleFullSystemForce getParameterSize framework/forces/OneAtomPair.h /^ static unsigned int getParameterSize() {$/;" f class:ProtoMol::OneAtomPair getParameterSize framework/forces/OneAtomPairFull.h /^ static unsigned int getParameterSize() {$/;" f class:ProtoMol::OneAtomPairFull getParameterSize framework/forces/OneAtomPairTwo.h /^ static unsigned int getParameterSize(){$/;" f class:ProtoMol::OneAtomPairTwo getParameterSize framework/forces/OneAtomPairTwoFull.h /^ static unsigned int getParameterSize(){$/;" f class:ProtoMol::OneAtomPairTwoFull getParameterSize framework/forces/OneMollyPair.h /^ static unsigned int getParameterSize() {$/;" f class:ProtoMol::OneMollyPair getParameterSize framework/forces/OneMollyPairTwo.h /^ static unsigned int getParameterSize(){$/;" f class:ProtoMol::OneMollyPairTwo getParameterSize framework/forces/PaulTrapExtendedForce.h /^ virtual unsigned int getParameterSize() const{return 8;}$/;" f class:ProtoMol::PaulTrapExtendedForce getParameterSize framework/forces/SphericalSystemForce.h /^ virtual unsigned int getParameterSize() const{return 4;}$/;" f class:ProtoMol::SphericalSystemForce getParameterSize framework/forces/TimeForce.cpp /^ unsigned int TimeForce::getParameterSize() const{$/;" f class:ProtoMol::TimeForce getParameterSize framework/forces/WrapperMetaForce.h /^ virtual unsigned int getParameterSize() const{return myParameterSize;}$/;" f class:ProtoMol::WrapperMetaForce getParameterSize framework/frontend/OutputBSDL.h /^ virtual unsigned int getParameterSize() const {return 5;}$/;" f class:ProtoMol::OutputBSDL getParameterSize framework/frontend/OutputDCDTrajectory.h /^ virtual unsigned int getParameterSize() const {return 3;}$/;" f class:ProtoMol::OutputDCDTrajectory getParameterSize framework/frontend/OutputDiffusion.h /^ virtual unsigned int getParameterSize() const {return 5;}$/;" f class:ProtoMol::OutputDiffusion getParameterSize framework/frontend/OutputDihedrals.h /^ virtual unsigned int getParameterSize() const {return 9;}$/;" f class:ProtoMol::OutputDihedrals getParameterSize framework/frontend/OutputEnergies.h /^ virtual unsigned int getParameterSize() const {return 7;}$/;" f class:ProtoMol::OutputEnergies getParameterSize framework/frontend/OutputFinalPDBPos.h /^ virtual unsigned int getParameterSize() const {return 2;}$/;" f class:ProtoMol::OutputFinalPDBPos getParameterSize framework/frontend/OutputFinalXYZBinPos.h /^ virtual unsigned int getParameterSize() const {return 2;}$/;" f class:ProtoMol::OutputFinalXYZBinPos getParameterSize framework/frontend/OutputFinalXYZBinVel.h /^ virtual unsigned int getParameterSize() const {return 1;}$/;" f class:ProtoMol::OutputFinalXYZBinVel getParameterSize framework/frontend/OutputFinalXYZPos.h /^ virtual unsigned int getParameterSize() const {return 2;}$/;" f class:ProtoMol::OutputFinalXYZPos getParameterSize framework/frontend/OutputFinalXYZVel.h /^ virtual unsigned int getParameterSize() const {return 1;}$/;" f class:ProtoMol::OutputFinalXYZVel getParameterSize framework/frontend/OutputMomentum.h /^ virtual unsigned int getParameterSize() const {return 5;}$/;" f class:ProtoMol::OutputMomentum getParameterSize framework/frontend/OutputPDBFramePos.h /^ virtual unsigned int getParameterSize() const {return 3;}$/;" f class:ProtoMol::OutputPDBFramePos getParameterSize framework/frontend/OutputPaulTrap.h /^ virtual unsigned int getParameterSize() const {return 10;}$/;" f class:ProtoMol::OutputPaulTrap getParameterSize framework/frontend/OutputREMExchangeRate.h /^ virtual unsigned int getParameterSize() const { return 5; }$/;" f class:ProtoMol::OutputREMExchangeRate getParameterSize framework/frontend/OutputREMHistory.h /^ virtual unsigned int getParameterSize() const { return 5; }$/;" f class:ProtoMol::OutputREMHistoryFile getParameterSize framework/frontend/OutputScreen.h /^ virtual unsigned int getParameterSize() const {return 2;}$/;" f class:ProtoMol::OutputScreen getParameterSize framework/frontend/OutputState.h /^ virtual unsigned int getParameterSize() const {return 6;}$/;" f class:ProtoMol::OutputState getParameterSize framework/frontend/OutputTemperatures.h /^ virtual unsigned int getParameterSize() const {return 6;}$/;" f class:ProtoMol::OutputTemperatures getParameterSize framework/frontend/OutputXYZBinTrajectoryPos.h /^ virtual unsigned int getParameterSize() const {return 3;}$/;" f class:ProtoMol::OutputXYZBinTrajectoryPos getParameterSize framework/frontend/OutputXYZBinTrajectoryVel.h /^ virtual unsigned int getParameterSize() const {return 2;}$/;" f class:ProtoMol::OutputXYZBinTrajectoryVel getParameterSize framework/frontend/OutputXYZTrajectoryForce.h /^ virtual unsigned int getParameterSize() const {return 2;}$/;" f class:ProtoMol::OutputXYZTrajectoryForce getParameterSize framework/frontend/OutputXYZTrajectoryPos.h /^ virtual unsigned int getParameterSize() const {return 3;}$/;" f class:ProtoMol::OutputXYZTrajectoryPos getParameterSize framework/frontend/OutputXYZTrajectoryVel.h /^ virtual unsigned int getParameterSize() const {return 2;}$/;" f class:ProtoMol::OutputXYZTrajectoryVel getParameterSize framework/imd/HapticSystemForce.h /^ virtual unsigned int getParameterSize() const{return 5;}$/;" f class:ProtoMol::HapticSystemForce getParameterSize framework/integrators/BBKIntegrator.h /^ virtual unsigned int getParameterSize() const{return 4;}$/;" f class:ProtoMol::BBKIntegrator getParameterSize framework/integrators/BSplineMOLLYIntegrator.h /^ virtual unsigned int getParameterSize() const{return 3;}$/;" f class:ProtoMol::BSplineMOLLYIntegrator getParameterSize framework/integrators/DLMCIntegrator.h /^ virtual unsigned int getParameterSize() const{return myNumParameters; }$/;" f class:ProtoMol::DLMCIntegrator getParameterSize framework/integrators/DMDLeapfrogIntegrator.h /^ virtual unsigned int getParameterSize() const{return 5;}$/;" f class:ProtoMol::DMDLeapfrogIntegrator getParameterSize framework/integrators/DihedralHMCIntegrator.h /^ virtual unsigned int getParameterSize() const{return 6;}$/;" f class:ProtoMol::DihedralHMCIntegrator getParameterSize framework/integrators/HMCIntegrator.h /^ virtual unsigned int getParameterSize() const{return myNumParameters; }$/;" f class:ProtoMol::HMCIntegrator getParameterSize framework/integrators/LangevinImpulseIntegrator.h /^ virtual unsigned int getParameterSize() const{return 4;}$/;" f class:ProtoMol::LangevinImpulseIntegrator getParameterSize framework/integrators/LeapfrogIntegrator.h /^ virtual unsigned int getParameterSize() const{return 1;}$/;" f class:ProtoMol::LeapfrogIntegrator getParameterSize framework/integrators/MTSIntegrator.h /^ virtual unsigned int getParameterSize() const{return 1;}$/;" f class:ProtoMol::MTSIntegrator getParameterSize framework/integrators/NPTVerletIntegrator.h /^ virtual unsigned int getParameterSize() const{return 6;}$/;" f class:ProtoMol::NPTVerletIntegrator getParameterSize framework/integrators/NVTVerletIntegrator.h /^ virtual unsigned int getParameterSize() const{return 3;}$/;" f class:ProtoMol::NVTVerletIntegrator getParameterSize framework/integrators/NoseNVTLeapfrogIntegrator.h /^ virtual unsigned int getParameterSize() const{return 4;}$/;" f class:ProtoMol::NoseNVTLeapfrogIntegrator getParameterSize framework/integrators/PLeapfrogIntegrator.h /^ virtual unsigned int getParameterSize() const{return 1;}$/;" f class:ProtoMol::PLeapfrogIntegrator getParameterSize framework/integrators/PaulTrapIntegrator.h /^ virtual unsigned int getParameterSize() const{return 9;}$/;" f class:ProtoMol::PaulTrapIntegrator getParameterSize framework/integrators/ShadowHMCIntegrator.h /^ virtual unsigned int getParameterSize() const{return 6;}$/;" f class:ProtoMol::ShadowHMCIntegrator getParameterSize framework/topology/C1SwitchingFunction.h /^ static unsigned int getParameterSize() {return 1;}$/;" f class:ProtoMol::C1SwitchingFunction getParameterSize framework/topology/C2SwitchingFunction.h /^ static unsigned int getParameterSize() { return 2;}$/;" f class:ProtoMol::C2SwitchingFunction getParameterSize framework/topology/CmpCnCnSwitchingFunction.h /^ static unsigned int getParameterSize() { return 4;}$/;" f class:ProtoMol::CmpCnCnSwitchingFunction getParameterSize framework/topology/CnSwitchingFunction.h /^ static unsigned int getParameterSize() { return 4;}$/;" f class:ProtoMol::CnSwitchingFunction getParameterSize framework/topology/ComplementSwitchingFunction.h /^ static unsigned int getParameterSize() {return TOriginalSwitchingFunction::getParameterSize();}$/;" f class:ProtoMol::ComplementSwitchingFunction getParameterSize framework/topology/CubicCellManager.h /^ unsigned int getParameterSize() const{return 1;}$/;" f class:ProtoMol::CubicCellManager getParameterSize framework/topology/CutoffSwitchingFunction.h /^ static unsigned int getParameterSize() {return 1;}$/;" f class:ProtoMol::CutoffSwitchingFunction getParameterSize framework/topology/PeriodicBoundaryConditions.h /^ static unsigned int getParameterSize() {return 4;}$/;" f class:ProtoMol::PeriodicBoundaryConditions getParameterSize framework/topology/RangeSwitchingFunction.h /^ static unsigned int getParameterSize() {return 2+TOriginalSwitchingFunction::getParameterSize();}$/;" f class:ProtoMol::RangeSwitchingFunction getParameterSize framework/topology/ShiftSwitchingFunction.h /^ static unsigned int getParameterSize() {return 1;}$/;" f class:ProtoMol::ShiftSwitchingFunction getParameterSize framework/topology/Topology.h /^ virtual unsigned int getParameterSize() const{$/;" f class:ProtoMol::Topology getParameterSize framework/topology/UniversalSwitchingFunction.h /^ static unsigned int getParameterSize() {return 0;}$/;" f class:ProtoMol::UniversalSwitchingFunction getParameterSize framework/topology/VacuumBoundaryConditions.h /^ static unsigned int getParameterSize() {return 0;}$/;" f class:ProtoMol::VacuumBoundaryConditions getParameters framework/base/Makeable.cpp /^ vector Makeable::getParameters() const{ $/;" f class:ProtoMol::Makeable getParameters framework/forces/AngleSystemForce.h /^ virtual void getParameters(std::vector&) const {}$/;" f class:ProtoMol::AngleSystemForce getParameters framework/forces/BondSystemForce.h /^ virtual void getParameters(std::vector&) const {}$/;" f class:ProtoMol::BondSystemForce getParameters framework/forces/CompareForce.cpp /^ void CompareForce::getParameters(vector& parameters) const{$/;" f class:ProtoMol::CompareForce getParameters framework/forces/CoulombEwaldRealForce.cpp /^ void CoulombEwaldRealForce::getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::CoulombEwaldRealForce getParameters framework/forces/CoulombEwaldRealTableForce.h /^ void getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::CoulombEwaldRealTableForce getParameters framework/forces/CoulombForce.h /^ void getParameters(std::vector&) const{}$/;" f class:ProtoMol::CoulombForce getParameters framework/forces/CoulombMultiGridDirectForce.h /^ void getParameters(std::vector¶meters) const{parameters.push_back(Parameter("-s",Value(myS,ConstraintValueType::Positive()),Text("MG smoothing distance")));}$/;" f class:ProtoMol::CoulombMultiGridDirectForce getParameters framework/forces/CoulombMultiGridDirectTableForce.h /^ void getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::CoulombMultiGridDirectTableForce getParameters framework/forces/CoulombTableForce.h /^ void getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::CoulombTableForce getParameters framework/forces/DihedralSystemForce.h /^ virtual void getParameters(std::vector&) const {}$/;" f class:ProtoMol::DihedralSystemForce getParameters framework/forces/ElectricFieldSystemForce.h /^ inline void ElectricFieldSystemForce::getParameters(std::vector& parameters) const {$/;" f class:ProtoMol::ElectricFieldSystemForce getParameters framework/forces/ExternalGravitationSystemForce.cpp /^ void ExternalGravitationSystemForce::getParameters(vector& parameters) const {$/;" f class:ProtoMol::ExternalGravitationSystemForce getParameters framework/forces/ExternalMagneticFieldExtendedForce.cpp /^ void ExternalMagneticFieldExtendedForce::getParameters(vector& parameters) const {$/;" f class:ProtoMol::ExternalMagneticFieldExtendedForce getParameters framework/forces/FrictionExtendedForce.cpp /^ void FrictionExtendedForce::getParameters(vector& parameters) const {$/;" f class:ProtoMol::FrictionExtendedForce getParameters framework/forces/GravitationForce.cpp /^ void GravitationForce::getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::GravitationForce getParameters framework/forces/HarmDihedralSystemForce.h /^ virtual void getParameters(std::vector& parameters) const {$/;" f class:ProtoMol::HarmDihedralSystemForce getParameters framework/forces/ImproperSystemForce.h /^ virtual void getParameters(std::vector&) const {}$/;" f class:ProtoMol::ImproperSystemForce getParameters framework/forces/LennardJonesForce.h /^ void getParameters(std::vector&) const{}$/;" f class:ProtoMol::LennardJonesForce getParameters framework/forces/LennardJonesTableForce.h /^ void getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::LennardJonesTableForce getParameters framework/forces/MagneticDipoleForce.cpp /^ void MagneticDipoleForce::getParameters(vector& parameters) const{$/;" f class:ProtoMol::MagneticDipoleForce getParameters framework/forces/MagneticDipoleMirrorSystemForce.h /^ inline void MagneticDipoleMirrorSystemForce::getParameters(std::vector& parameters) const {$/;" f class:ProtoMol::MagneticDipoleMirrorSystemForce getParameters framework/forces/NonbondedCutoffForce.h /^ void NonbondedCutoffForce::getParameters(std::vector& parameters) const {$/;" f class:ProtoMol::NonbondedCutoffForce getParameters framework/forces/NonbondedFullEwaldSystemForce.h /^ TSwitchingFunction>::getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::NonbondedFullEwaldSystemForce getParameters framework/forces/NonbondedFullSystemForce.h /^ void NonbondedFullSystemForce::getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::NonbondedFullSystemForce getParameters framework/forces/NonbondedMultiGridSystemForce.h /^ smooth>::getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::NonbondedMultiGridSystemForce getParameters framework/forces/NonbondedPMEwaldSystemForce.h /^ real,reciprocal,correction,TInterpolation,TSwitchingFunction>::getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::NonbondedPMEwaldSystemForce getParameters framework/forces/NonbondedSimpleFullSystemForce.h /^ virtual void getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::NonbondedSimpleFullSystemForce getParameters framework/forces/OneAtomPair.h /^ void getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::OneAtomPair getParameters framework/forces/OneAtomPairFull.h /^ void getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::OneAtomPairFull getParameters framework/forces/OneAtomPairTwo.h /^ void getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::OneAtomPairTwo getParameters framework/forces/OneAtomPairTwoFull.h /^ void getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::OneAtomPairTwoFull getParameters framework/forces/OneMollyPair.h /^ void getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::OneMollyPair getParameters framework/forces/OneMollyPairTwo.h /^ void getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::OneMollyPairTwo getParameters framework/forces/PaulTrapExtendedForce.h /^ inline void PaulTrapExtendedForce::getParameters(std::vector& parameters) const {$/;" f class:ProtoMol::PaulTrapExtendedForce getParameters framework/forces/SphericalSystemForce.cpp /^ void SphericalSystemForce::getParameters(vector& parameters) const {$/;" f class:ProtoMol::SphericalSystemForce getParameters framework/forces/TimeForce.cpp /^ void TimeForce::getParameters(vector& parameters) const{$/;" f class:ProtoMol::TimeForce getParameters framework/forces/WrapperMetaForce.h /^ virtual void getParameters(std::vector& parameters) const{parameters=myParameters;}$/;" f class:ProtoMol::WrapperMetaForce getParameters framework/frontend/OutputBSDL.cpp /^ void OutputBSDL::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputBSDL getParameters framework/frontend/OutputDCDTrajectory.cpp /^ void OutputDCDTrajectory::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputDCDTrajectory getParameters framework/frontend/OutputDihedrals.cpp /^ void OutputDihedrals::getParameters(std::vector ¶meter) const{$/;" f class:ProtoMol::OutputDihedrals getParameters framework/frontend/OutputEnergies.cpp /^ void OutputEnergies::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputEnergies getParameters framework/frontend/OutputFile.cpp /^ void OutputFile::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputFile getParameters framework/frontend/OutputFinalPDBPos.cpp /^ void OutputFinalPDBPos::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputFinalPDBPos getParameters framework/frontend/OutputFinalXYZBinPos.cpp /^ void OutputFinalXYZBinPos::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputFinalXYZBinPos getParameters framework/frontend/OutputFinalXYZBinVel.cpp /^ void OutputFinalXYZBinVel::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputFinalXYZBinVel getParameters framework/frontend/OutputFinalXYZPos.cpp /^ void OutputFinalXYZPos::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputFinalXYZPos getParameters framework/frontend/OutputFinalXYZVel.cpp /^ void OutputFinalXYZVel::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputFinalXYZVel getParameters framework/frontend/OutputPDBFramePos.cpp /^ void OutputPDBFramePos::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputPDBFramePos getParameters framework/frontend/OutputPaulTrap.cpp /^ void OutputPaulTrap::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputPaulTrap getParameters framework/frontend/OutputREMExchangeRate.cpp /^ void OutputREMExchangeRate::getParameters(vector ¶meter) const {$/;" f class:ProtoMol::OutputREMExchangeRate getParameters framework/frontend/OutputREMHistory.cpp /^ void OutputREMHistoryFile::getParameters(vector ¶meter) const {$/;" f class:ProtoMol::OutputREMHistoryFile getParameters framework/frontend/OutputScreen.cpp /^ void OutputScreen::getParameters(vector & parameter) const{$/;" f class:ProtoMol::OutputScreen getParameters framework/frontend/OutputState.cpp /^ void OutputState::getParameters(std::vector ¶meter) const{$/;" f class:ProtoMol::OutputState getParameters framework/frontend/OutputTemperatures.cpp /^ void OutputTemperatures::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputTemperatures getParameters framework/frontend/OutputXYZBinTrajectoryPos.cpp /^ void OutputXYZBinTrajectoryPos::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputXYZBinTrajectoryPos getParameters framework/frontend/OutputXYZBinTrajectoryVel.cpp /^ void OutputXYZBinTrajectoryVel::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputXYZBinTrajectoryVel getParameters framework/frontend/OutputXYZTrajectoryForce.cpp /^ void OutputXYZTrajectoryForce::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputXYZTrajectoryForce getParameters framework/frontend/OutputXYZTrajectoryPos.cpp /^ void OutputXYZTrajectoryPos::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputXYZTrajectoryPos getParameters framework/frontend/OutputXYZTrajectoryVel.cpp /^ void OutputXYZTrajectoryVel::getParameters(vector ¶meter) const{$/;" f class:ProtoMol::OutputXYZTrajectoryVel getParameters framework/imd/HapticSystemForce.cpp /^ void HapticSystemForce::getParameters(vector& parameters) const {$/;" f class:ProtoMol::HapticSystemForce getParameters framework/integrators/BBKIntegrator.cpp /^ void BBKIntegrator::getParameters(vector& parameters) const {$/;" f class:ProtoMol::BBKIntegrator getParameters framework/integrators/BSplineMOLLYIntegrator.cpp /^ void BSplineMOLLYIntegrator::getParameters(vector& parameters) const {$/;" f class:ProtoMol::BSplineMOLLYIntegrator getParameters framework/integrators/DMDLeapfrogIntegrator.cpp /^ void DMDLeapfrogIntegrator::getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::DMDLeapfrogIntegrator getParameters framework/integrators/DihedralHMCIntegrator.cpp /^ void DihedralHMCIntegrator::getParameters(vector< Parameter> ¶meters) const {$/;" f class:ProtoMol::DihedralHMCIntegrator getParameters framework/integrators/LangevinImpulseIntegrator.cpp /^ void LangevinImpulseIntegrator::getParameters(vector& parameters) const {$/;" f class:ProtoMol::LangevinImpulseIntegrator getParameters framework/integrators/MCIntegrator.cpp /^ void MCIntegrator::getParameters(vector< Parameter> ¶meters) const {$/;" f class:ProtoMol::MCIntegrator getParameters framework/integrators/MTSIntegrator.cpp /^ void MTSIntegrator::getParameters(vector& parameters) const {$/;" f class:ProtoMol::MTSIntegrator getParameters framework/integrators/NPTVerletIntegrator.cpp /^ void NPTVerletIntegrator::getParameters(vector& parameters) const {$/;" f class:ProtoMol::NPTVerletIntegrator getParameters framework/integrators/NVTVerletIntegrator.cpp /^ void NVTVerletIntegrator::getParameters(vector& parameters) const {$/;" f class:ProtoMol::NVTVerletIntegrator getParameters framework/integrators/NoseNVTLeapfrogIntegrator.cpp /^ void NoseNVTLeapfrogIntegrator::getParameters(vector& parameters) const {$/;" f class:ProtoMol::NoseNVTLeapfrogIntegrator getParameters framework/integrators/PaulTrapIntegrator.cpp /^ void PaulTrapIntegrator::getParameters(vector& parameters) const {$/;" f class:ProtoMol::PaulTrapIntegrator getParameters framework/integrators/STSIntegrator.cpp /^ void STSIntegrator::getParameters(std::vector ¶meter) const{$/;" f class:ProtoMol::STSIntegrator getParameters framework/integrators/ShadowHMCIntegrator.cpp /^ void ShadowHMCIntegrator::getParameters(vector< Parameter> ¶meters) const {$/;" f class:ProtoMol::ShadowHMCIntegrator getParameters framework/topology/C1SwitchingFunction.cpp /^ void C1SwitchingFunction::getParameters(vector& parameters) const{$/;" f class:ProtoMol::C1SwitchingFunction getParameters framework/topology/C2SwitchingFunction.cpp /^ void C2SwitchingFunction::getParameters(vector& parameters) const{$/;" f class:ProtoMol::C2SwitchingFunction getParameters framework/topology/CmpCnCnSwitchingFunction.cpp /^ void CmpCnCnSwitchingFunction::getParameters(vector& parameters) const{$/;" f class:ProtoMol::CmpCnCnSwitchingFunction getParameters framework/topology/CnSwitchingFunction.cpp /^ void CnSwitchingFunction::getParameters(vector& parameters) const{$/;" f class:ProtoMol::CnSwitchingFunction getParameters framework/topology/ComplementSwitchingFunction.h /^ void getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::ComplementSwitchingFunction getParameters framework/topology/CubicCellManager.cpp /^ void CubicCellManager::getParameters(vector& parameters) const{$/;" f class:ProtoMol::CubicCellManager getParameters framework/topology/CutoffSwitchingFunction.cpp /^ void CutoffSwitchingFunction::getParameters(vector& parameters) const{$/;" f class:ProtoMol::CutoffSwitchingFunction getParameters framework/topology/PeriodicBoundaryConditions.cpp /^ void PeriodicBoundaryConditions::getParameters(vector& parameters) const{$/;" f class:ProtoMol::PeriodicBoundaryConditions getParameters framework/topology/RangeSwitchingFunction.h /^ void RangeSwitchingFunction::getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::RangeSwitchingFunction getParameters framework/topology/ShiftSwitchingFunction.cpp /^ void ShiftSwitchingFunction::getParameters(vector& parameters) const{$/;" f class:ProtoMol::ShiftSwitchingFunction getParameters framework/topology/Topology.h /^ virtual void getParameters(std::vector& parameters) const{$/;" f class:ProtoMol::Topology getParameters framework/topology/UniversalSwitchingFunction.h /^ void getParameters(std::vector&) const{};$/;" f class:ProtoMol::UniversalSwitchingFunction getParameters framework/topology/VacuumBoundaryConditions.h /^ void getParameters(std::vector&) const{};$/;" f class:ProtoMol::VacuumBoundaryConditions getParameters tools/rem/sequential/replica.cc /^vector Replica::getParameters() const {$/;" f class:Replica getPipeSize framework/parallel/Parallel.h /^ static int getPipeSize() {return myPipeSize;}$/;" f class:ProtoMol::Parallel getPointer framework/topology/AngleInfo.cpp /^ unsigned int AngleInfo::getPointer() const{$/;" f class:ProtoMol::AngleInfo getPossibleValues framework/base/AbstractEnumType.h /^ std::string AbstractEnumType::getPossibleValues(std::string separator){$/;" f class:ProtoMol::AbstractEnumType getPostfixId framework/forces/oneAtomContraints.h /^ static std::string getPostfixId() {return "";}$/;" f struct:ProtoMol::HBondConstraint getPostfixId framework/forces/oneAtomContraints.h /^ static std::string getPostfixId() {return "";}$/;" f struct:ProtoMol::NoConstraint getPostfixId framework/forces/oneAtomContraints.h /^ static std::string getPostfixId() {return "DebugPost";}$/;" f struct:ProtoMol::DebugPostConstraint getPostfixId framework/forces/oneAtomContraints.h /^ static std::string getPostfixId() {return "DebugPre";}$/;" f struct:ProtoMol::DebugPreConstraint getPostfixId framework/forces/oneAtomContraints.h /^ static std::string getPostfixId() {return "NotSameMol";}$/;" f struct:ProtoMol::NotSameMoleculeConstraint getPostfixId framework/forces/oneAtomContraints.h /^ static std::string getPostfixId() {return "SameMol";}$/;" f struct:ProtoMol::SameMoleculeConstraint getPotentialEnergy tools/rem/sequential/replica.cc /^double Replica::getPotentialEnergy() const {$/;" f class:Replica getPrefixId framework/forces/oneAtomContraints.h /^ static std::string getPrefixId() {return "";}$/;" f struct:ProtoMol::DebugPostConstraint getPrefixId framework/forces/oneAtomContraints.h /^ static std::string getPrefixId() {return "";}$/;" f struct:ProtoMol::DebugPreConstraint getPrefixId framework/forces/oneAtomContraints.h /^ static std::string getPrefixId() {return "";}$/;" f struct:ProtoMol::NoConstraint getPrefixId framework/forces/oneAtomContraints.h /^ static std::string getPrefixId() {return "";}$/;" f struct:ProtoMol::NotSameMoleculeConstraint getPrefixId framework/forces/oneAtomContraints.h /^ static std::string getPrefixId() {return "";}$/;" f struct:ProtoMol::SameMoleculeConstraint getPrefixId framework/forces/oneAtomContraints.h /^ static std::string getPrefixId() {return "HBond";}$/;" f struct:ProtoMol::HBondConstraint getProcessTime framework/base/Timer.h /^ inline double TimeRep::getProcessTime() const$/;" f class:ProtoMol::TimeRep getPrototype framework/frontend/Factory.h /^ const Type* getPrototype(const std::string& id) const{$/;" f class:ProtoMol::FactoryBase getQ framework/base/Grid.h /^ void getQ(Real*& begin, Real*& end) {begin=&(myQ.begin()->re);end=&(myQ.end()->re);}$/;" f class:ProtoMol::Grid getQ framework/base/MultiGrid.h /^ void getQ(int level, Real*& begin, Real*& end) {begin=myQ[level].begin();end=myQ[level].end();}$/;" f class:ProtoMol::MultiGrid getRadius framework/io/XFigWriter.h /^ Real getRadius() const{return myRadius;}$/;" f class:ProtoMol::XFigWriter getRealCellSize framework/topology/CubicCellManager.h /^ Vector3D getRealCellSize(void) const {return myRealCellSize;}$/;" f class:ProtoMol::CubicCellManager getRealTime framework/base/Timer.h /^ inline double TimeRep::getRealTime() const $/;" f class:ProtoMol::TimeRep getRed framework/base/PGM.h /^ unsigned char getRed(unsigned int x, unsigned int y) const {return p[(h-y-1)*w+x];}$/;" f class:ProtoMol::PGM getRed framework/base/PPM.h /^ unsigned char getRed(unsigned int x, unsigned int y) const {return p[(h-y-1)*w*3+x*3];}$/;" f class:ProtoMol::PPM getRightFill framework/base/stringutilities.cpp /^ string getRightFill(const string& s,string::size_type n){$/;" f namespace:ProtoMol getScope framework/forces/Force.h /^ virtual std::string getScope() const{return scope;}$/;" f class:ProtoMol::Force getScope framework/frontend/Output.h /^ virtual std::string getScope() const{return scope;}$/;" f class:ProtoMol::Output getScope framework/integrators/Integrator.h /^ virtual std::string getScope() const{return scope;}$/;" f class:ProtoMol::Integrator getScope framework/topology/GenericTopology.h /^ virtual std::string getScope() const{return scope;}$/;" f class:ProtoMol::GenericTopology getString framework/base/AbstractEnumType.h /^ static const std::string & getString(Enum e){return T::str[static_cast(e)];}$/;" f class:ProtoMol::AbstractEnumType getString framework/base/AbstractEnumType.h /^ static const std::string& getString(int n){return T::str[static_cast(getEnum(n))];}$/;" f class:ProtoMol::AbstractEnumType getString framework/base/AbstractEnumType.h /^ std::string getString() const {return T::str[static_cast(myType)];}$/;" f class:ProtoMol::AbstractEnumType getString framework/base/Value.cpp /^ string Value::getString() const {$/;" f class:ProtoMol::Value getSystemTime framework/base/Timer.h /^ inline double TimeRep::getSystemTime() const $/;" f class:ProtoMol::TimeRep getTable framework/topology/ExclusionTable.h /^ const std::vector& getTable() const{return myTable;}$/;" f class:ProtoMol::ExclusionTable getTargetTemperature tools/rem/sequential/replica.cc /^double Replica::getTargetTemperature() const {$/;" f class:Replica getTemp framework/io/TempFileReader.h /^ Real getTemp() const { return myTemp; }$/;" f class:ProtoMol::TempFileReader getTemperature tools/rem/sequential/replica.cc /^double Replica::getTemperature() {$/;" f class:Replica getText framework/base/Configuration.cpp /^ string Configuration::getText(const std::string& keyword) const {$/;" f class:ProtoMol::Configuration getText framework/base/Makeable.h /^ virtual std::string getText() const{return std::string();}$/;" f class:ProtoMol::Makeable getTime framework/base/Timer.cpp /^ TimeRep Timer::getTime() const$/;" f class:ProtoMol::Timer getTimerSeed framework/base/mathutilities.cpp /^ int getTimerSeed(){$/;" f namespace:ProtoMol getTimestep framework/integrators/MTSIntegrator.h /^ inline Real MTSIntegrator::getTimestep () const{$/;" f class:ProtoMol::MTSIntegrator getTimestep framework/integrators/ModifierNPTRattle.h /^ virtual Real getTimestep()const{return myTheIntegrator->getTimestep();}$/;" f class:ProtoMol::ModifierNPTRattle getTimestep framework/integrators/ModifierNPTShake.h /^ virtual Real getTimestep()const{return myTheIntegrator->getTimestep();}$/;" f class:ProtoMol::ModifierNPTShake getTimestep framework/integrators/ModifierNVTRattle.h /^ virtual Real getTimestep()const{return myTheIntegrator->getTimestep();}$/;" f class:ProtoMol::ModifierNVTRattle getTimestep framework/integrators/ModifierNVTShake.h /^ virtual Real getTimestep()const{return myTheIntegrator->getTimestep();}$/;" f class:ProtoMol::ModifierNVTShake getTimestep framework/integrators/ModifierRattle.cpp /^ Real ModifierRattle::getTimestep()const {$/;" f class:ProtoMol::ModifierRattle getTimestep framework/integrators/ModifierShadow.cpp /^ Real ModifierShadow::getTimestep() const {$/;" f class:ProtoMol::ModifierShadow getTimestep framework/integrators/ModifierShake.cpp /^ Real ModifierShake::getTimestep()const {$/;" f class:ProtoMol::ModifierShake getTimestep framework/integrators/STSIntegrator.h /^ inline Real STSIntegrator::getTimestep() const {$/;" f class:ProtoMol::STSIntegrator getToZ framework/io/XFigWriter.h /^ Real getToZ() const{return myToZ;}$/;" f class:ProtoMol::XFigWriter getTransformation framework/io/XFigWriter.h /^ Matrix3by3 getTransformation() const{return myMat;}$/;" f class:ProtoMol::XFigWriter getType framework/base/Value.h /^ virtual ValueType::Enum getType() const {return (ValueType::Enum)ValueTrait::value;}$/;" f class:ProtoMol::Value::Holder getType framework/base/Value.h /^ inline ValueType::Enum Value::getType() const { $/;" f class:ProtoMol::Value getType framework/frontend/InputPosVel.cpp /^ InputPosVelType InputPosVel::getType() const{$/;" f class:ProtoMol::InputPosVel getTypeString framework/base/Value.h /^ virtual const std::string & getTypeString() const { return ValueType::getString((ValueType::Enum)ValueTrait::value);}$/;" f class:ProtoMol::Value::Holder getTypeString framework/base/Value.h /^ inline const std::string & Value::getTypeString() const{ $/;" f class:ProtoMol::Value getUserName framework/base/systemutilities.cpp /^ string getUserName(){$/;" f namespace:ProtoMol getUserTime framework/base/Timer.h /^ inline double TimeRep::getUserTime() const $/;" f class:ProtoMol::TimeRep getV framework/base/MultiGrid.h /^ void getV(int level, Real*& begin, Real*& end) {begin=myV[level].begin();end=myV[level].end();}$/;" f class:ProtoMol::MultiGrid getVolume framework/topology/PeriodicBoundaryConditions.h /^ Real getVolume() const {return myV;};$/;" f class:ProtoMol::PeriodicBoundaryConditions getVolume framework/topology/SemiGenericTopology.h /^ virtual Real getVolume() const{ return boundaryConditions.getVolume(); }$/;" f class:ProtoMol::SemiGenericTopology getVolume framework/topology/SemiGenericTopology.h /^ virtual Real getVolume(const Vector3DBlock& positions) const{$/;" f class:ProtoMol::SemiGenericTopology getVolume framework/topology/VacuumBoundaryConditions.cpp /^ Real VacuumBoundaryConditions::getVolume() const {$/;" f class:ProtoMol::VacuumBoundaryConditions getWorkState framework/parallel/Parallel-FD.cpp /^ Parallel::WorkState Parallel::getWorkState(){$/;" f class:ProtoMol::Parallel getWorkState framework/parallel/Parallel.cpp /^ Parallel::WorkState Parallel::getWorkState(){$/;" f class:ProtoMol::Parallel getXSC framework/integrators/Integrator.h /^ virtual XSC & getXSC() const { XSC *xsc = new XSC; return( *xsc ); };$/;" f class:ProtoMol::Integrator getXYZ framework/io/DCDTrajectoryReader.cpp /^ XYZ DCDTrajectoryReader::getXYZ() const{$/;" f class:ProtoMol::DCDTrajectoryReader getXYZ framework/io/XYZBinReader.cpp /^ XYZ XYZBinReader::getXYZ() const{$/;" f class:ProtoMol::XYZBinReader getXYZ framework/io/XYZReader.cpp /^ XYZ XYZReader::getXYZ() const{$/;" f class:ProtoMol::XYZReader getXYZ framework/io/XYZTrajectoryReader.cpp /^ XYZ XYZTrajectoryReader::getXYZ() const{$/;" f class:ProtoMol::XYZTrajectoryReader get_haptics framework/imd/IMDElf.cpp /^ int IMDElf::get_haptics(Vector3DBlock &h) {$/;" f class:ProtoMol::IMDElf getdihedralsfromatomset framework/frontend/OutputDihedrals.cpp /^ void OutputDihedrals::getdihedralsfromatomset(){$/;" f class:ProtoMol::OutputDihedrals getline framework/io/File.cpp /^ std::string File::getline(){$/;" f class:ProtoMol::File getticks framework/base/Cycles.h /^ static __inline ticks getticks(void)$/;" f namespace:ProtoMol::Private getticks framework/base/Cycles.h /^ static __inline__ ticks getticks(void)$/;" f namespace:ProtoMol::Private getticks framework/base/Cycles.h /^ static inline ticks getticks(void)$/;" f namespace:ProtoMol::Private getticks framework/base/Cycles.h /^ static inline unsigned long getticks(void)$/;" f namespace:ProtoMol::Private getticks framework/base/Cycles.h 114;" d getticks framework/base/Cycles.h 237;" d getticks framework/base/Cycles.h 425;" d gotoEndPair framework/topology/CellListEnumerator_periodicBoundaries.h /^ void gotoEndPair() {j=the_end;};$/;" f class:ProtoMol::CellListEnumerator gotoEndPair framework/topology/CellListEnumerator_standard.h /^ void gotoEndPair() {j=the_end;};$/;" f class:ProtoMol::CellListEnumerator greater framework/base/Value.cpp /^ inline bool Value::greater(const Value& v1, const Value& v2){$/;" f class:ProtoMol::Value greater framework/base/Value.cpp /^ inline bool Value::greater(const Value&, const Value&){return false;}$/;" f class:ProtoMol::Value greater framework/base/Value.cpp /^ inline bool Value::greater >(const Value&, const Value&){return false;}$/;" f class:ProtoMol::Value greaterEqual framework/base/Value.cpp /^ inline bool Value::greaterEqual(const Value& v1, const Value& v2){$/;" f class:ProtoMol::Value greaterEqual framework/base/Value.cpp /^ inline bool Value::greaterEqual(const Value&, const Value&){return false;}$/;" f class:ProtoMol::Value greaterEqual framework/base/Value.cpp /^ inline bool Value::greaterEqual >(const Value&, const Value&){return false;}$/;" f class:ProtoMol::Value h compilerTests/pngTest.cpp /^ unsigned int w,h;$/;" m class:PPM file: h framework/base/PGM.h /^ unsigned int w,h;$/;" m class:ProtoMol::PGM h framework/base/PPM.h /^ unsigned int w,h;$/;" m class:ProtoMol::PPM h framework/base/simpleTypes.h /^ int h;int k; int l;$/;" m struct:ProtoMol::TripleInt harmCalcTorsion framework/forces/HarmDihedralSystemForce.h /^ inline void HarmDihedralSystemForce::harmCalcTorsion(const GenericTopology* topo,$/;" f class:ProtoMol::HarmDihedralSystemForce hbonds framework/base/PAR.h /^ std::vector hbonds;$/;" m class:ProtoMol::PAR hdf framework/integrators/DLMCIntegrator.h /^ Force* hdf;$/;" m class:ProtoMol::DLMCIntegrator headString framework/base/stringutilities.cpp /^ string headString(const string& word){$/;" f namespace:ProtoMol height compilerTests/pngTest.cpp /^ unsigned int height() const{return h;}$/;" f class:PPM height framework/base/PGM.h /^ unsigned int height() const{return h;}$/;" f class:ProtoMol::PGM height framework/base/PPM.h /^ unsigned int height() const{return h;}$/;" f class:ProtoMol::PPM hessian framework/topology/C1SwitchingFunction.cpp /^ Matrix3by3 C1SwitchingFunction::hessian(const Vector3D& rij, Real a) const{$/;" f class:ProtoMol::C1SwitchingFunction hessian framework/topology/C2SwitchingFunction.cpp /^ Matrix3by3 C2SwitchingFunction::hessian(const Vector3D& rij, Real a) const{$/;" f class:ProtoMol::C2SwitchingFunction hessian framework/topology/CmpCnCnSwitchingFunction.cpp /^ Matrix3by3 CmpCnCnSwitchingFunction::hessian(const Vector3D& rij, Real a) const{$/;" f class:ProtoMol::CmpCnCnSwitchingFunction hessian framework/topology/CnSwitchingFunction.cpp /^ Matrix3by3 CnSwitchingFunction::hessian(const Vector3D& rij, Real a) const{$/;" f class:ProtoMol::CnSwitchingFunction hessian framework/topology/RangeSwitchingFunction.h /^ inline Matrix3by3 RangeSwitchingFunction::hessian(const Vector3D& rij, Real distSquared) const {$/;" f class:ProtoMol::RangeSwitchingFunction high framework/imd/imd.cpp /^ unsigned int high : 8;$/;" m struct:ProtoMol::IMD:: file: highBound framework/frontend/OutputState.h /^ Real highBound;$/;" m struct:ProtoMol::OutputState::orderParam highDeltas framework/topology/ExclusionTable.h /^ std::map highDeltas;$/;" m class:ProtoMol::ExclusionTable highest framework/imd/imd.cpp /^ unsigned int highest : 8;$/;" m struct:ProtoMol::IMD:: file: hint framework/base/Report.cpp /^ MyStreamer& hint(MyStreamer& stream){$/;" f namespace:ProtoMol::Report holder framework/base/Value.h /^ typename ValueTrait::RepType holder;$/;" m class:ProtoMol::Value::Holder hookup framework/imd/IMDElf.cpp /^ int IMDElf::hookup() {$/;" f class:ProtoMol::IMDElf hvyAtom framework/base/Atom.h /^ int hvyAtom;$/;" m struct:ProtoMol::Atom hvyAtomGrpsize framework/base/PDB.h /^ int hvyAtomGrpsize; \/\/\/< ??? throw in zeros $/;" m struct:ProtoMol::PDB::Atom i framework/base/LookUpTableBase.h /^ typedef union { TReal f; TInt i; } Conv;$/;" m union:ProtoMol::LookUpTableBase:: i framework/topology/CellListEnumerator_periodicBoundaries.h /^ CubicCellManager::CellListStructure::const_iterator i,j,the_beginning,the_end;$/;" m class:ProtoMol::CellListEnumerator i framework/topology/CellListEnumerator_standard.h /^ CubicCellManager::CellListStructure::const_iterator i,j,the_beginning,the_end;$/;" m class:ProtoMol::CellListEnumerator i tools/bccAnalyzer.cpp /^ int i;$/;" m class:Vector3DIdx file: i1 framework/integrators/EquilibriumMOLLYIntegrator.h /^ short i1; \/\/ Local index of atom 1 myHydrogenAtomGroups$/;" m struct:ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond i2 framework/integrators/EquilibriumMOLLYIntegrator.h /^ short i2; \/\/ Local index of atom 1 myHydrogenAtomGroups$/;" m struct:ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond iAmMaster framework/parallel/Parallel.h /^ static bool iAmMaster() {return myIAmMaster;}$/;" f class:ProtoMol::Parallel iAmSlave framework/parallel/Parallel.h /^ static bool iAmSlave() {return myIAmSlave;}$/;" f class:ProtoMol::Parallel iSGNumMols framework/topology/GenericTopology.h /^ std::vector iSGNumMols;$/;" m class:ProtoMol::GenericTopology iSGmodifierIndex framework/topology/Angle.h /^ int iSGmodifierIndex;$/;" m class:ProtoMol::Angle iSGmodifierIndex framework/topology/Bond.h /^ int iSGmodifierIndex;$/;" m class:ProtoMol::Bond iSGmodifierIndex framework/topology/Torsion.h /^ int iSGmodifierIndex; \/\/\/< The index # of this torsion type in the ModifierISG angle structure. $/;" m class:ProtoMol::Torsion iSGpar framework/frontend/OutputCache.h /^ const iSGPAR& iSGpar() const {return myiSGPAR;}$/;" f class:ProtoMol::OutputCache id framework/base/MakeableDefinition.h /^ std::string id; \/\/\/< keyword of the object$/;" m struct:ProtoMol::MakeableDefinition id framework/base/ObjectDefinition.h /^ std::string id;$/;" m struct:ProtoMol::ObjectDefinition id framework/frontend/HelpTextFactory.h /^ std::string id;$/;" m struct:ProtoMol::HelpText identity framework/base/Matrix3by3.cpp /^ void Matrix3by3::identity() $/;" f class:ProtoMol::Matrix3by3 identity framework/base/PSF.h /^ unsigned int identity; \/\/\/< atom's identity (for iSGMD)$/;" m struct:ProtoMol::PSF::Atom identity framework/base/ReducedHessAngle.cpp /^ void ReducedHessAngle::identity()$/;" f class:ProtoMol::ReducedHessAngle im framework/base/FFTComplex.h /^ double im;$/;" m im framework/base/fft.c /^ double im;$/;" m file: imd_disconnect framework/imd/imd.cpp /^ int imd_disconnect(void *s) {$/;" f namespace:ProtoMol::IMD imd_go framework/imd/imd.cpp /^ static int imd_go(void *s) {$/;" f namespace:ProtoMol::IMD file: imd_handshake framework/imd/imd.cpp /^ int imd_handshake(void *s) {$/;" f namespace:ProtoMol::IMD imd_htonl framework/imd/imd.cpp /^ static int32 imd_htonl(int32 h) {$/;" f namespace:ProtoMol::IMD file: imd_kill framework/imd/imd.cpp /^ int imd_kill(void *s) {$/;" f namespace:ProtoMol::IMD imd_ntohl framework/imd/imd.cpp /^ static int32 imd_ntohl(int32 n) {$/;" f namespace:ProtoMol::IMD file: imd_pause framework/imd/imd.cpp /^ int imd_pause(void *s) {$/;" f namespace:ProtoMol::IMD imd_readn framework/imd/imd.cpp /^ static int32 imd_readn(void *s, char *ptr, int32 n) {$/;" f namespace:ProtoMol::IMD file: imd_recv_energies framework/imd/imd.cpp /^ int imd_recv_energies(void *s, IMDEnergies *energies) {$/;" f namespace:ProtoMol::IMD imd_recv_fcoords framework/imd/imd.cpp /^ int imd_recv_fcoords(void *s, int32 n, float *coords) {$/;" f namespace:ProtoMol::IMD imd_recv_handshake framework/imd/imd.cpp /^ int imd_recv_handshake(void *s) {$/;" f namespace:ProtoMol::IMD imd_recv_header framework/imd/imd.cpp /^ IMDType imd_recv_header(void *s, int32 *length) {$/;" f namespace:ProtoMol::IMD imd_recv_header_nolengthswap framework/imd/imd.cpp /^ IMDType imd_recv_header_nolengthswap(void *s, int32 *length) {$/;" f namespace:ProtoMol::IMD imd_recv_mdcomm framework/imd/imd.cpp /^ int imd_recv_mdcomm(void *s, int32 n, int32 *indices, float *forces) {$/;" f namespace:ProtoMol::IMD imd_send_energies framework/imd/imd.cpp /^ int imd_send_energies(void *s, const IMDEnergies *energies) {$/;" f namespace:ProtoMol::IMD imd_send_fcoords framework/imd/imd.cpp /^ int imd_send_fcoords(void *s, int32 n, const float *coords) {$/;" f namespace:ProtoMol::IMD imd_send_mdcomm framework/imd/imd.cpp /^ int imd_send_mdcomm(void *s,int32 n,const int32 *indices,const float *forces) {$/;" f namespace:ProtoMol::IMD imd_trate framework/imd/imd.cpp /^ int imd_trate(void *s, int32 rate) {$/;" f namespace:ProtoMol::IMD imd_writen framework/imd/imd.cpp /^ static int32 imd_writen(void *s, const char *ptr, int32 n) {$/;" f namespace:ProtoMol::IMD file: improperList framework/base/Molecule.h /^ std::vector improperList;$/;" m struct:ProtoMol::Molecule impropers framework/base/PAR.h /^ std::vector impropers;$/;" m class:ProtoMol::PAR impropers framework/base/PSF.h /^ std::vector impropers;$/;" m class:ProtoMol::PSF impropers framework/topology/GenericTopology.h /^ std::vector impropers;$/;" m class:ProtoMol::GenericTopology indeces framework/integrators/ModifierShadow.h /^ std::vector< std::vector > indeces;$/;" m class:ProtoMol::ModifierShadow index framework/base/LookUpTableBase.h /^ void index(Real r, int& i, Real& dt) const{$/;" f class:ProtoMol::LookUpTableBase index framework/integrators/EquilibriumMOLLYIntegrator.cpp /^ int dim, const int (&index)[maxGDim],$/;" v index framework/integrators/EquilibriumMOLLYIntegrator.cpp /^ int dim, int (&index)[maxGDim],$/;" v index framework/integrators/EquilibriumMOLLYIntegrator.h /^ void luBksb(Real (&m)[maxGDim][maxGDim], int dim, const int (&index)[maxGDim], Real (&b)[maxGDim]) const;$/;" m class:ProtoMol::EquilibriumMOLLYIntegrator index framework/integrators/EquilibriumMOLLYIntegrator.h /^ void luDcmp(Real (&m)[maxGDim][maxGDim], int dim, int (&index)[maxGDim], Real& d) const;$/;" m class:ProtoMol::EquilibriumMOLLYIntegrator inertiaMomentum framework/topology/topologyutilities.cpp /^ Matrix3by3 inertiaMomentum(const Vector3DBlock *positions, $/;" f namespace:ProtoMol init compilerTests/glutTest.cpp /^static void init(){$/;" f file: init framework/base/Value.h /^ virtual bool init() { bool tmp = ok; holder = ValueTrait::init() ; ok = ValueTrait::check(Constraint(),holder); return tmp;}$/;" f class:ProtoMol::Value::Holder init framework/base/Value.h /^ inline bool Value::init() {$/;" f class:ProtoMol::Value init framework/base/ValueType.h /^ static RepType init(){return "";}$/;" f struct:ProtoMol::ValueTraits init framework/base/ValueType.h /^ static RepType init(){return 0.0;}$/;" f struct:ProtoMol::ValueTraits init framework/base/ValueType.h /^ static RepType init(){return 0;}$/;" f struct:ProtoMol::ValueTraits init framework/base/ValueType.h /^ static RepType init(){return Vector3D(0.0,0.0,0.0);}$/;" f struct:ProtoMol::ValueTraits init framework/base/ValueType.h /^ static RepType init(){return std::vector();}$/;" f struct:ProtoMol::ValueTraits init framework/base/ValueType.h /^ static RepType init(){return true;}$/;" f struct:ProtoMol::ValueTraits init framework/integrators/BSplineMOLLYIntegrator.cpp /^ void BSplineMOLLYIntegrator::init(){$/;" f class:ProtoMol::BSplineMOLLYIntegrator init framework/integrators/PaulTrapIntegrator.cpp /^ void PaulTrapIntegrator::init() {$/;" f class:ProtoMol::PaulTrapIntegrator init framework/parallel/Parallel-FD.cpp /^ void Parallel::init(int &argc, char **&argv){$/;" f class:ProtoMol::Parallel init framework/parallel/Parallel.cpp /^ void Parallel::init(int &argc, char **&argv){$/;" f class:ProtoMol::Parallel initialize framework/base/Array_Fastest.h /^ void initialize(const T & Init=T())$/;" f class:ProtoMol::Array initialize framework/base/Array_Fastest.h /^ void initialize(const T & Init=T())$/;" f class:ProtoMol::RefArray initialize framework/base/Array_NoPartialSpecialization.h /^ void initialize(const T & Init=T())$/;" f class:ProtoMol::Array::RefArray initialize framework/base/Array_NoPartialSpecialization.h /^ void initialize(const T & Init=T())$/;" f class:ProtoMol::Array initialize framework/base/FFTComplex.cpp /^ void FFTComplex::initialize(int x, int y, int z,zomplex* a){$/;" f class:ProtoMol::FFTComplex initialize framework/base/FFTComplex.cpp /^ void FFTInternal::initialize(int x, int y, int z,zomplex* a){$/;" f class:ProtoMol::FFTInternal initialize framework/base/Grid.h /^ void Grid::initialize(Real width, Real length, Real height, Real alpha,$/;" f class:ProtoMol::Grid initialize framework/base/MultiGrid.h /^ void MultiGrid::initialize(unsigned int n, Real s, int levels,$/;" f class:ProtoMol::MultiGrid initialize framework/forces/NonbondedFullEwaldSystemForce.h /^ TSwitchingFunction>::initialize(const RealTopologyType* realTopo, const Vector3DBlock* positions) {$/;" f class:ProtoMol::NonbondedFullEwaldSystemForce initialize framework/forces/NonbondedMultiGridSystemForce.h /^ smooth>::initialize(const RealTopologyType* realTopo, const Vector3DBlock* positions) {$/;" f class:ProtoMol::NonbondedMultiGridSystemForce initialize framework/forces/NonbondedPMEwaldSystemForce.h /^ TSwitchingFunction>::initialize(const RealTopologyType* realTopo, $/;" f class:ProtoMol::NonbondedPMEwaldSystemForce initialize framework/forces/OneAtomPair.h /^ void initialize(const SemiGenericTopology* topo, $/;" f class:ProtoMol::OneAtomPair initialize framework/forces/OneAtomPairFull.h /^ void initialize(const SemiGenericTopology* topo, $/;" f class:ProtoMol::OneAtomPairFull initialize framework/forces/OneAtomPairTwo.h /^ void initialize(const SemiGenericTopology* topo, $/;" f class:ProtoMol::OneAtomPairTwo initialize framework/forces/OneAtomPairTwoFull.h /^ void initialize(const SemiGenericTopology* topo, $/;" f class:ProtoMol::OneAtomPairTwoFull initialize framework/forces/OneMollyPair.h /^ void initialize(const SemiGenericTopology* topo, $/;" f class:ProtoMol::OneMollyPair initialize framework/forces/OneMollyPairTwo.h /^ void initialize(const SemiGenericTopology* topo, $/;" f class:ProtoMol::OneMollyPairTwo initialize framework/forces/PaulTrapExtendedForce.h /^ inline void PaulTrapExtendedForce::initialize(const GenericTopology* topo){ $/;" f class:ProtoMol::PaulTrapExtendedForce initialize framework/frontend/Output.cpp /^ void Output::initialize(const Configuration* config, const Integrator* integrator, const GenericTopology* topo,$/;" f class:ProtoMol::Output initialize framework/frontend/OutputCache.cpp /^ void OutputCache::initialize(const Configuration* config, const Integrator* integrator, const GenericTopology* topo,$/;" f class:ProtoMol::OutputCache initialize framework/frontend/OutputCollection.cpp /^ void OutputCollection::initialize(const Configuration* config, const Integrator* integrator, const GenericTopology* topo,$/;" f class:ProtoMol::OutputCollection initialize framework/integrators/BBKIntegrator.cpp /^ void BBKIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::BBKIntegrator initialize framework/integrators/BSplineMOLLYIntegrator.cpp /^ void BSplineMOLLYIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::BSplineMOLLYIntegrator initialize framework/integrators/DLMCIntegrator.cpp /^ void DLMCIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::DLMCIntegrator initialize framework/integrators/DMDLeapfrogIntegrator.cpp /^ void DMDLeapfrogIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::DMDLeapfrogIntegrator initialize framework/integrators/DihedralHMCIntegrator.cpp /^ void DihedralHMCIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::DihedralHMCIntegrator initialize framework/integrators/EquilibriumMOLLYIntegrator.cpp /^ void EquilibriumMOLLYIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::EquilibriumMOLLYIntegrator initialize framework/integrators/HMCIntegrator.cpp /^ void HMCIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::HMCIntegrator initialize framework/integrators/ImpulseIntegrator.cpp /^ void ImpulseIntegrator::initialize(GenericTopology *topo, Vector3DBlock$/;" f class:ProtoMol::ImpulseIntegrator initialize framework/integrators/Integrator.cpp /^ void Integrator::initialize(GenericTopology *topo, $/;" f class:ProtoMol::Integrator initialize framework/integrators/LangevinImpulseIntegrator.cpp /^ void LangevinImpulseIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::LangevinImpulseIntegrator initialize framework/integrators/LeapfrogIntegrator.cpp /^ void LeapfrogIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::LeapfrogIntegrator initialize framework/integrators/MCIntegrator.cpp /^ void MCIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::MCIntegrator initialize framework/integrators/MOLLYIntegrator.cpp /^ void MOLLYIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::MOLLYIntegrator initialize framework/integrators/MTSIntegrator.cpp /^ void MTSIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::MTSIntegrator initialize framework/integrators/Modifier.h /^ inline void Modifier::initialize(GenericTopology *topo, $/;" f class:ProtoMol::Modifier initialize framework/integrators/NPTVerletIntegrator.cpp /^ void NPTVerletIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::NPTVerletIntegrator initialize framework/integrators/NVTVerletIntegrator.cpp /^ void NVTVerletIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::NVTVerletIntegrator initialize framework/integrators/NoseNVTLeapfrogIntegrator.cpp /^ void NoseNVTLeapfrogIntegrator::initialize(GenericTopology *topo, $/;" f class:ProtoMol::NoseNVTLeapfrogIntegrator initialize framework/integrators/PLeapfrogIntegrator.cpp /^ void PLeapfrogIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::PLeapfrogIntegrator initialize framework/integrators/PaulTrapIntegrator.cpp /^ void PaulTrapIntegrator::initialize(GenericTopology *topo, $/;" f class:ProtoMol::PaulTrapIntegrator initialize framework/integrators/STSIntegrator.cpp /^ void STSIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::STSIntegrator initialize framework/integrators/ShadowHMCIntegrator.cpp /^ void ShadowHMCIntegrator::initialize( GenericTopology *topo,$/;" f class:ProtoMol::ShadowHMCIntegrator initialize framework/integrators/StandardIntegrator.cpp /^ void StandardIntegrator::initialize(GenericTopology *topo,$/;" f class:ProtoMol::StandardIntegrator initialize framework/topology/ArrayCellListStructure.cpp /^ void ArrayCellListStructure::initialize(const Vector3D& max, Vector3D cellSize){$/;" f class:ProtoMol::ArrayCellListStructure initialize framework/topology/CellListEnumerator_periodicBoundaries.h /^ void initialize(const Topology* topo,$/;" f class:ProtoMol::CellListEnumerator initialize framework/topology/CellListEnumerator_standard.h /^ void initialize(const Topology* topo,$/;" f class:ProtoMol::CellListEnumerator initialize framework/topology/CubicCellManager.cpp /^ void CubicCellManager::initialize(CellListStructure& cellList,const Vector3D& min, const Vector3D& max, bool pbc) const{$/;" f class:ProtoMol::CubicCellManager initializeForces framework/integrators/StandardIntegrator.cpp /^ void StandardIntegrator::initializeForces() {$/;" f class:ProtoMol::StandardIntegrator initializeModifiers framework/integrators/Integrator.cpp /^ void Integrator::initializeModifiers(){$/;" f class:ProtoMol::Integrator initialized framework/parallel/Parallel.h /^ static bool initialized() {return myInitialized;}$/;" f class:ProtoMol::Parallel insert framework/base/Vector3DBlock.h /^ iterator insert(iterator pos, const Vector3D& x) {return vec.insert(pos,x);} $/;" f class:ProtoMol::Vector3DBlock insert framework/base/Vector3DBlock.h /^ void insert(iterator pos, size_type n, const Vector3D& x) { vec.insert(pos,n,x);} $/;" f class:ProtoMol::Vector3DBlock insertionCode framework/base/PDB.h /^ std::string insertionCode; \/\/\/< insertion_code $/;" m struct:ProtoMol::PDB::Atom insertionCode framework/base/PDB.h /^ std::string insertionCode; \/\/\/< insertion_code $/;" m struct:ProtoMol::PDB::Ter instance framework/frontend/Factory.h /^ static Factory& instance(){$/;" f class:ProtoMol::Factory instance framework/frontend/HelpTextFactory.cpp /^ HelpTextFactory& HelpTextFactory::instance(){$/;" f class:ProtoMol::HelpTextFactory instance framework/parallel/Parallel-FD.cpp /^ Parallel& Parallel::instance(){$/;" f class:ProtoMol::Parallel instance framework/parallel/Parallel.cpp /^ Parallel& Parallel::instance(){$/;" f class:ProtoMol::Parallel int32 framework/imd/imd.h /^ typedef TypeSelection::Int<4>::type int32;$/;" t namespace:ProtoMol::IMD int32 framework/io/DCDTrajectoryReader.h /^ typedef TypeSelection::Int<4>::type int32;$/;" t class:ProtoMol::DCDTrajectoryReader int32 framework/io/DCDTrajectoryWriter.h /^ typedef TypeSelection::Int<4>::type int32;$/;" t class:ProtoMol::DCDTrajectoryWriter int_type framework/base/sstream_local.h /^ typedef int int_type;$/;" t class:std::stringbuf integrateNode framework/parallel/Parallel-FD.cpp /^ void Parallel::integrateNode() {$/;" f class:ProtoMol::Parallel integrateNode framework/parallel/Parallel.cpp /^ void Parallel::integrateNode() {$/;" f class:ProtoMol::Parallel integrator framework/integrators/IntegratorDefinition.h /^ MakeableDefinition integrator;$/;" m struct:ProtoMol::IntegratorDefinition interpolate framework/base/LookUpTableBase.h /^ void interpolate(Real a,Real b,Real c,Real d,Real dt,Real& energy, Real& force) const{$/;" f class:ProtoMol::LookUpTableBase interpolateForce framework/base/Grid.h /^ inline void Grid::interpolateForce(Real q, unsigned int index, Vector3D& force){$/;" f class:ProtoMol::Grid interpolateForce framework/base/MultiGrid.h /^ inline void MultiGrid::interpolateForce(Real q, unsigned int index, Vector3D& force){$/;" f class:ProtoMol::MultiGrid intoAdd framework/base/ScalarStructure.cpp /^ ScalarStructure & ScalarStructure::intoAdd(const ScalarStructure &e) {$/;" f class:ProtoMol::ScalarStructure intoAdd framework/base/Vector3D.h /^ Vector3D &intoAdd(const Vector3D& b) {return (*this)+=b;}$/;" f struct:ProtoMol::Vector3D intoAdd framework/base/Vector3DBlock.h /^ Vector3DBlock &intoAdd(const Vector3DBlock &x) { $/;" f class:ProtoMol::Vector3DBlock intoAssign framework/base/ScalarStructure.cpp /^ ScalarStructure & ScalarStructure::intoAssign(const ScalarStructure &e) {$/;" f class:ProtoMol::ScalarStructure intoAssign framework/base/Vector3DBlock.h /^ Vector3DBlock &intoAssign(const Vector3DBlock &x) { $/;" f class:ProtoMol::Vector3DBlock intoDivide framework/base/Vector3D.h /^ Vector3D &intoDivide(Real w) {return (*this)\/=w;}$/;" f struct:ProtoMol::Vector3D intoMultiply framework/base/Vector3D.h /^ Vector3D &intoMultiply(Real w) {return (*this)*=w;}$/;" f struct:ProtoMol::Vector3D intoSubtract framework/base/ScalarStructure.cpp /^ ScalarStructure & ScalarStructure::intoSubtract(const ScalarStructure &e) {$/;" f class:ProtoMol::ScalarStructure intoSubtract framework/base/Vector3D.h /^ Vector3D &intoSubtract(const Vector3D& b) {return (*this)-=b;}$/;" f struct:ProtoMol::Vector3D intoSubtract framework/base/Vector3DBlock.h /^ Vector3DBlock &intoSubtract(const Vector3DBlock &x) {$/;" f class:ProtoMol::Vector3DBlock intoWeighted framework/base/Vector3DBlock.h /^ Vector3DBlock &intoWeighted(Real weight, const Vector3DBlock &x) {$/;" f class:ProtoMol::Vector3DBlock intoWeightedAdd framework/base/Vector3D.h /^ Vector3D &intoWeightedAdd(Real w, const Vector3D& b) {$/;" f struct:ProtoMol::Vector3D intoWeightedAdd framework/base/Vector3DBlock.h /^ Vector3DBlock &intoWeightedAdd(Real weight, const Vector3DBlock &x) {$/;" f class:ProtoMol::Vector3DBlock intoWeightedSubtract framework/base/Vector3D.h /^ Vector3D &intoWeightedSubtract(Real w, const Vector3D& b) {$/;" f struct:ProtoMol::Vector3D intoWeightedSubtract framework/base/Vector3DBlock.h /^ Vector3DBlock &intoWeightedSubtract(Real weight, const Vector3DBlock &x) {$/;" f class:ProtoMol::Vector3DBlock invert framework/base/Matrix3by3.cpp /^ bool Matrix3by3::invert()$/;" f class:ProtoMol::Matrix3by3 isAccessible framework/base/systemutilities.cpp /^ bool isAccessible(const string& fileName){$/;" f namespace:ProtoMol isAccessible framework/io/File.cpp /^ bool File::isAccessible(){$/;" f class:ProtoMol::File isBCC tools/bccAnalyzer.cpp /^static bool isBCC(XYZ xyz, Real eps, Real rest, Vector3D& normal, Real& d, Real& err, Real& minimal, Real& maximal,$/;" f file: isBarrier framework/parallel/Parallel.h /^ static bool isBarrier() {return myUseBarrier;}$/;" f class:ProtoMol::Parallel isBlank framework/base/stringutilities.cpp /^ bool isBlank(const string& word){$/;" f namespace:ProtoMol isBool framework/base/stringutilities.cpp /^ bool isBool(const string& word){$/;" f namespace:ProtoMol isDynamic framework/parallel/Parallel.h /^ static bool isDynamic() {return (myMode != ParallelType::STATIC);}$/;" f class:ProtoMol::Parallel isEnabled framework/integrators/Modifier.h /^ bool isEnabled() const{return myEnable;}$/;" f class:ProtoMol::Modifier isExclusionAtom framework/topology/AngleInfo.cpp /^ bool AngleInfo::isExclusionAtom() const{$/;" f class:ProtoMol::AngleInfo isForward framework/integrators/Integrator.h /^ bool isForward() const {return myForward;}$/;" f class:ProtoMol::Integrator isIdDefined framework/frontend/Output.cpp /^ bool Output::isIdDefined(const Configuration* config) const{$/;" f class:ProtoMol::Output isIdDefined framework/frontend/OutputScreen.cpp /^ bool OutputScreen::isIdDefined(const Configuration* config) const{$/;" f class:ProtoMol::OutputScreen isInnerAtom framework/topology/AngleInfo.cpp /^ bool AngleInfo::isInnerAtom() const {$/;" f class:ProtoMol::AngleInfo isInt framework/base/stringutilities.cpp /^ bool isInt(const string& word){$/;" f namespace:ProtoMol isInternal framework/integrators/ModifierAveraging.h /^ virtual bool isInternal() const {return true;}$/;" f class:ProtoMol::ModifierAveraging isInternal framework/integrators/ModifierFriction.h /^ virtual bool isInternal() const {return true;}$/;" f class:ProtoMol::ModifierFriction isInternal framework/integrators/ModifierIncrementTimestep.h /^ virtual bool isInternal() const {return true;}$/;" f class:ProtoMol::ModifierIncrementTimestep isInternal framework/integrators/ModifierMetaRattleShake.h /^ virtual bool isInternal() const {return false;}$/;" f class:ProtoMol::ModifierMetaRattleShake isInternal framework/integrators/ModifierMollification.h /^ virtual bool isInternal() const {return true;}$/;" f class:ProtoMol::ModifierMollification isInternal framework/integrators/ModifierPostForceBarostat.h /^ virtual bool isInternal() const {return true;}$/;" f class:ProtoMol::ModifierPostForceBarostat isInternal framework/integrators/ModifierPostForceThermostat.h /^ virtual bool isInternal() const {return true;}$/;" f class:ProtoMol::ModifierPostForceThermostat isInternal framework/integrators/ModifierPreForceBarostat.h /^ virtual bool isInternal() const {return true;}$/;" f class:ProtoMol::ModifierPreForceBarostat isInternal framework/integrators/ModifierPreForceThermostat.h /^ virtual bool isInternal() const {return true;}$/;" f class:ProtoMol::ModifierPreForceThermostat isInternal framework/integrators/ModifierRemoveAngularMomentum.h /^ virtual bool isInternal() const {return false;}$/;" f class:ProtoMol::ModifierRemoveAngularMomentum isInternal framework/integrators/ModifierRemoveLinearMomentum.h /^ virtual bool isInternal() const {return false;}$/;" f class:ProtoMol::ModifierRemoveLinearMomentum isInternal framework/integrators/ModifierShadow.h /^ virtual bool isInternal() const { return( false ); }$/;" f class:ProtoMol::ModifierShadow isKeywordCharmm19 framework/io/PARReader.cpp /^ bool PARReader::isKeywordCharmm19(const string& word){$/;" f class:ProtoMol::PARReader isKeywordCharmm28 framework/io/PARReader.cpp /^ bool PARReader::isKeywordCharmm28(const string& word) {$/;" f class:ProtoMol::PARReader isLittleEndian framework/base/systemutilities.cpp /^ static bool isLittleEndian(){$/;" f struct:ProtoMol::Endian isMPI framework/parallel/Parallel-FD.cpp /^ const bool Parallel::isMPI = false;$/;" m class:ProtoMol::Parallel file: isMPI framework/parallel/Parallel-FD.cpp /^ const bool Parallel::isMPI = true;$/;" m class:ProtoMol::Parallel file: isMPI framework/parallel/Parallel.cpp /^ const bool Parallel::isMPI = false;$/;" m class:ProtoMol::Parallel file: isMPI framework/parallel/Parallel.cpp /^ const bool Parallel::isMPI = true;$/;" m class:ProtoMol::Parallel file: isMPI framework/parallel/Parallel.h /^ static const bool isMPI;$/;" m class:ProtoMol::Parallel isOrthogonal framework/topology/PeriodicBoundaryConditions.h /^ bool isOrthogonal() const {return myOrthogonal;};$/;" f class:ProtoMol::PeriodicBoundaryConditions isOrthogonal framework/topology/VacuumBoundaryConditions.h /^ bool isOrthogonal() const {return true;};$/;" f class:ProtoMol::VacuumBoundaryConditions isParallel framework/base/FFTComplex.cpp /^ bool FFTComplex::isParallel(){$/;" f class:ProtoMol::FFTComplex isParallel framework/base/TimerStatistic.h /^ static bool isParallel(void) {return myIsParallel;}$/;" f class:ProtoMol::TimerStatistic isParallel framework/parallel/Parallel.h /^ static bool isParallel() {return myIsParallel;}$/;" f class:ProtoMol::Parallel isPrintable framework/base/stringutilities.cpp /^ bool isPrintable(const string& word){$/;" f namespace:ProtoMol isReal framework/base/stringutilities.cpp /^ bool isReal(const string& word){$/;" f namespace:ProtoMol isSigma framework/base/BSpline.h /^ static bool isSigma(unsigned int order){return (BSpline(order,0.0).theta[order-1] == 0.0 && BSpline(order,0.0).dTheta[order-1] == 0.0);}$/;" f class:ProtoMol::BSpline isSigma framework/base/Hermite.h /^ static bool isSigma(unsigned int order){return (Hermite(order,0.0).theta[order-1] == 0.0 && Hermite(order,0.0).dTheta[order-1] == 0.0);}$/;" f class:ProtoMol::Hermite isSigma framework/base/Lagrange.h /^ static bool isSigma(unsigned int order){return (Lagrange(order,0.0).theta[order-1] == 0.0 && Lagrange(order,0.0).dTheta[order-1] == 0.0);}$/;" f class:ProtoMol::Lagrange isUInt framework/base/stringutilities.cpp /^ bool isUInt(const string& word){$/;" f namespace:ProtoMol isVector framework/base/stringutilities.cpp /^ bool isVector(const string& word){$/;" f namespace:ProtoMol isVector3D framework/base/stringutilities.cpp /^ bool isVector3D(const string& word){$/;" f namespace:ProtoMol isVisited framework/topology/AngleInfo.cpp /^ bool AngleInfo::isVisited() const{$/;" f class:ProtoMol::AngleInfo isblankchar framework/base/stringutilities.cpp /^ bool isblankchar(char c){$/;" f namespace:ProtoMol isgLJParms framework/topology/GenericTopology.h /^ BankLennardJonesParameterTable isgLJParms;$/;" m class:ProtoMol::GenericTopology isnan framework/base/mathutilities.h /^ inline int isnan(Real x) {$/;" f namespace:ProtoMol isolateNode framework/parallel/Parallel-FD.cpp /^ void Parallel::isolateNode() {$/;" f class:ProtoMol::Parallel isolateNode framework/parallel/Parallel.cpp /^ void Parallel::isolateNode() {$/;" f class:ProtoMol::Parallel isprintablechar framework/base/stringutilities.cpp /^ bool isprintablechar(char c){$/;" f namespace:ProtoMol istringstream framework/base/sstream_local.h /^ istringstream(const std::string& s, int which=ios::in) :$/;" f class:std::istringstream istringstream framework/base/sstream_local.h /^ istringstream(int which=ios::in) :$/;" f class:std::istringstream istringstream framework/base/sstream_local.h /^ class istringstream : public stringstreambase, public istream {$/;" c namespace:std iterator framework/base/Array_Fastest.h /^ typedef T * iterator;$/;" t class:ProtoMol::Array iterator framework/base/Array_Fastest.h /^ typedef T * iterator;$/;" t class:ProtoMol::RefArray iterator framework/base/Array_NoPartialSpecialization.h /^ typedef T * iterator;$/;" t class:ProtoMol::Array::RefArray iterator framework/base/Array_NoPartialSpecialization.h /^ typedef T * iterator;$/;" t class:ProtoMol::Array iterator framework/base/Configuration.h /^ typedef ValueMapType::iterator iterator;$/;" t class:ProtoMol::Configuration iterator framework/base/Vector3DBlock.h /^ typedef std::vector::iterator iterator; $/;" t class:ProtoMol::Vector3DBlock iterator framework/frontend/HelpTextFactory.h /^ typedef HelpTextMapType::iterator iterator;$/;" t class:ProtoMol::HelpTextFactory iterator framework/frontend/OutputCollection.h /^ typedef std::list::iterator iterator;$/;" t class:ProtoMol::OutputCollection iterator framework/topology/ArrayCellListStructure.h /^ typedef TContainer::iterator iterator;$/;" t class:ProtoMol::ArrayCellListStructure j framework/topology/CellListEnumerator_periodicBoundaries.h /^ CubicCellManager::CellListStructure::const_iterator i,j,the_beginning,the_end;$/;" m class:ProtoMol::CellListEnumerator j framework/topology/CellListEnumerator_standard.h /^ CubicCellManager::CellListStructure::const_iterator i,j,the_beginning,the_end;$/;" m class:ProtoMol::CellListEnumerator k framework/base/simpleTypes.h /^ int h;int k; int l;$/;" m struct:ProtoMol::TripleInt k framework/forces/HarmDihedralSystemForce.h /^ Real k;$/;" m class:ProtoMol::HarmDihedralSystemForce k_ub framework/base/PAR.h /^ Real k_ub; \/\/\/< Urey-Bradley force constant$/;" m struct:ProtoMol::PAR::Angle kappa framework/forces/MagneticDipoleForce.h /^ Real volum, expfactor, realChi, kappa;$/;" m class:ProtoMol::MagneticDipoleForce kbT framework/integrators/NPTVerletIntegrator.h /^ const Real kbT; \/\/ Target temperature multiplied by Boltzmann's constant. Units: (kcal\/mol)$/;" m class:ProtoMol::NPTVerletIntegrator kbT framework/integrators/NVTVerletIntegrator.h /^ const Real kbT; \/\/ Target temperature multiplied by Boltzmann's constant. Units: (kcal\/mol)$/;" m class:ProtoMol::NVTVerletIntegrator kernel framework/forces/CoulombForce.h /^ static Real kernel(Real r) {return (1.0\/r);}$/;" f class:ProtoMol::CoulombForce::C1 kernel framework/forces/CoulombForce.h /^ static Real kernel(Real r) {return (1.0\/r);}$/;" f class:ProtoMol::CoulombForce::C2 kernel framework/forces/CoulombForce.h /^ static Real kernel(Real r) {return (1.0\/r);}$/;" f class:ProtoMol::CoulombForce::C3 kernel framework/forces/CoulombForce.h /^ static Real kernel(Real r) {return (1.0\/r);}$/;" f class:ProtoMol::CoulombForce::C4 kernelR framework/forces/CoulombForce.h /^ static Real kernelR(Real rr) {return (rr);}$/;" f class:ProtoMol::CoulombForce::C1 kernelR framework/forces/CoulombForce.h /^ static Real kernelR(Real rr) {return (rr);}$/;" f class:ProtoMol::CoulombForce::C2 kernelR framework/forces/CoulombForce.h /^ static Real kernelR(Real rr) {return (rr);}$/;" f class:ProtoMol::CoulombForce::C3 kernelR framework/forces/CoulombForce.h /^ static Real kernelR(Real rr) {return (rr);}$/;" f class:ProtoMol::CoulombForce::C4 keyword framework/base/BSpline.h /^ static const std::string keyword;$/;" m class:ProtoMol::BSpline keyword framework/base/Hermite.h /^ static const std::string keyword;$/;" m class:ProtoMol::Hermite keyword framework/base/Lagrange.h /^ static const std::string keyword;$/;" m class:ProtoMol::Lagrange keyword framework/base/Parameter.h /^ std::string keyword;$/;" m struct:ProtoMol::Parameter keyword framework/forces/AngleSystemForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::AngleSystemForceBase keyword framework/forces/BondSystemForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::BondSystemForceBase keyword framework/forces/CompareForce.h /^ static const std::string keyword;$/;" m class:ProtoMol::CompareForce keyword framework/forces/CoulombEwaldRealForce.h /^ static const std::string keyword; $/;" m class:ProtoMol::CoulombEwaldRealForce keyword framework/forces/CoulombEwaldRealTableForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::CoulombEwaldRealTableForceBase keyword framework/forces/CoulombForce.h /^ static const std::string keyword; $/;" m class:ProtoMol::CoulombForce::C1 keyword framework/forces/CoulombForce.h /^ static const std::string keyword; $/;" m class:ProtoMol::CoulombForce::C2 keyword framework/forces/CoulombForce.h /^ static const std::string keyword; $/;" m class:ProtoMol::CoulombForce::C3 keyword framework/forces/CoulombForce.h /^ static const std::string keyword; $/;" m class:ProtoMol::CoulombForce::C4 keyword framework/forces/CoulombForce.h /^ static const std::string keyword; $/;" m class:ProtoMol::CoulombForce keyword framework/forces/CoulombMultiGridDirectForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::CoulombMultiGridDirectForceBase keyword framework/forces/CoulombMultiGridDirectTableForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::CoulombMultiGridDirectTableForceBase keyword framework/forces/CoulombTableForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::CoulombTableForceBase keyword framework/forces/DihedralSystemForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::DihedralSystemForceBase keyword framework/forces/ElectricFieldSystemForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::ElectricFieldSystemForceBase keyword framework/forces/ExternalGravitationSystemForce.h /^ static const std::string keyword;$/;" m class:ProtoMol::ExternalGravitationSystemForce keyword framework/forces/ExternalMagneticFieldExtendedForce.h /^ static const std::string keyword;$/;" m class:ProtoMol::ExternalMagneticFieldExtendedForce keyword framework/forces/FrictionExtendedForce.h /^ static const std::string keyword;$/;" m class:ProtoMol::FrictionExtendedForce keyword framework/forces/GravitationForce.h /^ static const std::string keyword; $/;" m class:ProtoMol::GravitationForce keyword framework/forces/HarmDihedralSystemForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::HarmDihedralSystemForceBase keyword framework/forces/ImproperSystemForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::ImproperSystemForceBase keyword framework/forces/LennardJonesForce.h /^ static const std::string keyword; $/;" m class:ProtoMol::LennardJonesForce keyword framework/forces/LennardJonesTableForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::LennardJonesTableForceBase keyword framework/forces/MagneticDipoleForce.h /^ static const std::string keyword; $/;" m class:ProtoMol::MagneticDipoleForce keyword framework/forces/MagneticDipoleMirrorSystemForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::MagneticDipoleMirrorSystemForceBase keyword framework/forces/NonbondedCutoffForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::NonbondedCutoffForceBase keyword framework/forces/NonbondedFullEwaldSystemForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForceBase keyword framework/forces/NonbondedFullSystemForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::NonbondedFullSystemForceBase keyword framework/forces/NonbondedMultiGridSystemForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::NonbondedMultiGridSystemForceBase keyword framework/forces/NonbondedPMEwaldSystemForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForceBase keyword framework/forces/NonbondedSimpleFullSystemForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::NonbondedSimpleFullSystemForceBase keyword framework/forces/PaulTrapExtendedForceBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::PaulTrapExtendedForceBase keyword framework/forces/SphericalSystemForce.h /^ static const std::string keyword;$/;" m class:ProtoMol::SphericalSystemForce keyword framework/forces/TimeForce.h /^ static const std::string keyword;$/;" m class:ProtoMol::TimeForce keyword framework/forces/WrapperMetaForce.h /^ const std::string keyword;$/;" m class:ProtoMol::WrapperMetaForce keyword framework/frontend/OutputBSDL.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputBSDL keyword framework/frontend/OutputDCDTrajectory.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputDCDTrajectory keyword framework/frontend/OutputDiffusion.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputDiffusion keyword framework/frontend/OutputDihedrals.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputDihedrals keyword framework/frontend/OutputEnergies.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputEnergies keyword framework/frontend/OutputFinalPDBPos.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputFinalPDBPos keyword framework/frontend/OutputFinalXYZBinPos.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputFinalXYZBinPos keyword framework/frontend/OutputFinalXYZBinVel.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputFinalXYZBinVel keyword framework/frontend/OutputFinalXYZPos.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputFinalXYZPos keyword framework/frontend/OutputFinalXYZVel.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputFinalXYZVel keyword framework/frontend/OutputMomentum.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputMomentum keyword framework/frontend/OutputPDBFramePos.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputPDBFramePos keyword framework/frontend/OutputPaulTrap.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputPaulTrap keyword framework/frontend/OutputREMExchangeRate.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputREMExchangeRate keyword framework/frontend/OutputREMHistory.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputREMHistoryFile keyword framework/frontend/OutputScreen.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputScreen keyword framework/frontend/OutputState.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputState keyword framework/frontend/OutputTemperatures.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputTemperatures keyword framework/frontend/OutputXYZBinTrajectoryPos.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputXYZBinTrajectoryPos keyword framework/frontend/OutputXYZBinTrajectoryVel.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputXYZBinTrajectoryVel keyword framework/frontend/OutputXYZTrajectoryForce.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputXYZTrajectoryForce keyword framework/frontend/OutputXYZTrajectoryPos.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputXYZTrajectoryPos keyword framework/frontend/OutputXYZTrajectoryVel.h /^ static const std::string keyword;$/;" m class:ProtoMol::OutputXYZTrajectoryVel keyword framework/imd/HapticSystemForce.h /^ static const std::string keyword;$/;" m class:ProtoMol::HapticSystemForce keyword framework/imd/HapticSystemForceBase.h /^ static const std::string keyword;$/;" m class:HapticSystemForceBase keyword framework/integrators/BBKIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::BBKIntegrator keyword framework/integrators/BSplineMOLLYIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::BSplineMOLLYIntegrator keyword framework/integrators/DLMCIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::DLMCIntegrator keyword framework/integrators/DMDLeapfrogIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::DMDLeapfrogIntegrator keyword framework/integrators/DihedralHMCIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::DihedralHMCIntegrator keyword framework/integrators/EquilibriumMOLLYIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::EquilibriumMOLLYIntegrator keyword framework/integrators/HMCIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::HMCIntegrator keyword framework/integrators/ImpulseIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::ImpulseIntegrator keyword framework/integrators/LangevinImpulseIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::LangevinImpulseIntegrator keyword framework/integrators/LeapfrogIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::LeapfrogIntegrator keyword framework/integrators/NPTVerletIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::NPTVerletIntegrator keyword framework/integrators/NVTVerletIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::NVTVerletIntegrator keyword framework/integrators/NoseNVTLeapfrogIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::NoseNVTLeapfrogIntegrator keyword framework/integrators/PLeapfrogIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::PLeapfrogIntegrator keyword framework/integrators/PaulTrapIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::PaulTrapIntegrator keyword framework/integrators/ShadowHMCIntegrator.h /^ static const std::string keyword;$/;" m class:ProtoMol::ShadowHMCIntegrator keyword framework/topology/C1SwitchingFunctionBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::C1SwitchingFunctionBase keyword framework/topology/C2SwitchingFunctionBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::C2SwitchingFunctionBase keyword framework/topology/CmpCnCnSwitchingFunctionBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::CmpCnCnSwitchingFunctionBase keyword framework/topology/CnSwitchingFunctionBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::CnSwitchingFunctionBase keyword framework/topology/ComplementSwitchingFunctionBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::ComplementSwitchingFunctionBase keyword framework/topology/CubicCellManager.h /^ static const std::string keyword;$/;" m class:ProtoMol::CubicCellManager keyword framework/topology/CutoffSwitchingFunctionBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::CutoffSwitchingFunctionBase keyword framework/topology/GenericTopology.h /^ static const std::string keyword;$/;" m class:ProtoMol::GenericTopology keyword framework/topology/PeriodicBoundaryConditions.h /^ static const std::string keyword;$/;" m class:ProtoMol::PeriodicBoundaryConditions keyword framework/topology/RangeSwitchingFunctionBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::RangeSwitchingFunctionBase keyword framework/topology/ShiftSwitchingFunctionBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::ShiftSwitchingFunctionBase keyword framework/topology/UniversalSwitchingFunctionBase.h /^ static const std::string keyword;$/;" m class:ProtoMol::UniversalSwitchingFunctionBase keyword framework/topology/VacuumBoundaryConditions.h /^ static const std::string keyword;$/;" m class:ProtoMol::VacuumBoundaryConditions keywords framework/frontend/HelpTextFactory.cpp /^ string HelpTextFactory::keywords(){$/;" f class:ProtoMol::HelpTextFactory kill framework/frontend/Factory.h /^ static void kill(){$/;" f class:ProtoMol::Factory kill framework/frontend/HelpTextFactory.cpp /^ void HelpTextFactory::kill(){$/;" f class:ProtoMol::HelpTextFactory kill framework/parallel/Parallel-FD.cpp /^ void Parallel::kill(){$/;" f class:ProtoMol::Parallel kill framework/parallel/Parallel.cpp /^ void Parallel::kill(){$/;" f class:ProtoMol::Parallel kineticEnergy framework/frontend/OutputCache.cpp /^ Real OutputCache::kineticEnergy() const{$/;" f class:ProtoMol::OutputCache kineticEnergy framework/topology/topologyutilities.cpp /^ Real kineticEnergy(const GenericTopology* topology,$/;" f namespace:ProtoMol kineticEnergyForAtomType framework/topology/topologyutilities.cpp /^ Real kineticEnergyForAtomType(const GenericTopology* topology,$/;" f namespace:ProtoMol kineticEnergyForNonWater framework/topology/topologyutilities.cpp /^ Real kineticEnergyForNonWater(const GenericTopology* topology,$/;" f namespace:ProtoMol kineticEnergyForWater framework/topology/topologyutilities.cpp /^ Real kineticEnergyForWater(const GenericTopology* topology,$/;" f namespace:ProtoMol l framework/base/simpleTypes.h /^ int h;int k; int l;$/;" m struct:ProtoMol::TripleInt l12 framework/integrators/EquilibriumMOLLYIntegrator.h /^ Real l12; \/\/ squared rest lenght of the constrain$/;" m struct:ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond lambda framework/base/Molecule.h /^ Real lambda;$/;" m struct:ProtoMol::Molecule lambda framework/integrators/EquilibriumMOLLYIntegrator.h /^ Real lambda;\/\/ Lambda of the constraint $/;" m struct:ProtoMol::EquilibriumMOLLYIntegrator::HydrogenBond lap framework/base/Timer.cpp /^ TimeRep Timer::lap()$/;" f class:ProtoMol::Timer lattice framework/forces/OneAtomPairFull.h /^ const std::vector* lattice;$/;" m class:ProtoMol::OneAtomPairFull lattice framework/forces/OneAtomPairTwoFull.h /^ const std::vector* lattice;$/;" m class:ProtoMol::OneAtomPairTwoFull len protomol_config_windows.cpp /^ int len;$/;" v len protomol_config_windows.cpp /^ socklen_t len;$/;" v length framework/imd/imd.cpp /^ int32 length;$/;" m struct:ProtoMol::IMD:: file: lennardJonesBank framework/topology/BankLennardJonesParameterTable.h /^ std::vector lennardJonesBank;$/;" m struct:ProtoMol::BankLennardJonesParameterTable lennardJonesParameters framework/topology/GenericTopology.h /^ LennardJonesParameterTable lennardJonesParameters;$/;" m class:ProtoMol::GenericTopology less framework/base/Value.cpp /^ inline bool Value::less(const Value& v1, const Value& v2){$/;" f class:ProtoMol::Value less framework/base/Value.cpp /^ inline bool Value::less(const Value&, const Value&){return false;}$/;" f class:ProtoMol::Value less framework/base/Value.cpp /^ inline bool Value::less >(const Value&, const Value&){return false;}$/;" f class:ProtoMol::Value lessEqual framework/base/Value.cpp /^ inline bool Value::lessEqual(const Value& v1, const Value& v2){$/;" f class:ProtoMol::Value lessEqual framework/base/Value.cpp /^ inline bool Value::lessEqual(const Value&, const Value&){return false;}$/;" f class:ProtoMol::Value lessEqual framework/base/Value.cpp /^ inline bool Value::lessEqual >(const Value&, const Value&){return false;}$/;" f class:ProtoMol::Value level framework/integrators/Integrator.cpp /^ int Integrator::level() const{$/;" f class:ProtoMol::Integrator lift framework/integrators/DLMCIntegrator.h /^ bool lift;$/;" m class:ProtoMol::DLMCIntegrator light_diffuse compilerTests/glutTest.cpp /^static GLfloat light_diffuse[] = {1.0, 0.0, 0.0, 1.0}; \/* Red diffuse light. *\/$/;" v file: light_position compilerTests/glutTest.cpp /^static GLfloat light_position[] = {1.0, 1.0, 1.0, 0.0}; \/* Infinite light location. *\/$/;" v file: linearMomentum framework/frontend/OutputCache.cpp /^ Vector3D OutputCache::linearMomentum() const{$/;" f class:ProtoMol::OutputCache linearMomentum framework/topology/topologyutilities.cpp /^ Vector3D linearMomentum(const Vector3DBlock *velocities, $/;" f namespace:ProtoMol listen framework/imd/IMDElf.cpp /^ int IMDElf::listen(int defport) {$/;" f class:ProtoMol::IMDElf longRangeTerm framework/forces/NonbondedMultiGridSystemForce.h /^ smooth>::longRangeTerm(const RealTopologyType* realTopo,$/;" f class:ProtoMol::NonbondedMultiGridSystemForce low framework/imd/imd.cpp /^ unsigned int low : 8;$/;" m struct:ProtoMol::IMD:: file: lowBound framework/frontend/OutputState.h /^ Real lowBound;$/;" m struct:ProtoMol::OutputState::orderParam lowDeltas framework/topology/ExclusionTable.h /^ ExclusionClass* lowDeltas;$/;" m class:ProtoMol::ExclusionTable lowerboundExp2 framework/base/mathutilities.cpp /^ Real lowerboundExp2(Real r){$/;" f namespace:ProtoMol lowercase framework/base/stringutilities.cpp /^ string lowercase (const string& word){$/;" f namespace:ProtoMol lowest framework/imd/imd.cpp /^ unsigned int lowest : 8;$/;" m struct:ProtoMol::IMD:: file: ltstrNocase framework/base/stringutilities.h /^ struct ltstrNocase {bool operator()(const std::string& s1, const std::string& s2) const;};$/;" s namespace:ProtoMol ltstrNocaseOp framework/base/stringutilities.cpp /^ bool ltstrNocaseOp (const string& s1, const string& s2){$/;" f namespace:ProtoMol m00 framework/base/Matrix3by3.h /^ Real m00, m01, m02;$/;" m class:ProtoMol::Matrix3by3 m01 framework/base/Matrix3by3.h /^ Real m00, m01, m02;$/;" m class:ProtoMol::Matrix3by3 m02 framework/base/Matrix3by3.h /^ Real m00, m01, m02;$/;" m class:ProtoMol::Matrix3by3 m10 framework/base/Matrix3by3.h /^ Real m10, m11, m12;$/;" m class:ProtoMol::Matrix3by3 m11 framework/base/Matrix3by3.h /^ Real m10, m11, m12;$/;" m class:ProtoMol::Matrix3by3 m12 framework/base/Matrix3by3.h /^ Real m10, m11, m12;$/;" m class:ProtoMol::Matrix3by3 m20 framework/base/Matrix3by3.h /^ Real m20, m21, m22;$/;" m class:ProtoMol::Matrix3by3 m21 framework/base/Matrix3by3.h /^ Real m20, m21, m22;$/;" m class:ProtoMol::Matrix3by3 m22 framework/base/Matrix3by3.h /^ Real m20, m21, m22;$/;" m class:ProtoMol::Matrix3by3 m_Dimensions framework/base/Array_Fastest.h /^ size_t m_Dimensions[1]; $/;" m class:ProtoMol::ArraySizes m_Dimensions framework/base/Array_Fastest.h /^ size_t m_Dimensions[N];$/;" m class:ProtoMol::ArraySize m_NDimensions framework/base/Array_Fastest.h /^ size_type m_NDimensions[N]; \/\/ Size of the N array dimensions$/;" m class:ProtoMol::Array m_NDimensions framework/base/Array_Fastest.h /^ size_type m_NDimensions; \/\/ Array dimension$/;" m class:ProtoMol::RefArray m_NDimensions framework/base/Array_Fastest.h /^ size_type m_NDimensions; \/\/ Array dimensions$/;" m class:ProtoMol::RefArray m_NDimensions framework/base/Array_NoPartialSpecialization.h /^ size_type m_NDimensions[N]; \/\/ Size of the N array dimensions$/;" m class:ProtoMol::Array m_SubArrayLen framework/base/Array_Fastest.h /^ size_type m_SubArrayLen[N]; \/\/ Size of each subarray$/;" m class:ProtoMol::Array m_SubArrayLen framework/base/Array_Fastest.h /^ size_type m_SubArrayLen; \/\/ SubArray dimensions$/;" m class:ProtoMol::RefArray m_SubArrayLen framework/base/Array_NoPartialSpecialization.h /^ size_type m_SubArrayLen[N]; \/\/ Size of each subarray$/;" m class:ProtoMol::Array m_TheSubArray framework/base/Array_Fastest.h /^ RefArray m_TheSubArray;\/\/ The only RefArray element used $/;" m class:ProtoMol::Array m_boolDummy framework/base/Array_Fastest.h /^ mutable bool m_boolDummy;$/;" m class:ProtoMol::RefArray m_elem framework/base/Stack.h /^ T *m_elem;$/;" m class:ProtoMol::Stack m_nArrayElements framework/base/Array_Fastest.h /^ size_type m_nArrayElements; \/\/ Total number of array elements$/;" m class:ProtoMol::Array m_nArrayElements framework/base/Array_NoPartialSpecialization.h /^ size_type m_nArrayElements; \/\/ Total number of array elements$/;" m class:ProtoMol::Array m_numElements framework/base/Stack.h /^ unsigned int m_numElements;$/;" m class:ProtoMol::Stack m_pArrayElements framework/base/Array_Fastest.h /^ T * m_pArrayElements; \/\/ Pointer to actual array elements$/;" m class:ProtoMol::Array m_pArrayElements framework/base/Array_NoPartialSpecialization.h /^ T * m_pArrayElements; \/\/ Pointer to actual array elements$/;" m class:ProtoMol::Array m_pElements framework/base/Array_Fastest.h /^ mutable T * m_pElements; \/\/ Point to SubArray with elements within Array$/;" m class:ProtoMol::RefArray m_pElements framework/base/Array_Fastest.h /^ mutable T * m_pElements; \/\/ Point to elements within Array$/;" m class:ProtoMol::RefArray m_pElements framework/base/Array_NoPartialSpecialization.h /^ T * const m_pElements; \/\/ Point to elements within Array$/;" m class:ProtoMol::Array::RefArray m_pElements framework/base/Array_NoPartialSpecialization.h /^ T * const m_pElements; \/\/ Point to SubArray with elements within Array$/;" m class:ProtoMol::Array::RefArray m_pNDimensions framework/base/Array_NoPartialSpecialization.h /^ const size_type * const m_pNDimensions; \/\/ Array dimension$/;" m class:ProtoMol::Array::RefArray m_pNDimensions framework/base/Array_NoPartialSpecialization.h /^ const size_type * const m_pNDimensions; \/\/ Array dimensions$/;" m class:ProtoMol::Array::RefArray m_pSubArrayLen framework/base/Array_NoPartialSpecialization.h /^ const size_type * const m_pSubArrayLen; \/\/ SubArray dimensions$/;" m class:ProtoMol::Array::RefArray m_size framework/base/Stack.h /^ unsigned int m_size;$/;" m class:ProtoMol::Stack main applications/protomol-app/protomol.cpp /^int main(int argc, char **argv) {$/;" f main compilerTests/glutTest.cpp /^int main(int argc, char **argv) {$/;" f main compilerTests/pngTest.cpp /^int main(int argc, char **argv) {$/;" f main tools/bccAnalyzer.cpp /^int main(int argc, char **argv) {$/;" f main tools/imageMerger.cpp /^int main(int argc, char **argv) {$/;" f main tools/molOrientAnalyzer.cpp /^int main(int argc, char **argv) {$/;" f main tools/par2par.cpp /^int main(int argc, char **argv) {$/;" f main tools/paulTrap.cpp /^int main(int argc, char **argv) {$/;" f main tools/pdb2pdb.cpp /^int main(int argc, char **argv) {$/;" f main tools/rem/sequential/main.cc /^int main(int argc, char* argv[]) {$/;" f make framework/forces/CoulombEwaldRealForce.cpp /^ CoulombEwaldRealForce CoulombEwaldRealForce::make(std::string& , const std::vector& values) {$/;" f class:ProtoMol::CoulombEwaldRealForce make framework/forces/CoulombEwaldRealTableForce.h /^ static CoulombEwaldRealTableForce make(std::string& errMsg, const std::vector& values){$/;" f class:ProtoMol::CoulombEwaldRealTableForce make framework/forces/CoulombForce.h /^ static CoulombForce make(std::string&, const std::vector&) {$/;" f class:ProtoMol::CoulombForce make framework/forces/CoulombMultiGridDirectForce.h /^ static CoulombMultiGridDirectForce make(std::string&, const std::vector& values){return CoulombMultiGridDirectForce(values[0]);}$/;" f class:ProtoMol::CoulombMultiGridDirectForce make framework/forces/CoulombMultiGridDirectTableForce.h /^ static CoulombMultiGridDirectTableForce make(std::string&, const std::vector& values){$/;" f class:ProtoMol::CoulombMultiGridDirectTableForce make framework/forces/CoulombTableForce.h /^ static CoulombTableForce make(std::string& errMsg, const std::vector& values){$/;" f class:ProtoMol::CoulombTableForce make framework/forces/Force.cpp /^ Force* Force::make(string& errMsg, const vector& values) const{$/;" f class:ProtoMol::Force make framework/forces/GravitationForce.cpp /^ GravitationForce GravitationForce::make(std::string& ,const std::vector& values) {$/;" f class:ProtoMol::GravitationForce make framework/forces/LennardJonesForce.h /^ static LennardJonesForce make(std::string& , const std::vector&) {$/;" f class:ProtoMol::LennardJonesForce make framework/forces/LennardJonesTableForce.h /^ static LennardJonesTableForce make(std::string& errMsg, const std::vector& values){$/;" f class:ProtoMol::LennardJonesTableForce make framework/forces/MagneticDipoleForce.cpp /^ MagneticDipoleForce MagneticDipoleForce::make(string& , const vector& values) {$/;" f class:ProtoMol::MagneticDipoleForce make framework/forces/OneAtomPair.h /^ static OneAtomPair make(std::string& errMsg, std::vector values) {$/;" f class:ProtoMol::OneAtomPair make framework/forces/OneAtomPairFull.h /^ static OneAtomPairFull make(std::string& errMsg, std::vector values) {$/;" f class:ProtoMol::OneAtomPairFull make framework/forces/OneAtomPairTwo.h /^ static OneAtomPairTwo make(std::string& errMsg, std::vector values) {$/;" f class:ProtoMol::OneAtomPairTwo make framework/forces/OneAtomPairTwoFull.h /^ static OneAtomPairTwoFull make(std::string& errMsg, std::vector values) {$/;" f class:ProtoMol::OneAtomPairTwoFull make framework/forces/OneMollyPair.h /^ static OneMollyPair make(std::string& errMsg, std::vector values) {$/;" f class:ProtoMol::OneMollyPair make framework/forces/OneMollyPairTwo.h /^ static OneMollyPairTwo make(std::string& errMsg, std::vector values) {$/;" f class:ProtoMol::OneMollyPairTwo make framework/frontend/ForceFactoryDetails.cpp /^ Force* ForceFactoryDetails::make(string& errMsg, const string& id, vector values){$/;" f class:ProtoMol::ForceFactoryDetails make framework/frontend/IntegratorFactoryDetails.cpp /^ Integrator* IntegratorFactoryDetails::make(string& errMsg, const string& definition){$/;" f class:ProtoMol::IntegratorFactoryDetails make framework/frontend/Output.cpp /^ Output* Output::make(string& errMsg, const vector& values) const{$/;" f class:ProtoMol::Output make framework/frontend/OutputFactoryDetails.cpp /^ Output* OutputFactoryDetails::make(string& errMsg, const string& id, const vector& values){$/;" f class:ProtoMol::OutputFactoryDetails make framework/frontend/TopologyFactoryDetails.cpp /^ GenericTopology* TopologyFactoryDetails::make(string& errMsg, const Configuration* config){$/;" f class:ProtoMol::TopologyFactoryDetails make framework/frontend/TopologyFactoryDetails.cpp /^ GenericTopology* TopologyFactoryDetails::make(string& errMsg, const string& id, const vector& values){$/;" f class:ProtoMol::TopologyFactoryDetails make framework/integrators/MTSIntegrator.cpp /^ MTSIntegrator* MTSIntegrator::make(string& errMsg, const vector& values, ForceGroup* fg, StandardIntegrator *nextIntegrator)const{$/;" f class:ProtoMol::MTSIntegrator make framework/integrators/STSIntegrator.cpp /^ STSIntegrator* STSIntegrator::make(string& errMsg, const vector& values, ForceGroup* fg)const{$/;" f class:ProtoMol::STSIntegrator make framework/topology/C1SwitchingFunction.cpp /^ C1SwitchingFunction C1SwitchingFunction::make(string&, vector values) {$/;" f class:ProtoMol::C1SwitchingFunction make framework/topology/C2SwitchingFunction.cpp /^ C2SwitchingFunction C2SwitchingFunction::make(string& errMsg, vector values) {$/;" f class:ProtoMol::C2SwitchingFunction make framework/topology/CmpCnCnSwitchingFunction.cpp /^ CmpCnCnSwitchingFunction CmpCnCnSwitchingFunction::make(string& errMsg, vector values) {$/;" f class:ProtoMol::CmpCnCnSwitchingFunction make framework/topology/CnSwitchingFunction.cpp /^ CnSwitchingFunction CnSwitchingFunction::make(string& errMsg, vector values) {$/;" f class:ProtoMol::CnSwitchingFunction make framework/topology/ComplementSwitchingFunction.h /^ static ComplementSwitchingFunction make(std::string& errMsg,std::vector values) {$/;" f class:ProtoMol::ComplementSwitchingFunction make framework/topology/CubicCellManager.cpp /^ CubicCellManager CubicCellManager::make(string& errMsg, vector values){$/;" f class:ProtoMol::CubicCellManager make framework/topology/CutoffSwitchingFunction.cpp /^ CutoffSwitchingFunction CutoffSwitchingFunction::make(string& , vector values) {$/;" f class:ProtoMol::CutoffSwitchingFunction make framework/topology/GenericTopology.cpp /^ GenericTopology* GenericTopology::make(string& errMsg, const vector& values)const{$/;" f class:ProtoMol::GenericTopology make framework/topology/PeriodicBoundaryConditions.cpp /^ PeriodicBoundaryConditions PeriodicBoundaryConditions::make(string& errMsg, vector values){$/;" f class:ProtoMol::PeriodicBoundaryConditions make framework/topology/RangeSwitchingFunction.h /^ RangeSwitchingFunction RangeSwitchingFunction::make(std::string& errMsg,std::vector values) {$/;" f class:ProtoMol::RangeSwitchingFunction make framework/topology/ShiftSwitchingFunction.cpp /^ ShiftSwitchingFunction ShiftSwitchingFunction::make(string& , vector values) {$/;" f class:ProtoMol::ShiftSwitchingFunction make framework/topology/UniversalSwitchingFunction.h /^ static UniversalSwitchingFunction make(std::string&, std::vector) {$/;" f class:ProtoMol::UniversalSwitchingFunction make framework/topology/VacuumBoundaryConditions.cpp /^ VacuumBoundaryConditions VacuumBoundaryConditions::make(string& , vector) {$/;" f class:ProtoMol::VacuumBoundaryConditions makeCollection framework/frontend/OutputFactoryDetails.cpp /^ OutputCollection* OutputFactoryDetails::makeCollection(string& errMsg, const Configuration* config){$/;" f class:ProtoMol::OutputFactoryDetails makeCompareForce framework/forces/ExtendedForce.cpp /^ CompareForce* ExtendedForce::makeCompareForce(Force* actualForce, CompareForce* compareForce) const{$/;" f class:ProtoMol::ExtendedForce makeCompareForce framework/forces/Force.cpp /^ CompareForce* Force::makeCompareForce(Force* actualForce, CompareForce* compareForce) const{$/;" f class:ProtoMol::Force makeCompareForce framework/forces/SystemForce.cpp /^ CompareForce* SystemForce::makeCompareForce(Force* actualForce, CompareForce* compareForce) const{$/;" f class:ProtoMol::SystemForce makeTimeForce framework/forces/ExtendedForce.cpp /^ TimeForce* ExtendedForce::makeTimeForce(Force* actualForce) const{$/;" f class:ProtoMol::ExtendedForce makeTimeForce framework/forces/Force.cpp /^ TimeForce* Force::makeTimeForce(Force* actualForce) const{$/;" f class:ProtoMol::Force makeTimeForce framework/forces/SystemForce.cpp /^ TimeForce* SystemForce::makeTimeForce(Force* actualForce) const{$/;" f class:ProtoMol::SystemForce mass framework/base/AtomType.h /^ Real mass; \/\/\/< The mass of this atom type.$/;" m struct:ProtoMol::AtomType mass framework/base/Molecule.h /^ Real mass;$/;" m struct:ProtoMol::Molecule mass framework/base/PSF.h /^ Real mass; \/\/\/< mass [amu]$/;" m struct:ProtoMol::PSF::Atom mass framework/frontend/OutputCache.cpp /^ Real OutputCache::mass() const{$/;" f class:ProtoMol::OutputCache master framework/parallel/Parallel-FD.cpp /^ static const int master = 0;$/;" v file: master framework/parallel/Parallel.cpp /^ static const int master = 0;$/;" v file: max framework/base/fft.c 31;" d file: max framework/base/mathutilities.h /^ inline T max(const T& a, const T& b, const T& c){ $/;" f namespace:ProtoMol max framework/base/mathutilities.h /^ inline T max(const T& a, const T& b, const T& c, const T& d) {$/;" f namespace:ProtoMol max framework/topology/GenericTopology.h /^ mutable Vector3D max;$/;" m class:ProtoMol::GenericTopology maxGDim framework/integrators/EquilibriumMOLLYIntegrator.h /^ enum { maxGDim=4};$/;" e enum:ProtoMol::EquilibriumMOLLYIntegrator:: maxItems framework/base/mathutilities.h /^ unsigned int maxItems;$/;" m class:ProtoMol::WindowAve max_size framework/base/Vector3DBlock.h /^ size_type max_size() const {return vec.max_size();} $/;" f class:ProtoMol::Vector3DBlock mediForceModify framework/integrators/Integrator.cpp /^ void Integrator::mediForceModify(){$/;" f class:ProtoMol::Integrator mergeString framework/base/stringutilities.cpp /^ string mergeString(const vector& id){$/;" f namespace:ProtoMol metropolisTest framework/integrators/DihedralHMCIntegrator.cpp /^ bool DihedralHMCIntegrator::metropolisTest(Real newEnergy, Real oldEnergy, Real theTemperature, Real &acceptProb) {$/;" f class:ProtoMol::DihedralHMCIntegrator metropolisTest framework/integrators/MCIntegrator.cpp /^ bool MCIntegrator::metropolisTest( Real newValue, Real oldValue ) {$/;" f class:ProtoMol::MCIntegrator metropolisTest framework/integrators/MCIntegrator.cpp /^ bool MCIntegrator::metropolisTest( Real newValue, Real oldValue,$/;" f class:ProtoMol::MCIntegrator metropolisTest framework/integrators/MCIntegrator.cpp /^ bool MCIntegrator::metropolisTest() {$/;" f class:ProtoMol::MCIntegrator min framework/base/fft.c 28;" d file: min framework/base/mathutilities.h /^ inline T min(const T& a, const T& b, const T& c){ $/;" f namespace:ProtoMol min framework/base/mathutilities.h /^ inline T min(const T& a, const T& b, const T& c, const T& d) {$/;" f namespace:ProtoMol min framework/topology/GenericTopology.h /^ mutable Vector3D min;$/;" m class:ProtoMol::GenericTopology minimalDifference framework/topology/PeriodicBoundaryConditions.h /^ Vector3D minimalDifference(const Vector3D &c1, const Vector3D &c2) const{$/;" f class:ProtoMol::PeriodicBoundaryConditions minimalDifference framework/topology/PeriodicBoundaryConditions.h /^ Vector3D minimalDifference(const Vector3D &c1, const Vector3D &c2, Real& distSquared) const{$/;" f class:ProtoMol::PeriodicBoundaryConditions minimalDifference framework/topology/SemiGenericTopology.h /^ virtual Vector3D minimalDifference(const Vector3D &c1, const Vector3D &c2) const{ return boundaryConditions.minimalDifference(c1,c2); }$/;" f class:ProtoMol::SemiGenericTopology minimalDifference framework/topology/VacuumBoundaryConditions.h /^ Vector3D minimalDifference(const Vector3D &c1, const Vector3D &c2) const {Vector3D diff(c2); diff -= c1; return diff; }$/;" f class:ProtoMol::VacuumBoundaryConditions minimalDifference framework/topology/VacuumBoundaryConditions.h /^ Vector3D minimalDifference(const Vector3D &c1, const Vector3D &c2, Real& distSquared) const{Vector3D diff(c2); diff -= c1;distSquared = diff.normSquared(); return diff;}$/;" f class:ProtoMol::VacuumBoundaryConditions minimalImage framework/topology/SemiGenericTopology.h /^ virtual void minimalImage(Vector3DBlock& positions){$/;" f class:ProtoMol::SemiGenericTopology minimalMolecularDistances framework/topology/GenericTopology.h /^ bool minimalMolecularDistances;$/;" m class:ProtoMol::GenericTopology minimalPosition framework/topology/PeriodicBoundaryConditions.h /^ Vector3D minimalPosition(const Vector3D &c) const{$/;" f class:ProtoMol::PeriodicBoundaryConditions minimalPosition framework/topology/SemiGenericTopology.h /^ virtual Vector3D minimalPosition(const Vector3D &c) const{ return Vector3D(boundaryConditions.minimalPosition(c)); }$/;" f class:ProtoMol::SemiGenericTopology minimalPosition framework/topology/VacuumBoundaryConditions.h /^ Vector3D minimalPosition(const Vector3D &c) const {return c;}$/;" f class:ProtoMol::VacuumBoundaryConditions minimalPositions framework/frontend/OutputCache.cpp /^ const Vector3DBlock* OutputCache::minimalPositions() const{$/;" f class:ProtoMol::OutputCache minimalTranslationDifference framework/topology/PeriodicBoundaryConditions.h /^ Vector3D minimalTranslationDifference(const Vector3D & c1, const Vector3D &c2) const {$/;" f class:ProtoMol::PeriodicBoundaryConditions minimalTranslationDifference framework/topology/VacuumBoundaryConditions.h /^ Vector3D minimalTranslationDifference(const Vector3D &, const Vector3D &) const {return Vector3D(0.0,0.0,0.0); }$/;" f class:ProtoMol::VacuumBoundaryConditions minimalTranslationPosition framework/topology/PeriodicBoundaryConditions.h /^ Vector3D minimalTranslationPosition(const Vector3D &c) const {$/;" f class:ProtoMol::PeriodicBoundaryConditions minimalTranslationPosition framework/topology/VacuumBoundaryConditions.h /^ Vector3D minimalTranslationPosition(const Vector3D &) const {return Vector3D(0.0,0.0,0.0); }$/;" f class:ProtoMol::VacuumBoundaryConditions mode framework/base/sstream_local.h /^ ios::open_mode mode;$/;" m class:std::stringbuf molecularCenterOfMass framework/topology/topologyutilities.cpp /^ Vector3D molecularCenterOfMass(const vector &atomList, $/;" f namespace:ProtoMol molecularKineticEnergy framework/frontend/OutputCache.cpp /^ Real OutputCache::molecularKineticEnergy() const{$/;" f class:ProtoMol::OutputCache molecularKineticEnergy framework/topology/topologyutilities.cpp /^ Real molecularKineticEnergy(const GenericTopology* topology,$/;" f namespace:ProtoMol molecularMomentum framework/topology/topologyutilities.cpp /^ Vector3D molecularMomentum(const vector &atomList, $/;" f namespace:ProtoMol molecularPressure framework/base/ScalarStructure.h /^ inline Real ScalarStructure::molecularPressure(Real volume) const {$/;" f class:ProtoMol::ScalarStructure molecularPressure framework/frontend/OutputCache.cpp /^ Real OutputCache::molecularPressure() const{$/;" f class:ProtoMol::OutputCache molecularTemperature framework/frontend/OutputCache.cpp /^ Real OutputCache::molecularTemperature() const{$/;" f class:ProtoMol::OutputCache molecularVirial framework/base/ScalarStructure.cpp /^ bool ScalarStructure::molecularVirial(bool doMolecularVirial){$/;" f class:ProtoMol::ScalarStructure molecularVirial framework/base/ScalarStructure.h /^ bool molecularVirial() const {return myDoMolecularVirial;}$/;" f class:ProtoMol::ScalarStructure molecule framework/base/Atom.h /^ int molecule;$/;" m struct:ProtoMol::Atom molecules framework/topology/GenericTopology.h /^ std::vector molecules; $/;" m class:ProtoMol::GenericTopology mollification framework/integrators/MOLLYIntegrator.cpp /^ void MOLLYIntegrator::mollification(){$/;" f class:ProtoMol::MOLLYIntegrator momentum framework/base/Molecule.h /^ Vector3D momentum;$/;" m struct:ProtoMol::Molecule mpiAbort framework/parallel/Parallel-FD.cpp /^ void mpiAbort(){$/;" f namespace:ProtoMol mpiAbort framework/parallel/Parallel.cpp /^ void mpiAbort(){$/;" f namespace:ProtoMol mpiEndSerial framework/parallel/Parallel-FD.cpp /^ void mpiEndSerial(bool exludeMaster){$/;" f namespace:ProtoMol mpiEndSerial framework/parallel/Parallel.cpp /^ void mpiEndSerial(bool exludeMaster){$/;" f namespace:ProtoMol mpiExit framework/parallel/Parallel-FD.cpp /^ void mpiExit(){$/;" f namespace:ProtoMol mpiExit framework/parallel/Parallel.cpp /^ void mpiExit(){$/;" f namespace:ProtoMol mpiStartSerial framework/parallel/Parallel-FD.cpp /^ void mpiStartSerial(bool exludeMaster){$/;" f namespace:ProtoMol mpiStartSerial framework/parallel/Parallel.cpp /^ void mpiStartSerial(bool exludeMaster){$/;" f namespace:ProtoMol multiplicity framework/base/PAR.h /^ int multiplicity; \/\/\/< multiplicity$/;" m struct:ProtoMol::PAR::Dihedral multiplicity framework/topology/Torsion.h /^ int multiplicity; \/\/\/< The number of terms describing the potential energy of this torsion.$/;" m class:ProtoMol::Torsion multiply framework/base/Vector3D.h /^ Vector3D multiply(Real w) const {return (*this)*w;}$/;" f struct:ProtoMol::Vector3D my05Cutoff_3 framework/topology/C1SwitchingFunction.h /^ Real myCutoff, myCutoff2, myCutoff_3, my15Cutoff_1,my05Cutoff_3,my15Cutoff_3;$/;" m class:ProtoMol::C1SwitchingFunction my15Cutoff_1 framework/topology/C1SwitchingFunction.h /^ Real myCutoff, myCutoff2, myCutoff_3, my15Cutoff_1,my05Cutoff_3,my15Cutoff_3;$/;" m class:ProtoMol::C1SwitchingFunction my15Cutoff_3 framework/topology/C1SwitchingFunction.h /^ Real myCutoff, myCutoff2, myCutoff_3, my15Cutoff_1,my05Cutoff_3,my15Cutoff_3;$/;" m class:ProtoMol::C1SwitchingFunction my2AlphaPI framework/forces/CoulombEwaldRealForce.h /^ Real my2AlphaPI;$/;" m class:ProtoMol::CoulombEwaldRealForce my2AlphaPI framework/forces/NonbondedFullEwaldSystemForce.h /^ Real my2AlphaPI;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce my2AlphaPI framework/forces/NonbondedPMEwaldSystemForce.h /^ Real my2AlphaPI;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce my4Cutoff_2 framework/topology/ShiftSwitchingFunction.h /^ Real my4Cutoff_2;$/;" m class:ProtoMol::ShiftSwitchingFunction myA framework/forces/ElectricFieldSystemForce.h /^ Real myA;$/;" m class:ProtoMol::ElectricFieldSystemForce myA framework/forces/PaulTrapExtendedForce.h /^ Real myA;$/;" m class:ProtoMol::PaulTrapExtendedForce myAbort framework/base/Report.h /^ bool myAbort;$/;" m class:ProtoMol::Report::MyStreamer myAbortFunction framework/base/systemutilities.cpp /^ static void (*myAbortFunction)() = NULL;$/;" v file: myAccuracy framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myAccuracy;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myAccuracy framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myAccuracy;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myActualForce framework/forces/CompareForce.h /^ Force* myActualForce;$/;" m class:ProtoMol::CompareForce myActualForce framework/forces/TimeForce.h /^ Force* myActualForce;$/;" m class:ProtoMol::TimeForce myAlias framework/base/Makeable.h /^ std::string myAlias;$/;" m class:ProtoMol::Makeable myAliasExemplars framework/frontend/Factory.h /^ std::map myAliasExemplars; $/;" m class:ProtoMol::FactoryBase myAliases framework/base/Configuration.h /^ AliasMapType myAliases;$/;" m class:ProtoMol::Configuration myAlign framework/base/LookUpTableBase.h /^ unsigned int myAlign;$/;" m class:ProtoMol::LookUpTableBase myAllNodes framework/base/Report.h /^ bool myAllNodes;$/;" m class:ProtoMol::Report::MyStreamer myAllNodesSerial framework/base/Report.h /^ bool myAllNodesSerial;$/;" m class:ProtoMol::Report::MyStreamer myAllSlavesSerial framework/base/Report.h /^ bool myAllSlavesSerial;$/;" m class:ProtoMol::Report::MyStreamer myAlpha framework/base/Grid.h /^ Real myAlpha;$/;" m class:ProtoMol::Grid myAlpha framework/forces/CoulombEwaldRealForce.h /^ Real myAlpha;$/;" m class:ProtoMol::CoulombEwaldRealForce myAlpha framework/forces/CoulombEwaldRealTableForce.h /^ Real myAlpha;$/;" m class:ProtoMol::CoulombEwaldRealTableForce myAlpha framework/forces/CoulombEwaldRealTableForceBase.h /^ Real myAlpha;$/;" m class:ProtoMol::CoulombEwaldRealTableForceBase::LookUpValues myAlpha framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myAlpha; \/\/ $/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myAlpha framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myAlpha; \/\/ $/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myAlpha framework/forces/PaulTrapExtendedForce.h /^ Real myAlpha;$/;" m class:ProtoMol::PaulTrapExtendedForce myAlphaDefault framework/forces/NonbondedFullEwaldSystemForce.h /^ bool myAlphaDefault;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myAlphaDefault framework/forces/NonbondedPMEwaldSystemForce.h /^ bool myAlphaDefault;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myAlphaR04 framework/forces/PaulTrapExtendedForce.h /^ Real myAlphaR04;$/;" m class:ProtoMol::PaulTrapExtendedForce myAlphaSquared framework/forces/CoulombEwaldRealForce.h /^ Real myAlphaSquared;$/;" m class:ProtoMol::CoulombEwaldRealForce myAlphaSquared framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myAlphaSquared;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myAlphaSquared framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myAlphaSquared;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myAlphaSquaredr framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myAlphaSquaredr;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myAlphaSquaredr framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myAlphaSquaredr;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myAngle framework/integrators/BSplineMOLLYIntegrator.h /^ bool myAngle;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myAngleFilter framework/forces/OneMollyPair.h /^ std::vector< ReducedHessAngle > *myAngleFilter;$/;" m class:ProtoMol::OneMollyPair myAngleFilter framework/forces/OneMollyPairTwo.h /^ std::vector< ReducedHessAngle > *myAngleFilter;$/;" m class:ProtoMol::OneMollyPairTwo myAngleFilter framework/integrators/BSplineMOLLYIntegrator.h /^ std::vector *myAngleFilter; $/;" m class:ProtoMol::BSplineMOLLYIntegrator myAngleIndexes framework/integrators/BSplineMOLLYIntegrator.h /^ std::vector myAngleIndexes;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myAngles framework/integrators/DihedralHMCIntegrator.h /^ std::vector< Real >* myAngles;$/;" m class:ProtoMol::DihedralHMCIntegrator myAnglesSet framework/integrators/DihedralHMCIntegrator.h /^ bool myAnglesSet; $/;" m class:ProtoMol::DihedralHMCIntegrator myAngularMomentum framework/frontend/OutputCache.h /^ mutable Vector3D myAngularMomentum;$/;" m class:ProtoMol::OutputCache myArray framework/base/FFTComplex.cpp /^ zomplex* myArray;$/;" m class:ProtoMol::FFTInternal file: myArray framework/topology/ArrayCellListStructure.h /^ TContainer myArray;$/;" m class:ProtoMol::ArrayCellListStructure myAtomCount framework/base/Grid.h /^ unsigned int myAtomCount;$/;" m class:ProtoMol::Grid myAtomTypes framework/io/XYZTrajectoryWriter.h /^ const std::vector* myAtomTypes;$/;" m class:ProtoMol::XYZTrajectoryWriter myAtoms framework/frontend/OutputCache.h /^ std::vector myAtoms;$/;" m class:ProtoMol::OutputCache myAtoms framework/io/PDBReader.h /^ std::vector* myAtoms;$/;" m class:ProtoMol::PDBReader myAtoms framework/io/XYZTrajectoryWriter.h /^ const std::vector* myAtoms;$/;" m class:ProtoMol::XYZTrajectoryWriter myAutofit framework/io/XFigWriter.h /^ bool myAutofit;$/;" m class:ProtoMol::XFigWriter myAvailableId framework/parallel/Parallel-FD.cpp /^ int Parallel::myAvailableId = 0;$/;" m class:ProtoMol::Parallel file: myAvailableId framework/parallel/Parallel.cpp /^ int Parallel::myAvailableId = 0;$/;" m class:ProtoMol::Parallel file: myAvailableId framework/parallel/Parallel.h /^ static int myAvailableId; \/\/\/< Actual master-slave id, -1 for the master$/;" m class:ProtoMol::Parallel myAvailableNum framework/parallel/Parallel-FD.cpp /^ int Parallel::myAvailableNum = 1;$/;" m class:ProtoMol::Parallel file: myAvailableNum framework/parallel/Parallel.cpp /^ int Parallel::myAvailableNum = 1;$/;" m class:ProtoMol::Parallel file: myAvailableNum framework/parallel/Parallel.h /^ static int myAvailableNum; \/\/\/< Available number of nodes for computation$/;" m class:ProtoMol::Parallel myAveragedPositions framework/integrators/EquilibriumMOLLYIntegrator.h /^ Vector3DBlock* myAveragedPositions;$/;" m class:ProtoMol::EquilibriumMOLLYIntegrator myAxes framework/io/XFigWriter.h /^ bool myAxes;$/;" m class:ProtoMol::XFigWriter myB framework/forces/ExternalMagneticFieldExtendedForce.h /^ Vector3D myB;$/;" m class:ProtoMol::ExternalMagneticFieldExtendedForce myB framework/integrators/BSplineMOLLYIntegrator.h /^ Vector3DBlock *myB;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myBathPosition framework/integrators/NoseNVTLeapfrogIntegrator.h /^ Real myBathPosition;$/;" m class:ProtoMol::NoseNVTLeapfrogIntegrator myBathPosition framework/integrators/PaulTrapIntegrator.h /^ Real myBathPosition;$/;" m class:ProtoMol::PaulTrapIntegrator myBathVelocity framework/integrators/PaulTrapIntegrator.h /^ Real myBathVelocity;$/;" m class:ProtoMol::PaulTrapIntegrator myBegin framework/topology/ArrayCellListStructure.h /^ iterator myBegin,myEnd;$/;" m class:ProtoMol::ArrayCellListStructure myBeginConst framework/topology/ArrayCellListStructure.h /^ const_iterator myBeginConst,myEndConst;$/;" m class:ProtoMol::ArrayCellListStructure myBeta framework/integrators/Integrator.cpp /^ Real Integrator::myBeta = 0.;$/;" m class:ProtoMol::Integrator file: myBeta framework/integrators/Integrator.h /^ static Real myBeta;$/;" m class:ProtoMol::Integrator myBeta framework/integrators/ModifierShadow.h /^ Real & myBeta;$/;" m class:ProtoMol::ModifierShadow myBlockList framework/parallel/Parallel-FD.cpp /^ vector Parallel::myBlockList;$/;" m class:ProtoMol::Parallel file: myBlockList framework/parallel/Parallel.cpp /^ vector Parallel::myBlockList;$/;" m class:ProtoMol::Parallel file: myBlockList framework/parallel/Parallel.h /^ static std::vector myBlockList; \/\/\/< List of of the force partitioning$/;" m class:ProtoMol::Parallel myBlockSize framework/forces/NonbondedFullSystemForce.h /^ unsigned int myBlockSize;$/;" m class:ProtoMol::NonbondedFullSystemForce myBlockSize framework/forces/NonbondedSimpleFullSystemForce.h /^ unsigned int myBlockSize;$/;" m class:ProtoMol::NonbondedSimpleFullSystemForce myBlocksCorrection framework/base/MultiGrid.h /^ std::vector > myBlocksCorrection; \/\/\/< List of blocks for the correction$/;" m class:ProtoMol::MultiGrid myBond framework/integrators/BSplineMOLLYIntegrator.h /^ bool myBond;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myBrentMaxima framework/frontend/OutputCache.h /^ mutable std::vector< std::vector< Real > >* myBrentMaxima;$/;" m class:ProtoMol::OutputCache myBuffer framework/frontend/OutputFile.h /^ std::stringstream myBuffer;$/;" m class:ProtoMol::OutputFile myBuffer framework/parallel/Parallel-FD.cpp /^ int* Parallel::myBuffer = NULL;$/;" m class:ProtoMol::Parallel file: myBuffer framework/parallel/Parallel.cpp /^ int* Parallel::myBuffer = NULL;$/;" m class:ProtoMol::Parallel file: myBuffer framework/parallel/Parallel.h /^ static int* myBuffer; \/\/\/< Bsend buffer$/;" m class:ProtoMol::Parallel myBxAngle framework/integrators/BSplineMOLLYIntegrator.h /^ std::vector *myBxAngle;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myC framework/forces/ElectricFieldSystemForce.h /^ Real myC;$/;" m class:ProtoMol::ElectricFieldSystemForce myC framework/integrators/ShadowHMCIntegrator.h /^ Real myC,$/;" m class:ProtoMol::ShadowHMCIntegrator myCMax framework/base/MultiGrid.h /^ Vector3D myCMax; \/\/ $/;" m class:ProtoMol::MultiGrid myCMin framework/base/MultiGrid.h /^ Vector3D myCMin; \/\/ $/;" m class:ProtoMol::MultiGrid myCache framework/frontend/Factory.h /^ mutable bool myCache;$/;" m class:ProtoMol::FactoryBase myCache framework/frontend/Output.h /^ const OutputCache* myCache; \/\/\/< Pointer to the shared cache object $/;" m class:ProtoMol::Output myCache framework/frontend/OutputCollection.h /^ OutputCache* myCache;$/;" m class:ProtoMol::OutputCollection myCacheFreq framework/frontend/OutputFile.h /^ int myCacheFreq;$/;" m class:ProtoMol::OutputFile myCacheSize framework/frontend/OutputFile.h /^ int myCacheSize;$/;" m class:ProtoMol::OutputFile myCached framework/forces/NonbondedFullEwaldSystemForce.h /^ bool myCached;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myCached framework/forces/NonbondedFullSystemForce.h /^ bool myCached;$/;" m class:ProtoMol::NonbondedFullSystemForce myCached framework/forces/NonbondedMultiGridSystemForce.h /^ bool myCached;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myCached framework/forces/NonbondedPMEwaldSystemForce.h /^ bool myCached;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myCached framework/forces/NonbondedSimpleFullSystemForce.h /^ bool myCached;$/;" m class:ProtoMol::NonbondedSimpleFullSystemForce myCached framework/forces/PaulTrapExtendedForce.h /^ bool myCached;$/;" m class:ProtoMol::PaulTrapExtendedForce myCached framework/imd/HapticSystemForce.h /^ bool myCached;$/;" m class:ProtoMol::HapticSystemForce myCached framework/integrators/BSplineMOLLYIntegrator.h /^ bool myCached;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myCached framework/integrators/PaulTrapIntegrator.h /^ bool myCached;$/;" m class:ProtoMol::PaulTrapIntegrator myCachedAngularMomentum framework/frontend/OutputCache.h /^ mutable bool myCachedAngularMomentum;$/;" m class:ProtoMol::OutputCache myCachedBrentMaxima framework/frontend/OutputCache.h /^ mutable bool myCachedBrentMaxima;$/;" m class:ProtoMol::OutputCache myCachedCenterOfMass framework/frontend/OutputCache.h /^ mutable bool myCachedCenterOfMass;$/;" m class:ProtoMol::OutputCache myCachedDensity framework/frontend/OutputCache.h /^ mutable bool myCachedDensity;$/;" m class:ProtoMol::OutputCache myCachedDiffusion framework/frontend/OutputCache.h /^ mutable bool myCachedDiffusion;$/;" m class:ProtoMol::OutputCache myCachedDihedralPhi framework/frontend/OutputCache.h /^ mutable int myCachedDihedralPhi;$/;" m class:ProtoMol::OutputCache myCachedDihedralPhis framework/frontend/OutputCache.h /^ mutable bool myCachedDihedralPhis;$/;" m class:ProtoMol::OutputCache myCachedKE framework/frontend/OutputCache.h /^ mutable bool myCachedKE;$/;" m class:ProtoMol::OutputCache myCachedLinearMomentum framework/frontend/OutputCache.h /^ mutable bool myCachedLinearMomentum;$/;" m class:ProtoMol::OutputCache myCachedMass framework/frontend/OutputCache.h /^ mutable bool myCachedMass;$/;" m class:ProtoMol::OutputCache myCachedMinimalPositions framework/frontend/OutputCache.h /^ mutable bool myCachedMinimalPositions;$/;" m class:ProtoMol::OutputCache myCachedMolKE framework/frontend/OutputCache.h /^ mutable bool myCachedMolKE;$/;" m class:ProtoMol::OutputCache myCachedMolP framework/frontend/OutputCache.h /^ mutable bool myCachedMolP;$/;" m class:ProtoMol::OutputCache myCachedMolT framework/frontend/OutputCache.h /^ mutable bool myCachedMolT;$/;" m class:ProtoMol::OutputCache myCachedNonWaterT framework/frontend/OutputCache.h /^ mutable bool myCachedNonWaterT;$/;" m class:ProtoMol::OutputCache myCachedP framework/frontend/OutputCache.h /^ mutable bool myCachedP;$/;" m class:ProtoMol::OutputCache myCachedPE framework/frontend/OutputCache.h /^ mutable bool myCachedPE;$/;" m class:ProtoMol::OutputCache myCachedV framework/frontend/OutputCache.h /^ mutable bool myCachedV;$/;" m class:ProtoMol::OutputCache myCachedWaterT framework/frontend/OutputCache.h /^ mutable bool myCachedWaterT;$/;" m class:ProtoMol::OutputCache myCellListStruct framework/topology/CellListEnumerator_periodicBoundaries.h /^ const CubicCellManager::CellListStructure *myCellListStruct;$/;" m class:ProtoMol::CellListEnumerator myCellListStruct framework/topology/CellListEnumerator_standard.h /^ const CubicCellManager::CellListStructure *myCellListStruct;$/;" m class:ProtoMol::CellListEnumerator myCellSize framework/topology/ArrayCellListStructure.h /^ Vector3D myCellSize;$/;" m class:ProtoMol::ArrayCellListStructure myCellSize framework/topology/CellListEnumerator_periodicBoundaries.h /^ Vector3D myCellSize; $/;" m class:ProtoMol::CellListEnumerator myCellSize framework/topology/CellListEnumerator_standard.h /^ Vector3D myCellSize; $/;" m class:ProtoMol::CellListEnumerator myCellSize framework/topology/CubicCellManager.h /^ Real myCellSize;$/;" m class:ProtoMol::CubicCellManager myCenter framework/forces/SphericalSystemForce.h /^ Vector3D myCenter;$/;" m class:ProtoMol::SphericalSystemForce myCenter framework/imd/HapticSystemForce.h /^ Vector3D myCenter;$/;" m class:ProtoMol::HapticSystemForce myCenterOfMass framework/frontend/OutputCache.h /^ mutable Vector3D myCenterOfMass;$/;" m class:ProtoMol::OutputCache myChargedSystemEnergy framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myChargedSystemEnergy;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myChargedSystemEnergy framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myChargedSystemEnergy;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myCharmmType framework/io/AMBERReader.h /^ PAR::CharmmTypeEnum myCharmmType;$/;" m class:ProtoMol::AMBERReader myCharmmType framework/io/PARReader.h /^ PAR::CharmmTypeEnum myCharmmType;$/;" m class:ProtoMol::PARReader myCharmmType framework/io/PARWriter.h /^ PAR::CharmmTypeEnum myCharmmType;$/;" m class:ProtoMol::PARWriter myCharmmTypeDetected framework/io/AMBERReader.h /^ PAR::CharmmTypeEnum myCharmmTypeDetected;$/;" m class:ProtoMol::AMBERReader myCharmmTypeDetected framework/io/PARReader.h /^ PAR::CharmmTypeEnum myCharmmTypeDetected;$/;" m class:ProtoMol::PARReader myChi framework/forces/MagneticDipoleForce.h /^ Real myChi, myR, myOmega, myPhi, myHx, myHy, myHz, myD;$/;" m class:ProtoMol::MagneticDipoleForce myChi framework/forces/MagneticDipoleMirrorSystemForce.h /^ Real myChi, myR, myD, myHx, myHy, myHz, myF;$/;" m class:ProtoMol::MagneticDipoleMirrorSystemForce myCloseTime framework/frontend/OutputFile.h /^ Real myCloseTime;$/;" m class:ProtoMol::OutputFile myColor framework/io/XFigWriter.h /^ bool myColor;$/;" m class:ProtoMol::XFigWriter myColortable framework/frontend/OutputBSDL.h /^ std::map myColortable;$/;" m class:ProtoMol::OutputBSDL myComment framework/io/File.h /^ std::string myComment; \/\/ Reader has get and Writer has set method$/;" m class:ProtoMol::File myCompareForce framework/forces/CompareForce.h /^ CompareForce* myCompareForce;$/;" m class:ProtoMol::CompareForce myCompareForcename framework/forces/CompareForce.h /^ std::string myCompareForcename;$/;" m class:ProtoMol::CompareForce myCompoff framework/topology/CmpCnCnSwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, myCompoff, myCompoff2, myOrder;$/;" m class:ProtoMol::CmpCnCnSwitchingFunction myCompoff2 framework/topology/CmpCnCnSwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, myCompoff, myCompoff2, myOrder;$/;" m class:ProtoMol::CmpCnCnSwitchingFunction myConfig framework/frontend/Output.h /^ const Configuration* myConfig; $/;" m class:ProtoMol::Output myConfig framework/frontend/OutputCache.h /^ const Configuration* myConfig; $/;" m class:ProtoMol::OutputCache myConfig framework/frontend/OutputCollection.h /^ const Configuration* myConfig; $/;" m class:ProtoMol::OutputCollection myConfig framework/io/ConfigurationReader.h /^ Configuration* myConfig;$/;" m class:ProtoMol::ConfigurationReader myConfig framework/io/REMConfigurationReader.h /^ Configuration* myConfig;$/;" m class:ProtoMol::REMConfigurationReader myConfig tools/rem/sequential/replica.h /^ string myConfig;$/;" m class:Replica myConfstrings framework/frontend/OutputDihedrals.h /^ std::set< std::string > myConfstrings;$/;" m class:ProtoMol::OutputDihedrals myCoords framework/io/CRDReader.h /^ Vector3DBlock* myCoords;$/;" m class:ProtoMol::CRDReader myCoords framework/io/DCDTrajectoryReader.h /^ Vector3DBlock* myCoords;$/;" m class:ProtoMol::DCDTrajectoryReader myCoords framework/io/PDBReader.h /^ Vector3DBlock* myCoords;$/;" m class:ProtoMol::PDBReader myCoords framework/io/XYZBinReader.h /^ Vector3DBlock* myCoords;$/;" m class:ProtoMol::XYZBinReader myCoords framework/io/XYZReader.h /^ Vector3DBlock* myCoords;$/;" m class:ProtoMol::XYZReader myCoords framework/io/XYZTrajectoryReader.h /^ Vector3DBlock* myCoords;$/;" m class:ProtoMol::XYZTrajectoryReader myCoords framework/io/XYZTrajectoryWriter.h /^ const Vector3DBlock* myCoords;$/;" m class:ProtoMol::XYZTrajectoryWriter myCoulomb framework/integrators/BSplineMOLLYIntegrator.h /^ bool myCoulomb;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myCount framework/base/Proxy.h /^ mutable int myCount;$/;" m class:ProtoMol::Proxy myCount framework/frontend/OutputFile.h /^ int myCount;$/;" m class:ProtoMol::OutputFile myCount framework/integrators/PaulTrapIntegrator.h /^ unsigned int myCount;$/;" m class:ProtoMol::PaulTrapIntegrator myCounter framework/forces/CompareForce.cpp /^ unsigned int CompareForce::myCounter = 0;$/;" m class:ProtoMol::CompareForce file: myCounter framework/forces/CompareForce.h /^ static unsigned int myCounter;$/;" m class:ProtoMol::CompareForce myCounter framework/forces/TimeForce.cpp /^ unsigned int TimeForce::myCounter = 0;$/;" m class:ProtoMol::TimeForce file: myCounter framework/forces/TimeForce.h /^ static unsigned int myCounter;$/;" m class:ProtoMol::TimeForce myCounter framework/frontend/OutputBSDL.h /^ int myCounter;$/;" m class:ProtoMol::OutputBSDL myCounterCorrection framework/base/MultiGrid.h /^ long myCounterCorrection;$/;" m class:ProtoMol::MultiGrid myCounterCorrection framework/forces/NonbondedMultiGridSystemForce.h /^ long myCounterCorrection;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myCounterDirect framework/base/MultiGrid.h /^ long myCounterDirect;$/;" m class:ProtoMol::MultiGrid myCounterDirect framework/forces/NonbondedMultiGridSystemForce.h /^ long myCounterDirect;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myCurrentSize framework/topology/ExclusionTable.h /^ int myCurrentSize;$/;" m class:ProtoMol::ExclusionTable myCurrentSize framework/topology/LennardJonesParameterTable.h /^ int myCurrentSize;$/;" m class:ProtoMol::LennardJonesParameterTable myCutoff framework/forces/CoulombEwaldRealTableForce.h /^ Real myCutoff;$/;" m class:ProtoMol::CoulombEwaldRealTableForce myCutoff framework/forces/CoulombMultiGridDirectTableForce.h /^ Real myCutoff;$/;" m class:ProtoMol::CoulombMultiGridDirectTableForce myCutoff framework/forces/CoulombTableForce.h /^ Real myCutoff;$/;" m class:ProtoMol::CoulombTableForce myCutoff framework/forces/LennardJonesTableForce.h /^ Real myCutoff;$/;" m class:ProtoMol::LennardJonesTableForce myCutoff framework/forces/NonbondedCutoffForce.h /^ Real myCutoff;$/;" m class:ProtoMol::NonbondedCutoffForce myCutoff framework/forces/NonbondedFullSystemForce.h /^ Real myCutoff;$/;" m class:ProtoMol::NonbondedFullSystemForce myCutoff framework/topology/C1SwitchingFunction.h /^ Real myCutoff, myCutoff2, myCutoff_3, my15Cutoff_1,my05Cutoff_3,my15Cutoff_3;$/;" m class:ProtoMol::C1SwitchingFunction myCutoff framework/topology/C2SwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, mySwitch1, mySwitch2, mySwitch3;$/;" m class:ProtoMol::C2SwitchingFunction myCutoff framework/topology/CellListEnumerator_periodicBoundaries.h /^ Real myCutoff;$/;" m class:ProtoMol::CellListEnumerator myCutoff framework/topology/CellListEnumerator_standard.h /^ Real myCutoff;$/;" m class:ProtoMol::CellListEnumerator myCutoff framework/topology/CmpCnCnSwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, myCompoff, myCompoff2, myOrder;$/;" m class:ProtoMol::CmpCnCnSwitchingFunction myCutoff framework/topology/CnSwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, myOrder, mySwitchoff;$/;" m class:ProtoMol::CnSwitchingFunction myCutoff framework/topology/CutoffSwitchingFunction.h /^ Real myCutoff, myCutoff2;$/;" m class:ProtoMol::CutoffSwitchingFunction myCutoff framework/topology/ShiftSwitchingFunction.h /^ Real myCutoff;$/;" m class:ProtoMol::ShiftSwitchingFunction myCutoff2 framework/forces/CoulombEwaldRealTableForce.h /^ Real myCutoff2;$/;" m class:ProtoMol::CoulombEwaldRealTableForce myCutoff2 framework/forces/CoulombMultiGridDirectTableForce.h /^ Real myCutoff2;$/;" m class:ProtoMol::CoulombMultiGridDirectTableForce myCutoff2 framework/forces/CoulombTableForce.h /^ Real myCutoff2;$/;" m class:ProtoMol::CoulombTableForce myCutoff2 framework/forces/LennardJonesTableForce.h /^ Real myCutoff2;$/;" m class:ProtoMol::LennardJonesTableForce myCutoff2 framework/topology/C1SwitchingFunction.h /^ Real myCutoff, myCutoff2, myCutoff_3, my15Cutoff_1,my05Cutoff_3,my15Cutoff_3;$/;" m class:ProtoMol::C1SwitchingFunction myCutoff2 framework/topology/C2SwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, mySwitch1, mySwitch2, mySwitch3;$/;" m class:ProtoMol::C2SwitchingFunction myCutoff2 framework/topology/CmpCnCnSwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, myCompoff, myCompoff2, myOrder;$/;" m class:ProtoMol::CmpCnCnSwitchingFunction myCutoff2 framework/topology/CnSwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, myOrder, mySwitchoff;$/;" m class:ProtoMol::CnSwitchingFunction myCutoff2 framework/topology/CutoffSwitchingFunction.h /^ Real myCutoff, myCutoff2;$/;" m class:ProtoMol::CutoffSwitchingFunction myCutoff2 framework/topology/ShiftSwitchingFunction.h /^ Real myCutoff2;$/;" m class:ProtoMol::ShiftSwitchingFunction myCutoff_2 framework/topology/ShiftSwitchingFunction.h /^ Real myCutoff_2;$/;" m class:ProtoMol::ShiftSwitchingFunction myCutoff_3 framework/topology/C1SwitchingFunction.h /^ Real myCutoff, myCutoff2, myCutoff_3, my15Cutoff_1,my05Cutoff_3,my15Cutoff_3;$/;" m class:ProtoMol::C1SwitchingFunction myCycleLength framework/integrators/MTSIntegrator.h /^ const int myCycleLength;$/;" m class:ProtoMol::MTSIntegrator myD framework/forces/MagneticDipoleForce.h /^ Real myChi, myR, myOmega, myPhi, myHx, myHy, myHz, myD;$/;" m class:ProtoMol::MagneticDipoleForce myD framework/forces/MagneticDipoleMirrorSystemForce.h /^ Real myChi, myR, myD, myHx, myHy, myHz, myF;$/;" m class:ProtoMol::MagneticDipoleMirrorSystemForce myD framework/topology/PeriodicBoundaryConditions.h /^ Real myD; \/\/\/< maximal distance between two positions where plain subtraction if safe$/;" m class:ProtoMol::PeriodicBoundaryConditions myDCD framework/frontend/OutputDCDTrajectory.h /^ DCDTrajectoryWriter* myDCD;$/;" m class:ProtoMol::OutputDCDTrajectory myDCD framework/frontend/OutputDihedrals.h /^ DCDTrajectoryWriter* myDCD;$/;" m class:ProtoMol::OutputDihedrals myDX framework/topology/PeriodicBoundaryConditions.h /^ Real myDX;$/;" m class:ProtoMol::PeriodicBoundaryConditions myDY framework/topology/PeriodicBoundaryConditions.h /^ Real myDY;$/;" m class:ProtoMol::PeriodicBoundaryConditions myDZ framework/topology/PeriodicBoundaryConditions.h /^ Real myDZ;$/;" m class:ProtoMol::PeriodicBoundaryConditions myData framework/topology/LennardJonesParameterTable.h /^ LennardJonesParameters* myData;$/;" m class:ProtoMol::LennardJonesParameterTable myDeltaList framework/topology/CellListEnumerator_periodicBoundaries.h /^ std::vector myDeltaList;$/;" m class:ProtoMol::CellListEnumerator myDeltaList framework/topology/CellListEnumerator_standard.h /^ std::vector myDeltaList;$/;" m class:ProtoMol::CellListEnumerator myDensity framework/frontend/OutputCache.h /^ mutable Real myDensity;$/;" m class:ProtoMol::OutputCache myDhmcAnSetFile framework/integrators/DihedralHMCIntegrator.h /^ std::string myDhmcAnSetFile;$/;" m class:ProtoMol::DihedralHMCIntegrator myDhmcDiSetFile framework/integrators/DihedralHMCIntegrator.h /^ std::string myDhmcDiSetFile;$/;" m class:ProtoMol::DihedralHMCIntegrator myDiffusion framework/frontend/OutputCache.h /^ mutable Real myDiffusion;$/;" m class:ProtoMol::OutputCache myDihedral framework/forces/HarmDihedralSystemForce.h /^ int myDihedral;$/;" m class:ProtoMol::HarmDihedralSystemForce myDihedralFile tools/rem/sequential/replica.h /^ string myDihedralFile;$/;" m class:Replica myDihedralIndex framework/frontend/OutputDihedrals.h /^ int myDihedralIndex;$/;" m class:ProtoMol::OutputDihedrals myDihedralIndex framework/integrators/DihedralHMCIntegrator.h /^ int myDihedralIndex;$/;" m class:ProtoMol::DihedralHMCIntegrator myDihedralPhi framework/frontend/OutputCache.h /^ mutable Real myDihedralPhi;$/;" m class:ProtoMol::OutputCache myDihedralPhis framework/frontend/OutputCache.h /^ mutable std::vector* myDihedralPhis;$/;" m class:ProtoMol::OutputCache myDihedralReference framework/forces/HarmDihedralSystemForce.h /^ Real myDihedralReference;$/;" m class:ProtoMol::HarmDihedralSystemForce myDihedralSetFile tools/rem/sequential/replica.h /^ string myDihedralSetFile;$/;" m class:Replica myDihedrals framework/frontend/OutputDihedrals.h /^ std::vector< int > myDihedrals;$/;" m class:ProtoMol::OutputDihedrals myDihedrals framework/integrators/DihedralHMCIntegrator.h /^ std::vector< int >* myDihedrals;$/;" m class:ProtoMol::DihedralHMCIntegrator myDihedralsSet framework/frontend/OutputDihedrals.h /^ bool myDihedralsSet;$/;" m class:ProtoMol::OutputDihedrals myDihedralsSet framework/integrators/DihedralHMCIntegrator.h /^ bool myDihedralsSet;$/;" m class:ProtoMol::DihedralHMCIntegrator myDihedralsSetfile framework/frontend/OutputDihedrals.h /^ std::string myDihedralsSetfile;$/;" m class:ProtoMol::OutputDihedrals myDim framework/base/MultiGrid.h /^ std::vector myDim; \/\/\/< Dimension of the grids$/;" m class:ProtoMol::MultiGrid myDir tools/rem/sequential/replica.h /^ string myDir;$/;" m class:Replica myDissipativeCutoff framework/integrators/DMDLeapfrogIntegrator.h /^ Real myDissipativeCutoff;$/;" m class:ProtoMol::DMDLeapfrogIntegrator myDissipativeForces framework/integrators/DMDLeapfrogIntegrator.h /^ Vector3DBlock *myDissipativeForces;$/;" m class:ProtoMol::DMDLeapfrogIntegrator myDoHint framework/base/Report.h /^ bool myDoHint;$/;" m class:ProtoMol::Report::MyStreamer myDoMolecularTemperature framework/frontend/OutputEnergies.h /^ bool myDoMolecularTemperature;$/;" m class:ProtoMol::OutputEnergies myDoMolecularVirial framework/base/ScalarStructure.h /^ bool myDoMolecularVirial;$/;" m class:ProtoMol::ScalarStructure myDoOutput framework/base/ScalarStructure.h /^ bool myDoOutput;$/;" m class:ProtoMol::ScalarStructure myDoPaulLow framework/frontend/OutputPaulTrap.h /^ bool myDoPaulLow;$/;" m class:ProtoMol::OutputPaulTrap myDoShadow framework/frontend/OutputEnergies.h /^ bool myDoShadow;$/;" m class:ProtoMol::OutputEnergies myDoTrajectory framework/base/ScalarStructure.h /^ bool myDoTrajectory;$/;" m class:ProtoMol::ScalarStructure myDoVirial framework/base/ScalarStructure.h /^ bool myDoVirial;$/;" m class:ProtoMol::ScalarStructure myDone framework/parallel/Parallel-FD.cpp /^ vector Parallel::myDone;$/;" m class:ProtoMol::Parallel file: myDone framework/parallel/Parallel.cpp /^ vector Parallel::myDone;$/;" m class:ProtoMol::Parallel file: myDone framework/parallel/Parallel.h /^ static std::vector myDone; \/\/\/< Master, keeps track of slave have got already their work$/;" m class:ProtoMol::Parallel myE framework/forces/ElectricFieldSystemForce.h /^ Real myE;$/;" m class:ProtoMol::ElectricFieldSystemForce myE1 framework/topology/PeriodicBoundaryConditions.h /^ Vector3D myE1;$/;" m class:ProtoMol::PeriodicBoundaryConditions myE1r framework/topology/PeriodicBoundaryConditions.h /^ Vector3D myE1r;$/;" m class:ProtoMol::PeriodicBoundaryConditions myE2 framework/topology/PeriodicBoundaryConditions.h /^ Vector3D myE2;$/;" m class:ProtoMol::PeriodicBoundaryConditions myE2r framework/topology/PeriodicBoundaryConditions.h /^ Vector3D myE2r;$/;" m class:ProtoMol::PeriodicBoundaryConditions myE3 framework/topology/PeriodicBoundaryConditions.h /^ Vector3D myE3;$/;" m class:ProtoMol::PeriodicBoundaryConditions myE3r framework/topology/PeriodicBoundaryConditions.h /^ Vector3D myE3r;$/;" m class:ProtoMol::PeriodicBoundaryConditions myEnable framework/integrators/Modifier.h /^ mutable bool myEnable;$/;" m class:ProtoMol::Modifier myEnd framework/topology/ArrayCellListStructure.h /^ iterator myBegin,myEnd;$/;" m class:ProtoMol::ArrayCellListStructure myEndConst framework/topology/ArrayCellListStructure.h /^ const_iterator myBeginConst,myEndConst;$/;" m class:ProtoMol::ArrayCellListStructure myEndSerial framework/base/systemutilities.cpp /^ static void (*myEndSerial)(bool) = NULL;$/;" v file: myEndTime framework/base/Cycles.h /^ ticks myEndTime;$/;" m class:ProtoMol::Cycles myEnergies framework/forces/CompareForce.h /^ ScalarStructure* myEnergies;$/;" m class:ProtoMol::CompareForce myEnergies framework/frontend/Output.h /^ const ScalarStructure* myEnergies;$/;" m class:ProtoMol::Output myEnergies framework/frontend/OutputCache.h /^ const ScalarStructure* myEnergies;$/;" m class:ProtoMol::OutputCache myEnergies framework/frontend/OutputCollection.h /^ const ScalarStructure* myEnergies;$/;" m class:ProtoMol::OutputCollection myEnergies framework/integrators/Integrator.h /^ ScalarStructure *myEnergies;$/;" m class:ProtoMol::Integrator myEnergies framework/integrators/Modifier.h /^ ScalarStructure* myEnergies;$/;" m class:ProtoMol::Modifier myEnergyFile tools/rem/sequential/replica.h /^ string myEnergyFile;$/;" m class:Replica myEpsilon framework/integrators/ModifierMetaRattleShake.h /^ Real myEpsilon;$/;" m class:ProtoMol::ModifierMetaRattleShake myEpsilonVel framework/integrators/NPTVerletIntegrator.h /^ Real myEpsilonVel; \/\/ Barostat strain rate velocity. Units: (fs)^-1$/;" m class:ProtoMol::NPTVerletIntegrator myErrors framework/forces/CompareForce.h /^ std::vector myErrors;$/;" m class:ProtoMol::CompareForce myEta framework/integrators/NPTVerletIntegrator.h /^ Real myEta; \/\/ Nose-Hoover particle thermostat variable. Units: (dimensionless)$/;" m class:ProtoMol::NPTVerletIntegrator myEta framework/integrators/NVTVerletIntegrator.h /^ Real myEta; \/\/ Nose-Hoover particle thermostat variable. Units: (dimensionless)$/;" m class:ProtoMol::NVTVerletIntegrator myEtaV framework/integrators/NPTVerletIntegrator.h /^ Real myEtaV; \/\/ Nose-Hoover volume thermostat variable. Units: (dimensionless)$/;" m class:ProtoMol::NPTVerletIntegrator myEtaVel framework/integrators/NPTVerletIntegrator.h /^ Real myEtaVel; \/\/ Velocity of the thermostat variable. Units: (fs)^-1$/;" m class:ProtoMol::NPTVerletIntegrator myEtaVel framework/integrators/NVTVerletIntegrator.h /^ Real myEtaVel; \/\/ Velocity of the thermostat variable. Units: (fs)^-1$/;" m class:ProtoMol::NVTVerletIntegrator myEtaVolVel framework/integrators/NPTVerletIntegrator.h /^ Real myEtaVolVel; \/\/ Velocity of the volume thermostat variable. Units: (fs)^-1$/;" m class:ProtoMol::NPTVerletIntegrator myExemplars framework/frontend/Factory.h /^ std::map myExemplars; $/;" m class:ProtoMol::FactoryBase myExemplars framework/frontend/HelpTextFactory.h /^ HelpTextMapType myExemplars; $/;" m class:ProtoMol::HelpTextFactory myExitFunction framework/base/systemutilities.cpp /^ static void (*myExitFunction)() = NULL;$/;" v file: myExpX framework/base/Grid.h /^ Real* myExpX;$/;" m class:ProtoMol::Grid myExpY framework/base/Grid.h /^ Real* myExpY;$/;" m class:ProtoMol::Grid myExpZ framework/base/Grid.h /^ Real* myExpZ;$/;" m class:ProtoMol::Grid myExpansionFactor framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myExpansionFactor;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myExpansionFactor framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myExpansionFactor;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myExtendedForcesList framework/forces/ForceGroup.h /^ std::list myExtendedForcesList;$/;" m class:ProtoMol::ForceGroup myF framework/forces/FrictionExtendedForce.h /^ Real myF;$/;" m class:ProtoMol::FrictionExtendedForce myF framework/forces/MagneticDipoleMirrorSystemForce.h /^ Real myChi, myR, myD, myHx, myHy, myHz, myF;$/;" m class:ProtoMol::MagneticDipoleMirrorSystemForce myFFT framework/base/Grid.h /^ FFTComplex myFFT;$/;" m class:ProtoMol::Grid myFFTCoeff framework/base/FFTComplex.cpp /^ zomplex* myFFTCoeff;$/;" m class:ProtoMol::FFTInternal file: myFFTInternal framework/base/FFTComplex.h /^ FFTInternal* myFFTInternal;$/;" m class:ProtoMol::FFTComplex myFac framework/base/Grid.h /^ Real myFac;$/;" m class:ProtoMol::Grid myFac framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myFac;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myFactor framework/frontend/OutputPaulTrap.h /^ Real myFactor;$/;" m class:ProtoMol::OutputPaulTrap myFactor framework/frontend/OutputScreen.h /^ Real myFactor;$/;" m class:ProtoMol::OutputScreen myFastDeltaMax framework/topology/ExclusionTable.h /^ int myFastDeltaMax;$/;" m class:ProtoMol::ExclusionTable myFile framework/frontend/OutputFile.h /^ std::ofstream myFile;$/;" m class:ProtoMol::OutputFile myFile framework/io/File.h /^ std::fstream myFile;$/;" m class:ProtoMol::File myFilename framework/frontend/InputPosVel.h /^ std::string myFilename;$/;" m class:ProtoMol::InputPosVel myFilename framework/frontend/OutputBSDL.h /^ std::string myFilename;$/;" m class:ProtoMol::OutputBSDL myFilename framework/frontend/OutputFile.h /^ std::string myFilename;$/;" m class:ProtoMol::OutputFile myFilename framework/frontend/OutputFinalPDBPos.h /^ std::string myFilename;$/;" m class:ProtoMol::OutputFinalPDBPos myFilename framework/frontend/OutputFinalXYZBinPos.h /^ std::string myFilename;$/;" m class:ProtoMol::OutputFinalXYZBinPos myFilename framework/frontend/OutputFinalXYZBinVel.h /^ std::string myFilename;$/;" m class:ProtoMol::OutputFinalXYZBinVel myFilename framework/frontend/OutputFinalXYZPos.h /^ std::string myFilename;$/;" m class:ProtoMol::OutputFinalXYZPos myFilename framework/frontend/OutputFinalXYZVel.h /^ std::string myFilename;$/;" m class:ProtoMol::OutputFinalXYZVel myFilename framework/frontend/OutputPDBFramePos.h /^ std::string myFilename;$/;" m class:ProtoMol::OutputPDBFramePos myFilename framework/io/File.h /^ std::string myFilename;$/;" m class:ProtoMol::File myFilenameLow framework/frontend/OutputPaulTrap.h /^ std::string myFilenameLow;$/;" m class:ProtoMol::OutputPaulTrap myFinalPos tools/rem/sequential/replica.h /^ string myFinalPos;$/;" m class:Replica myFinalVel tools/rem/sequential/replica.h /^ string myFinalVel;$/;" m class:Replica myFinalized framework/parallel/Parallel-FD.cpp /^ bool Parallel::myFinalized = false;$/;" m class:ProtoMol::Parallel file: myFinalized framework/parallel/Parallel.cpp /^ bool Parallel::myFinalized = false;$/;" m class:ProtoMol::Parallel file: myFinalized framework/parallel/Parallel.h /^ static bool myFinalized; \/\/ \/ myForceTypes;$/;" m class:ProtoMol::ForceFactoryDetails myForceTypesSorted framework/frontend/ForceFactoryDetails.h /^ mutable std::map myForceTypesSorted;$/;" m class:ProtoMol::ForceFactoryDetails myForcename framework/forces/CompareForce.h /^ std::string myForcename;$/;" m class:ProtoMol::CompareForce myForcename framework/forces/TimeForce.h /^ std::string myForcename;$/;" m class:ProtoMol::TimeForce myForces framework/forces/CompareForce.h /^ Vector3DBlock* myForces;$/;" m class:ProtoMol::CompareForce myForces framework/forces/WrapperMetaForce.h /^ std::vector myForces;$/;" m class:ProtoMol::WrapperMetaForce myForces framework/integrators/Integrator.h /^ Vector3DBlock *myForces;$/;" m class:ProtoMol::Integrator myForces framework/integrators/Modifier.h /^ Vector3DBlock* myForces; $/;" m class:ProtoMol::Modifier myForcesToEvaluate framework/integrators/Integrator.h /^ ForceGroup *myForcesToEvaluate;$/;" m class:ProtoMol::Integrator myForward framework/integrators/Integrator.h /^ bool myForward;$/;" m class:ProtoMol::Integrator myFreq framework/integrators/ModifierRemoveAngularMomentum.h /^ int myFreq;$/;" m class:ProtoMol::ModifierRemoveAngularMomentum myFreq framework/integrators/ModifierRemoveLinearMomentum.h /^ int myFreq;$/;" m class:ProtoMol::ModifierRemoveLinearMomentum myFreq framework/integrators/ModifierShadow.h /^ myFreq;$/;" m class:ProtoMol::ModifierShadow myFromRange framework/forces/NonbondedFullSystemForce.h /^ std::vector myFromRange;$/;" m class:ProtoMol::NonbondedFullSystemForce myFromRange framework/forces/NonbondedSimpleFullSystemForce.h /^ std::vector myFromRange;$/;" m class:ProtoMol::NonbondedSimpleFullSystemForce myFromZ framework/io/XFigWriter.h /^ Real myFromZ;$/;" m class:ProtoMol::XFigWriter myG framework/forces/ExternalGravitationSystemForce.h /^ Vector3D myG;$/;" m class:ProtoMol::ExternalGravitationSystemForce myG framework/forces/GravitationForce.h /^ Real myG;$/;" m class:ProtoMol::GravitationForce myGCorrDimX framework/base/MultiGrid.h /^ int myGCorrDimX; \/\/\/< Dimensions of G_correction$/;" m class:ProtoMol::MultiGrid myGCorrDimY framework/base/MultiGrid.h /^ int myGCorrDimY;$/;" m class:ProtoMol::MultiGrid myGCorrDimZ framework/base/MultiGrid.h /^ int myGCorrDimZ;$/;" m class:ProtoMol::MultiGrid myGCorrection framework/base/MultiGrid.h /^ Array myGCorrection; \/\/\/< G_Correction for other levels, G->V $/;" m class:ProtoMol::MultiGrid myGDirect framework/base/MultiGrid.h /^ Array myGDirect; \/\/\/< G_direct for top level, G->V$/;" m class:ProtoMol::MultiGrid myGamma framework/integrators/BBKIntegrator.h /^ Real myGamma;$/;" m class:ProtoMol::BBKIntegrator myGamma framework/integrators/DMDLeapfrogIntegrator.h /^ Real myGamma;$/;" m class:ProtoMol::DMDLeapfrogIntegrator myGamma framework/integrators/LangevinImpulseIntegrator.h /^ Real myGamma;$/;" m class:ProtoMol::LangevinImpulseIntegrator myGrid framework/forces/NonbondedMultiGridSystemForce.h /^ MultiGrid myGrid;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myGrid framework/forces/NonbondedPMEwaldSystemForce.h /^ Grid myGrid;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myGridInterpolation framework/base/MultiGrid.h /^ std::vector myGridInterpolation; \/\/\/< Interpolation between grids$/;" m class:ProtoMol::MultiGrid myH framework/base/MultiGrid.h /^ Vector3D myH; \/\/ $/;" m class:ProtoMol::MultiGrid myH framework/forces/NonbondedMultiGridSystemForce.h /^ Vector3D myH;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myH framework/topology/PeriodicBoundaryConditions.h /^ Vector3D myH;$/;" m class:ProtoMol::PeriodicBoundaryConditions myH2 framework/topology/PeriodicBoundaryConditions.h /^ Vector3D myH2;$/;" m class:ProtoMol::PeriodicBoundaryConditions myHBondForces framework/integrators/BSplineMOLLYIntegrator.h /^ ForceGroup *myHBondForces;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myHKLmax framework/forces/NonbondedFullEwaldSystemForce.h /^ int myHKLmax;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myHX framework/base/Grid.h /^ Real myHX;$/;" m class:ProtoMol::Grid myHX framework/base/MultiGrid.h /^ Real myHX; \/\/\/< h_x at level 0$/;" m class:ProtoMol::MultiGrid myHXr framework/base/Grid.h /^ Real myHXr;$/;" m class:ProtoMol::Grid myHXr framework/base/MultiGrid.h /^ Real myHXr; \/\/\/< 1\/h_x at level 0$/;" m class:ProtoMol::MultiGrid myHY framework/base/Grid.h /^ Real myHY;$/;" m class:ProtoMol::Grid myHY framework/base/MultiGrid.h /^ Real myHY; \/\/\/< h_y at level 0$/;" m class:ProtoMol::MultiGrid myHYr framework/base/Grid.h /^ Real myHYr;$/;" m class:ProtoMol::Grid myHYr framework/base/MultiGrid.h /^ Real myHYr; \/\/\/< 1\/h_y at level 0$/;" m class:ProtoMol::MultiGrid myHZ framework/base/Grid.h /^ Real myHZ;$/;" m class:ProtoMol::Grid myHZ framework/base/MultiGrid.h /^ Real myHZ; \/\/\/< h_z at level 0$/;" m class:ProtoMol::MultiGrid myHZr framework/base/Grid.h /^ Real myHZr;$/;" m class:ProtoMol::Grid myHZr framework/base/MultiGrid.h /^ Real myHZr; \/\/\/< 1\/h_z at level 0$/;" m class:ProtoMol::MultiGrid myHapticForces framework/imd/HapticSystemForce.h /^ Vector3DBlock* myHapticForces;$/;" m class:ProtoMol::HapticSystemForce myHeight framework/base/Grid.h /^ Real myHeight;$/;" m class:ProtoMol::Grid myHeightr framework/base/Grid.h /^ Real myHeightr;$/;" m class:ProtoMol::Grid myHmax framework/forces/NonbondedFullEwaldSystemForce.h /^ int myHmax;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myHx framework/forces/MagneticDipoleForce.h /^ Real myChi, myR, myOmega, myPhi, myHx, myHy, myHz, myD;$/;" m class:ProtoMol::MagneticDipoleForce myHx framework/forces/MagneticDipoleMirrorSystemForce.h /^ Real myChi, myR, myD, myHx, myHy, myHz, myF;$/;" m class:ProtoMol::MagneticDipoleMirrorSystemForce myHy framework/forces/MagneticDipoleForce.h /^ Real myChi, myR, myOmega, myPhi, myHx, myHy, myHz, myD;$/;" m class:ProtoMol::MagneticDipoleForce myHy framework/forces/MagneticDipoleMirrorSystemForce.h /^ Real myChi, myR, myD, myHx, myHy, myHz, myF;$/;" m class:ProtoMol::MagneticDipoleMirrorSystemForce myHydrogenAtomGroups framework/integrators/EquilibriumMOLLYIntegrator.h /^ std::vector > myHydrogenAtomGroups;$/;" m class:ProtoMol::EquilibriumMOLLYIntegrator myHydrogenConstraintGroups framework/integrators/EquilibriumMOLLYIntegrator.h /^ std::vector > myHydrogenConstraintGroups;$/;" m class:ProtoMol::EquilibriumMOLLYIntegrator myHz framework/forces/MagneticDipoleForce.h /^ Real myChi, myR, myOmega, myPhi, myHx, myHy, myHz, myD;$/;" m class:ProtoMol::MagneticDipoleForce myHz framework/forces/MagneticDipoleMirrorSystemForce.h /^ Real myChi, myR, myD, myHx, myHy, myHz, myF;$/;" m class:ProtoMol::MagneticDipoleMirrorSystemForce myI framework/parallel/Parallel-FD.cpp /^ int Parallel::myI;$/;" m class:ProtoMol::Parallel file: myI framework/parallel/Parallel.cpp /^ int Parallel::myI;$/;" m class:ProtoMol::Parallel file: myI framework/parallel/Parallel.h /^ static int myI; \/\/\/< Index of the actual work package (only master)$/;" m class:ProtoMol::Parallel myIAmMaster framework/base/Report.h /^ bool myIAmMaster;$/;" m class:ProtoMol::Report::MyStreamer myIAmMaster framework/parallel/Parallel-FD.cpp /^ bool Parallel::myIAmMaster = true;$/;" m class:ProtoMol::Parallel file: myIAmMaster framework/parallel/Parallel.cpp /^ bool Parallel::myIAmMaster = true;$/;" m class:ProtoMol::Parallel file: myIAmMaster framework/parallel/Parallel.h /^ static bool myIAmMaster; \/\/\/< If this node is master$/;" m class:ProtoMol::Parallel myIAmSlave framework/parallel/Parallel-FD.cpp /^ bool Parallel::myIAmSlave = true;$/;" m class:ProtoMol::Parallel file: myIAmSlave framework/parallel/Parallel.cpp /^ bool Parallel::myIAmSlave = true;$/;" m class:ProtoMol::Parallel file: myIAmSlave framework/parallel/Parallel.h /^ static bool myIAmSlave; \/\/\/< If this node is slave\/worker$/;" m class:ProtoMol::Parallel myIMDElf framework/imd/HapticSystemForce.h /^ IMDElf* myIMDElf;$/;" m class:ProtoMol::HapticSystemForce myIRange framework/topology/CmpCnCnSwitchingFunction.h /^ Real myIRange[MAXEQNCM];$/;" m class:ProtoMol::CmpCnCnSwitchingFunction myIRange framework/topology/CnSwitchingFunction.h /^ Real myIRange[MAXEQNN];$/;" m class:ProtoMol::CnSwitchingFunction myId framework/parallel/Parallel-FD.cpp /^ int Parallel::myId = 0;$/;" m class:ProtoMol::Parallel file: myId framework/parallel/Parallel.cpp /^ int Parallel::myId = 0;$/;" m class:ProtoMol::Parallel file: myId framework/parallel/Parallel.h /^ static int myId; \/\/\/< Actual id of the node, [0,1,...,N-1]$/;" m class:ProtoMol::Parallel myIdNumber framework/forces/CompareForce.h /^ unsigned int myIdNumber;$/;" m class:ProtoMol::CompareForce myIdNumber framework/forces/TimeForce.h /^ unsigned int myIdNumber;$/;" m class:ProtoMol::TimeForce myIncludeView framework/frontend/OutputBSDL.h /^ bool myIncludeView;$/;" m class:ProtoMol::OutputBSDL myInerpolationModX framework/base/Grid.h /^ Real* myInerpolationModX;$/;" m class:ProtoMol::Grid myInerpolationModY framework/base/Grid.h /^ Real* myInerpolationModY;$/;" m class:ProtoMol::Grid myInerpolationModZ framework/base/Grid.h /^ Real* myInerpolationModZ;$/;" m class:ProtoMol::Grid myInitialPositions framework/frontend/OutputCache.h /^ Vector3DBlock* myInitialPositions;$/;" m class:ProtoMol::OutputCache myInitialTemperature framework/integrators/DihedralHMCIntegrator.h /^ Real myInitialTemperature;$/;" m class:ProtoMol::DihedralHMCIntegrator myInitialTemperature framework/integrators/MCIntegrator.h /^ Real myInitialTemperature;$/;" m class:ProtoMol::MCIntegrator myInitialized framework/parallel/Parallel-FD.cpp /^ bool Parallel::myInitialized = false;$/;" m class:ProtoMol::Parallel file: myInitialized framework/parallel/Parallel.cpp /^ bool Parallel::myInitialized = false;$/;" m class:ProtoMol::Parallel file: myInitialized framework/parallel/Parallel.h /^ static bool myInitialized; \/\/\/< If Parallel is initialized$/;" m class:ProtoMol::Parallel myIntegrator framework/frontend/Output.h /^ const Integrator* myIntegrator;$/;" m class:ProtoMol::Output myIntegrator framework/frontend/OutputCache.h /^ const Integrator* myIntegrator;$/;" m class:ProtoMol::OutputCache myIntegrator framework/frontend/OutputCollection.h /^ const Integrator* myIntegrator;$/;" m class:ProtoMol::OutputCollection myIntegrator framework/integrators/ModifierShadow.h /^ const Integrator *myIntegrator;$/;" m class:ProtoMol::ModifierShadow myInterOrder framework/base/BSpline.h /^ unsigned int myInterOrder;$/;" m class:ProtoMol::BSpline myInterOrder framework/base/Grid.h /^ unsigned int myInterOrder;$/;" m class:ProtoMol::Grid myInterOrder framework/base/Hermite.h /^ unsigned int myInterOrder;$/;" m class:ProtoMol::Hermite myInterOrder framework/base/Lagrange.h /^ unsigned int myInterOrder;$/;" m class:ProtoMol::Lagrange myInterOrder framework/base/MultiGrid.h /^ int myInterOrder; \/\/\/< Interpolation order$/;" m class:ProtoMol::MultiGrid myInterOrder framework/forces/NonbondedMultiGridSystemForce.h /^ unsigned int myInterOrder;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myInterOrder framework/forces/NonbondedPMEwaldSystemForce.h /^ unsigned int myInterOrder;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myInterpolations framework/base/Grid.h /^ std::vector myInterpolations;$/;" m class:ProtoMol::Grid myInterpolations framework/base/MultiGrid.h /^ std::vector myInterpolations; \/\/\/< Interpolation weights for each particle $/;" m class:ProtoMol::MultiGrid myIntra framework/forces/NonbondedFullEwaldSystemForce.h /^ Timer myIntra;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myIntra framework/forces/NonbondedPMEwaldSystemForce.h /^ Timer myIntra;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myIsLittleEndian framework/io/DCDTrajectoryWriter.h /^ bool myIsLittleEndian;$/;" m class:ProtoMol::DCDTrajectoryWriter myIsLittleEndian framework/io/XYZBinWriter.h /^ bool myIsLittleEndian;$/;" m class:ProtoMol::XYZBinWriter myIsParallel framework/base/TimerStatistic.cpp /^ bool TimerStatistic::myIsParallel = false;$/;" m class:ProtoMol::TimerStatistic file: myIsParallel framework/base/TimerStatistic.h /^ static bool myIsParallel;$/;" m class:ProtoMol::TimerStatistic myIsParallel framework/parallel/Parallel-FD.cpp /^ bool Parallel::myIsParallel = Parallel::isMPI;$/;" m class:ProtoMol::Parallel file: myIsParallel framework/parallel/Parallel.cpp /^ bool Parallel::myIsParallel = Parallel::isMPI;$/;" m class:ProtoMol::Parallel file: myIsParallel framework/parallel/Parallel.h /^ static bool myIsParallel; \/\/\/< If environment has more that 1 node$/;" m class:ProtoMol::Parallel myIsolated framework/parallel/Parallel-FD.cpp /^ bool Parallel::myIsolated = false;$/;" m class:ProtoMol::Parallel file: myIsolated framework/parallel/Parallel.cpp /^ bool Parallel::myIsolated = false;$/;" m class:ProtoMol::Parallel file: myIsolated framework/parallel/Parallel.h /^ static bool myIsolated; \/\/\/< Saves isolation state$/;" m class:ProtoMol::Parallel myItRange framework/topology/CmpCnCnSwitchingFunction.h /^ Real myItRange[MAXEQNCM];$/;" m class:ProtoMol::CmpCnCnSwitchingFunction myJ framework/forces/SphericalSystemForce.h /^ int myJ;$/;" m class:ProtoMol::SphericalSystemForce myK framework/forces/NonbondedFullEwaldSystemForce.h /^ std::vector myK; \/\/ Reciprocal lattice vector (h*2PI\/Lx,k*2PI\/Ly,l*2PI\/Lz)$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myK framework/forces/PaulTrapExtendedForce.h /^ Vector3D myK;$/;" m class:ProtoMol::PaulTrapExtendedForce myK framework/forces/SphericalSystemForce.h /^ Real myK;$/;" m class:ProtoMol::SphericalSystemForce myKE framework/frontend/OutputCache.h /^ mutable Real myKE;$/;" m class:ProtoMol::OutputCache myKInt framework/forces/NonbondedFullEwaldSystemForce.h /^ std::vector myKInt; \/\/ Reciprocal lattice vector (h,k,l)$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myKSquared framework/forces/NonbondedFullEwaldSystemForce.h /^ std::vector myKSquared; \/\/ Squared norm of the reciprocal lattice vector$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myKc framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myKc; \/\/ Cutoff reciprocal term$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myKc framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myKc; \/\/ Cutoff reciprocal term$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myKeep framework/integrators/PaulTrapIntegrator.h /^ std::vector myKeep;$/;" m class:ProtoMol::PaulTrapIntegrator myKmax framework/forces/NonbondedFullEwaldSystemForce.h /^ int myKmax;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myLX framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myLX, myLY, myLZ;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myLX framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myLX, myLY, myLZ;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myLXr framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myLXr,myLYr,myLZr;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myLXr framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myLXr,myLYr,myLZr;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myLY framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myLX, myLY, myLZ;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myLY framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myLX, myLY, myLZ;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myLYr framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myLXr,myLYr,myLZr;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myLYr framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myLXr,myLYr,myLZr;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myLZ framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myLX, myLY, myLZ;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myLZ framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myLX, myLY, myLZ;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myLZr framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myLXr,myLYr,myLZr;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myLZr framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myLXr,myLYr,myLZr;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myLangevinTemperature framework/integrators/BBKIntegrator.h /^ Real myLangevinTemperature;$/;" m class:ProtoMol::BBKIntegrator myLangevinTemperature framework/integrators/LangevinImpulseIntegrator.h /^ Real myLangevinTemperature;$/;" m class:ProtoMol::LangevinImpulseIntegrator myLapTime framework/base/Timer.h /^ TimeRep myLapTime;$/;" m class:ProtoMol::Timer myLast framework/base/LookUpTableBase.h /^ int myLast;$/;" m class:ProtoMol::LookUpTableBase myLastCompareForce framework/frontend/ForceFactoryDetails.h /^ mutable CompareForce* myLastCompareForce;$/;" m class:ProtoMol::ForceFactoryDetails myLastLapTime framework/base/Timer.h /^ TimeRep myLastLapTime;$/;" m class:ProtoMol::Timer myLastPositions framework/integrators/ModifierMetaRattleShake.h /^ Vector3DBlock myLastPositions;$/;" m class:ProtoMol::ModifierMetaRattleShake myLastSinCos framework/forces/NonbondedFullEwaldSystemForce.h /^ Real* myLastSinCos;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myLastStep framework/frontend/Output.h /^ int myLastStep;$/;" m class:ProtoMol::Output myLattice framework/forces/NonbondedFullEwaldSystemForce.h /^ std::vector myLattice;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myLattice framework/forces/NonbondedFullSystemForce.h /^ std::vector myLattice;$/;" m class:ProtoMol::NonbondedFullSystemForce myLattice framework/forces/NonbondedPMEwaldSystemForce.h /^ std::vector myLattice;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myLayer framework/integrators/PaulTrapIntegrator.h /^ std::vector > myLayer;$/;" m class:ProtoMol::PaulTrapIntegrator myLegend framework/io/XFigWriter.h /^ bool myLegend;$/;" m class:ProtoMol::XFigWriter myLength framework/base/Grid.h /^ Real myLength;$/;" m class:ProtoMol::Grid myLengthr framework/base/Grid.h /^ Real myLengthr;$/;" m class:ProtoMol::Grid myLennardJones framework/integrators/BSplineMOLLYIntegrator.h /^ bool myLennardJones;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myLevel framework/base/Report.h /^ short myLevel;$/;" m class:ProtoMol::Report::MyStreamer myLevel framework/base/Report.h /^ short myLevel;$/;" m class:ProtoMol::Report::debug myLevels framework/base/MultiGrid.h /^ int myLevels; \/\/\/< Number of levels, 0,1,2,...,myLevels-1$/;" m class:ProtoMol::MultiGrid myLevels framework/forces/NonbondedMultiGridSystemForce.h /^ int myLevels;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myLinearMomentum framework/frontend/OutputCache.h /^ mutable Vector3D myLinearMomentum;$/;" m class:ProtoMol::OutputCache myListModifiers framework/integrators/Integrator.h /^ std::set myListModifiers;$/;" m class:ProtoMol::Integrator myListOfConstraints framework/integrators/ModifierMetaRattleShake.h /^ const std::vector* myListOfConstraints;$/;" m class:ProtoMol::ModifierMetaRattleShake myLmax framework/forces/NonbondedFullEwaldSystemForce.h /^ int myLmax;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myLowComment framework/frontend/OutputPaulTrap.h /^ std::string myLowComment;$/;" m class:ProtoMol::OutputPaulTrap myLowOut framework/frontend/OutputPaulTrap.h /^ std::string myLowOut;$/;" m class:ProtoMol::OutputPaulTrap myLowXYZ framework/frontend/OutputPaulTrap.h /^ Vector3DBlock myLowXYZ;$/;" m class:ProtoMol::OutputPaulTrap myMOLLYEnergies framework/integrators/BSplineMOLLYIntegrator.h /^ ScalarStructure *myMOLLYEnergies;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myMOLLYForces framework/integrators/BSplineMOLLYIntegrator.h /^ Vector3DBlock *myMOLLYForces;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myMOLLYForcesBonded framework/integrators/BSplineMOLLYIntegrator.h /^ ForceGroup *myMOLLYForcesBonded;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myMOLLYForcesHBonded framework/integrators/BSplineMOLLYIntegrator.h /^ ForceGroup *myMOLLYForcesHBonded;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myMOLLYPositions framework/integrators/BSplineMOLLYIntegrator.h /^ Vector3DBlock *myMOLLYPositions;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myMOLLYStepsize framework/integrators/BSplineMOLLYIntegrator.h /^ Real myMOLLYStepsize;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myMOLLYStepsize framework/integrators/EquilibriumMOLLYIntegrator.h /^ Real myMOLLYStepsize;$/;" m class:ProtoMol::EquilibriumMOLLYIntegrator myMOLLYStepsizeP framework/integrators/BSplineMOLLYIntegrator.h /^ Real myMOLLYStepsizeP;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myMOLLYStepsizeSquare framework/integrators/BSplineMOLLYIntegrator.h /^ Real myMOLLYStepsizeSquare;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myMOLLYVelocities framework/integrators/BSplineMOLLYIntegrator.h /^ Vector3DBlock *myMOLLYVelocities;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myMask framework/base/LookUpTableBase.h /^ static const TInt myMask;$/;" m class:ProtoMol::LookUpTableBase myMask framework/base/LookUpTableBase.h /^ const typename LookUpTableBase::TInt LookUpTableBase::myMask=~((1LL< > myMaximas;$/;" m class:ProtoMol::OutputDihedrals myMediForceModifiers framework/integrators/Integrator.h /^ std::set myMediForceModifiers;$/;" m class:ProtoMol::Integrator myMem framework/base/LookUpTableBase.h /^ TReal* myMem;$/;" m class:ProtoMol::LookUpTableBase myMetaForcesList framework/forces/ForceGroup.h /^ std::list myMetaForcesList;$/;" m class:ProtoMol::ForceGroup myMin framework/base/MultiGrid.h /^ Vector3D myMin; \/\/ $/;" m class:ProtoMol::MultiGrid myMin framework/forces/NonbondedMultiGridSystemForce.h /^ Vector3D myMin;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myMin framework/topology/PeriodicBoundaryConditions.h /^ Vector3D myMin;$/;" m class:ProtoMol::PeriodicBoundaryConditions myMinimal framework/forces/WrapperMetaForce.h /^ bool myMinimal;$/;" m class:ProtoMol::WrapperMetaForce myMinimalImage framework/frontend/OutputBSDL.h /^ bool myMinimalImage;$/;" m class:ProtoMol::OutputBSDL myMinimalImage framework/frontend/OutputDCDTrajectory.h /^ bool myMinimalImage;$/;" m class:ProtoMol::OutputDCDTrajectory myMinimalImage framework/frontend/OutputDihedrals.h /^ bool myMinimalImage;$/;" m class:ProtoMol::OutputDihedrals myMinimalImage framework/frontend/OutputFinalPDBPos.h /^ bool myMinimalImage;$/;" m class:ProtoMol::OutputFinalPDBPos myMinimalImage framework/frontend/OutputFinalXYZBinPos.h /^ bool myMinimalImage;$/;" m class:ProtoMol::OutputFinalXYZBinPos myMinimalImage framework/frontend/OutputFinalXYZPos.h /^ bool myMinimalImage;$/;" m class:ProtoMol::OutputFinalXYZPos myMinimalImage framework/frontend/OutputPDBFramePos.h /^ bool myMinimalImage;$/;" m class:ProtoMol::OutputPDBFramePos myMinimalImage framework/frontend/OutputXYZBinTrajectoryPos.h /^ bool myMinimalImage;$/;" m class:ProtoMol::OutputXYZBinTrajectoryPos myMinimalImage framework/frontend/OutputXYZTrajectoryPos.h /^ bool myMinimalImage;$/;" m class:ProtoMol::OutputXYZTrajectoryPos myMinimalPositions framework/frontend/OutputCache.h /^ mutable Vector3DBlock* myMinimalPositions;$/;" m class:ProtoMol::OutputCache myMinimas framework/frontend/OutputDihedrals.h /^ std::vector< std::vector< Real > > myMinimas; $/;" m class:ProtoMol::OutputDihedrals myMode framework/io/File.h /^ std::ios::openmode myMode;$/;" m class:ProtoMol::File myMode framework/parallel/Parallel-FD.cpp /^ ParallelType Parallel::myMode = ParallelType::STATIC;$/;" m class:ProtoMol::Parallel file: myMode framework/parallel/Parallel.cpp /^ ParallelType Parallel::myMode = ParallelType::STATIC;$/;" m class:ProtoMol::Parallel file: myMode framework/parallel/Parallel.h /^ static ParallelType myMode; \/\/\/< Parallelization scheme$/;" m class:ProtoMol::Parallel myMolKE framework/frontend/OutputCache.h /^ mutable Real myMolKE;$/;" m class:ProtoMol::OutputCache myMolP framework/frontend/OutputCache.h /^ mutable Real myMolP;$/;" m class:ProtoMol::OutputCache myMolT framework/frontend/OutputCache.h /^ mutable Real myMolT;$/;" m class:ProtoMol::OutputCache myMolecularDistance framework/frontend/OutputBSDL.h /^ bool myMolecularDistance;$/;" m class:ProtoMol::OutputBSDL myMolecule framework/base/XSC.h /^ unsigned int myMolecule, old_type, new_type;$/;" m struct:ProtoMol::XSC myMollyForcesList framework/forces/ForceGroup.h /^ std::list myMollyForcesList;$/;" m class:ProtoMol::ForceGroup myNX framework/base/FFTComplex.cpp /^ int myNX;$/;" m class:ProtoMol::FFTInternal file: myNX framework/base/Grid.h /^ unsigned int myNX;$/;" m class:ProtoMol::Grid myNX framework/base/MultiGrid.h /^ int myNX; \/\/\/< x dimension of the grid level 0$/;" m class:ProtoMol::MultiGrid myNX framework/forces/NonbondedMultiGridSystemForce.h /^ unsigned int myNX;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myNX framework/forces/NonbondedPMEwaldSystemForce.h /^ unsigned int myNX;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myNX framework/topology/ArrayCellListStructure.h /^ int myNX,myNY,myNZ;$/;" m class:ProtoMol::ArrayCellListStructure myNX1 framework/topology/ArrayCellListStructure.h /^ int myNX1,myNY1,myNZ1;$/;" m class:ProtoMol::ArrayCellListStructure myNXOffset framework/base/Grid.h /^ int myNXOffset;$/;" m class:ProtoMol::Grid myNXOffset framework/base/MultiGrid.h /^ int myNXOffset; \/\/\/< x index offset between to grid levels$/;" m class:ProtoMol::MultiGrid myNY framework/base/FFTComplex.cpp /^ int myNY;$/;" m class:ProtoMol::FFTInternal file: myNY framework/base/Grid.h /^ unsigned int myNY;$/;" m class:ProtoMol::Grid myNY framework/base/MultiGrid.h /^ int myNY; \/\/\/< y dimension of the grid level 0$/;" m class:ProtoMol::MultiGrid myNY framework/forces/NonbondedMultiGridSystemForce.h /^ unsigned int myNY;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myNY framework/forces/NonbondedPMEwaldSystemForce.h /^ unsigned int myNY;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myNY framework/topology/ArrayCellListStructure.h /^ int myNX,myNY,myNZ;$/;" m class:ProtoMol::ArrayCellListStructure myNY1 framework/topology/ArrayCellListStructure.h /^ int myNX1,myNY1,myNZ1;$/;" m class:ProtoMol::ArrayCellListStructure myNYOffset framework/base/Grid.h /^ int myNYOffset;$/;" m class:ProtoMol::Grid myNYOffset framework/base/MultiGrid.h /^ int myNYOffset; \/\/\/< y index offset between to grid levels$/;" m class:ProtoMol::MultiGrid myNZ framework/base/FFTComplex.cpp /^ int myNZ;$/;" m class:ProtoMol::FFTInternal file: myNZ framework/base/Grid.h /^ unsigned int myNZ;$/;" m class:ProtoMol::Grid myNZ framework/base/MultiGrid.h /^ int myNZ; \/\/\/< z dimension of the grid level 0$/;" m class:ProtoMol::MultiGrid myNZ framework/forces/NonbondedMultiGridSystemForce.h /^ unsigned int myNZ;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myNZ framework/forces/NonbondedPMEwaldSystemForce.h /^ unsigned int myNZ;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myNZ framework/topology/ArrayCellListStructure.h /^ int myNX,myNY,myNZ;$/;" m class:ProtoMol::ArrayCellListStructure myNZ1 framework/topology/ArrayCellListStructure.h /^ int myNX1,myNY1,myNZ1;$/;" m class:ProtoMol::ArrayCellListStructure myNZOffset framework/base/Grid.h /^ int myNZOffset;$/;" m class:ProtoMol::Grid myNZOffset framework/base/MultiGrid.h /^ int myNZOffset; \/\/\/< z index offset between to grid levels$/;" m class:ProtoMol::MultiGrid myName tools/rem/sequential/replica.h /^ string myName;$/;" m class:Replica myNames framework/io/XYZReader.h /^ std::vector* myNames;$/;" m class:ProtoMol::XYZReader myNames framework/io/XYZTrajectoryReader.h /^ std::vector* myNames;$/;" m class:ProtoMol::XYZTrajectoryReader myNames framework/io/XYZTrajectoryWriter.h /^ const std::vector* myNames;$/;" m class:ProtoMol::XYZTrajectoryWriter myNext framework/parallel/Parallel-FD.cpp /^ int Parallel::myNext = 0;$/;" m class:ProtoMol::Parallel file: myNext framework/parallel/Parallel.cpp /^ int Parallel::myNext = 0;$/;" m class:ProtoMol::Parallel file: myNext framework/parallel/Parallel.h /^ static int myNext; \/\/\/< Counter of next() calls$/;" m class:ProtoMol::Parallel myNextIntegrator framework/integrators/MTSIntegrator.h /^ StandardIntegrator *myNextIntegrator;$/;" m class:ProtoMol::MTSIntegrator myNextRange framework/parallel/Parallel-FD.cpp /^ int Parallel::myNextRange[2] = {0,0};$/;" m class:ProtoMol::Parallel file: myNextRange framework/parallel/Parallel.cpp /^ int Parallel::myNextRange[2] = {0,0};$/;" m class:ProtoMol::Parallel file: myNextRange framework/parallel/Parallel.h /^ static int myNextRange[2]; \/\/\/< Actual work package to work on [from,to]$/;" m class:ProtoMol::Parallel myNextStep framework/frontend/Output.h /^ int myNextStep;$/;" m class:ProtoMol::Output myNextStep tools/rem/sequential/replica.h /^ int myNextStep;$/;" m class:Replica myNonWaterAtomTypes framework/frontend/OutputTemperatures.h /^ std::vector myNonWaterAtomTypes;$/;" m class:ProtoMol::OutputTemperatures myNonWaterT framework/frontend/OutputCache.h /^ mutable Real myNonWaterT;$/;" m class:ProtoMol::OutputCache myNum framework/parallel/Parallel-FD.cpp /^ int Parallel::myNum = 1;$/;" m class:ProtoMol::Parallel file: myNum framework/parallel/Parallel.cpp /^ int Parallel::myNum = 1;$/;" m class:ProtoMol::Parallel file: myNum framework/parallel/Parallel.h /^ static int myNum; \/\/\/< Number of nodes, N$/;" m class:ProtoMol::Parallel myNumFree framework/integrators/NPTVerletIntegrator.h /^ unsigned int myNumFree; \/\/ Total # of degrees of freedom = (3*Natoms - 3) - NumConstraints$/;" m class:ProtoMol::NPTVerletIntegrator myNumFree framework/integrators/NVTVerletIntegrator.h /^ unsigned int myNumFree; \/\/ Total # of degrees of freedom = (3*Natoms - 3) - NumConstraints$/;" m class:ProtoMol::NVTVerletIntegrator myNumIter framework/integrators/BSplineMOLLYIntegrator.h /^ unsigned int myNumIter;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myNumIter framework/integrators/DMDLeapfrogIntegrator.h /^ int myNumIter;$/;" m class:ProtoMol::DMDLeapfrogIntegrator myNumParameters framework/integrators/DLMCIntegrator.h /^ static const int myNumParameters;$/;" m class:ProtoMol::DLMCIntegrator myNumParameters framework/integrators/HMCIntegrator.h /^ static const int myNumParameters;$/;" m class:ProtoMol::HMCIntegrator myNumSteps tools/rem/sequential/replica.h /^ int myNumSteps;$/;" m class:Replica myOk framework/frontend/InputPosVel.h /^ bool myOk;$/;" m class:ProtoMol::InputPosVel myOldAtomCount framework/forces/NonbondedFullEwaldSystemForce.h /^ unsigned int myOldAtomCount; \/\/ Keep track of old values and hope$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myOldEnergies framework/integrators/DihedralHMCIntegrator.h /^ ScalarStructure* myOldEnergies;$/;" m class:ProtoMol::DihedralHMCIntegrator myOldEnergies framework/integrators/MCIntegrator.h /^ ScalarStructure* myOldEnergies;$/;" m class:ProtoMol::MCIntegrator myOldForces framework/integrators/Integrator.h /^ Vector3DBlock *myOldForces;$/;" m class:ProtoMol::Integrator myOldForces framework/integrators/ShadowHMCIntegrator.h /^ Vector3DBlock myOldForces;$/;" m class:ProtoMol::ShadowHMCIntegrator myOldHKLmax framework/forces/NonbondedFullEwaldSystemForce.h /^ int myOldHKLmax; \/\/ we do not need to reallocate memory ...$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myOldId framework/parallel/Parallel-FD.cpp /^ int Parallel::myOldId = 0;$/;" m class:ProtoMol::Parallel file: myOldId framework/parallel/Parallel.cpp /^ int Parallel::myOldId = 0;$/;" m class:ProtoMol::Parallel file: myOldId framework/parallel/Parallel.h /^ static int myOldId; \/\/\/< Saves processor id when switching MPI off$/;" m class:ProtoMol::Parallel myOldKineticEnergy framework/integrators/MCIntegrator.h /^ Real myOldKineticEnergy;$/;" m class:ProtoMol::MCIntegrator myOldMode framework/parallel/Parallel-FD.cpp /^ ParallelType Parallel::myOldMode = ParallelType::STATIC;$/;" m class:ProtoMol::Parallel file: myOldMode framework/parallel/Parallel.cpp /^ ParallelType Parallel::myOldMode = ParallelType::STATIC;$/;" m class:ProtoMol::Parallel file: myOldMode framework/parallel/Parallel.h /^ static ParallelType myOldMode; \/\/\/< Saves parallelization scheme when switching MPI off$/;" m class:ProtoMol::Parallel myOldNum framework/parallel/Parallel-FD.cpp /^ int Parallel::myOldNum = 1;$/;" m class:ProtoMol::Parallel file: myOldNum framework/parallel/Parallel.cpp /^ int Parallel::myOldNum = 1;$/;" m class:ProtoMol::Parallel file: myOldNum framework/parallel/Parallel.h /^ static int myOldNum; \/\/\/< Saves number of processors when switching MPI off$/;" m class:ProtoMol::Parallel myOldPositions framework/integrators/DihedralHMCIntegrator.h /^ Vector3DBlock* myOldPositions;$/;" m class:ProtoMol::DihedralHMCIntegrator myOldPositions framework/integrators/MCIntegrator.h /^ Vector3DBlock* myOldPositions;$/;" m class:ProtoMol::MCIntegrator myOldVelocities framework/integrators/DihedralHMCIntegrator.h /^ Vector3DBlock* myOldVelocities;$/;" m class:ProtoMol::DihedralHMCIntegrator myOldVelocities framework/integrators/MCIntegrator.h /^ Vector3DBlock* myOldVelocities;$/;" m class:ProtoMol::MCIntegrator myOmega framework/forces/MagneticDipoleForce.h /^ Real myChi, myR, myOmega, myPhi, myHx, myHy, myHz, myD;$/;" m class:ProtoMol::MagneticDipoleForce myOmega framework/forces/PaulTrapExtendedForce.h /^ Real myOmega;$/;" m class:ProtoMol::PaulTrapExtendedForce myOmegaR framework/forces/PaulTrapExtendedForce.h /^ std::vector myOmegaR;$/;" m class:ProtoMol::PaulTrapExtendedForce myOmegaR framework/frontend/OutputPaulTrap.h /^ Real myOmegaR;$/;" m class:ProtoMol::OutputPaulTrap myOmegaR1 framework/forces/PaulTrapExtendedForce.h /^ Real myOmegaR1;$/;" m class:ProtoMol::PaulTrapExtendedForce myOmegaZ framework/forces/PaulTrapExtendedForce.h /^ std::vector myOmegaZ;$/;" m class:ProtoMol::PaulTrapExtendedForce myOmegaZ framework/frontend/OutputPaulTrap.h /^ Real myOmegaZ;$/;" m class:ProtoMol::OutputPaulTrap myOmegaZ1 framework/forces/PaulTrapExtendedForce.h /^ Real myOmegaZ1;$/;" m class:ProtoMol::PaulTrapExtendedForce myOneAtomPair framework/forces/NonbondedCutoffForce.h /^ TOneAtomPair myOneAtomPair;$/;" m class:ProtoMol::NonbondedCutoffForce myOneAtomPair framework/forces/NonbondedFullSystemForce.h /^ TOneAtomPair myOneAtomPair;$/;" m class:ProtoMol::NonbondedFullSystemForce myOneAtomPair framework/forces/NonbondedSimpleFullSystemForce.h /^ TOneAtomPair myOneAtomPair;$/;" m class:ProtoMol::NonbondedSimpleFullSystemForce myOptimize framework/integrators/ShadowHMCIntegrator.h /^ bool myOptimize;$/;" m class:ProtoMol::ShadowHMCIntegrator myOrder framework/integrators/Modifier.h /^ int myOrder;$/;" m class:ProtoMol::Modifier myOrder framework/integrators/ShadowHMCIntegrator.h /^ unsigned int myOrder,$/;" m class:ProtoMol::ShadowHMCIntegrator myOrder framework/topology/CmpCnCnSwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, myCompoff, myCompoff2, myOrder;$/;" m class:ProtoMol::CmpCnCnSwitchingFunction myOrder framework/topology/CnSwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, myOrder, mySwitchoff;$/;" m class:ProtoMol::CnSwitchingFunction myOrder2k framework/integrators/ModifierShadow.h /^ unsigned int myOrder2k,$/;" m class:ProtoMol::ModifierShadow myOrigFunc framework/topology/ComplementSwitchingFunction.h /^ TOriginalSwitchingFunction myOrigFunc;$/;" m class:ProtoMol::ComplementSwitchingFunction myOrigFunc framework/topology/RangeSwitchingFunction.h /^ TOriginalSwitchingFunction myOrigFunc;$/;" m class:ProtoMol::RangeSwitchingFunction myOrigin framework/base/MultiGrid.h /^ Vector3D myOrigin; \/\/ $/;" m class:ProtoMol::MultiGrid myOrigin framework/forces/ElectricFieldSystemForce.h /^ Vector3D myOrigin;$/;" m class:ProtoMol::ElectricFieldSystemForce myOrigin framework/forces/NonbondedFullEwaldSystemForce.h /^ Vector3D myOrigin;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myOrigin framework/forces/NonbondedMultiGridSystemForce.h /^ Vector3D myOrigin;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myOrigin framework/forces/NonbondedPMEwaldSystemForce.h /^ Vector3D myOrigin;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myOrigin framework/topology/PeriodicBoundaryConditions.h /^ Vector3D myOrigin;$/;" m class:ProtoMol::PeriodicBoundaryConditions myOrthogonal framework/topology/PeriodicBoundaryConditions.h /^ bool myOrthogonal;$/;" m class:ProtoMol::PeriodicBoundaryConditions myOutputFreq framework/frontend/Output.h /^ int myOutputFreq; \/\/\/< Output freqeuncy$/;" m class:ProtoMol::Output myOutputList framework/frontend/OutputCollection.h /^ Container myOutputList;$/;" m class:ProtoMol::OutputCollection myP framework/frontend/OutputCache.h /^ mutable Real myP;$/;" m class:ProtoMol::OutputCache myP framework/parallel/Parallel-FD.cpp /^ int Parallel::myP;$/;" m class:ProtoMol::Parallel file: myP framework/parallel/Parallel.cpp /^ int Parallel::myP;$/;" m class:ProtoMol::Parallel file: myP framework/parallel/Parallel.h /^ static int myP; \/\/\/< Node number$/;" m class:ProtoMol::Parallel myPAR framework/frontend/OutputCache.h /^ PAR myPAR;$/;" m class:ProtoMol::OutputCache myPAR framework/io/AMBERReader.h /^ PAR *myPAR;$/;" m class:ProtoMol::AMBERReader myPAR framework/io/PARReader.h /^ PAR* myPAR;$/;" m class:ProtoMol::PARReader myPARFile tools/rem/sequential/replica.h /^ string myPARFile;$/;" m class:Replica myPDBFile tools/rem/sequential/replica.h /^ string myPDBFile;$/;" m class:Replica myPE framework/frontend/OutputCache.h /^ mutable Real myPE;$/;" m class:ProtoMol::OutputCache myPGM framework/io/PGMReader.h /^ PGM* myPGM;$/;" m class:ProtoMol::PGMReader myPOSA framework/frontend/OutputState.h /^ XYZTrajectoryWriter* myPOSA;$/;" m class:ProtoMol::OutputState myPOSB framework/frontend/OutputState.h /^ XYZTrajectoryWriter* myPOSB;$/;" m class:ProtoMol::OutputState myPPM framework/io/PPMReader.h /^ PPM* myPPM;$/;" m class:ProtoMol::PPMReader myPSF framework/frontend/OutputCache.h /^ PSF myPSF;$/;" m class:ProtoMol::OutputCache myPSF framework/io/AMBERReader.h /^ PSF *myPSF;$/;" m class:ProtoMol::AMBERReader myPSF framework/io/PSFReader.h /^ PSF* myPSF;$/;" m class:ProtoMol::PSFReader myPSFFile tools/rem/sequential/replica.h /^ string myPSFFile;$/;" m class:Replica myParameterSize framework/forces/WrapperMetaForce.h /^ unsigned int myParameterSize;$/;" m class:ProtoMol::WrapperMetaForce myParameters framework/forces/WrapperMetaForce.h /^ std::vector myParameters;$/;" m class:ProtoMol::WrapperMetaForce myParameters tools/rem/sequential/replica.h /^ vector myParameters;$/;" m class:Replica myParentDir tools/rem/sequential/replica.h /^ string myParentDir;$/;" m class:Replica myPart framework/integrators/PaulTrapIntegrator.h /^ Real myPart;$/;" m class:ProtoMol::PaulTrapIntegrator myPartReal framework/integrators/PaulTrapIntegrator.h /^ Real myPartReal;$/;" m class:ProtoMol::PaulTrapIntegrator myPaulA framework/frontend/OutputPaulTrap.h /^ Real myPaulA;$/;" m class:ProtoMol::OutputPaulTrap myPaulF framework/forces/PaulTrapExtendedForce.h /^ Real myPaulF;$/;" m class:ProtoMol::PaulTrapExtendedForce myPaulF framework/frontend/OutputPaulTrap.h /^ Real myPaulF;$/;" m class:ProtoMol::OutputPaulTrap myPaulF2 framework/frontend/OutputPaulTrap.h /^ Real myPaulF2;$/;" m class:ProtoMol::OutputPaulTrap myPaulK framework/frontend/OutputPaulTrap.h /^ Real myPaulK;$/;" m class:ProtoMol::OutputPaulTrap myPaulLow framework/frontend/OutputPaulTrap.h /^ Real myPaulLow;$/;" m class:ProtoMol::OutputPaulTrap myPaulM framework/frontend/OutputPaulTrap.h /^ Real myPaulM;$/;" m class:ProtoMol::OutputPaulTrap myPaulOmega framework/frontend/OutputPaulTrap.h /^ Real myPaulOmega;$/;" m class:ProtoMol::OutputPaulTrap myPaulQ framework/frontend/OutputPaulTrap.h /^ Real myPaulQ;$/;" m class:ProtoMol::OutputPaulTrap myPaulR framework/frontend/OutputPaulTrap.h /^ Real myPaulR;$/;" m class:ProtoMol::OutputPaulTrap myPaulUHom framework/forces/PaulTrapExtendedForce.h /^ Real myPaulUHom;$/;" m class:ProtoMol::PaulTrapExtendedForce myPaulUHom framework/frontend/OutputPaulTrap.h /^ Real myPaulUHom;$/;" m class:ProtoMol::OutputPaulTrap myPhi framework/forces/MagneticDipoleForce.h /^ Real myChi, myR, myOmega, myPhi, myHx, myHy, myHz, myD;$/;" m class:ProtoMol::MagneticDipoleForce myPipeSize framework/parallel/Parallel-FD.cpp /^ int Parallel::myPipeSize = 1;$/;" m class:ProtoMol::Parallel file: myPipeSize framework/parallel/Parallel.cpp /^ int Parallel::myPipeSize = 1;$/;" m class:ProtoMol::Parallel file: myPipeSize framework/parallel/Parallel.h /^ static int myPipeSize; \/\/\/< Number of add. work packages to push to slaves$/;" m class:ProtoMol::Parallel myPointSelfEnergy framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myPointSelfEnergy; \/\/ Precomputed energy terms$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myPointSelfEnergy framework/forces/NonbondedMultiGridSystemForce.h /^ Real myPointSelfEnergy;\/\/ Precomputed energy terms$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myPointSelfEnergy framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myPointSelfEnergy; \/\/ Precomputed energy terms$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myPointers framework/frontend/Factory.h /^ std::set myPointers;$/;" m class:ProtoMol::FactoryBase myPort framework/imd/HapticSystemForce.h /^ int myPort;$/;" m class:ProtoMol::HapticSystemForce myPositions framework/frontend/Output.h /^ const Vector3DBlock* myPositions;$/;" m class:ProtoMol::Output myPositions framework/frontend/OutputCache.h /^ const Vector3DBlock* myPositions;$/;" m class:ProtoMol::OutputCache myPositions framework/frontend/OutputCollection.h /^ const Vector3DBlock* myPositions;$/;" m class:ProtoMol::OutputCollection myPositions framework/integrators/Integrator.h /^ Vector3DBlock *myPositions;$/;" m class:ProtoMol::Integrator myPositions framework/integrators/Modifier.h /^ Vector3DBlock* myPositions;$/;" m class:ProtoMol::Modifier myPostDriftOrNextModifiers framework/integrators/Integrator.h /^ std::set myPostDriftOrNextModifiers;$/;" m class:ProtoMol::Integrator myPostForceModifiers framework/integrators/Integrator.h /^ std::set myPostForceModifiers;$/;" m class:ProtoMol::Integrator myPostStepModifiers framework/integrators/Integrator.h /^ std::set myPostStepModifiers;$/;" m class:ProtoMol::Integrator myPotEnergy framework/integrators/Integrator.h /^ Real myPotEnergy;$/;" m class:ProtoMol::Integrator myPreDriftOrNextModifiers framework/integrators/Integrator.h /^ std::set myPreDriftOrNextModifiers;$/;" m class:ProtoMol::Integrator myPreForceModifiers framework/integrators/Integrator.h /^ std::set myPreForceModifiers;$/;" m class:ProtoMol::Integrator myPreStepModifiers framework/integrators/Integrator.h /^ std::set myPreStepModifiers;$/;" m class:ProtoMol::Integrator myPreviousIntegrator framework/integrators/StandardIntegrator.h /^ StandardIntegrator *myPreviousIntegrator;$/;" m class:ProtoMol::StandardIntegrator myProtomol tools/rem/sequential/replica.h /^ string myProtomol;$/;" m class:Replica myPxAngle framework/integrators/BSplineMOLLYIntegrator.h /^ std::vector *myPxAngle; $/;" m class:ProtoMol::BSplineMOLLYIntegrator myQ framework/base/Grid.h /^ Array myQ; $/;" m class:ProtoMol::Grid myQ framework/base/MultiGrid.h /^ std::vector > myQ; \/\/\/< Arrays of charges$/;" m class:ProtoMol::MultiGrid myQTmp framework/base/Grid.h /^ Array myQTmp; $/;" m class:ProtoMol::Grid myQuit framework/base/Report.h /^ bool myQuit;$/;" m class:ProtoMol::Report::MyStreamer myR framework/forces/MagneticDipoleForce.h /^ Real myChi, myR, myOmega, myPhi, myHx, myHy, myHz, myD;$/;" m class:ProtoMol::MagneticDipoleForce myR framework/forces/MagneticDipoleMirrorSystemForce.h /^ Real myChi, myR, myD, myHx, myHy, myHz, myF;$/;" m class:ProtoMol::MagneticDipoleMirrorSystemForce myR0 framework/forces/PaulTrapExtendedForce.h /^ Real myR0;$/;" m class:ProtoMol::PaulTrapExtendedForce myR0 framework/topology/RangeSwitchingFunction.h /^ Real myR0;$/;" m class:ProtoMol::RangeSwitchingFunction myR0Squared framework/topology/RangeSwitchingFunction.h /^ Real myR0Squared;$/;" m class:ProtoMol::RangeSwitchingFunction myR1 framework/topology/RangeSwitchingFunction.h /^ Real myR1; $/;" m class:ProtoMol::RangeSwitchingFunction myR1Squared framework/topology/RangeSwitchingFunction.h /^ Real myR1Squared; $/;" m class:ProtoMol::RangeSwitchingFunction myREMRates framework/frontend/OutputCache.h /^ std::vector myREMRates;$/;" m class:ProtoMol::OutputCache myRS framework/base/MultiGrid.h /^ Real myRS; \/\/\/< 1 \/ Softening distance$/;" m class:ProtoMol::MultiGrid myRS framework/forces/CoulombMultiGridDirectForce.h /^ Real myRS;$/;" m class:ProtoMol::CoulombMultiGridDirectForce myRS framework/forces/NonbondedMultiGridSystemForce.h /^ Real myRS;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myRadius framework/forces/SphericalSystemForce.h /^ Real myRadius;$/;" m class:ProtoMol::SphericalSystemForce myRadius framework/io/XFigWriter.h /^ Real myRadius;$/;" m class:ProtoMol::XFigWriter myRadius2 framework/forces/SphericalSystemForce.h /^ Real myRadius2;$/;" m class:ProtoMol::SphericalSystemForce myRandomForces framework/integrators/DMDLeapfrogIntegrator.h /^ Vector3DBlock *myRandomForces;$/;" m class:ProtoMol::DMDLeapfrogIntegrator myRatio framework/base/MultiGrid.h /^ int myRatio; \/\/\/< Ratio between to levels, usually 2$/;" m class:ProtoMol::MultiGrid myRatio framework/forces/NonbondedMultiGridSystemForce.h /^ unsigned int myRatio;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myRatio framework/integrators/ShadowHMCIntegrator.h /^ Real myRatio;$/;" m class:ProtoMol::ShadowHMCIntegrator myRc framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myRc; \/\/ Cutoff real term$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myRc framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myRc; \/\/ Cutoff real term$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myRcSquared framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myRcSquared; \/\/ Cutoff squared real term$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myRcSquared framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myRcSquared; \/\/ Cutoff squared real term$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myReal framework/forces/NonbondedFullEwaldSystemForce.h /^ Timer myReal;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myReal framework/forces/NonbondedPMEwaldSystemForce.h /^ Timer myReal;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myRealCellSize framework/topology/CubicCellManager.h /^ mutable Vector3D myRealCellSize;$/;" m class:ProtoMol::CubicCellManager myRealRCellSize framework/topology/CubicCellManager.h /^ mutable Vector3D myRealRCellSize;$/;" m class:ProtoMol::CubicCellManager myRealTime framework/base/Timer.h /^ double myRealTime;$/;" m class:ProtoMol::TimeRep myReciprocal framework/forces/NonbondedFullEwaldSystemForce.h /^ Timer myReciprocal;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myReciprocal framework/forces/NonbondedPMEwaldSystemForce.h /^ Timer myReciprocal;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myRecv framework/parallel/Parallel-FD.cpp /^ int Parallel::myRecv;$/;" m class:ProtoMol::Parallel file: myRecv framework/parallel/Parallel.cpp /^ int Parallel::myRecv;$/;" m class:ProtoMol::Parallel file: myRecv framework/parallel/Parallel.h /^ static int myRecv; \/\/\/< Number of outstanding receives$/;" m class:ProtoMol::Parallel myRemoveAngularMotion framework/integrators/PaulTrapIntegrator.h /^ bool myRemoveAngularMotion;$/;" m class:ProtoMol::PaulTrapIntegrator myRemoveCommonMotion framework/integrators/PaulTrapIntegrator.h /^ bool myRemoveCommonMotion;$/;" m class:ProtoMol::PaulTrapIntegrator myReplicaHistory framework/frontend/OutputCache.h /^ const Real *myReplicaHistory;$/;" m class:ProtoMol::OutputCache myReportLevel framework/base/Report.h /^ short myReportLevel;$/;" m class:ProtoMol::Report::MyStreamer myReportlevel framework/base/Report.h /^ short myReportlevel;$/;" m class:ProtoMol::Report::reportlevel myResetFlags framework/base/Report.h /^ std::ios::fmtflags myResetFlags;\/\/ Resest\/default flags$/;" m class:ProtoMol::Report::MyStreamer myRnd framework/forces/FrictionExtendedForce.h /^ Vector3D myRnd;$/;" m class:ProtoMol::FrictionExtendedForce myRunningFlag framework/base/Cycles.h /^ bool myRunningFlag;$/;" m class:ProtoMol::Cycles myRunningFlag framework/base/Timer.h /^ bool myRunningFlag;$/;" m class:ProtoMol::Timer myS framework/base/MultiGrid.h /^ Real myS; \/\/\/< Softening distance$/;" m class:ProtoMol::MultiGrid myS framework/forces/CoulombMultiGridDirectForce.h /^ Real myS;$/;" m class:ProtoMol::CoulombMultiGridDirectForce myS framework/forces/CoulombMultiGridDirectTableForce.h /^ Real myS;$/;" m class:ProtoMol::CoulombMultiGridDirectTableForce myS framework/forces/CoulombMultiGridDirectTableForceBase.h /^ Real myS;$/;" m class:ProtoMol::CoulombMultiGridDirectTableForceBase::LookUpValues myS framework/forces/NonbondedMultiGridSystemForce.h /^ Real myS;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myS2 framework/forces/NonbondedMultiGridSystemForce.h /^ Real myS2;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myScale framework/base/MultiGrid.h /^ std::vector myScale; \/\/\/< Scaling factor for each level$/;" m class:ProtoMol::MultiGrid myScale framework/frontend/OutputBSDL.h /^ Real myScale;$/;" m class:ProtoMol::OutputBSDL myScaledParticleIntPositions framework/base/Grid.h /^ std::vector myScaledParticleIntPositions;$/;" m class:ProtoMol::Grid myScaledParticleIntPositions framework/base/MultiGrid.h /^ std::vector myScaledParticleIntPositions; \/\/\/< Starting index for anter\/-interpolation$/;" m class:ProtoMol::MultiGrid myScreen framework/frontend/OutputPaulTrap.h /^ bool myScreen;$/;" m class:ProtoMol::OutputPaulTrap mySeed framework/integrators/BBKIntegrator.h /^ int mySeed;$/;" m class:ProtoMol::BBKIntegrator mySeed framework/integrators/DMDLeapfrogIntegrator.h /^ int mySeed;$/;" m class:ProtoMol::DMDLeapfrogIntegrator mySeed framework/integrators/LangevinImpulseIntegrator.h /^ int mySeed;$/;" m class:ProtoMol::LangevinImpulseIntegrator mySeparateWater framework/frontend/OutputTemperatures.h /^ bool mySeparateWater;$/;" m class:ProtoMol::OutputTemperatures mySet framework/topology/ExclusionTable.h /^ std::set mySet;$/;" m class:ProtoMol::ExclusionTable myShadowK framework/integrators/ModifierShadow.h /^ myShadowK,$/;" m class:ProtoMol::ModifierShadow myShadowK framework/integrators/ShadowHMCIntegrator.h /^ myShadowK;$/;" m class:ProtoMol::ShadowHMCIntegrator mySigma framework/base/MultiGrid.h /^ int mySigma; \/\/\/< 1 if interpolation weights ...,0 for w=0, 0 else$/;" m class:ProtoMol::MultiGrid mySigma framework/integrators/DMDLeapfrogIntegrator.h /^ Real mySigma;$/;" m class:ProtoMol::DMDLeapfrogIntegrator mySilentHint framework/base/Report.h /^ short mySilentHint;$/;" m class:ProtoMol::Report::MyStreamer mySinCos framework/forces/NonbondedFullEwaldSystemForce.h /^ Vector3D* mySinCos;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce mySinCosA framework/forces/NonbondedFullEwaldSystemForce.h /^ Real* mySinCosA; \/\/ Look up tables$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce mySize framework/base/LookUpTableBase.h /^ int mySize;$/;" m class:ProtoMol::LookUpTableBase mySize framework/io/XYZBinWriter.h /^ unsigned int mySize;$/;" m class:ProtoMol::XYZBinWriter mySize framework/topology/ArrayCellListStructure.h /^ size_type mySize;$/;" m class:ProtoMol::ArrayCellListStructure mySourceConfig tools/rem/sequential/replica.h /^ string mySourceConfig;$/;" m class:Replica mySquaredCutoff framework/forces/ElectricFieldSystemForce.h /^ Real mySquaredCutoff;$/;" m class:ProtoMol::ElectricFieldSystemForce mySquaredCutoff framework/forces/OneAtomPair.h /^ Real mySquaredCutoff;$/;" m class:ProtoMol::OneAtomPair mySquaredCutoff framework/forces/OneAtomPairTwo.h /^ Real mySquaredCutoff;$/;" m class:ProtoMol::OneAtomPairTwo myStartSerial framework/base/systemutilities.cpp /^ static void (*myStartSerial)(bool) = NULL;$/;" v file: myStartTime framework/base/Cycles.h /^ ticks myStartTime;$/;" m class:ProtoMol::Cycles myStartTime framework/base/Timer.h /^ TimeRep myStartTime;$/;" m class:ProtoMol::Timer myStatesFile framework/frontend/OutputState.h /^ std::string myStatesFile;$/;" m class:ProtoMol::OutputState myStep framework/integrators/ModifierRemoveAngularMomentum.h /^ int myStep;$/;" m class:ProtoMol::ModifierRemoveAngularMomentum myStep framework/integrators/ModifierRemoveLinearMomentum.h /^ int myStep;$/;" m class:ProtoMol::ModifierRemoveLinearMomentum myStepCounter framework/imd/HapticSystemForce.h /^ int myStepCounter;$/;" m class:ProtoMol::HapticSystemForce myStepInc framework/imd/HapticSystemForce.h /^ int myStepInc;$/;" m class:ProtoMol::HapticSystemForce myStoredBeta framework/integrators/ModifierShadow.h /^ std::deque< Real > myStoredBeta;$/;" m class:ProtoMol::ModifierShadow myStoredPos framework/integrators/ModifierShadow.h /^ std::deque< Vector3DBlock > myStoredPos,$/;" m class:ProtoMol::ModifierShadow myStoredVel framework/integrators/ModifierShadow.h /^ myStoredVel;$/;" m class:ProtoMol::ModifierShadow myStream framework/base/Report.h /^ std::ostream* myStream;$/;" m class:ProtoMol::Report::MyStreamer mySumMass framework/integrators/NoseNVTLeapfrogIntegrator.h /^ Real mySumMass;$/;" m class:ProtoMol::NoseNVTLeapfrogIntegrator mySurface framework/forces/NonbondedFullEwaldSystemForce.h /^ Timer mySurface;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce mySurface framework/forces/NonbondedPMEwaldSystemForce.h /^ Timer mySurface;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce mySwapEndian framework/io/DCDTrajectoryReader.h /^ bool mySwapEndian;$/;" m class:ProtoMol::DCDTrajectoryReader mySwapPositions framework/integrators/MOLLYIntegrator.h /^ Vector3DBlock* mySwapPositions;$/;" m class:ProtoMol::MOLLYIntegrator mySwitch1 framework/topology/C2SwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, mySwitch1, mySwitch2, mySwitch3;$/;" m class:ProtoMol::C2SwitchingFunction mySwitch2 framework/topology/C2SwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, mySwitch1, mySwitch2, mySwitch3;$/;" m class:ProtoMol::C2SwitchingFunction mySwitch3 framework/topology/C2SwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, mySwitch1, mySwitch2, mySwitch3;$/;" m class:ProtoMol::C2SwitchingFunction mySwitchoff framework/topology/CnSwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, myOrder, mySwitchoff;$/;" m class:ProtoMol::CnSwitchingFunction mySwitchon framework/topology/C2SwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, mySwitch1, mySwitch2, mySwitch3;$/;" m class:ProtoMol::C2SwitchingFunction mySwitchon framework/topology/CmpCnCnSwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, myCompoff, myCompoff2, myOrder;$/;" m class:ProtoMol::CmpCnCnSwitchingFunction mySwitchon framework/topology/CnSwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, myOrder, mySwitchoff;$/;" m class:ProtoMol::CnSwitchingFunction mySwitchon2 framework/topology/C2SwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, mySwitch1, mySwitch2, mySwitch3;$/;" m class:ProtoMol::C2SwitchingFunction mySwitchon2 framework/topology/CmpCnCnSwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, myCompoff, myCompoff2, myOrder;$/;" m class:ProtoMol::CmpCnCnSwitchingFunction mySwitchon2 framework/topology/CnSwitchingFunction.h /^ Real mySwitchon, mySwitchon2, myCutoff, myCutoff2, myOrder, mySwitchoff;$/;" m class:ProtoMol::CnSwitchingFunction mySystemForcesList framework/forces/ForceGroup.h /^ std::list mySystemForcesList;$/;" m class:ProtoMol::ForceGroup mySystemTime framework/base/Timer.h /^ double mySystemTime;$/;" m class:ProtoMol::TimeRep myT framework/frontend/OutputCache.h /^ mutable Real myT;$/;" m class:ProtoMol::OutputCache myT framework/integrators/PaulTrapIntegrator.h /^ std::vector myT;$/;" m class:ProtoMol::PaulTrapIntegrator myTRate framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myTRate; \/\/$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myTRate framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myTRate; \/\/$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myTable framework/base/LookUpTableBase.h /^ TReal* myTable;$/;" m class:ProtoMol::LookUpTableBase myTable framework/base/ScalarStructure.h /^ Real myTable[LAST-FIRST];$/;" m class:ProtoMol::ScalarStructure myTable framework/topology/ExclusionTable.h /^ std::vector myTable;$/;" m class:ProtoMol::ExclusionTable myTargetKE framework/integrators/NoseNVTLeapfrogIntegrator.h /^ Real myTargetKE;$/;" m class:ProtoMol::NoseNVTLeapfrogIntegrator myTargetPres framework/integrators/NPTVerletIntegrator.h /^ const Real myTargetPres; \/\/ Target pressure. Units: (bar)$/;" m class:ProtoMol::NPTVerletIntegrator myTargetTemp framework/integrators/NPTVerletIntegrator.h /^ const Real myTargetTemp; \/\/ Target temperature. Units: (K)$/;" m class:ProtoMol::NPTVerletIntegrator myTargetTemp framework/integrators/NVTVerletIntegrator.h /^ const Real myTargetTemp; \/\/ Target temperature. Units: (K)$/;" m class:ProtoMol::NVTVerletIntegrator myTargetTemperature tools/rem/sequential/replica.h /^ double myTargetTemperature;$/;" m class:Replica myTauP framework/integrators/NPTVerletIntegrator.h /^ const Real myTauP; \/\/ box volumr oscillation time constant. Units: (fs)$/;" m class:ProtoMol::NPTVerletIntegrator myTauT framework/integrators/NPTVerletIntegrator.h /^ const Real myTauT; \/\/ thermostat oscillation period. Units: (fs)$/;" m class:ProtoMol::NPTVerletIntegrator myTauT framework/integrators/NVTVerletIntegrator.h /^ const Real myTauT; \/\/ thermostat oscillation time period. Units: (fs)$/;" m class:ProtoMol::NVTVerletIntegrator myTauV framework/integrators/NPTVerletIntegrator.h /^ const Real myTauV; \/\/ box volume thermostat oscillation period. Units: (fs)$/;" m class:ProtoMol::NPTVerletIntegrator myTemp framework/io/REMConfigurationReader.h /^ Real myTemp;$/;" m class:ProtoMol::REMConfigurationReader myTemp framework/io/TempFileReader.h /^ Real myTemp;$/;" m class:ProtoMol::TempFileReader myTempForces framework/integrators/PLeapfrogIntegrator.h /^ Vector3DBlock* myTempForces;$/;" m class:ProtoMol::PLeapfrogIntegrator myTemperature framework/integrators/DMDLeapfrogIntegrator.h /^ Real myTemperature;$/;" m class:ProtoMol::DMDLeapfrogIntegrator myTemperature framework/integrators/NoseNVTLeapfrogIntegrator.h /^ const Real myTemperature;$/;" m class:ProtoMol::NoseNVTLeapfrogIntegrator myTemperature framework/integrators/PaulTrapIntegrator.h /^ const Real myTemperature;$/;" m class:ProtoMol::PaulTrapIntegrator myTemperatureFile tools/rem/sequential/replica.h /^ string myTemperatureFile;$/;" m class:Replica myTers framework/io/PDBReader.h /^ std::vector* myTers;$/;" m class:ProtoMol::PDBReader myTexts framework/base/Configuration.h /^ TextMapType myTexts;$/;" m class:ProtoMol::Configuration myTheIntegrator framework/integrators/ModifierAveraging.h /^ MOLLYIntegrator* myTheIntegrator;$/;" m class:ProtoMol::ModifierAveraging myTheIntegrator framework/integrators/ModifierFriction.h /^ NoseNVTLeapfrogIntegrator* myTheIntegrator;$/;" m class:ProtoMol::ModifierFriction myTheIntegrator framework/integrators/ModifierIncrementTimestep.h /^ STSIntegrator* myTheIntegrator;$/;" m class:ProtoMol::ModifierIncrementTimestep myTheIntegrator framework/integrators/ModifierMollification.h /^ MOLLYIntegrator* myTheIntegrator;$/;" m class:ProtoMol::ModifierMollification myTheIntegrator framework/integrators/ModifierNPTRattle.h /^ const TIntegrator* myTheIntegrator;$/;" m class:ProtoMol::ModifierNPTRattle myTheIntegrator framework/integrators/ModifierNPTShake.h /^ const TIntegrator* myTheIntegrator;$/;" m class:ProtoMol::ModifierNPTShake myTheIntegrator framework/integrators/ModifierNVTRattle.h /^ const TIntegrator* myTheIntegrator;$/;" m class:ProtoMol::ModifierNVTRattle myTheIntegrator framework/integrators/ModifierNVTShake.h /^ const TIntegrator* myTheIntegrator;$/;" m class:ProtoMol::ModifierNVTShake myTheIntegrator framework/integrators/ModifierPostForceBarostat.h /^ TIntegrator* myTheIntegrator;$/;" m class:ProtoMol::ModifierPostForceBarostat myTheIntegrator framework/integrators/ModifierPostForceThermostat.h /^ TIntegrator* myTheIntegrator;$/;" m class:ProtoMol::ModifierPostForceThermostat myTheIntegrator framework/integrators/ModifierPreForceBarostat.h /^ TIntegrator* myTheIntegrator;$/;" m class:ProtoMol::ModifierPreForceBarostat myTheIntegrator framework/integrators/ModifierPreForceThermostat.h /^ TIntegrator* myTheIntegrator;$/;" m class:ProtoMol::ModifierPreForceThermostat myTheIntegrator framework/integrators/ModifierRattle.h /^ const Integrator* myTheIntegrator;$/;" m class:ProtoMol::ModifierRattle myTheIntegrator framework/integrators/ModifierShake.h /^ const Integrator* myTheIntegrator;$/;" m class:ProtoMol::ModifierShake myThermalInertia framework/integrators/NoseNVTLeapfrogIntegrator.h /^ const Real myThermalInertia;$/;" m class:ProtoMol::NoseNVTLeapfrogIntegrator myThermalInertia framework/integrators/PaulTrapIntegrator.h /^ const Real myThermalInertia;$/;" m class:ProtoMol::PaulTrapIntegrator myThermostatType framework/integrators/PaulTrapIntegrator.h /^ ThermostatType myThermostatType;$/;" m class:ProtoMol::PaulTrapIntegrator myTime framework/integrators/PaulTrapIntegrator.h /^ std::vector myTime;$/;" m class:ProtoMol::PaulTrapIntegrator myTimeAnterpolate framework/forces/NonbondedMultiGridSystemForce.h /^ Timer myTimeAnterpolate;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myTimeCoarseToFine framework/forces/NonbondedMultiGridSystemForce.h /^ std::vector myTimeCoarseToFine;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myTimeCorrection framework/forces/NonbondedMultiGridSystemForce.h /^ Timer myTimeCorrection;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myTimeCorrectionMG framework/forces/NonbondedMultiGridSystemForce.h /^ std::vector myTimeCorrectionMG; $/;" m class:ProtoMol::NonbondedMultiGridSystemForce myTimeDirect framework/forces/NonbondedMultiGridSystemForce.h /^ Timer myTimeDirect;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myTimeFineToCoarse framework/forces/NonbondedMultiGridSystemForce.h /^ std::vector myTimeFineToCoarse;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myTimeInit framework/forces/NonbondedMultiGridSystemForce.h /^ Timer myTimeInit; $/;" m class:ProtoMol::NonbondedMultiGridSystemForce myTimeInterpolate framework/forces/NonbondedMultiGridSystemForce.h /^ Timer myTimeInterpolate;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myTimeList framework/forces/TimeForce.h /^ std::vector myTimeList;$/;" m class:ProtoMol::TimeForce myTimeLong framework/forces/NonbondedMultiGridSystemForce.h /^ Timer myTimeLong; $/;" m class:ProtoMol::NonbondedMultiGridSystemForce myTimeShort framework/forces/NonbondedMultiGridSystemForce.h /^ Timer myTimeShort; $/;" m class:ProtoMol::NonbondedMultiGridSystemForce myTimeStep framework/io/DCDTrajectoryWriter.h /^ Real myTimeStep;$/;" m class:ProtoMol::DCDTrajectoryWriter myTimer framework/forces/TimeForce.h /^ Timer myTimer;$/;" m class:ProtoMol::TimeForce myTimer framework/frontend/OutputFile.h /^ Timer myTimer;$/;" m class:ProtoMol::OutputFile myTimestep framework/integrators/STSIntegrator.h /^ Real myTimestep;$/;" m class:ProtoMol::STSIntegrator myToRange framework/forces/NonbondedFullSystemForce.h /^ std::vector myToRange;$/;" m class:ProtoMol::NonbondedFullSystemForce myToRange framework/forces/NonbondedSimpleFullSystemForce.h /^ std::vector myToRange;$/;" m class:ProtoMol::NonbondedSimpleFullSystemForce myToZ framework/io/XFigWriter.h /^ Real myToZ;$/;" m class:ProtoMol::XFigWriter myTopo framework/integrators/Integrator.h /^ GenericTopology *myTopo;$/;" m class:ProtoMol::Integrator myTopology framework/frontend/Output.h /^ const GenericTopology* myTopology; $/;" m class:ProtoMol::Output myTopology framework/frontend/OutputCache.h /^ const GenericTopology* myTopology; $/;" m class:ProtoMol::OutputCache myTopology framework/frontend/OutputCollection.h /^ const GenericTopology* myTopology; $/;" m class:ProtoMol::OutputCollection myTopology framework/integrators/Modifier.h /^ GenericTopology* myTopology; $/;" m class:ProtoMol::Modifier myTotalTime framework/base/Timer.h /^ TimeRep myTotalTime;$/;" m class:ProtoMol::Timer myType framework/base/AbstractEnumType.h /^ Enum myType;$/;" m class:ProtoMol::AbstractEnumType myType framework/frontend/InputPosVel.h /^ InputPosVelType myType;$/;" m class:ProtoMol::InputPosVel myTypeOfBSpline framework/integrators/BSplineMOLLYIntegrator.h /^ BSplineType myTypeOfBSpline;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myU0 framework/forces/PaulTrapExtendedForce.h /^ Real myU0;$/;" m class:ProtoMol::PaulTrapExtendedForce myUnit framework/frontend/OutputPaulTrap.h /^ std::string myUnit;$/;" m class:ProtoMol::OutputPaulTrap myUnit framework/frontend/OutputScreen.h /^ std::string myUnit;$/;" m class:ProtoMol::OutputScreen myUseBarrier framework/parallel/Parallel-FD.cpp /^ bool Parallel::myUseBarrier = false;$/;" m class:ProtoMol::Parallel file: myUseBarrier framework/parallel/Parallel.cpp /^ bool Parallel::myUseBarrier = false;$/;" m class:ProtoMol::Parallel file: myUseBarrier framework/parallel/Parallel.h /^ static bool myUseBarrier; \/\/\/< Flag to signal usage of MPI_Barrier$/;" m class:ProtoMol::Parallel myUserTime framework/base/Timer.h /^ double myUserTime;$/;" m class:ProtoMol::TimeRep myV framework/base/Grid.h /^ Real myV;$/;" m class:ProtoMol::Grid myV framework/base/MultiGrid.h /^ std::vector > myV; \/\/\/< Arrays of potentials$/;" m class:ProtoMol::MultiGrid myV framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myV,myVr;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myV framework/forces/NonbondedMultiGridSystemForce.h /^ Real myV;$/;" m class:ProtoMol::NonbondedMultiGridSystemForce myV framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myV,myVr;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myV framework/frontend/OutputCache.h /^ mutable Real myV;$/;" m class:ProtoMol::OutputCache myV framework/topology/PeriodicBoundaryConditions.h /^ Real myV;$/;" m class:ProtoMol::PeriodicBoundaryConditions myVELA framework/frontend/OutputState.h /^ XYZTrajectoryWriter* myVELA;$/;" m class:ProtoMol::OutputState myVELB framework/frontend/OutputState.h /^ XYZTrajectoryWriter* myVELB;$/;" m class:ProtoMol::OutputState myValue framework/base/Value.h /^ PlaceHolder* myValue;$/;" m class:ProtoMol::Value myValue framework/frontend/InputValue.h /^ Value myValue;$/;" m class:ProtoMol::InputValue myValues framework/base/Configuration.h /^ ValueMapType myValues;$/;" m class:ProtoMol::Configuration myVector framework/base/Vector.h /^ std::vector & myVector;$/;" m class:ProtoMol::VectorPacker myVector framework/base/Vector.h /^ std::vector myVector; $/;" m class:ProtoMol::Vector myVelocities framework/frontend/Output.h /^ const Vector3DBlock* myVelocities; $/;" m class:ProtoMol::Output myVelocities framework/frontend/OutputCache.h /^ const Vector3DBlock* myVelocities; $/;" m class:ProtoMol::OutputCache myVelocities framework/frontend/OutputCollection.h /^ const Vector3DBlock* myVelocities; $/;" m class:ProtoMol::OutputCollection myVelocities framework/integrators/Integrator.h /^ Vector3DBlock *myVelocities;$/;" m class:ProtoMol::Integrator myVelocities framework/integrators/Modifier.h /^ Vector3DBlock* myVelocities; $/;" m class:ProtoMol::Modifier myVhat framework/integrators/DMDLeapfrogIntegrator.h /^ Vector3DBlock *myVhat;$/;" m class:ProtoMol::DMDLeapfrogIntegrator myView framework/frontend/OutputBSDL.h /^ std::string myView;$/;" m class:ProtoMol::OutputBSDL myVolume framework/integrators/NPTVerletIntegrator.h /^ Real myVolume; \/\/ Current cubic volume. Units (AA^3)$/;" m class:ProtoMol::NPTVerletIntegrator myVr framework/forces/NonbondedFullEwaldSystemForce.h /^ Real myV,myVr;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce myVr framework/forces/NonbondedPMEwaldSystemForce.h /^ Real myV,myVr;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce myWater framework/frontend/OutputBSDL.h /^ bool myWater;$/;" m class:ProtoMol::OutputBSDL myWaterAtomTypes framework/frontend/OutputTemperatures.h /^ std::vector myWaterAtomTypes;$/;" m class:ProtoMol::OutputTemperatures myWaterT framework/frontend/OutputCache.h /^ mutable Real myWaterT;$/;" m class:ProtoMol::OutputCache myWidth framework/base/Grid.h /^ Real myWidth;$/;" m class:ProtoMol::Grid myWidthr framework/base/Grid.h /^ Real myWidthr;$/;" m class:ProtoMol::Grid myWorkState framework/parallel/Parallel-FD.cpp /^ Parallel::WorkState Parallel::myWorkState = Parallel::SEQUENTIAL;$/;" m class:ProtoMol::Parallel file: myWorkState framework/parallel/Parallel.cpp /^ Parallel::WorkState Parallel::myWorkState = Parallel::SEQUENTIAL;$/;" m class:ProtoMol::Parallel file: myWorkState framework/parallel/Parallel.h /^ static WorkState myWorkState; \/\/\/< Actual work state$/;" m class:ProtoMol::Parallel myX framework/io/DCDTrajectoryReader.h /^ std::vector myX;$/;" m class:ProtoMol::DCDTrajectoryReader myX framework/io/DCDTrajectoryWriter.h /^ std::vector myX;$/;" m class:ProtoMol::DCDTrajectoryWriter myXYZ framework/frontend/OutputXYZBinTrajectoryPos.h /^ XYZBinWriter* myXYZ;$/;" m class:ProtoMol::OutputXYZBinTrajectoryPos myXYZ framework/frontend/OutputXYZBinTrajectoryVel.h /^ XYZBinWriter* myXYZ;$/;" m class:ProtoMol::OutputXYZBinTrajectoryVel myXYZ framework/frontend/OutputXYZTrajectoryForce.h /^ XYZTrajectoryWriter* myXYZ;$/;" m class:ProtoMol::OutputXYZTrajectoryForce myXYZ framework/frontend/OutputXYZTrajectoryPos.h /^ XYZTrajectoryWriter* myXYZ;$/;" m class:ProtoMol::OutputXYZTrajectoryPos myXYZ framework/frontend/OutputXYZTrajectoryVel.h /^ XYZTrajectoryWriter* myXYZ;$/;" m class:ProtoMol::OutputXYZTrajectoryVel myXxAngle framework/integrators/BSplineMOLLYIntegrator.h /^ std::vector *myXxAngle;$/;" m class:ProtoMol::BSplineMOLLYIntegrator myY framework/io/DCDTrajectoryReader.h /^ std::vector myY;$/;" m class:ProtoMol::DCDTrajectoryReader myY framework/io/DCDTrajectoryWriter.h /^ std::vector myY;$/;" m class:ProtoMol::DCDTrajectoryWriter myZ framework/io/DCDTrajectoryReader.h /^ std::vector myZ;$/;" m class:ProtoMol::DCDTrajectoryReader myZ framework/io/DCDTrajectoryWriter.h /^ std::vector myZ;$/;" m class:ProtoMol::DCDTrajectoryWriter my_angle framework/topology/AngleInfo.h /^ Real my_angle;$/;" m class:ProtoMol::AngleInfo my_angleType framework/topology/AngleInfo.h /^ AngleType my_angleType;$/;" m class:ProtoMol::AngleInfo my_atomID framework/topology/AngleInfo.h /^ unsigned int my_atomID;$/;" m class:ProtoMol::AngleInfo my_bondedAtoms framework/topology/AngleInfo.h /^ std::vector my_bondedAtoms;$/;" m class:ProtoMol::AngleInfo my_isExclusionAtom framework/topology/AngleInfo.h /^ bool my_isExclusionAtom;$/;" m class:ProtoMol::AngleInfo my_isInnerAtom framework/topology/AngleInfo.h /^ bool my_isInnerAtom;$/;" m class:ProtoMol::AngleInfo my_pointer framework/topology/AngleInfo.h /^ unsigned int my_pointer;$/;" m class:ProtoMol::AngleInfo my_visited framework/topology/AngleInfo.h /^ bool my_visited;$/;" m class:ProtoMol::AngleInfo mybonds framework/base/Atom.h /^ std::vector< int > mybonds;$/;" m struct:ProtoMol::Atom myerf framework/base/mathutilities.cpp /^ Real myerf(Real x){$/;" f namespace:ProtoMol myiSGPAR framework/frontend/OutputCache.h /^ iSGPAR myiSGPAR;$/;" m class:ProtoMol::OutputCache n compilerTests/glutTest.cpp /^static GLfloat n[6][3] = { \/* Normals for the 6 faces of a cube. *\/$/;" v file: name framework/base/Atom.h /^ std::string name;$/;" m struct:ProtoMol::Atom name framework/base/AtomType.h /^ std::string name; \/\/\/< The name of this atom type.$/;" m struct:ProtoMol::AtomType name framework/base/Molecule.h /^ std::string name;$/;" m struct:ProtoMol::Molecule names framework/base/XYZ.h /^ std::vector names;$/;" m struct:ProtoMol::XYZ nbfixs framework/base/PAR.h /^ std::vector nbfixs;$/;" m class:ProtoMol::PAR negative framework/base/PAR.h /^ bool negative; $/;" m struct:ProtoMol::PAR::Nonbonded negative2 framework/base/PAR.h /^ bool negative2; \/\/\/< flag for a negative VDW paramenter second term (see above), default to true$/;" m struct:ProtoMol::PAR::Nonbonded netint framework/imd/imd.cpp /^ } netint;$/;" t namespace:ProtoMol::IMD file: new_type framework/base/XSC.h /^ unsigned int myMolecule, old_type, new_type;$/;" m struct:ProtoMol::XSC newtype framework/base/Molecule.h /^ unsigned int type, newtype;$/;" m struct:ProtoMol::Molecule next framework/integrators/MTSIntegrator.h /^ inline Integrator* MTSIntegrator::next(){$/;" f class:ProtoMol::MTSIntegrator next framework/integrators/MTSIntegrator.h /^ inline const Integrator* MTSIntegrator::next() const{$/;" f class:ProtoMol::MTSIntegrator next framework/integrators/STSIntegrator.h /^ virtual Integrator* next(){return NULL;}$/;" f class:ProtoMol::STSIntegrator next framework/integrators/STSIntegrator.h /^ virtual const Integrator* next() const {return NULL;}$/;" f class:ProtoMol::STSIntegrator next framework/parallel/Parallel-FD.cpp /^ bool Parallel::next(){$/;" f class:ProtoMol::Parallel next framework/parallel/Parallel.cpp /^ bool Parallel::next(){$/;" f class:ProtoMol::Parallel next framework/topology/CellListEnumerator_periodicBoundaries.h /^ void next(void){$/;" f class:ProtoMol::CellListEnumerator next framework/topology/CellListEnumerator_standard.h /^ void next(){$/;" f class:ProtoMol::CellListEnumerator nextMaster framework/parallel/Parallel-FD.cpp /^ void Parallel::nextMaster(){$/;" f class:ProtoMol::Parallel nextMaster framework/parallel/Parallel.cpp /^ void Parallel::nextMaster(){$/;" f class:ProtoMol::Parallel nextNewPair framework/topology/CellListEnumerator_periodicBoundaries.h /^ void nextNewPair(int inc){$/;" f class:ProtoMol::CellListEnumerator nextNewPair framework/topology/CellListEnumerator_standard.h /^ void nextNewPair(int inc){$/;" f class:ProtoMol::CellListEnumerator ngrp framework/base/PSF.h /^ std::vector ngrp;$/;" m class:ProtoMol::PSF node framework/io/TempFileReader.h /^ int node;$/;" m class:ProtoMol::TempFileReader nonbondedForceFunction framework/forces/OneAtomPair.h /^ TNonbondedForce nonbondedForceFunction; $/;" m class:ProtoMol::OneAtomPair nonbondedForceFunction framework/forces/OneAtomPairFull.h /^ TNonbondedForce nonbondedForceFunction;$/;" m class:ProtoMol::OneAtomPairFull nonbondedForceFunction framework/forces/OneMollyPair.h /^ TNonbondedForce nonbondedForceFunction; $/;" m class:ProtoMol::OneMollyPair nonbondedForceFunctionFirst framework/forces/OneAtomPairTwo.h /^ TNonbondedForceFirst nonbondedForceFunctionFirst; $/;" m class:ProtoMol::OneAtomPairTwo nonbondedForceFunctionFirst framework/forces/OneAtomPairTwoFull.h /^ TNonbondedForceFirst nonbondedForceFunctionFirst; $/;" m class:ProtoMol::OneAtomPairTwoFull nonbondedForceFunctionFirst framework/forces/OneMollyPairTwo.h /^ TNonbondedForceFirst nonbondedForceFunctionFirst; $/;" m class:ProtoMol::OneMollyPairTwo nonbondedForceFunctionSecond framework/forces/OneAtomPairTwo.h /^ TNonbondedForceSecond nonbondedForceFunctionSecond; $/;" m class:ProtoMol::OneAtomPairTwo nonbondedForceFunctionSecond framework/forces/OneAtomPairTwoFull.h /^ TNonbondedForceSecond nonbondedForceFunctionSecond; $/;" m class:ProtoMol::OneAtomPairTwoFull nonbondedForceFunctionSecond framework/forces/OneMollyPairTwo.h /^ TNonbondedForceSecond nonbondedForceFunctionSecond; $/;" m class:ProtoMol::OneMollyPairTwo nonbondedHessian framework/forces/OneMollyPair.h /^ typename ReducedHessTraits::Hessian nonbondedHessian;$/;" m class:ProtoMol::OneMollyPair nonbondedHessianFirst framework/forces/OneMollyPairTwo.h /^ typename ReducedHessTraits::Hessian nonbondedHessianFirst;$/;" m class:ProtoMol::OneMollyPairTwo nonbondedHessianSecond framework/forces/OneMollyPairTwo.h /^ typename ReducedHessTraits::Hessian nonbondedHessianSecond;$/;" m class:ProtoMol::OneMollyPairTwo nonbondeds framework/base/PAR.h /^ std::vector nonbondeds;$/;" m class:ProtoMol::PAR nonbondeds framework/base/PSF.h /^ std::vector nonbondeds;$/;" m class:ProtoMol::PSF norm framework/base/Vector3D.h /^ Real norm() const {$/;" f struct:ProtoMol::Vector3D norm framework/base/mathutilities.cpp /^ Real norm(Real a, Real b) { $/;" f namespace:ProtoMol normSquared framework/base/Vector3D.h /^ Real normSquared() const {$/;" f struct:ProtoMol::Vector3D normVector3DOp framework/topology/PeriodicBoundaryConditions.cpp /^ static bool normVector3DOp (const Vector3D& v1, const Vector3D& v2){$/;" f namespace:ProtoMol file: normalize framework/base/Vector3D.h /^ Real normalize() {$/;" f struct:ProtoMol::Vector3D normalizeString framework/base/stringutilities.cpp /^ string normalizeString(const string& word){$/;" f namespace:ProtoMol normalized framework/base/Vector3D.h /^ Vector3D normalized() const {$/;" f struct:ProtoMol::Vector3D notSameCell framework/topology/CellListEnumerator_periodicBoundaries.h /^ bool notSameCell(){return (i != j);}$/;" f class:ProtoMol::CellListEnumerator notSameCell framework/topology/CellListEnumerator_standard.h /^ bool notSameCell(){return (i != j);}$/;" f class:ProtoMol::CellListEnumerator numBonds framework/topology/AngleInfo.cpp /^ unsigned int AngleInfo::numBonds()const {$/;" f class:ProtoMol::AngleInfo numComps framework/topology/BankLennardJonesParameterTable.h /^ unsigned int numComps;$/;" m struct:ProtoMol::BankLennardJonesParameterTable numTables framework/topology/BankLennardJonesParameterTable.h /^ unsigned int numTables;$/;" m struct:ProtoMol::BankLennardJonesParameterTable number framework/base/PAR.h /^ int number; \/\/\/< nonbonded number$/;" m struct:ProtoMol::PAR::Nonbonded number framework/base/PAR.h /^ int number; \/\/\/< angle number$/;" m struct:ProtoMol::PAR::Angle number framework/base/PAR.h /^ int number; \/\/\/< bond number$/;" m struct:ProtoMol::PAR::Bond number framework/base/PAR.h /^ int number; \/\/\/< dihedral number$/;" m struct:ProtoMol::PAR::Dihedral number framework/base/PAR.h /^ int number; \/\/\/< improper number$/;" m struct:ProtoMol::PAR::Improper number framework/base/PAR.h /^ int number; \/\/\/< nbfi number$/;" m struct:ProtoMol::PAR::Nbfix number framework/base/PAR.h /^ int number; \/\/\/< hydrogen bond number$/;" m struct:ProtoMol::PAR::Hbond number framework/base/PSF.h /^ int number; \/\/\/< atom number$/;" m struct:ProtoMol::PSF::Atom number framework/base/PSF.h /^ int number; \/\/\/< acceptor number$/;" m struct:ProtoMol::PSF::Acceptor number framework/base/PSF.h /^ int number; \/\/\/< angle number$/;" m struct:ProtoMol::PSF::Angle number framework/base/PSF.h /^ int number; \/\/\/< bond number$/;" m struct:ProtoMol::PSF::Bond number framework/base/PSF.h /^ int number; \/\/\/< dihedral number$/;" m struct:ProtoMol::PSF::Dihedral number framework/base/PSF.h /^ int number; \/\/\/< donor number$/;" m struct:ProtoMol::PSF::Donor number framework/base/PSF.h /^ int number; \/\/\/< improper number$/;" m struct:ProtoMol::PSF::Improper number framework/base/PSF.h /^ int number; \/\/\/< ngrp number$/;" m struct:ProtoMol::PSF::Ngrp number framework/base/PSF.h /^ int number; \/\/\/< nonbonded structure number$/;" m struct:ProtoMol::PSF::Nonbonded numberOfBlocks framework/forces/AngleSystemForce.h /^ inline unsigned int AngleSystemForce::numberOfBlocks(const GenericTopology* topo, $/;" f class:ProtoMol::AngleSystemForce numberOfBlocks framework/forces/BondSystemForce.h /^ inline unsigned int BondSystemForce::numberOfBlocks(const GenericTopology* topo, $/;" f class:ProtoMol::BondSystemForce numberOfBlocks framework/forces/CompareForce.cpp /^ unsigned int CompareForce::numberOfBlocks(const GenericTopology* topo,$/;" f class:ProtoMol::CompareForce numberOfBlocks framework/forces/DihedralSystemForce.h /^ inline unsigned int DihedralSystemForce::numberOfBlocks(const GenericTopology* topo, $/;" f class:ProtoMol::DihedralSystemForce numberOfBlocks framework/forces/ElectricFieldSystemForce.h /^ inline unsigned int ElectricFieldSystemForce::numberOfBlocks(const GenericTopology*,$/;" f class:ProtoMol::ElectricFieldSystemForce numberOfBlocks framework/forces/ExternalGravitationSystemForce.cpp /^ unsigned int ExternalGravitationSystemForce::numberOfBlocks(const GenericTopology*, $/;" f class:ProtoMol::ExternalGravitationSystemForce numberOfBlocks framework/forces/ExternalMagneticFieldExtendedForce.cpp /^ unsigned int ExternalMagneticFieldExtendedForce::numberOfBlocks(const GenericTopology*, $/;" f class:ProtoMol::ExternalMagneticFieldExtendedForce numberOfBlocks framework/forces/Force.h /^ virtual unsigned int numberOfBlocks(const GenericTopology*,const Vector3DBlock*){return 1;}$/;" f class:ProtoMol::Force numberOfBlocks framework/forces/FrictionExtendedForce.cpp /^ unsigned int FrictionExtendedForce::numberOfBlocks(const GenericTopology*, $/;" f class:ProtoMol::FrictionExtendedForce numberOfBlocks framework/forces/HarmDihedralSystemForce.h /^ inline unsigned int HarmDihedralSystemForce::numberOfBlocks(const GenericTopology* topo, $/;" f class:ProtoMol::HarmDihedralSystemForce numberOfBlocks framework/forces/ImproperSystemForce.h /^ inline unsigned int ImproperSystemForce::numberOfBlocks(const GenericTopology* topo, $/;" f class:ProtoMol::ImproperSystemForce numberOfBlocks framework/forces/NonbondedCutoffForce.h /^ virtual unsigned int numberOfBlocks(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedCutoffForce numberOfBlocks framework/forces/NonbondedFullEwaldSystemForce.h /^ TSwitchingFunction>::numberOfBlocks(const GenericTopology* topo,$/;" f class:ProtoMol::NonbondedFullEwaldSystemForce numberOfBlocks framework/forces/NonbondedFullSystemForce.h /^ virtual unsigned int numberOfBlocks(const GenericTopology*, const Vector3DBlock*){return Parallel::getAvailableNum();} $/;" f class:ProtoMol::NonbondedFullSystemForce numberOfBlocks framework/forces/NonbondedMultiGridSystemForce.h /^ smooth>::numberOfBlocks(const GenericTopology* topo, const Vector3DBlock* positions){$/;" f class:ProtoMol::NonbondedMultiGridSystemForce numberOfBlocks framework/forces/NonbondedPMEwaldSystemForce.h /^ real,reciprocal,correction,TInterpolation,TSwitchingFunction>::numberOfBlocks(const GenericTopology* topo,$/;" f class:ProtoMol::NonbondedPMEwaldSystemForce numberOfBlocks framework/forces/NonbondedSimpleFullSystemForce.h /^ virtual unsigned int numberOfBlocks(const GenericTopology*, const Vector3DBlock*){$/;" f class:ProtoMol::NonbondedSimpleFullSystemForce numberOfBlocks framework/forces/PaulTrapExtendedForce.h /^ inline unsigned int PaulTrapExtendedForce::numberOfBlocks(const GenericTopology*,$/;" f class:ProtoMol::PaulTrapExtendedForce numberOfBlocks framework/forces/SphericalSystemForce.cpp /^ unsigned int SphericalSystemForce::numberOfBlocks(const GenericTopology* , $/;" f class:ProtoMol::SphericalSystemForce numberOfBlocks framework/forces/TimeForce.cpp /^ unsigned int TimeForce::numberOfBlocks(const GenericTopology* topo,$/;" f class:ProtoMol::TimeForce obj framework/frontend/Factory.h /^ static Factory* obj;$/;" m class:ProtoMol::Factory obj framework/frontend/Factory.h /^ Factory* Factory::obj=NULL;$/;" m class:ProtoMol::Factory obj framework/frontend/HelpTextFactory.h /^ static HelpTextFactory* obj;$/;" m class:ProtoMol::HelpTextFactory obj framework/parallel/Parallel-FD.cpp /^ Parallel* Parallel::obj = NULL;$/;" m class:ProtoMol::Parallel file: obj framework/parallel/Parallel.cpp /^ Parallel* Parallel::obj = NULL;$/;" m class:ProtoMol::Parallel file: obj framework/parallel/Parallel.h /^ static Parallel* obj; \/\/\/< Instance$/;" m class:ProtoMol::Parallel occupancy framework/base/PDB.h /^ Real occupancy; \/\/\/< occupancy $/;" m struct:ProtoMol::PDB::Atom off_type framework/base/sstream_local.h /^ typedef streamoff off_type;$/;" t class:std::stringbuf ok framework/base/Value.h /^ bool ok;$/;" m class:ProtoMol::Value::Holder ok framework/parallel/Parallel-FD.cpp /^ bool Parallel::ok(const string& err){$/;" f class:ProtoMol::Parallel ok framework/parallel/Parallel.cpp /^ bool Parallel::ok(const string& err){$/;" f class:ProtoMol::Parallel ok framework/parallel/Parallel.h /^ static bool ok() {return (myInitialized && !myFinalized);}$/;" f class:ProtoMol::Parallel old_type framework/base/XSC.h /^ unsigned int myMolecule, old_type, new_type;$/;" m struct:ProtoMol::XSC oldconformstring framework/frontend/OutputDihedrals.h /^ std::string oldconformstring;$/;" m class:ProtoMol::OutputDihedrals open framework/frontend/InputPosVel.cpp /^ bool InputPosVel::open(){$/;" f class:ProtoMol::InputPosVel open framework/frontend/InputPosVel.cpp /^ bool InputPosVel::open(const string& filename){$/;" f class:ProtoMol::InputPosVel open framework/frontend/OutputFile.cpp /^ bool OutputFile::open(){$/;" f class:ProtoMol::OutputFile open framework/io/AMBERReader.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::AMBERReader open framework/io/AMBERReader.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::AMBERReader open framework/io/AMBERReader.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::AMBERReader open framework/io/CRDReader.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::CRDReader open framework/io/CRDReader.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::CRDReader open framework/io/CRDReader.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::CRDReader open framework/io/ConfigurationReader.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::ConfigurationReader open framework/io/ConfigurationReader.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::ConfigurationReader open framework/io/ConfigurationReader.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::ConfigurationReader open framework/io/DCDTrajectoryReader.h /^ virtual bool open(){myFirst=true;return File::open();}$/;" f class:ProtoMol::DCDTrajectoryReader open framework/io/DCDTrajectoryReader.h /^ virtual bool open(const char* filename){myFirst=true;return File::open(filename);}$/;" f class:ProtoMol::DCDTrajectoryReader open framework/io/DCDTrajectoryReader.h /^ virtual bool open(const std::string& filename){myFirst=true;return File::open(filename);}$/;" f class:ProtoMol::DCDTrajectoryReader open framework/io/DCDTrajectoryWriter.cpp /^ bool DCDTrajectoryWriter::open(Real timestep, unsigned int firststep, bool isLittleEndian){$/;" f class:ProtoMol::DCDTrajectoryWriter open framework/io/DCDTrajectoryWriter.cpp /^ bool DCDTrajectoryWriter::open(const char* filename, Real timestep, unsigned int firststep, bool isLittleEndian){$/;" f class:ProtoMol::DCDTrajectoryWriter open framework/io/DCDTrajectoryWriter.cpp /^ bool DCDTrajectoryWriter::open(const string& filename, Real timestep, unsigned int firststep, bool isLittleEndian){$/;" f class:ProtoMol::DCDTrajectoryWriter open framework/io/DCDTrajectoryWriter.h /^ virtual bool open(){myFirst = false;return File::open();}$/;" f class:ProtoMol::DCDTrajectoryWriter open framework/io/DCDTrajectoryWriter.h /^ virtual bool open(const char* filename){myFirst = false;return File::open(filename);}$/;" f class:ProtoMol::DCDTrajectoryWriter open framework/io/DCDTrajectoryWriter.h /^ virtual bool open(const std::string& filename){myFirst = false;return File::open(filename);}$/;" f class:ProtoMol::DCDTrajectoryWriter open framework/io/File.cpp /^ bool File::open(){$/;" f class:ProtoMol::File open framework/io/File.cpp /^ bool File::open(const char* filename){$/;" f class:ProtoMol::File open framework/io/File.cpp /^ bool File::open(const string& filename){$/;" f class:ProtoMol::File open framework/io/PARReader.cpp /^ bool PARReader::open(PAR::CharmmTypeEnum charmmType){$/;" f class:ProtoMol::PARReader open framework/io/PARReader.cpp /^ bool PARReader::open(const std::string& filename, PAR::CharmmTypeEnum charmmType){$/;" f class:ProtoMol::PARReader open framework/io/PARReader.h /^ virtual bool open(){return File::open();};$/;" f class:ProtoMol::PARReader open framework/io/PARReader.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::PARReader open framework/io/PARReader.h /^ virtual bool open(const std::string& filename){return File::open(filename);};$/;" f class:ProtoMol::PARReader open framework/io/PARReader.h /^ inline bool PARReader::open(const char* filename, PAR::CharmmTypeEnum charmmType){$/;" f class:ProtoMol::PARReader open framework/io/PARWriter.cpp /^ bool PARWriter::open(PAR::CharmmTypeEnum charmmType){$/;" f class:ProtoMol::PARWriter open framework/io/PARWriter.cpp /^ bool PARWriter::open(const char* filename, PAR::CharmmTypeEnum charmmType){$/;" f class:ProtoMol::PARWriter open framework/io/PARWriter.cpp /^ bool PARWriter::open(const std::string& filename, PAR::CharmmTypeEnum charmmType){$/;" f class:ProtoMol::PARWriter open framework/io/PARWriter.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::PARWriter open framework/io/PARWriter.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::PARWriter open framework/io/PARWriter.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::PARWriter open framework/io/PDBReader.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::PDBReader open framework/io/PDBReader.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::PDBReader open framework/io/PDBReader.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::PDBReader open framework/io/PDBWriter.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::PDBWriter open framework/io/PDBWriter.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::PDBWriter open framework/io/PDBWriter.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::PDBWriter open framework/io/PGMReader.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::PGMReader open framework/io/PGMReader.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::PGMReader open framework/io/PGMReader.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::PGMReader open framework/io/PGMWriter.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::PGMWriter open framework/io/PGMWriter.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::PGMWriter open framework/io/PGMWriter.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::PGMWriter open framework/io/PNGWriter.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::PNGWriter open framework/io/PNGWriter.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::PNGWriter open framework/io/PNGWriter.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::PNGWriter open framework/io/PPMReader.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::PPMReader open framework/io/PPMReader.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::PPMReader open framework/io/PPMReader.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::PPMReader open framework/io/PPMWriter.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::PPMWriter open framework/io/PPMWriter.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::PPMWriter open framework/io/PPMWriter.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::PPMWriter open framework/io/PSFReader.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::PSFReader open framework/io/PSFReader.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::PSFReader open framework/io/PSFReader.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::PSFReader open framework/io/PSFWriter.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::PSFWriter open framework/io/PSFWriter.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::PSFWriter open framework/io/PSFWriter.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::PSFWriter open framework/io/REMConfigurationReader.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::REMConfigurationReader open framework/io/REMConfigurationReader.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::REMConfigurationReader open framework/io/REMConfigurationReader.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::REMConfigurationReader open framework/io/TempFileReader.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::TempFileReader open framework/io/TempFileReader.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::TempFileReader open framework/io/TempFileReader.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::TempFileReader open framework/io/XFigWriter.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::XFigWriter open framework/io/XFigWriter.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::XFigWriter open framework/io/XFigWriter.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::XFigWriter open framework/io/XYZBinReader.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::XYZBinReader open framework/io/XYZBinReader.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::XYZBinReader open framework/io/XYZBinReader.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::XYZBinReader open framework/io/XYZBinWriter.cpp /^ bool XYZBinWriter::open(bool isLittleEndian, unsigned int size){$/;" f class:ProtoMol::XYZBinWriter open framework/io/XYZBinWriter.cpp /^ bool XYZBinWriter::open(const char* filename, bool isLittleEndian, unsigned int size){$/;" f class:ProtoMol::XYZBinWriter open framework/io/XYZBinWriter.cpp /^ bool XYZBinWriter::open(const std::string& filename, bool isLittleEndian, unsigned int size){$/;" f class:ProtoMol::XYZBinWriter open framework/io/XYZBinWriter.h /^ virtual bool open(){return File::open();};$/;" f class:ProtoMol::XYZBinWriter open framework/io/XYZBinWriter.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::XYZBinWriter open framework/io/XYZBinWriter.h /^ virtual bool open(const std::string& filename){return File::open(filename);};$/;" f class:ProtoMol::XYZBinWriter open framework/io/XYZReader.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::XYZReader open framework/io/XYZReader.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::XYZReader open framework/io/XYZReader.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::XYZReader open framework/io/XYZTrajectoryReader.h /^ virtual bool open(){myFirst=true;return File::open();}$/;" f class:ProtoMol::XYZTrajectoryReader open framework/io/XYZTrajectoryReader.h /^ virtual bool open(const char* filename){myFirst=true;return File::open(filename);}$/;" f class:ProtoMol::XYZTrajectoryReader open framework/io/XYZTrajectoryReader.h /^ virtual bool open(const std::string& filename){myFirst=true;return File::open(filename);}$/;" f class:ProtoMol::XYZTrajectoryReader open framework/io/XYZTrajectoryWriter.cpp /^ bool XYZTrajectoryWriter::open(const XYZ& xyz){$/;" f class:ProtoMol::XYZTrajectoryWriter open framework/io/XYZTrajectoryWriter.cpp /^ bool XYZTrajectoryWriter::open(const std::string& filename, const XYZ& xyz){$/;" f class:ProtoMol::XYZTrajectoryWriter open framework/io/XYZTrajectoryWriter.cpp /^ bool XYZTrajectoryWriter::open(const std::string& filename, const std::vector& names){$/;" f class:ProtoMol::XYZTrajectoryWriter open framework/io/XYZTrajectoryWriter.cpp /^ bool XYZTrajectoryWriter::open(const std::string& filename,const std::vector& atoms, const std::vector& atomTypes){$/;" f class:ProtoMol::XYZTrajectoryWriter open framework/io/XYZTrajectoryWriter.cpp /^ bool XYZTrajectoryWriter::open(const std::vector& atoms, const std::vector& atomTypes){$/;" f class:ProtoMol::XYZTrajectoryWriter open framework/io/XYZTrajectoryWriter.cpp /^ bool XYZTrajectoryWriter::open(const std::vector& names){$/;" f class:ProtoMol::XYZTrajectoryWriter open framework/io/XYZTrajectoryWriter.h /^ virtual bool open(){myFirst = false;return File::open();}$/;" f class:ProtoMol::XYZTrajectoryWriter open framework/io/XYZTrajectoryWriter.h /^ virtual bool open(const char* filename){myFirst = false;return File::open(filename);}$/;" f class:ProtoMol::XYZTrajectoryWriter open framework/io/XYZTrajectoryWriter.h /^ virtual bool open(const std::string& filename){myFirst = false;return File::open(filename);}$/;" f class:ProtoMol::XYZTrajectoryWriter open framework/io/XYZWriter.h /^ virtual bool open(){return File::open();}$/;" f class:ProtoMol::XYZWriter open framework/io/XYZWriter.h /^ virtual bool open(const char* filename){return File::open(filename);}$/;" f class:ProtoMol::XYZWriter open framework/io/XYZWriter.h /^ virtual bool open(const std::string& filename){return File::open(filename);}$/;" f class:ProtoMol::XYZWriter operator ! framework/frontend/InputPosVel.cpp /^ bool InputPosVel::operator!() const { $/;" f class:ProtoMol::InputPosVel operator ! framework/io/File.cpp /^ bool File::operator!() const { $/;" f class:ProtoMol::File operator != framework/base/AbstractEnumType.h /^ bool operator!=(Enum a) {return (a != myType);}$/;" f class:ProtoMol::AbstractEnumType operator != framework/base/AbstractEnumType.h /^ bool operator!=(const AbstractEnumType& a) {return (a.myType != myType);}$/;" f class:ProtoMol::AbstractEnumType operator != framework/base/Array_Fastest.h /^ inline bool operator != (const Array & A, const Array & B) $/;" f namespace:ProtoMol operator != framework/base/Array_NoPartialSpecialization.h /^ bool operator != (const Array & A, const Array & B) $/;" f namespace:ProtoMol operator != framework/base/Matrix3by3.cpp /^ bool Matrix3by3::operator!=(const Matrix3by3& tm) const$/;" f class:ProtoMol::Matrix3by3 operator != framework/base/Value.h /^ friend bool operator!=(const T& v1, const Value& v2) {return !(Value(v1) == v2);}$/;" f class:ProtoMol::Value operator != framework/base/Value.h /^ friend bool operator!=(const Value& v1, const T& v2) {return !(v1 == Value(v2));}$/;" f class:ProtoMol::Value operator != framework/base/Value.h /^ friend bool operator!=(const Value& v1, const Value& v2){return !(v1 == v2);}$/;" f class:ProtoMol::Value operator != framework/base/Vector3D.h /^ bool operator!=(const Vector3D& b) const {$/;" f struct:ProtoMol::Vector3D operator () framework/base/Array_Fastest.h /^ ArraySize<2> operator () (size_t dim) $/;" f class:ProtoMol::ArraySizes operator () framework/base/Array_Fastest.h /^ ArraySize operator () (size_t dim) $/;" f class:ProtoMol::ArraySize operator () framework/base/Array_NoPartialSpecialization.h /^ ArraySize<2> operator () (unsigned int dim) $/;" f class:ProtoMol::ArraySizes operator () framework/base/Array_NoPartialSpecialization.h /^ ArraySize operator () (unsigned int dim) $/;" f class:ProtoMol::ArraySize operator () framework/base/Matrix3by3.cpp /^ Real Matrix3by3::operator()(int i, int j) const$/;" f class:ProtoMol::Matrix3by3 operator () framework/base/Matrix3by3.cpp /^ void Matrix3by3::operator()(Real x00, Real x01, Real x02,$/;" f class:ProtoMol::Matrix3by3 operator () framework/base/Matrix3by3.cpp /^ void Matrix3by3::operator()(int i, int j, Real x)$/;" f class:ProtoMol::Matrix3by3 operator () framework/base/ReducedHessAngle.cpp /^ Matrix3by3 ReducedHessAngle::operator()(int i, int j) const$/;" f class:ProtoMol::ReducedHessAngle operator () framework/base/ReducedHessAngle.cpp /^ void ReducedHessAngle::operator()(int i, int j, Matrix3by3 x) $/;" f class:ProtoMol::ReducedHessAngle operator () framework/base/Report.cpp /^ MyStreamer& debug::operator()(MyStreamer& stream) const{$/;" f class:ProtoMol::Report::debug operator () framework/base/Report.cpp /^ MyStreamer& reportlevel::operator()(MyStreamer& stream) const{$/;" f class:ProtoMol::Report::reportlevel operator () framework/base/Vector.h /^ VectorPacker operator () (T elm){ $/;" f class:ProtoMol::Vector operator () framework/base/Vector.h /^ VectorPacker operator () (T elm) { $/;" f class:ProtoMol::VectorPacker operator () framework/base/stringutilities.cpp /^ bool ltstrNocase::operator()(const string& s1, const string& s2) const{$/;" f class:ProtoMol::ltstrNocase operator () framework/forces/CoulombEwaldRealForce.h /^ void operator()(Real &energy, $/;" f class:ProtoMol::CoulombEwaldRealForce operator () framework/forces/CoulombEwaldRealTableForce.h /^ void operator()(Real &energy, $/;" f class:ProtoMol::CoulombEwaldRealTableForce operator () framework/forces/CoulombForce.h /^ void operator()(Real &energy, $/;" f class:ProtoMol::CoulombForce operator () framework/forces/CoulombMultiGridDirectForce.h /^ void operator()(Real &energy, $/;" f class:ProtoMol::CoulombMultiGridDirectForce operator () framework/forces/CoulombMultiGridDirectTableForce.h /^ void operator()(Real &energy, $/;" f class:ProtoMol::CoulombMultiGridDirectTableForce operator () framework/forces/CoulombTableForce.h /^ void operator()(Real &energy, $/;" f class:ProtoMol::CoulombTableForce operator () framework/forces/GravitationForce.h /^ void operator()(Real &energy, $/;" f class:ProtoMol::GravitationForce operator () framework/forces/LennardJonesForce.h /^ void operator()(Real &energy, $/;" f class:ProtoMol::LennardJonesForce operator () framework/forces/LennardJonesTableForce.h /^ void operator()(Real &energy, $/;" f class:ProtoMol::LennardJonesTableForce operator () framework/forces/MagneticDipoleForce.cpp /^ void MagneticDipoleForce::operator()(Real &energy, $/;" f class:ProtoMol::MagneticDipoleForce operator () framework/forces/ReducedHessCoulomb.cpp /^ Matrix3by3 ReducedHessCoulomb::operator()(const Real rawEnergy,$/;" f class:ProtoMol::ReducedHessCoulomb operator () framework/forces/ReducedHessLennardJones.cpp /^ Matrix3by3 ReducedHessLennardJones::operator()(const Real rawEnergy,$/;" f class:ProtoMol::ReducedHessLennardJones operator () framework/topology/BankLennardJonesParameterTable.h /^ const LennardJonesParameters& operator()(int i, int j, int type1, int type2) const{$/;" f struct:ProtoMol::BankLennardJonesParameterTable operator () framework/topology/C1SwitchingFunction.h /^ void operator()(Real &value, Real &derivOverD, Real distSquared) const{$/;" f class:ProtoMol::C1SwitchingFunction operator () framework/topology/C2SwitchingFunction.h /^ void operator()(Real &value, Real &deriv, Real distSquared) const{$/;" f class:ProtoMol::C2SwitchingFunction operator () framework/topology/CmpCnCnSwitchingFunction.h /^ void operator()(Real &value, Real &deriv, Real distSquared) const{$/;" f class:ProtoMol::CmpCnCnSwitchingFunction operator () framework/topology/CnSwitchingFunction.cpp /^ void CnSwitchingFunction::operator()( Real &value, Real &deriv,$/;" f class:ProtoMol::CnSwitchingFunction operator () framework/topology/ComplementSwitchingFunction.h /^ void operator()(Real &value, Real &derivOverD, Real distSquared) const{$/;" f class:ProtoMol::ComplementSwitchingFunction operator () framework/topology/CutoffSwitchingFunction.h /^ void operator()(Real &value, Real &derivOverD, Real distSquared) const{$/;" f class:ProtoMol::CutoffSwitchingFunction operator () framework/topology/LennardJonesParameterTable.h /^ const LennardJonesParameters& operator()(int type1, int type2) const{$/;" f class:ProtoMol::LennardJonesParameterTable operator () framework/topology/RangeSwitchingFunction.h /^ inline void RangeSwitchingFunction::operator()(Real &value, Real &derivOverD, Real distSquared) const {$/;" f class:ProtoMol::RangeSwitchingFunction operator () framework/topology/ShiftSwitchingFunction.h /^ void operator()(Real &value, Real &derivOverD, Real distSquared) const{$/;" f class:ProtoMol::ShiftSwitchingFunction operator () framework/topology/UniversalSwitchingFunction.h /^ void operator()(Real &value, Real &deriv, Real \/*distSquared*\/) const{ value=1.0; deriv=0.0;}$/;" f class:ProtoMol::UniversalSwitchingFunction operator () tools/bccAnalyzer.cpp /^ bool operator()(const PairVector3D& a, const PairVector3D& b) const {$/;" f class:PairVector3D operator () tools/bccAnalyzer.cpp /^ bool operator()(const Vector3D& v1, const Vector3D& v2) const{$/;" f class:radialCmpVector3D operator () tools/bccAnalyzer.cpp /^ bool operator()(const Vector3DIdx& v1, const Vector3DIdx& v2) const{$/;" f class:radialCmpVector3D operator * framework/base/Matrix3by3.cpp /^ Matrix3by3 Matrix3by3::operator*(const Matrix3by3& tm) const $/;" f class:ProtoMol::Matrix3by3 operator * framework/base/Matrix3by3.cpp /^ Matrix3by3 Matrix3by3::operator*(const Real tm) const $/;" f class:ProtoMol::Matrix3by3 operator * framework/base/Matrix3by3.cpp /^ Vector3D Matrix3by3::operator*(const Vector3D& tm) const $/;" f class:ProtoMol::Matrix3by3 operator * framework/base/Matrix3by3.cpp /^ Vector3D operator*(const Vector3D& point, const Matrix3by3& tm)$/;" f namespace:ProtoMol operator * framework/base/ReducedHessAngle.cpp /^ ReducedHessAngle ReducedHessAngle::operator*(const Real tm) $/;" f class:ProtoMol::ReducedHessAngle operator * framework/base/ReducedHessAngle.cpp /^ ReducedHessAngle ReducedHessAngle::operator*(const ReducedHessAngle& tm) $/;" f class:ProtoMol::ReducedHessAngle operator * framework/base/Vector3D.h /^ Real operator*(const Vector3D& b) const{$/;" f struct:ProtoMol::Vector3D operator * framework/base/Vector3D.h /^ Vector3D operator*(Real w) const {$/;" f struct:ProtoMol::Vector3D operator *= framework/base/Matrix3by3.cpp /^ Matrix3by3& Matrix3by3::operator*=(const Matrix3by3& tm)$/;" f class:ProtoMol::Matrix3by3 operator *= framework/base/Matrix3by3.cpp /^ Matrix3by3& Matrix3by3::operator*=(const Real tm)$/;" f class:ProtoMol::Matrix3by3 operator *= framework/base/ReducedHessAngle.cpp /^ ReducedHessAngle& ReducedHessAngle::operator*=(const Real tm) $/;" f class:ProtoMol::ReducedHessAngle operator *= framework/base/Vector3D.h /^ Vector3D &operator*=(Real w) {$/;" f struct:ProtoMol::Vector3D operator + framework/base/Matrix3by3.cpp /^ Matrix3by3 Matrix3by3::operator+(const Matrix3by3& tm) const $/;" f class:ProtoMol::Matrix3by3 operator + framework/base/ReducedHessAngle.cpp /^ ReducedHessAngle ReducedHessAngle::operator+(const ReducedHessAngle& tm) $/;" f class:ProtoMol::ReducedHessAngle operator + framework/base/Timer.cpp /^ TimeRep TimeRep::operator+(const TimeRep& time) const$/;" f class:ProtoMol::TimeRep operator + framework/base/Vector3D.h /^ Vector3D operator+(const Vector3D& b) const {$/;" f struct:ProtoMol::Vector3D operator + framework/topology/CubicCellLocation.h /^ CubicCellLocation operator+(const CubicCellLocation& b) const {return CubicCellLocation(x+b.x,y+b.y,z+b.z);}$/;" f class:ProtoMol::CubicCellLocation operator += framework/base/Matrix3by3.cpp /^ Matrix3by3& Matrix3by3::operator+=(const Matrix3by3& tm)$/;" f class:ProtoMol::Matrix3by3 operator += framework/base/ReducedHessAngle.cpp /^ ReducedHessAngle& ReducedHessAngle::operator+=(const ReducedHessAngle& tm) $/;" f class:ProtoMol::ReducedHessAngle operator += framework/base/Timer.cpp /^ TimeRep& TimeRep::operator+=(const TimeRep& time)$/;" f class:ProtoMol::TimeRep operator += framework/base/Timer.cpp /^ Timer& Timer::operator+=(const TimeRep& time)$/;" f class:ProtoMol::Timer operator += framework/base/Vector3D.h /^ Vector3D &operator+=(const Vector3D& b) {$/;" f struct:ProtoMol::Vector3D operator - framework/base/Matrix3by3.cpp /^ Matrix3by3 Matrix3by3::operator-(const Matrix3by3& tm) const $/;" f class:ProtoMol::Matrix3by3 operator - framework/base/Matrix3by3.cpp /^ Matrix3by3 Matrix3by3::operator-(void) const $/;" f class:ProtoMol::Matrix3by3 operator - framework/base/ReducedHessAngle.cpp /^ ReducedHessAngle ReducedHessAngle::operator-(const ReducedHessAngle& tm) $/;" f class:ProtoMol::ReducedHessAngle operator - framework/base/Timer.cpp /^ TimeRep TimeRep::operator-(const TimeRep& time) const$/;" f class:ProtoMol::TimeRep operator - framework/base/Vector3D.h /^ Vector3D operator-() const {$/;" f struct:ProtoMol::Vector3D operator - framework/base/Vector3D.h /^ Vector3D operator-(const Vector3D& b) const {$/;" f struct:ProtoMol::Vector3D operator - framework/topology/CubicCellLocation.h /^ CubicCellLocation operator-(const CubicCellLocation& b) const {return CubicCellLocation(x-b.x,y-b.y,z-b.z);}$/;" f class:ProtoMol::CubicCellLocation operator -= framework/base/Matrix3by3.cpp /^ Matrix3by3& Matrix3by3::operator-=(const Matrix3by3& tm)$/;" f class:ProtoMol::Matrix3by3 operator -= framework/base/ReducedHessAngle.cpp /^ ReducedHessAngle& ReducedHessAngle::operator-=(const ReducedHessAngle& tm) $/;" f class:ProtoMol::ReducedHessAngle operator -= framework/base/Timer.cpp /^ TimeRep& TimeRep::operator-=(const TimeRep& time)$/;" f class:ProtoMol::TimeRep operator -= framework/base/Timer.cpp /^ Timer& Timer::operator-=(const TimeRep& time)$/;" f class:ProtoMol::Timer operator -= framework/base/Vector3D.h /^ Vector3D &operator-=(const Vector3D& b) {$/;" f struct:ProtoMol::Vector3D operator / framework/base/Matrix3by3.cpp /^ Matrix3by3 Matrix3by3::operator\/(const Real tm) const$/;" f class:ProtoMol::Matrix3by3 operator / framework/base/ReducedHessAngle.cpp /^ ReducedHessAngle ReducedHessAngle::operator\/(const Real tm) $/;" f class:ProtoMol::ReducedHessAngle operator / framework/base/Vector3D.h /^ Vector3D operator\/(Real w) const {$/;" f struct:ProtoMol::Vector3D operator /= framework/base/Matrix3by3.cpp /^ Matrix3by3& Matrix3by3::operator\/=(const Real tm)$/;" f class:ProtoMol::Matrix3by3 operator /= framework/base/ReducedHessAngle.cpp /^ ReducedHessAngle& ReducedHessAngle::operator\/=(const Real tm) $/;" f class:ProtoMol::ReducedHessAngle operator /= framework/base/Vector3D.h /^ Vector3D &operator\/=(Real w) {$/;" f struct:ProtoMol::Vector3D operator < framework/base/Value.cpp /^ bool operator<(const Value& v1, const Value& v2){$/;" f namespace:ProtoMol operator < framework/base/Value.h /^ friend bool operator<(const T& v1, const Value& v2) {return (Value(v1) < v2);}$/;" f class:ProtoMol::Value operator < framework/base/Value.h /^ friend bool operator<(const Value& v1, const T& v2) {return (v1 < Value(v2));}$/;" f class:ProtoMol::Value operator < framework/base/Vector3DBlock.h /^ inline bool operator<(const Vector3DBlock& a, const Vector3DBlock& b){return a.vec == b.vec;} $/;" f namespace:ProtoMol operator < framework/base/simpleTypes.h /^ bool operator<(const PairIntSorted& p) const{$/;" f struct:ProtoMol::PairIntSorted operator < framework/integrators/BSplineMOLLYIntegrator.h /^ bool operator<(const BondIndex& a) const {$/;" f struct:ProtoMol::BSplineMOLLYIntegrator::BondIndex operator < framework/integrators/Modifier.h /^ inline bool Modifier::operator<(const Modifier & m) const {$/;" f class:ProtoMol::Modifier operator < framework/topology/CubicCellLocation.h /^ inline bool CubicCellLocation::operator<(const CubicCellLocation &c) const {$/;" f class:ProtoMol::CubicCellLocation operator < framework/topology/ExclusionTable.cpp /^ bool ExclusionPair::operator<(const ExclusionPair & e) const{$/;" f class:ProtoMol::ExclusionPair operator << framework/base/AbstractEnumType.h /^ friend Report::MyStreamer& operator<< (Report::MyStreamer& OS, const AbstractEnumType& b){return (OS< & operator = (const Array & A)$/;" f class:ProtoMol::Array operator = framework/base/Array_NoPartialSpecialization.h /^ Array & operator = (const Array & A)$/;" f class:ProtoMol::Array operator = framework/base/LookUpTableBase.h /^ LookUpTableBase& operator=(LookUpTableBase const& rhs){$/;" f class:ProtoMol::LookUpTableBase operator = framework/base/PGM.cpp /^ PGM& PGM::operator=(const PPM& ppm){$/;" f class:ProtoMol::PGM operator = framework/base/PPM.cpp /^ PPM& PPM::operator=(const PGM& pgm){$/;" f class:ProtoMol::PPM operator = framework/base/Value.cpp /^ Value & Value::operator=(const Value & rhs) {$/;" f class:ProtoMol::Value operator = framework/base/Value.h /^ Value& operator=(const T& value){$/;" f class:ProtoMol::Value operator = framework/base/Vector3D.h /^ Vector3D& operator=(const Vector3D &c) {$/;" f struct:ProtoMol::Vector3D operator = framework/frontend/Factory.h /^ Factory& operator=(const Factory&){return *this;}$/;" f class:ProtoMol::Factory operator = framework/frontend/Factory.h /^ FactoryBase& operator=(const FactoryBase&){return *this;}$/;" f class:ProtoMol::FactoryBase operator = framework/frontend/ForceFactoryDetails.cpp /^ ForceFactoryDetails& ForceFactoryDetails::operator=(const ForceFactoryDetails&){return *this;}$/;" f class:ProtoMol::ForceFactoryDetails operator = framework/frontend/HelpTextFactory.cpp /^ HelpTextFactory& HelpTextFactory::operator=(const HelpTextFactory&){return *this;}$/;" f class:ProtoMol::HelpTextFactory operator = framework/frontend/InputValue.h /^ InputValue & operator=(const InputValue & rhs) {$/;" f class:ProtoMol::InputValue operator = framework/frontend/InputValue.h /^ InputValue& operator=(const T& value){$/;" f class:ProtoMol::InputValue operator = framework/frontend/InputValue.h /^ InputValue& operator=(const char* value){return operator=(std::string(value));}$/;" f class:ProtoMol::InputValue operator = framework/frontend/IntegratorFactoryDetails.cpp /^ IntegratorFactoryDetails& IntegratorFactoryDetails::operator=(const IntegratorFactoryDetails&){return *this;}$/;" f class:ProtoMol::IntegratorFactoryDetails operator = framework/frontend/OutputFactoryDetails.cpp /^ OutputFactoryDetails& OutputFactoryDetails::operator=(const OutputFactoryDetails&){return *this;}$/;" f class:ProtoMol::OutputFactoryDetails operator = framework/frontend/TopologyFactoryDetails.cpp /^ TopologyFactoryDetails& TopologyFactoryDetails::operator=(const TopologyFactoryDetails&){return *this;}$/;" f class:ProtoMol::TopologyFactoryDetails operator = framework/parallel/Parallel.h /^ Parallel& operator=(const Parallel&){return *this;}$/;" f class:ProtoMol::Parallel operator == framework/base/AbstractEnumType.h /^ bool operator==(Enum a) {return (a == myType);}$/;" f class:ProtoMol::AbstractEnumType operator == framework/base/AbstractEnumType.h /^ bool operator==(const AbstractEnumType& a) {return (a.myType == myType);}$/;" f class:ProtoMol::AbstractEnumType operator == framework/base/Array_Fastest.h /^ inline bool operator == (const Array & A, const Array & B)$/;" f namespace:ProtoMol operator == framework/base/Array_NoPartialSpecialization.h /^ bool operator == (const Array & A, const Array & B)$/;" f namespace:ProtoMol operator == framework/base/Matrix3by3.cpp /^ bool Matrix3by3::operator==(const Matrix3by3& tm) const$/;" f class:ProtoMol::Matrix3by3 operator == framework/base/Value.cpp /^ bool operator==(const Value& v1, const Value& v2){$/;" f namespace:ProtoMol operator == framework/base/Value.h /^ friend bool operator==(const T& v1, const Value& v2){return (Value(v1) == v2);}$/;" f class:ProtoMol::Value operator == framework/base/Value.h /^ friend bool operator==(const Value& v1, const T& v2){return (v1 == Value(v2));}$/;" f class:ProtoMol::Value operator == framework/base/Vector3D.h /^ bool operator==(const Vector3D& b) const {$/;" f struct:ProtoMol::Vector3D operator == framework/base/Vector3DBlock.h /^ inline bool operator==(const Vector3DBlock& a, const Vector3DBlock& b){return a.vec == b.vec;} $/;" f namespace:ProtoMol operator == framework/base/simpleTypes.h /^ bool operator==(const PairIntSorted& p) const {return (first == p.first && second == p.second);}$/;" f struct:ProtoMol::PairIntSorted operator == framework/topology/CubicCellLocation.h /^ bool operator==(const CubicCellLocation& c) const {return (x == c.x && y == c.y && z == c.z);}$/;" f class:ProtoMol::CubicCellLocation operator > framework/base/Value.cpp /^ bool operator>(const Value& v1, const Value& v2){$/;" f namespace:ProtoMol operator > framework/base/Value.h /^ friend bool operator>(const T& v1, const Value& v2) {return (Value(v1) > v2);}$/;" f class:ProtoMol::Value operator > framework/base/Value.h /^ friend bool operator>(const Value& v1, const T& v2) {return (v1 > Value(v2));}$/;" f class:ProtoMol::Value operator >= framework/base/Value.cpp /^ bool operator>=(const Value& v1, const Value& v2){$/;" f namespace:ProtoMol operator >= framework/base/Value.h /^ friend bool operator>=(const T& v1, const Value& v2){return (Value(v1) >= v2);}$/;" f class:ProtoMol::Value operator >= framework/base/Value.h /^ friend bool operator>=(const Value& v1, const T& v2){return (v1 >= Value(v2));}$/;" f class:ProtoMol::Value operator >> framework/base/Value.h /^ friend std::istream& operator>>(std::istream& is, Value& v){ v.read(is); return is;}$/;" f class:ProtoMol::Value operator >> framework/base/Vector3D.h /^ friend std::istream& operator>>(std::istream& OS, Vector3D & coords){$/;" f struct:ProtoMol::Vector3D operator >> framework/frontend/InputPosVel.cpp /^ InputPosVel& operator>>(InputPosVel& posReader, PDB& pdb){$/;" f namespace:ProtoMol operator >> framework/frontend/InputPosVel.cpp /^ InputPosVel& operator>>(InputPosVel& posReader, Vector3DBlock& coords){$/;" f namespace:ProtoMol operator >> framework/frontend/InputPosVel.cpp /^ InputPosVel& operator>>(InputPosVel& posReader, XYZ& xyz){$/;" f namespace:ProtoMol operator >> framework/io/AMBERReader.cpp /^ AMBERReader& operator>>(AMBERReader& topReader, PAR& par){$/;" f namespace:ProtoMol operator >> framework/io/AMBERReader.cpp /^ AMBERReader& operator>>(AMBERReader& topReader, PSF& psf){$/;" f namespace:ProtoMol operator >> framework/io/CRDReader.cpp /^ CRDReader& operator>>(CRDReader& crdReader, Vector3DBlock& coords){$/;" f namespace:ProtoMol operator >> framework/io/ConfigurationReader.cpp /^ ConfigurationReader& operator>>(ConfigurationReader& configReader, Configuration& config){$/;" f namespace:ProtoMol operator >> framework/io/DCDTrajectoryReader.cpp /^ DCDTrajectoryReader& operator>>(DCDTrajectoryReader& dcdTrajectoryReader, Vector3DBlock& coords){$/;" f namespace:ProtoMol operator >> framework/io/DCDTrajectoryReader.cpp /^ DCDTrajectoryReader& operator>>(DCDTrajectoryReader& dcdTrajectoryReader, XYZ& xyz){$/;" f namespace:ProtoMol operator >> framework/io/PARReader.cpp /^ PARReader& operator>>(PARReader& parReader, PAR& par){$/;" f namespace:ProtoMol operator >> framework/io/PDBReader.cpp /^ PDBReader& operator>>(PDBReader& pdbReader, PDB& pdb){$/;" f namespace:ProtoMol operator >> framework/io/PDBReader.cpp /^ PDBReader& operator>>(PDBReader& pdbReader, Vector3DBlock& coords){$/;" f namespace:ProtoMol operator >> framework/io/PDBReader.cpp /^ PDBReader& operator>>(PDBReader& pdbReader, XYZ& xyz){$/;" f namespace:ProtoMol operator >> framework/io/PGMReader.cpp /^ PGMReader& operator>>(PGMReader& pgmReader, PGM& pgm){$/;" f namespace:ProtoMol operator >> framework/io/PGMReader.cpp /^ PGMReader& operator>>(PGMReader& pgmReader, PPM& ppm){$/;" f namespace:ProtoMol operator >> framework/io/PPMReader.cpp /^ PPMReader& operator>>(PPMReader& ppmReader, PGM& pgm){$/;" f namespace:ProtoMol operator >> framework/io/PPMReader.cpp /^ PPMReader& operator>>(PPMReader& ppmReader, PPM& ppm){$/;" f namespace:ProtoMol operator >> framework/io/PSFReader.cpp /^ PSFReader& operator>>(PSFReader& psfReader, PSF& psf){$/;" f namespace:ProtoMol operator >> framework/io/REMConfigurationReader.cpp /^ REMConfigurationReader& operator>>(REMConfigurationReader& configReader, Configuration& config){$/;" f namespace:ProtoMol operator >> framework/io/TempFileReader.cpp /^ TempFileReader &operator>>(TempFileReader &reader, Real &temp) {$/;" f namespace:ProtoMol operator >> framework/io/XYZBinReader.cpp /^ XYZBinReader& operator>>(XYZBinReader& xyzbinReader, Vector3DBlock& coords){$/;" f namespace:ProtoMol operator >> framework/io/XYZBinReader.cpp /^ XYZBinReader& operator>>(XYZBinReader& xyzbinReader, XYZ& xyz){$/;" f namespace:ProtoMol operator >> framework/io/XYZReader.cpp /^ XYZReader& operator>>(XYZReader& xyzReader, Vector3DBlock& coords){$/;" f namespace:ProtoMol operator >> framework/io/XYZReader.cpp /^ XYZReader& operator>>(XYZReader& xyzReader, XYZ& xyz){$/;" f namespace:ProtoMol operator >> framework/io/XYZTrajectoryReader.cpp /^ XYZTrajectoryReader& operator>>(XYZTrajectoryReader& xyzReader, Vector3DBlock& coords){$/;" f namespace:ProtoMol operator >> framework/io/XYZTrajectoryReader.cpp /^ XYZTrajectoryReader& operator>>(XYZTrajectoryReader& xyzReader, XYZ& xyz){$/;" f namespace:ProtoMol operator Enum framework/base/AbstractEnumType.h /^ operator Enum() const{return myType;}$/;" f class:ProtoMol::AbstractEnumType operator Enum framework/base/ConstraintValueType.h /^ operator Enum() const{return e;}$/;" f struct:ProtoMol::ConstraintValueEnum::Enum2Type operator Enum framework/base/ValueType.h /^ operator Enum() const{return e;}$/;" f struct:ProtoMol::ValueEnum::Enum2ValueType operator Real framework/base/Value.cpp /^ Value::operator Real() const {$/;" f class:ProtoMol::Value operator T framework/frontend/InputValue.h /^ operator T() const {$/;" f class:ProtoMol::InputValue operator UIntArrayN framework/base/Array_Fastest.h /^ operator UIntArrayN () const { return m_Dimensions; }$/;" f class:ProtoMol::ArraySize operator Value framework/frontend/InputValue.h /^ operator Value() const{return myValue;}$/;" f class:ProtoMol::InputValue operator Vector3D framework/base/Value.cpp /^ Value::operator Vector3D() const {$/;" f class:ProtoMol::Value operator [] framework/base/Array_Fastest.h /^ RefArray & operator [](size_type Index) $/;" f class:ProtoMol::Array operator [] framework/base/Array_Fastest.h /^ RefArray & operator [](size_type Index)$/;" f class:ProtoMol::RefArray operator [] framework/base/Array_Fastest.h /^ const RefArray & operator [](size_type Index) const $/;" f class:ProtoMol::Array operator [] framework/base/Array_Fastest.h /^ const RefArray & operator [](size_type Index) const$/;" f class:ProtoMol::RefArray operator [] framework/base/Array_Fastest.h /^ const_reference operator [](size_type Index) const$/;" f class:ProtoMol::RefArray operator [] framework/base/Array_Fastest.h /^ reference operator [](size_type Index)$/;" f class:ProtoMol::RefArray operator [] framework/base/Array_NoPartialSpecialization.h /^ RefArray operator [](size_type Index)$/;" f class:ProtoMol::Array::RefArray operator [] framework/base/Array_NoPartialSpecialization.h /^ const RefArray operator [](size_type Index) const$/;" f class:ProtoMol::Array::RefArray operator [] framework/base/Array_NoPartialSpecialization.h /^ const_reference operator [](size_type Index) const$/;" f class:ProtoMol::Array::RefArray operator [] framework/base/Array_NoPartialSpecialization.h /^ reference operator [](size_type Index)$/;" f class:ProtoMol::Array::RefArray operator [] framework/base/Array_NoPartialSpecialization.h /^ RefArray operator [](size_type Index) $/;" f class:ProtoMol::Array operator [] framework/base/Array_NoPartialSpecialization.h /^ const RefArray operator [](size_type Index) const $/;" f class:ProtoMol::Array operator [] framework/base/Configuration.cpp /^ Value& Configuration::operator[](const string& keyword){$/;" f class:ProtoMol::Configuration operator [] framework/base/Configuration.cpp /^ const Value& Configuration::operator[](const string& keyword) const{$/;" f class:ProtoMol::Configuration operator [] framework/base/Molecule.h /^ int operator [](int i ){return atoms[i];}$/;" f struct:ProtoMol::Molecule operator [] framework/base/ScalarStructure.h /^ Real operator [](Index i) const{return myTable[static_cast(i)];}$/;" f class:ProtoMol::ScalarStructure operator [] framework/base/ScalarStructure.h /^ Real& operator [](Index i){return myTable[static_cast(i)];}$/;" f class:ProtoMol::ScalarStructure operator [] framework/base/Vector3D.h /^ Real operator[](int index) const{$/;" f struct:ProtoMol::Vector3D operator [] framework/base/Vector3D.h /^ Real& operator[](int index){$/;" f struct:ProtoMol::Vector3D operator [] framework/base/Vector3DBlock.h /^ const_reference operator[](size_type n) const {return vec[n];} $/;" f class:ProtoMol::Vector3DBlock operator [] framework/base/Vector3DBlock.h /^ reference operator[](size_type n) {return vec[n];} $/;" f class:ProtoMol::Vector3DBlock operator [] framework/topology/ArrayCellListStructure.h /^ T2& operator[](const T1& t1){$/;" f class:ProtoMol::ArrayCellListStructure operator ^ framework/base/Vector3D.h /^ Vector3D operator^(const Vector3D& b) const {$/;" f struct:ProtoMol::Vector3D operator bool framework/base/Value.cpp /^ Value::operator bool() const {$/;" f class:ProtoMol::Value operator int framework/base/Value.cpp /^ Value::operator int() const {$/;" f class:ProtoMol::Value operator std::string framework/base/AbstractEnumType.h /^ operator std::string() const{return getString(myType);}$/;" f class:ProtoMol::AbstractEnumType operator std::string framework/base/Value.cpp /^ Value::operator std::string() const {$/;" f class:ProtoMol::Value operator std::string framework/base/ValueType.h /^ operator std::string() const{return str;}$/;" f struct:ProtoMol::ValueEnum::Enum2ValueType operator std::vector framework/base/Vector.h /^ operator std::vector () {return myVector;};$/;" f class:ProtoMol::VectorPacker operator std::vector framework/base/Vector.h /^ operator std::vector(){return myVector;};$/;" f class:ProtoMol::Vector operator unsigned int framework/base/Value.cpp /^ Value::operator unsigned int() const {$/;" f class:ProtoMol::Value operator vector framework/base/Value.cpp /^ Value::operator vector() const {$/;" f class:ProtoMol::Value operator void* framework/frontend/InputPosVel.cpp /^ InputPosVel::operator void*() const{$/;" f class:ProtoMol::InputPosVel operator void* framework/io/File.cpp /^ File::operator void*() const{$/;" f class:ProtoMol::File optimize framework/topology/ExclusionTable.cpp /^ void ExclusionTable::optimize(){$/;" f class:ProtoMol::ExclusionTable optimizeC framework/integrators/ShadowHMCIntegrator.cpp /^ void ShadowHMCIntegrator::optimizeC( Real ratio ) {$/;" f class:ProtoMol::ShadowHMCIntegrator ordIdx framework/topology/CmpCnCnSwitchingFunction.h /^ int ordInt, ordIdx;$/;" m class:ProtoMol::CmpCnCnSwitchingFunction ordIdx framework/topology/CnSwitchingFunction.h /^ int ordInt, ordIdx;$/;" m class:ProtoMol::CnSwitchingFunction ordInt framework/topology/CmpCnCnSwitchingFunction.h /^ int ordInt, ordIdx;$/;" m class:ProtoMol::CmpCnCnSwitchingFunction ordInt framework/topology/CnSwitchingFunction.h /^ int ordInt, ordIdx;$/;" m class:ProtoMol::CnSwitchingFunction order framework/integrators/Modifier.h /^ int order() const{return myOrder;}$/;" f class:ProtoMol::Modifier orderParam framework/frontend/OutputState.h /^ struct orderParam{$/;" s class:ProtoMol::OutputState origin framework/topology/PeriodicBoundaryConditions.h /^ const Vector3D& origin() const {return myOrigin;}$/;" f class:ProtoMol::PeriodicBoundaryConditions origin framework/topology/VacuumBoundaryConditions.cpp /^ Vector3D VacuumBoundaryConditions::origin() const {return Vector3D(0,0,0);}$/;" f class:ProtoMol::VacuumBoundaryConditions orphanAtoms framework/io/PDBReader.cpp /^ std::vector* PDBReader::orphanAtoms(){$/;" f class:ProtoMol::PDBReader orphanConfiguration framework/io/ConfigurationReader.cpp /^ Configuration* ConfigurationReader::orphanConfiguration(){$/;" f class:ProtoMol::ConfigurationReader orphanConfiguration framework/io/REMConfigurationReader.cpp /^ Configuration* REMConfigurationReader::orphanConfiguration(){$/;" f class:ProtoMol::REMConfigurationReader orphanCoords framework/io/DCDTrajectoryReader.cpp /^ Vector3DBlock* DCDTrajectoryReader::orphanCoords(){$/;" f class:ProtoMol::DCDTrajectoryReader orphanCoords framework/io/PDBReader.cpp /^ Vector3DBlock* PDBReader::orphanCoords(){$/;" f class:ProtoMol::PDBReader orphanCoords framework/io/XYZBinReader.cpp /^ Vector3DBlock* XYZBinReader::orphanCoords(){$/;" f class:ProtoMol::XYZBinReader orphanCoords framework/io/XYZReader.cpp /^ Vector3DBlock* XYZReader::orphanCoords(){$/;" f class:ProtoMol::XYZReader orphanCoords framework/io/XYZTrajectoryReader.cpp /^ Vector3DBlock* XYZTrajectoryReader::orphanCoords(){$/;" f class:ProtoMol::XYZTrajectoryReader orphanNames framework/io/XYZReader.cpp /^ vector* XYZReader::orphanNames(){$/;" f class:ProtoMol::XYZReader orphanNames framework/io/XYZTrajectoryReader.cpp /^ vector* XYZTrajectoryReader::orphanNames(){$/;" f class:ProtoMol::XYZTrajectoryReader orphanPAR framework/io/AMBERReader.cpp /^ PAR* AMBERReader::orphanPAR(){$/;" f class:ProtoMol::AMBERReader orphanPAR framework/io/PARReader.cpp /^ PAR* PARReader::orphanPAR(){$/;" f class:ProtoMol::PARReader orphanPGM framework/io/PGMReader.cpp /^ PGM* PGMReader::orphanPGM(){$/;" f class:ProtoMol::PGMReader orphanPPM framework/io/PPMReader.cpp /^ PPM* PPMReader::orphanPPM(){$/;" f class:ProtoMol::PPMReader orphanPSF framework/io/AMBERReader.cpp /^ PSF* AMBERReader::orphanPSF(){$/;" f class:ProtoMol::AMBERReader orphanPSF framework/io/PSFReader.cpp /^ PSF* PSFReader::orphanPSF(){$/;" f class:ProtoMol::PSFReader orphanTers framework/io/PDBReader.cpp /^ std::vector* PDBReader::orphanTers(){$/;" f class:ProtoMol::PDBReader ostringstream framework/base/sstream_local.h /^ ostringstream(const std::string& s, int which=ios::out) :$/;" f class:std::ostringstream ostringstream framework/base/sstream_local.h /^ ostringstream(int which=ios::out) :$/;" f class:std::ostringstream ostringstream framework/base/sstream_local.h /^ class ostringstream : public stringstreambase, public ostream {$/;" c namespace:std ourIdentity framework/base/Matrix3by3.cpp /^ const Matrix3by3 Matrix3by3::ourIdentity = Matrix3by3(1,0,0, 0,1,0, 0,0,1);$/;" m class:ProtoMol::Matrix3by3 file: ourIdentity framework/base/Matrix3by3.h /^ static const Matrix3by3 ourIdentity;$/;" m class:ProtoMol::Matrix3by3 output framework/base/ScalarStructure.cpp /^ bool ScalarStructure::output(bool doOutput){$/;" f class:ProtoMol::ScalarStructure output framework/base/ScalarStructure.h /^ bool output() const {return myDoOutput;}$/;" f class:ProtoMol::ScalarStructure overflow framework/base/sstream_local.h /^inline int std::stringbuf::overflow(int ch)$/;" f class:std::stringbuf p compilerTests/pngTest.cpp /^ unsigned char* p;$/;" m class:PPM file: p framework/base/PGM.h /^ unsigned char* p;$/;" m class:ProtoMol::PGM p framework/base/PPM.h /^ unsigned char* p;$/;" m class:ProtoMol::PPM pairs framework/base/Molecule.h /^ std::vector pairs;$/;" m struct:ProtoMol::Molecule par framework/frontend/OutputCache.h /^ const PAR& par() const {return myPAR;}$/;" f class:ProtoMol::OutputCache parallelEvaluate framework/forces/AngleSystemForce.h /^ inline void AngleSystemForce::parallelEvaluate(const GenericTopology* topo,$/;" f class:ProtoMol::AngleSystemForce parallelEvaluate framework/forces/BondSystemForce.h /^ inline void BondSystemForce::parallelEvaluate(const GenericTopology* topo,$/;" f class:ProtoMol::BondSystemForce parallelEvaluate framework/forces/DihedralSystemForce.h /^ inline void DihedralSystemForce::parallelEvaluate(const GenericTopology* topo,$/;" f class:ProtoMol::DihedralSystemForce parallelEvaluate framework/forces/ElectricFieldSystemForce.h /^ inline void ElectricFieldSystemForce::parallelEvaluate(const GenericTopology* topo,$/;" f class:ProtoMol::ElectricFieldSystemForce parallelEvaluate framework/forces/ExtendedCompareForce.cpp /^ void ExtendedCompareForce::parallelEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::ExtendedCompareForce parallelEvaluate framework/forces/ExtendedForce.h /^ inline void ExtendedForce::parallelEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::ExtendedForce parallelEvaluate framework/forces/ExtendedTimeForce.cpp /^ void ExtendedTimeForce::parallelEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::ExtendedTimeForce parallelEvaluate framework/forces/ExternalGravitationSystemForce.cpp /^ void ExternalGravitationSystemForce::parallelEvaluate(const GenericTopology* topo,$/;" f class:ProtoMol::ExternalGravitationSystemForce parallelEvaluate framework/forces/ExternalMagneticFieldExtendedForce.cpp /^ void ExternalMagneticFieldExtendedForce::parallelEvaluate(const GenericTopology* topo,$/;" f class:ProtoMol::ExternalMagneticFieldExtendedForce parallelEvaluate framework/forces/FrictionExtendedForce.cpp /^ void FrictionExtendedForce::parallelEvaluate(const GenericTopology* topo,$/;" f class:ProtoMol::FrictionExtendedForce parallelEvaluate framework/forces/HarmDihedralSystemForce.h /^ inline void HarmDihedralSystemForce::parallelEvaluate(const GenericTopology* topo,$/;" f class:ProtoMol::HarmDihedralSystemForce parallelEvaluate framework/forces/ImproperSystemForce.h /^ inline void ImproperSystemForce::parallelEvaluate(const GenericTopology* topo,$/;" f class:ProtoMol::ImproperSystemForce parallelEvaluate framework/forces/MollyForce.h /^ inline void MollyForce::parallelEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::MollyForce parallelEvaluate framework/forces/NonbondedCutoffMollyForce.h /^ void NonbondedCutoffMollyForce::parallelEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedCutoffMollyForce parallelEvaluate framework/forces/NonbondedCutoffSystemForce.h /^ void NonbondedCutoffSystemForce::parallelEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedCutoffSystemForce parallelEvaluate framework/forces/NonbondedFullEwaldSystemForce.h /^ TSwitchingFunction>::parallelEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedFullEwaldSystemForce parallelEvaluate framework/forces/NonbondedFullSystemForce.h /^ virtual void parallelEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedFullSystemForce parallelEvaluate framework/forces/NonbondedMultiGridSystemForce.h /^ smooth>::parallelEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedMultiGridSystemForce parallelEvaluate framework/forces/NonbondedPMEwaldSystemForce.h /^ real,reciprocal,correction,TInterpolation,TSwitchingFunction>::parallelEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedPMEwaldSystemForce parallelEvaluate framework/forces/NonbondedSimpleFullSystemForce.h /^ virtual void parallelEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::NonbondedSimpleFullSystemForce parallelEvaluate framework/forces/PaulTrapExtendedForce.h /^ inline void PaulTrapExtendedForce::parallelEvaluate(const GenericTopology* topo,$/;" f class:ProtoMol::PaulTrapExtendedForce parallelEvaluate framework/forces/SphericalSystemForce.cpp /^ void SphericalSystemForce::parallelEvaluate(const GenericTopology* topo,$/;" f class:ProtoMol::SphericalSystemForce parallelEvaluate framework/forces/SystemCompareForce.cpp /^ void SystemCompareForce::parallelEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::SystemCompareForce parallelEvaluate framework/forces/SystemForce.h /^ inline void SystemForce::parallelEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::SystemForce parallelEvaluate framework/forces/SystemTimeForce.cpp /^ void SystemTimeForce::parallelEvaluate(const GenericTopology* topo, $/;" f class:ProtoMol::SystemTimeForce parameters framework/base/MakeableDefinition.h /^ std::vector parameters; \/\/\/< parameters of the obejct$/;" m struct:ProtoMol::MakeableDefinition parameters framework/base/ObjectDefinition.h /^ std::vector parameters;$/;" m struct:ProtoMol::ObjectDefinition parameters framework/frontend/HelpTextFactory.h /^ std::vector parameters;$/;" m struct:ProtoMol::HelpText parseCommandLine framework/frontend/parseCommandLine.cpp /^ vector > parseCommandLine (int argc, char **argv, $/;" f namespace:ProtoMol parseParameters tools/rem/sequential/main.cc /^vector parseParameters(const string& parameterString) {$/;" f pauseCalc framework/integrators/ModifierShadow.h /^ inline void ModifierShadow::pauseCalc() {$/;" f class:ProtoMol::ModifierShadow paused framework/integrators/ModifierShadow.h /^ bool paused;$/;" m class:ProtoMol::ModifierShadow pdb framework/frontend/OutputCache.h /^ const std::vector& pdb() const {return myAtoms;}$/;" f class:ProtoMol::OutputCache periodicCell framework/topology/ArrayCellListStructure.h /^ T1 periodicCell(const T1& t1) const{$/;" f class:ProtoMol::ArrayCellListStructure periodicity framework/base/PAR.h /^ int periodicity; \/\/\/< periodicity$/;" m struct:ProtoMol::PAR::Improper periodicity framework/base/PAR.h /^ std::vector< int > periodicity; \/\/\/< periodicity$/;" m struct:ProtoMol::PAR::Dihedral periodicity framework/topology/Torsion.h /^ std::vector< int > periodicity; \/\/\/< The periodicity ($n$ value) for this interaction.$/;" m class:ProtoMol::Torsion perturbSystem framework/integrators/DLMCIntegrator.cpp /^ void DLMCIntegrator::perturbSystem() {$/;" f class:ProtoMol::DLMCIntegrator perturbSystem framework/integrators/HMCIntegrator.cpp /^ void HMCIntegrator::perturbSystem() {$/;" f class:ProtoMol::HMCIntegrator perturbSystem framework/integrators/ShadowHMCIntegrator.cpp /^ void ShadowHMCIntegrator::perturbSystem() {$/;" f class:ProtoMol::ShadowHMCIntegrator phaseShift framework/base/PAR.h /^ Real phaseShift; \/\/\/< phase shift$/;" m struct:ProtoMol::PAR::Improper phaseShift framework/base/PAR.h /^ std::vector< Real > phaseShift; \/\/\/< phase shift$/;" m struct:ProtoMol::PAR::Dihedral phaseShift framework/topology/Torsion.h /^ std::vector< Real > phaseShift; \/\/\/< The phase shift ($\\delta$ value) for this interaction, in radians. $/;" m class:ProtoMol::Torsion plain framework/base/Report.cpp /^ MyStreamer& plain(MyStreamer& stream){$/;" f namespace:ProtoMol::Report pointer framework/base/Array_Fastest.h /^ typedef T * pointer;$/;" t class:ProtoMol::Array pointer framework/base/Array_Fastest.h /^ typedef T * pointer;$/;" t class:ProtoMol::RefArray pointer framework/base/Array_NoPartialSpecialization.h /^ typedef T * pointer;$/;" t class:ProtoMol::Array::RefArray pointer framework/base/Array_NoPartialSpecialization.h /^ typedef T * pointer;$/;" t class:ProtoMol::Array pointer framework/base/Vector3DBlock.h /^ typedef std::vector::pointer pointer; $/;" t class:ProtoMol::Vector3DBlock pointer framework/topology/ArrayCellListStructure.h /^ typedef TContainer::pointer pointer;$/;" t class:ProtoMol::ArrayCellListStructure polarizability framework/base/PAR.h /^ Real polarizability; \/\/\/< polarizability or ignore (see description of negative below), default to zero$/;" m struct:ProtoMol::PAR::Nonbonded polarizability2 framework/base/PAR.h /^ Real polarizability2; \/\/\/< VDW parameter polarizability, default to zero$/;" m struct:ProtoMol::PAR::Nonbonded policies framework/frontend/ForceFactoryDetails.h /^ std::set policies;$/;" m struct:ProtoMol::ForceFactoryDetails::ForceType policiesSorted framework/frontend/ForceFactoryDetails.h /^ std::map policiesSorted;$/;" m struct:ProtoMol::ForceFactoryDetails::ForceType policy framework/frontend/ForceFactoryDetails.h /^ std::set policy;$/;" m struct:ProtoMol::ForceFactoryDetails::ForceType poly5 framework/base/mathutilities.cpp /^ Real poly5(Real ar){$/;" f namespace:ProtoMol popElement framework/base/Stack.h /^ T Stack::popElement() {$/;" f class:ProtoMol::Stack pop_back framework/base/Vector3DBlock.h /^ void pop_back() {return vec.pop_back();} $/;" f class:ProtoMol::Vector3DBlock port framework/imd/IMDElf.h /^ int port;$/;" m class:ProtoMol::IMDElf pos_type framework/base/sstream_local.h /^ typedef streampos pos_type;$/;" t class:std::stringbuf position framework/base/Molecule.h /^ Vector3D position;$/;" m struct:ProtoMol::Molecule positions framework/forces/OneAtomPair.h /^ const Vector3DBlock* positions;$/;" m class:ProtoMol::OneAtomPair positions framework/forces/OneAtomPairFull.h /^ const Vector3DBlock* positions;$/;" m class:ProtoMol::OneAtomPairFull positions framework/forces/OneAtomPairTwo.h /^ const Vector3DBlock* positions;$/;" m class:ProtoMol::OneAtomPairTwo positions framework/forces/OneAtomPairTwoFull.h /^ const Vector3DBlock* positions;$/;" m class:ProtoMol::OneAtomPairTwoFull positions framework/forces/OneMollyPair.h /^ const Vector3DBlock* positions;$/;" m class:ProtoMol::OneMollyPair positions framework/forces/OneMollyPairTwo.h /^ const Vector3DBlock* positions;$/;" m class:ProtoMol::OneMollyPairTwo postDriftOrNextModify framework/integrators/Integrator.cpp /^ void Integrator::postDriftOrNextModify(){$/;" f class:ProtoMol::Integrator postForceModify framework/integrators/Integrator.cpp /^ void Integrator::postForceModify(){$/;" f class:ProtoMol::Integrator postStepModify framework/integrators/Integrator.cpp /^ void Integrator::postStepModify(){$/;" f class:ProtoMol::Integrator postprocess framework/forces/CompareForce.cpp /^ void CompareForce::postprocess(const GenericTopology* topo, Vector3DBlock* forces,ScalarStructure* energies){$/;" f class:ProtoMol::CompareForce postprocess framework/forces/TimeForce.cpp /^ void TimeForce::postprocess(const GenericTopology* , Vector3DBlock*,ScalarStructure* ){$/;" f class:ProtoMol::TimeForce potentialEnergy framework/base/ScalarStructure.h /^ inline Real ScalarStructure::potentialEnergy() const {$/;" f class:ProtoMol::ScalarStructure potentialEnergy framework/frontend/OutputCache.cpp /^ Real OutputCache::potentialEnergy() const{$/;" f class:ProtoMol::OutputCache power framework/base/mathutilities.cpp /^ Real power(Real x, int n){$/;" f namespace:ProtoMol power framework/base/mathutilities.h /^ static Real power(Real x){ return 1\/x;}$/;" f struct:ProtoMol::Private::Power power framework/base/mathutilities.h /^ static Real power(Real x){ return x;}$/;" f struct:ProtoMol::Private::Power power framework/base/mathutilities.h /^ static Real power(Real x){$/;" f struct:ProtoMol::Private::Power power framework/base/mathutilities.h /^ static Real power(Real){ return 1;}$/;" f struct:ProtoMol::Private::Power power framework/base/mathutilities.h /^ template inline Real power(Real x) {$/;" f namespace:ProtoMol power framework/base/mathutilities.h /^ template<> inline Real power<-1>(Real x) {return 1.\/x;}$/;" f namespace:ProtoMol power framework/base/mathutilities.h /^ template<> inline Real power<0>(Real) {return 1;}$/;" f namespace:ProtoMol power framework/base/mathutilities.h /^ template<> inline Real power<1>(Real x) {return x;}$/;" f namespace:ProtoMol power framework/base/mathutilities.h /^ template inline Real power(Real x){$/;" f namespace:ProtoMol preDriftOrNextModify framework/integrators/Integrator.cpp /^ void Integrator::preDriftOrNextModify(){$/;" f class:ProtoMol::Integrator preForceModify framework/integrators/Integrator.cpp /^ void Integrator::preForceModify(){$/;" f class:ProtoMol::Integrator preStepModify framework/integrators/Integrator.cpp /^ void Integrator::preStepModify(){$/;" f class:ProtoMol::Integrator precision framework/base/Report.cpp /^ void MyStreamer::precision(int prec){$/;" f class:ProtoMol::Report::MyStreamer precomputeG framework/base/MultiGrid.h /^ inline void MultiGrid::precomputeG(){$/;" f class:ProtoMol::MultiGrid preprocess framework/forces/CompareForce.cpp /^ void CompareForce::preprocess(unsigned int numAtoms){$/;" f class:ProtoMol::CompareForce preprocess framework/forces/TimeForce.cpp /^ void TimeForce::preprocess(unsigned int){$/;" f class:ProtoMol::TimeForce pressure framework/base/ScalarStructure.h /^ inline Real ScalarStructure::pressure(Real volume) const {$/;" f class:ProtoMol::ScalarStructure pressure framework/frontend/OutputCache.cpp /^ Real OutputCache::pressure() const{$/;" f class:ProtoMol::OutputCache previous framework/integrators/StandardIntegrator.cpp /^ Integrator* StandardIntegrator::previous(){$/;" f class:ProtoMol::StandardIntegrator previous framework/integrators/StandardIntegrator.cpp /^ const Integrator* StandardIntegrator::previous() const{$/;" f class:ProtoMol::StandardIntegrator print framework/base/Configuration.cpp /^ string Configuration::print() const{$/;" f class:ProtoMol::Configuration print framework/base/Grid.h /^ void Grid::print(){$/;" f class:ProtoMol::Grid print framework/base/MultiGrid.h /^ void print(int level){printQ(level);printV(level);}$/;" f class:ProtoMol::MultiGrid print framework/base/Report.h /^ inline bool MyStreamer::print() const{$/;" f class:ProtoMol::Report::MyStreamer print framework/base/pmconstants.cpp /^ string print(){$/;" f namespace:ProtoMol::Constant print framework/frontend/Factory.h /^ static std::string print(){$/;" f class:ProtoMol::Factory print framework/integrators/IntegratorDefinition.cpp /^ string IntegratorDefinition::print() const{$/;" f class:ProtoMol::IntegratorDefinition print framework/integrators/Modifier.h /^ std::string print() const{$/;" f class:ProtoMol::Modifier print framework/topology/Topology.h /^ virtual std::string print(const Vector3DBlock* positions=NULL) const{$/;" f class:ProtoMol::Topology printConst framework/base/MultiGrid.h /^ void MultiGrid::printConst(){$/;" f class:ProtoMol::MultiGrid printQ framework/base/MultiGrid.h /^ void MultiGrid::printQ(int level){$/;" f class:ProtoMol::MultiGrid printV framework/base/MultiGrid.h /^ void MultiGrid::printV(int level){$/;" f class:ProtoMol::MultiGrid protomolAbort framework/base/systemutilities.cpp /^ void protomolAbort(){$/;" f namespace:ProtoMol protomolEndSerial framework/base/systemutilities.cpp /^ void protomolEndSerial(bool exludeMaster){$/;" f namespace:ProtoMol protomolExit framework/base/systemutilities.cpp /^ void protomolExit(){$/;" f namespace:ProtoMol protomolStartSerial framework/base/systemutilities.cpp /^ void protomolStartSerial(bool exludeMaster){$/;" f namespace:ProtoMol prototype framework/frontend/IntegratorFactoryDetails.h /^ const Integrator* prototype;$/;" m struct:ProtoMol::IntegratorFactoryDetails::IntegratorInput psf framework/frontend/OutputCache.h /^ const PSF& psf() const {return myPSF;}$/;" f class:ProtoMol::OutputCache push_back framework/base/Vector3DBlock.h /^ void push_back(const Vector3D& t) {return vec.push_back(t);} $/;" f class:ProtoMol::Vector3DBlock quit framework/base/Report.cpp /^ MyStreamer& quit(MyStreamer& stream){$/;" f namespace:ProtoMol::Report rFavg framework/forces/CompareForce.h /^ Real absF2,rFavg,rFmax,rPE; $/;" m struct:ProtoMol::CompareForce::CompareError rFmax framework/forces/CompareForce.h /^ Real absF2,rFavg,rFmax,rPE; $/;" m struct:ProtoMol::CompareForce::CompareError rPE framework/forces/CompareForce.h /^ Real absF2,rFavg,rFmax,rPE; $/;" m struct:ProtoMol::CompareForce::CompareError r_ub framework/base/PAR.h /^ Real r_ub; \/\/\/< Urey-Bradley radius$/;" m struct:ProtoMol::PAR::Angle radialCmpVector3D tools/bccAnalyzer.cpp /^ radialCmpVector3D():c(Vector3D(0.0,0.0,0.0)){}$/;" f class:radialCmpVector3D radialCmpVector3D tools/bccAnalyzer.cpp /^ radialCmpVector3D(const Vector3D& a):c(a){}$/;" f class:radialCmpVector3D radialCmpVector3D tools/bccAnalyzer.cpp /^class radialCmpVector3D {$/;" c file: radix2b_ framework/base/fft.c /^int radix2b_(double *a1, double *a2, double *b1, double *b2,int * b, int *ldb, double *c2, double *d2)$/;" f radix2f_ framework/base/fft.c /^int radix2f_(double *a1,double * a2, double *b1,double * b2,int * b,int *ldb, double *c2,double * d2)$/;" f radix3b_ framework/base/fft.c /^int radix3b_(double *a1,double * a2, double *a3,double * b1,double * b2,double * b3, int *b, int *ldb, double *c2, double *d2, double *c3, double *d3)$/;" f radix3f_ framework/base/fft.c /^int radix3f_(double *a1, double *a2, double *a3, double *b1, double *b2, double *b3, int *b, int *ldb, double *c2, double *d2, double *c3, double *d3)$/;" f radix4b_ framework/base/fft.c /^int radix4b_(double *a1, double *a2, double *a3, double *a4, double *b1, double *b2, double *b3, double *b4, int *b, int *ldb, double *c2, double *d2, double *c3, double *d3, double *c4, double *d4)$/;" f radix4f_ framework/base/fft.c /^int radix4f_(double *a1, double *a2, double *a3, double *a4, double *b1, double *b2, double *b3, double *b4, int *b, int *ldb, double *c2, double *d2, double *c3, double *d3, double *c4, double *d4)$/;" f radix5b_ framework/base/fft.c /^int radix5b_(double *a1,double * a2,double * a3,double * a4,double * a5,double * b1,double * b2,double * b3,double * b4,double * b5,int * b,int *ldb, double *c2,double * d2,double * c3,double * d3,double * c4,double * d4, double *c5, double *d5)$/;" f radix5f_ framework/base/fft.c /^int radix5f_(double *a1,double * a2,double * a3,double * a4,double * a5,double * b1,double * b2,double * b3,double * b4,double * b5,int *b, int *ldb, double *c2,double * d2,double * c3,double * d3,double * c4,double * d4,double * c5,double * d5)$/;" f radix7b_ framework/base/fft.c /^int radix7b_(double *a1, double *a2,double * a3,double * a4,double * a5,double * a6,double * a7,double * b1,double * b2,double * b3,double * b4,double * b5, double *b6, double *b7, int *b, int *ldb)$/;" f radix7f_ framework/base/fft.c /^int radix7f_(double *a1,double * a2,double * a3, double *a4,double * a5,double * a6,double * a7,double * b1,double * b2,double * b3,double * b4,double * b5, double *b6,double * b7,int * b,int * ldb)$/;" f randomGaussian framework/base/mathutilities.cpp /^ Real randomGaussian(Real sdv, unsigned int seed){$/;" f namespace:ProtoMol randomGaussianNumber framework/base/mathutilities.cpp /^ Real randomGaussianNumber(Real mean, Real stdev, unsigned int iseed) {$/;" f namespace:ProtoMol randomGaussianNumber framework/base/mathutilities.cpp /^ Real randomGaussianNumber(unsigned int seed) {$/;" f namespace:ProtoMol randomNumber framework/base/mathutilities.cpp /^ Real randomNumber(unsigned int seed) {$/;" f namespace:ProtoMol randomVelocity framework/topology/topologyutilities.cpp /^ void randomVelocity(Real temperature,$/;" f namespace:ProtoMol randomVelocity framework/topology/topologyutilities.cpp /^ void randomVelocity(Real temperatureFrom,$/;" f namespace:ProtoMol rbegin framework/base/Vector3DBlock.h /^ const_reverse_iterator rbegin() const {return vec.rbegin();} $/;" f class:ProtoMol::Vector3DBlock rbegin framework/base/Vector3DBlock.h /^ reverse_iterator rbegin() {return vec.rbegin();} $/;" f class:ProtoMol::Vector3DBlock rc framework/imd/IMDElf.h /^ int rc;$/;" m class:ProtoMol::IMDElf rdbuf framework/base/sstream_local.h /^ stringbuf* rdbuf()$/;" f class:std::stringstreambase re framework/base/FFTComplex.h /^ double re;$/;" m re framework/base/fft.c /^ double re;$/;" m file: read framework/base/Value.cpp /^ void Value::read(std::istream& is){$/;" f class:ProtoMol::Value read framework/base/Value.h /^ virtual void read(std::istream& is){ ok = ValueTrait::read(is,holder) && ValueTrait::check(Constraint(),holder);}$/;" f class:ProtoMol::Value::Holder read framework/base/ValueType.h /^ static bool read(std::istream& is, RepType & v){ $/;" f struct:ProtoMol::ValueTraits read framework/base/ValueType.h /^ static bool read(std::istream& is, RepType & v){ std::string tmp; is >> tmp; return toReal(tmp,v);}$/;" f struct:ProtoMol::ValueTraits read framework/base/ValueType.h /^ static bool read(std::istream& is, RepType & v){ std::string tmp; is >> tmp; return toUInt(tmp,v);}$/;" f struct:ProtoMol::ValueTraits read framework/base/ValueType.h /^ static bool read(std::istream& is, RepType & v){ std::string x,y,z; is >> x >> y >> z; return toVector3D(x+" "+y+" "+z,v);}$/;" f struct:ProtoMol::ValueTraits read framework/base/ValueType.h /^ static bool read(std::istream& is, RepType & v){ $/;" f struct:ProtoMol::ValueTraits read framework/base/ValueType.h /^ static bool read(std::istream& is, RepType & v){ is >> v; return true;}$/;" f struct:ProtoMol::ValueTraits read framework/base/ValueType.h /^ static bool read(std::istream& is, RepType & v){ std::string tmp; is >> tmp; return toBool(tmp,v);}$/;" f struct:ProtoMol::ValueTraits read framework/base/ValueType.h /^ static bool read(std::istream& is, RepType & v){ std::string tmp; is >> tmp; return toInt(tmp,v);}$/;" f struct:ProtoMol::ValueTraits read framework/io/AMBERReader.cpp /^ bool AMBERReader::read() {$/;" f class:ProtoMol::AMBERReader read framework/io/AMBERReader.cpp /^ bool AMBERReader::read(PSF& psf,PAR& par) {$/;" f class:ProtoMol::AMBERReader read framework/io/CRDReader.cpp /^ bool CRDReader::read() {$/;" f class:ProtoMol::CRDReader read framework/io/CRDReader.cpp /^ bool CRDReader::read(Vector3DBlock& coords) {$/;" f class:ProtoMol::CRDReader read framework/io/ConfigurationReader.cpp /^ bool ConfigurationReader::read() {$/;" f class:ProtoMol::ConfigurationReader read framework/io/ConfigurationReader.cpp /^ bool ConfigurationReader::read(Configuration& config){$/;" f class:ProtoMol::ConfigurationReader read framework/io/DCDTrajectoryReader.cpp /^ bool DCDTrajectoryReader::read() {$/;" f class:ProtoMol::DCDTrajectoryReader read framework/io/DCDTrajectoryReader.cpp /^ bool DCDTrajectoryReader::read(Vector3DBlock& coords) {$/;" f class:ProtoMol::DCDTrajectoryReader read framework/io/File.cpp /^ std::fstream& File::read(char* c, std::streamsize count){$/;" f class:ProtoMol::File read framework/io/PARReader.cpp /^ bool PARReader::read() {$/;" f class:ProtoMol::PARReader read framework/io/PARReader.cpp /^ bool PARReader::read(PAR& par) {$/;" f class:ProtoMol::PARReader read framework/io/PDBReader.cpp /^ bool PDBReader::read() {$/;" f class:ProtoMol::PDBReader read framework/io/PDBReader.cpp /^ bool PDBReader::read(PDB& pdb){$/;" f class:ProtoMol::PDBReader read framework/io/PDBReader.cpp /^ bool PDBReader::read(Vector3DBlock& coords, std::vector& atoms, std::vector& ters) {$/;" f class:ProtoMol::PDBReader read framework/io/PGMReader.cpp /^ bool PGMReader::read() {$/;" f class:ProtoMol::PGMReader read framework/io/PGMReader.cpp /^ bool PGMReader::read(PGM& pgm) {$/;" f class:ProtoMol::PGMReader read framework/io/PGMReader.cpp /^ bool PGMReader::read(PPM& ppm) {$/;" f class:ProtoMol::PGMReader read framework/io/PPMReader.cpp /^ bool PPMReader::read() {$/;" f class:ProtoMol::PPMReader read framework/io/PPMReader.cpp /^ bool PPMReader::read(PGM& pgm) {$/;" f class:ProtoMol::PPMReader read framework/io/PPMReader.cpp /^ bool PPMReader::read(PPM& ppm) {$/;" f class:ProtoMol::PPMReader read framework/io/PSFReader.cpp /^ bool PSFReader::read() {$/;" f class:ProtoMol::PSFReader read framework/io/PSFReader.cpp /^ bool PSFReader::read(PSF& psf) {$/;" f class:ProtoMol::PSFReader read framework/io/REMConfigurationReader.cpp /^ bool REMConfigurationReader::read() {$/;" f class:ProtoMol::REMConfigurationReader read framework/io/REMConfigurationReader.cpp /^ bool REMConfigurationReader::read(Configuration& config){$/;" f class:ProtoMol::REMConfigurationReader read framework/io/TempFileReader.cpp /^ bool TempFileReader::read() {$/;" f class:ProtoMol::TempFileReader read framework/io/TempFileReader.cpp /^ bool TempFileReader::read(Real &temp) {$/;" f class:ProtoMol::TempFileReader read framework/io/XYZBinReader.cpp /^ bool XYZBinReader::read() {$/;" f class:ProtoMol::XYZBinReader read framework/io/XYZBinReader.cpp /^ bool XYZBinReader::read(Vector3DBlock& coords) {$/;" f class:ProtoMol::XYZBinReader read framework/io/XYZReader.cpp /^ bool XYZReader::read() {$/;" f class:ProtoMol::XYZReader read framework/io/XYZReader.cpp /^ bool XYZReader::read(Vector3DBlock& coords, std::vector& names){$/;" f class:ProtoMol::XYZReader read framework/io/XYZReader.cpp /^ bool XYZReader::read(XYZ& xyz) {$/;" f class:ProtoMol::XYZReader read framework/io/XYZTrajectoryReader.cpp /^ bool XYZTrajectoryReader::read() {$/;" f class:ProtoMol::XYZTrajectoryReader read framework/io/XYZTrajectoryReader.cpp /^ bool XYZTrajectoryReader::read(Vector3DBlock& coords, std::vector& names){$/;" f class:ProtoMol::XYZTrajectoryReader read framework/io/XYZTrajectoryReader.cpp /^ bool XYZTrajectoryReader::read(XYZ& xyz) {$/;" f class:ProtoMol::XYZTrajectoryReader readInput tools/rem/sequential/main.cc /^void readInput(char* fileName,$/;" f realChi framework/forces/MagneticDipoleForce.h /^ Real volum, expfactor, realChi, kappa;$/;" m class:ProtoMol::MagneticDipoleForce realTerm framework/forces/NonbondedFullEwaldSystemForce.h /^ TSwitchingFunction>::realTerm(const RealTopologyType* realTopo,$/;" f class:ProtoMol::NonbondedFullEwaldSystemForce realTerm framework/forces/NonbondedPMEwaldSystemForce.h /^ TSwitchingFunction>::realTerm(const RealTopologyType* realTopo,$/;" f class:ProtoMol::NonbondedPMEwaldSystemForce realTopo framework/forces/OneAtomPair.h /^ const SemiGenericTopology* realTopo;$/;" m class:ProtoMol::OneAtomPair realTopo framework/forces/OneAtomPairFull.h /^ const SemiGenericTopology* realTopo;$/;" m class:ProtoMol::OneAtomPairFull realTopo framework/forces/OneAtomPairTwo.h /^ const SemiGenericTopology* realTopo;$/;" m class:ProtoMol::OneAtomPairTwo realTopo framework/forces/OneAtomPairTwoFull.h /^ const SemiGenericTopology* realTopo;$/;" m class:ProtoMol::OneAtomPairTwoFull realTopo framework/forces/OneMollyPair.h /^ const SemiGenericTopology* realTopo;$/;" m class:ProtoMol::OneMollyPair realTopo framework/forces/OneMollyPairTwo.h /^ const SemiGenericTopology* realTopo;$/;" m class:ProtoMol::OneMollyPairTwo realclear framework/base/systemutilities.h /^ void realclear(T& t){$/;" f namespace:ProtoMol reciprocalTerm framework/forces/NonbondedFullEwaldSystemForce.h /^ TSwitchingFunction>::reciprocalTerm(const RealTopologyType* realTopo,$/;" f class:ProtoMol::NonbondedFullEwaldSystemForce reciprocalTerm framework/forces/NonbondedPMEwaldSystemForce.h /^ TSwitchingFunction>::reciprocalTerm(const RealTopologyType* realTopo,$/;" f class:ProtoMol::NonbondedPMEwaldSystemForce reciprocalTermParallel framework/forces/NonbondedPMEwaldSystemForce.h /^ TSwitchingFunction>::reciprocalTermParallel(const RealTopologyType* realTopo,$/;" f class:ProtoMol::NonbondedPMEwaldSystemForce reclose framework/frontend/OutputFile.cpp /^ bool OutputFile::reclose(){$/;" f class:ProtoMol::OutputFile recoverable framework/base/Report.cpp /^ MyStreamer& recoverable(MyStreamer& stream){$/;" f namespace:ProtoMol::Report recv framework/parallel/Parallel-FD.cpp /^ void Parallel::recv(Real *, int, int) {}$/;" f class:ProtoMol::Parallel recv framework/parallel/Parallel-FD.cpp /^ void Parallel::recv(Real *data, int num, int address) {$/;" f class:ProtoMol::Parallel recv framework/parallel/Parallel-FD.cpp /^ void Parallel::recv(Vector3DBlock *, int) {}$/;" f class:ProtoMol::Parallel recv framework/parallel/Parallel-FD.cpp /^ void Parallel::recv(Vector3DBlock *vect, int address) {$/;" f class:ProtoMol::Parallel recv framework/parallel/Parallel.cpp /^ void Parallel::recv(Real *, int, int) {}$/;" f class:ProtoMol::Parallel recv framework/parallel/Parallel.cpp /^ void Parallel::recv(Real *data, int num, int address) {$/;" f class:ProtoMol::Parallel recv framework/parallel/Parallel.cpp /^ void Parallel::recv(Vector3DBlock *, int) {}$/;" f class:ProtoMol::Parallel recv framework/parallel/Parallel.cpp /^ void Parallel::recv(Vector3DBlock *vect, int address) {$/;" f class:ProtoMol::Parallel recvcounts framework/parallel/Parallel-FD.cpp /^ int* recvcounts = NULL;$/;" v reduce framework/base/Proxy.h /^ void reduce() const {myCount--;}$/;" f class:ProtoMol::Proxy reduce framework/parallel/Parallel-FD.cpp /^ void Parallel::reduce(ScalarStructure* energies, Vector3DBlock* coords){$/;" f class:ProtoMol::Parallel reduce framework/parallel/Parallel-FD.cpp /^ void Parallel::reduce(ScalarStructure*, Vector3DBlock*){}$/;" f class:ProtoMol::Parallel reduce framework/parallel/Parallel.cpp /^ void Parallel::reduce(ScalarStructure* energies, Vector3DBlock* coords){$/;" f class:ProtoMol::Parallel reduce framework/parallel/Parallel.cpp /^ void Parallel::reduce(ScalarStructure*, Vector3DBlock*){}$/;" f class:ProtoMol::Parallel reduceSlaves framework/parallel/Parallel-FD.cpp /^ void Parallel::reduceSlaves(Real* begin, Real* end) {$/;" f class:ProtoMol::Parallel reduceSlaves framework/parallel/Parallel-FD.cpp /^ void Parallel::reduceSlaves(Real*, Real*) {}$/;" f class:ProtoMol::Parallel reduceSlaves framework/parallel/Parallel.cpp /^ void Parallel::reduceSlaves(Real* begin, Real* end) {$/;" f class:ProtoMol::Parallel reduceSlaves framework/parallel/Parallel.cpp /^ void Parallel::reduceSlaves(Real*, Real*) {}$/;" f class:ProtoMol::Parallel reducedHessBond framework/base/reducedHessBond.cpp /^ Matrix3by3 reducedHessBond(const Vector3D& atom_i,$/;" f namespace:ProtoMol reference framework/base/Array_Fastest.h /^ typedef T & reference;$/;" t class:ProtoMol::Array reference framework/base/Array_Fastest.h /^ typedef T & reference;$/;" t class:ProtoMol::RefArray reference framework/base/Array_NoPartialSpecialization.h /^ typedef T & reference;$/;" t class:ProtoMol::Array::RefArray reference framework/base/Array_NoPartialSpecialization.h /^ typedef T & reference;$/;" t class:ProtoMol::Array reference framework/base/Vector3DBlock.h /^ typedef std::vector::reference reference; $/;" t class:ProtoMol::Vector3DBlock reference framework/topology/ArrayCellListStructure.h /^ typedef TContainer::reference reference;$/;" t class:ProtoMol::ArrayCellListStructure registerAliases framework/base/Configuration.cpp /^ void Configuration::registerAliases(const string& keyword, const vector& aliases){$/;" f class:ProtoMol::Configuration registerAllExemplarsConfiguration framework/frontend/OutputFactoryDetails.cpp /^ void OutputFactoryDetails::registerAllExemplarsConfiguration(Configuration* config){$/;" f class:ProtoMol::OutputFactoryDetails registerAllExemplarsConfiguration framework/frontend/TopologyFactoryDetails.cpp /^ void TopologyFactoryDetails::registerAllExemplarsConfiguration(Configuration* config){$/;" f class:ProtoMol::TopologyFactoryDetails registerConfiguration framework/frontend/InputValue.h /^ static void registerConfiguration(Configuration* config){$/;" f class:ProtoMol::InputValue registerConfiguration framework/frontend/InputValue.h /^ static void registerConfiguration(Configuration* config, const Text& txt){$/;" f class:ProtoMol::InputValue registerConfiguration framework/frontend/InputValue.h /^ static void registerConfiguration(Configuration* config,T v) {$/;" f class:ProtoMol::InputValue registerConfiguration framework/frontend/InputValue.h /^ static void registerConfiguration(Configuration* config,T v, const Text& txt) {$/;" f class:ProtoMol::InputValue registerConfiguration framework/frontend/InputValue.h /^ static void registerConfiguration(Configuration* config,Value v) {$/;" f class:ProtoMol::InputValue registerConfiguration framework/frontend/InputValue.h /^ static void registerConfiguration(Configuration* config,Value v, const Text& txt) {$/;" f class:ProtoMol::InputValue registerExemplar framework/frontend/Factory.h /^ static void registerExemplar(const Type* exemplar, std::string id=""){$/;" f class:ProtoMol::Factory registerExemplar framework/frontend/Factory.h /^ static void registerExemplar(const Type* exemplar,const std::vector& aliases, std::string id=""){$/;" f class:ProtoMol::Factory registerExemplar framework/frontend/HelpTextFactory.cpp /^ void HelpTextFactory::registerExemplar(const string& id, const HelpText& helpText){$/;" f class:ProtoMol::HelpTextFactory registerExemplars framework/frontend/HelpTextFactory.cpp /^ void HelpTextFactory::registerExemplars(const Configuration* config){$/;" f class:ProtoMol::HelpTextFactory registerForceExemplars framework/factories/registerForceExemplars.cpp /^ void registerForceExemplars(const GenericTopology* topo){$/;" f namespace:ProtoMol registerForceExemplarsBonded framework/factories/registerForceExemplarsBonded.cpp /^ void registerForceExemplarsBonded(const PeriodicBoundaryConditions*){$/;" f namespace:ProtoMol registerForceExemplarsBonded framework/factories/registerForceExemplarsBonded.cpp /^ void registerForceExemplarsBonded(const VacuumBoundaryConditions*){$/;" f namespace:ProtoMol registerForceExemplarsCutoff framework/factories/registerForceExemplarsCutoff.cpp /^ void registerForceExemplarsCutoff(const PeriodicBoundaryConditions*, const CubicCellManager*){$/;" f namespace:ProtoMol registerForceExemplarsCutoff framework/factories/registerForceExemplarsCutoff.cpp /^ void registerForceExemplarsCutoff(const VacuumBoundaryConditions*, const CubicCellManager*){$/;" f namespace:ProtoMol registerForceExemplarsDispatch framework/factories/registerForceExemplars.cpp /^ inline void registerForceExemplarsDispatch(const Topology* topo){$/;" f namespace:ProtoMol registerForceExemplarsFastElectrostatic framework/factories/registerForceExemplarsFastElectrostatic.cpp /^ void registerForceExemplarsFastElectrostatic(const PeriodicBoundaryConditions*, const CubicCellManager*){$/;" f namespace:ProtoMol registerForceExemplarsFastElectrostatic framework/factories/registerForceExemplarsFastElectrostatic.cpp /^ void registerForceExemplarsFastElectrostatic(const VacuumBoundaryConditions*, const CubicCellManager*){ $/;" f namespace:ProtoMol registerForceExemplarsFull framework/factories/registerForceExemplarsFull.cpp /^ void registerForceExemplarsFull(const PeriodicBoundaryConditions*){$/;" f namespace:ProtoMol registerForceExemplarsFull framework/factories/registerForceExemplarsFull.cpp /^ void registerForceExemplarsFull(const VacuumBoundaryConditions*){$/;" f namespace:ProtoMol registerForceExemplarsOther framework/factories/registerForceExemplarsOther.cpp /^ void registerForceExemplarsOther(){ $/;" f namespace:ProtoMol registerForceExemplarsOther framework/factories/registerForceExemplarsOther.cpp /^ void registerForceExemplarsOther(const PeriodicBoundaryConditions*){$/;" f namespace:ProtoMol registerForceExemplarsOther framework/factories/registerForceExemplarsOther.cpp /^ void registerForceExemplarsOther(const PeriodicBoundaryConditions*, const CubicCellManager*){$/;" f namespace:ProtoMol registerForceExemplarsOther framework/factories/registerForceExemplarsOther.cpp /^ void registerForceExemplarsOther(const VacuumBoundaryConditions*){$/;" f namespace:ProtoMol registerForceExemplarsOther framework/factories/registerForceExemplarsOther.cpp /^ void registerForceExemplarsOther(const VacuumBoundaryConditions*, const CubicCellManager*){ $/;" f namespace:ProtoMol registerForceExemplarsSimpleFull framework/factories/registerForceExemplarsSimpleFull.cpp /^ void registerForceExemplarsSimpleFull(const PeriodicBoundaryConditions*){$/;" f namespace:ProtoMol registerForceExemplarsSimpleFull framework/factories/registerForceExemplarsSimpleFull.cpp /^ void registerForceExemplarsSimpleFull(const VacuumBoundaryConditions*){$/;" f namespace:ProtoMol registerHelpText framework/frontend/Factory.h /^ static void registerHelpText(){$/;" f class:ProtoMol::Factory registerIntegratorExemplars framework/factories/registerIntegratorExemplars.cpp /^ void registerIntegratorExemplars(){$/;" f namespace:ProtoMol registerKeyword framework/base/Configuration.cpp /^ void Configuration::registerKeyword(const string& keyword, Value value){$/;" f class:ProtoMol::Configuration registerOutputExemplars framework/factories/registerOutputExemplars.cpp /^ void registerOutputExemplars(){$/;" f namespace:ProtoMol registerTopologyExemplars framework/factories/registerTopologyExemplars.cpp /^ void registerTopologyExemplars(){$/;" f namespace:ProtoMol removeAngularMomentum framework/topology/topologyutilities.cpp /^ Vector3D removeAngularMomentum(const Vector3DBlock *positions, $/;" f namespace:ProtoMol removeBeginEndBlanks framework/base/stringutilities.cpp /^ string removeBeginEndBlanks(const string& s){$/;" f namespace:ProtoMol removeLinearMomentum framework/topology/topologyutilities.cpp /^ Vector3D removeLinearMomentum(Vector3DBlock *velocities, $/;" f namespace:ProtoMol removeModifier framework/integrators/Integrator.cpp /^ bool Integrator::removeModifier( const std::string modifierName ) {$/;" f class:ProtoMol::Integrator removeModifier framework/integrators/Integrator.cpp /^ bool Integrator::removeModifier(const Modifier* modifier){$/;" f class:ProtoMol::Integrator rend framework/base/Vector3DBlock.h /^ const_reverse_iterator rend() const {return vec.rend();} $/;" f class:ProtoMol::Vector3DBlock rend framework/base/Vector3DBlock.h /^ reverse_iterator rend() {return vec.rend();} $/;" f class:ProtoMol::Vector3DBlock reopen framework/frontend/OutputFile.cpp /^ bool OutputFile::reopen(){$/;" f class:ProtoMol::OutputFile reopen framework/io/DCDTrajectoryWriter.cpp /^ bool DCDTrajectoryWriter::reopen(unsigned int numAtoms){$/;" f class:ProtoMol::DCDTrajectoryWriter reopen framework/io/XYZTrajectoryWriter.cpp /^ bool XYZTrajectoryWriter::reopen(){$/;" f class:ProtoMol::XYZTrajectoryWriter replicaHistory framework/frontend/OutputCache.h /^ const Real *replicaHistory() const {return myReplicaHistory;}$/;" f class:ProtoMol::OutputCache reportlevel framework/base/Report.h /^ reportlevel() : myReportlevel(0) {}$/;" f class:ProtoMol::Report::reportlevel reportlevel framework/base/Report.h /^ reportlevel(short l) : myReportlevel(l) {}$/;" f class:ProtoMol::Report::reportlevel reportlevel framework/base/Report.h /^ class reportlevel{$/;" c namespace:ProtoMol::Report rescaleVolume framework/topology/SemiGenericTopology.h /^ virtual void rescaleVolume(Real fac){$/;" f class:ProtoMol::SemiGenericTopology reserve framework/base/Vector3DBlock.h /^ void reserve(size_t n) { vec.reserve(n);} $/;" f class:ProtoMol::Vector3DBlock reset framework/base/Cycles.h /^ void reset(){myRunningFlag = false;}$/;" f class:ProtoMol::Cycles reset framework/base/Report.cpp /^ void MyStreamer::reset(){$/;" f class:ProtoMol::Report::MyStreamer reset framework/base/Stack.h /^ void Stack::reset(bool delMem) {$/;" f class:ProtoMol::Stack reset framework/base/Timer.cpp /^ void TimeRep::reset()$/;" f class:ProtoMol::TimeRep reset framework/base/Timer.cpp /^ void Timer::reset()$/;" f class:ProtoMol::Timer resetHistory framework/integrators/ModifierShadow.cpp /^ void ModifierShadow::resetHistory() {$/;" f class:ProtoMol::ModifierShadow resetNext framework/parallel/Parallel-FD.cpp /^ void Parallel::resetNext(const vector& blocks){$/;" f class:ProtoMol::Parallel resetNext framework/parallel/Parallel.cpp /^ void Parallel::resetNext(const vector& blocks){$/;" f class:ProtoMol::Parallel resetNext framework/parallel/Parallel.h /^ static void resetNext(){myNext = 0;myNextRange[0] =0;myNextRange[1]=0;myWorkState = getWorkState();}$/;" f class:ProtoMol::Parallel residueName framework/base/PDB.h /^ std::string residueName; \/\/\/< residue_name $/;" m struct:ProtoMol::PDB::Atom residueName framework/base/PDB.h /^ std::string residueName; \/\/\/< residue_name $/;" m struct:ProtoMol::PDB::Ter residueNum framework/base/PDB.h /^ int residueNum; \/\/\/< residue_sequence $/;" m struct:ProtoMol::PDB::Atom residueNum framework/base/PDB.h /^ int residueNum; \/\/\/< residue_sequence $/;" m struct:ProtoMol::PDB::Ter residue_name framework/base/PSF.h /^ std::string residue_name; \/\/\/< residue name$/;" m struct:ProtoMol::PSF::Atom residue_sequence framework/base/PSF.h /^ int residue_sequence; \/\/\/< residue sequence$/;" m struct:ProtoMol::PSF::Atom resize compilerTests/pngTest.cpp /^void PPM::resize(unsigned int width, unsigned int height){$/;" f class:PPM resize framework/base/Array_NoPartialSpecialization.h /^ bool resize(const ArraySize & Dimensions, const T & Init=T(), bool PreserveElems=false)$/;" f class:ProtoMol::Array resize framework/base/Array_NoPartialSpecialization.h /^ bool resize(const unsigned int * Dimensions, const T & Init=T(), bool PreserveElems=false)$/;" f class:ProtoMol::Array resize framework/base/PDB.h /^ void resize(size_t n){coords.resize(n),atoms.resize(n);}$/;" f struct:ProtoMol::PDB resize framework/base/PGM.cpp /^ void PGM::resize(unsigned int width, unsigned int height){$/;" f class:ProtoMol::PGM resize framework/base/PPM.cpp /^ void PPM::resize(unsigned int width, unsigned int height){$/;" f class:ProtoMol::PPM resize framework/base/Vector3DBlock.h /^ void resize(size_type n, Vector3D t = Vector3D(0.0,0.0,0.0)) { vec.resize(n,t);} $/;" f class:ProtoMol::Vector3DBlock resize framework/base/XYZ.h /^ void resize(size_t n){coords.resize(n),names.resize(n);}$/;" f struct:ProtoMol::XYZ resize framework/topology/ExclusionTable.cpp /^ void ExclusionTable::resize(int count) {$/;" f class:ProtoMol::ExclusionTable resize framework/topology/LennardJonesParameterTable.cpp /^ void LennardJonesParameterTable::resize(int count) {$/;" f class:ProtoMol::LennardJonesParameterTable restAngle framework/topology/Angle.h /^ Real restAngle;$/;" m class:ProtoMol::Angle restLength framework/topology/Bond.h /^ Real restLength;$/;" m struct:ProtoMol::Bond::Constraint restLength framework/topology/Bond.h /^ Real restLength;$/;" m class:ProtoMol::Bond restoreForces framework/integrators/Integrator.cpp /^ void Integrator::restoreForces() {$/;" f class:ProtoMol::Integrator restoreValues framework/integrators/DLMCIntegrator.cpp /^ void DLMCIntegrator::restoreValues(){$/;" f class:ProtoMol::DLMCIntegrator restoreValues framework/integrators/DihedralHMCIntegrator.cpp /^ void DihedralHMCIntegrator::restoreValues(){$/;" f class:ProtoMol::DihedralHMCIntegrator restoreValues framework/integrators/MCIntegrator.cpp /^ void MCIntegrator::restoreValues() {$/;" f class:ProtoMol::MCIntegrator restoreValues framework/integrators/ShadowHMCIntegrator.cpp /^ void ShadowHMCIntegrator::restoreValues() {$/;" f class:ProtoMol::ShadowHMCIntegrator reverse_iterator framework/base/Vector3DBlock.h /^ typedef std::vector::reverse_iterator reverse_iterator; $/;" t class:ProtoMol::Vector3DBlock rint framework/base/Real.h 14;" d rmin framework/base/PAR.h /^ Real rmin; \/\/\/< minimum radius$/;" m struct:ProtoMol::PAR::Hbond rotate framework/base/Matrix3by3.cpp /^ void Matrix3by3::rotate(const Vector3D& axis, Real alpha)$/;" f class:ProtoMol::Matrix3by3 rotate framework/base/Matrix3by3.cpp /^ void Matrix3by3::rotate(const Vector3D& axis, Real sinAlpha, Real cosAlpha)$/;" f class:ProtoMol::Matrix3by3 rotate framework/base/Matrix3by3.cpp /^ void Matrix3by3::rotate(const Vector3D& from, const Vector3D& to)$/;" f class:ProtoMol::Matrix3by3 rotateDihedral framework/topology/topologyutilities.cpp /^ void rotateDihedral(const GenericTopology* topology,$/;" f namespace:ProtoMol roughTest framework/topology/C1SwitchingFunction.h /^ bool roughTest(Real distSquared) const { return (distSquared <= myCutoff2);}$/;" f class:ProtoMol::C1SwitchingFunction roughTest framework/topology/C2SwitchingFunction.h /^ bool roughTest(Real distSquared) const{return (distSquared <= myCutoff2);}$/;" f class:ProtoMol::C2SwitchingFunction roughTest framework/topology/CmpCnCnSwitchingFunction.h /^ bool roughTest(Real distSquared) const{return (distSquared <= myCutoff2);}$/;" f class:ProtoMol::CmpCnCnSwitchingFunction roughTest framework/topology/CnSwitchingFunction.h /^ bool roughTest(Real distSquared) const{return (distSquared <= myCutoff2);}$/;" f class:ProtoMol::CnSwitchingFunction roughTest framework/topology/ComplementSwitchingFunction.h /^ bool roughTest(Real \/*distSquared*\/) const{return true;}$/;" f class:ProtoMol::ComplementSwitchingFunction roughTest framework/topology/CutoffSwitchingFunction.h /^ bool roughTest(Real distSquared) const{return (distSquared <= myCutoff2);}$/;" f class:ProtoMol::CutoffSwitchingFunction roughTest framework/topology/RangeSwitchingFunction.h /^ inline bool RangeSwitchingFunction::roughTest(Real distSquared) const {$/;" f class:ProtoMol::RangeSwitchingFunction roughTest framework/topology/ShiftSwitchingFunction.h /^ bool roughTest(Real distSquared) const{return (distSquared <= myCutoff2);}$/;" f class:ProtoMol::ShiftSwitchingFunction roughTest framework/topology/UniversalSwitchingFunction.h /^ bool roughTest(Real \/*distSquared*\/) const {return true;};$/;" f class:ProtoMol::UniversalSwitchingFunction rpos framework/base/sstream_local.h /^ std::string::size_type rpos;$/;" m class:std::stringbuf rtod framework/base/mathutilities.cpp /^ vector rtod(const vector& rad){$/;" f namespace:ProtoMol rtod framework/base/mathutilities.h /^ inline Real rtod(Real rad){ $/;" f namespace:ProtoMol run framework/frontend/Output.cpp /^ void Output::run(int step){$/;" f class:ProtoMol::Output run framework/frontend/OutputCollection.cpp /^ void OutputCollection::run(int step){$/;" f class:ProtoMol::OutputCollection run framework/integrators/BBKIntegrator.cpp /^ void BBKIntegrator::run (int numTimesteps) {$/;" f class:ProtoMol::BBKIntegrator run framework/integrators/DMDLeapfrogIntegrator.cpp /^ void DMDLeapfrogIntegrator::run (int numTimesteps) {$/;" f class:ProtoMol::DMDLeapfrogIntegrator run framework/integrators/DihedralHMCIntegrator.cpp /^ void DihedralHMCIntegrator::run(int numTimesteps){$/;" f class:ProtoMol::DihedralHMCIntegrator run framework/integrators/HMCIntegrator.cpp /^ void HMCIntegrator::run( int numTimesteps ) {$/;" f class:ProtoMol::HMCIntegrator run framework/integrators/LeapfrogIntegrator.cpp /^ void LeapfrogIntegrator::run(int numTimesteps) {$/;" f class:ProtoMol::LeapfrogIntegrator run framework/integrators/MCIntegrator.cpp /^ void MCIntegrator::run(int numTimesteps) {$/;" f class:ProtoMol::MCIntegrator run framework/integrators/NPTVerletIntegrator.cpp /^ void NPTVerletIntegrator::run(int numTimesteps) {$/;" f class:ProtoMol::NPTVerletIntegrator run framework/integrators/NVTVerletIntegrator.cpp /^ void NVTVerletIntegrator::run(int numTimesteps) {$/;" f class:ProtoMol::NVTVerletIntegrator run framework/integrators/PLeapfrogIntegrator.cpp /^ void PLeapfrogIntegrator::run(int numTimesteps) {$/;" f class:ProtoMol::PLeapfrogIntegrator run framework/integrators/ShadowHMCIntegrator.cpp /^ void ShadowHMCIntegrator::run( int numTimesteps ) {$/;" f class:ProtoMol::ShadowHMCIntegrator run framework/integrators/StandardIntegrator.cpp /^ void StandardIntegrator::run(int numTimesteps){$/;" f class:ProtoMol::StandardIntegrator run tools/rem/sequential/replica.cc /^void Replica::run() {$/;" f class:Replica runPreSteps framework/integrators/ShadowHMCIntegrator.cpp /^ void ShadowHMCIntegrator::runPreSteps( int numTimesteps ) {$/;" f class:ProtoMol::ShadowHMCIntegrator saveForces framework/integrators/Integrator.cpp /^ void Integrator::saveForces() {$/;" f class:ProtoMol::Integrator saveValues framework/integrators/DLMCIntegrator.cpp /^ void DLMCIntegrator::saveValues(){$/;" f class:ProtoMol::DLMCIntegrator saveValues framework/integrators/DihedralHMCIntegrator.cpp /^ void DihedralHMCIntegrator::saveValues() {$/;" f class:ProtoMol::DihedralHMCIntegrator saveValues framework/integrators/MCIntegrator.cpp /^ void MCIntegrator::saveValues() {$/;" f class:ProtoMol::MCIntegrator saveValues framework/integrators/ShadowHMCIntegrator.cpp /^ void ShadowHMCIntegrator::saveValues() {$/;" f class:ProtoMol::ShadowHMCIntegrator savedPE framework/integrators/ShadowHMCIntegrator.h /^ savedPE;$/;" m class:ProtoMol::ShadowHMCIntegrator scalarSum framework/base/Grid.h /^ Real Grid::scalarSum(ScalarStructure* energies){$/;" f class:ProtoMol::Grid scalarSum framework/base/Grid.h /^ Real Grid::scalarSum(ScalarStructure* energies, unsigned int block, unsigned int nBlocks){$/;" f class:ProtoMol::Grid scale framework/base/Matrix3by3.cpp /^ void Matrix3by3::scale(Real s)$/;" f class:ProtoMol::Matrix3by3 scale framework/base/Matrix3by3.cpp /^ void Matrix3by3::scale(Real sx, Real sy, Real sz)$/;" f class:ProtoMol::Matrix3by3 scale framework/base/Matrix3by3.cpp /^ void Matrix3by3::scale(const Vector3D& scaleFactor)$/;" f class:ProtoMol::Matrix3by3 scaleToTemperature tools/rem/sequential/replica.cc /^void Replica::scaleToTemperature(double newTemp) {$/;" f class:Replica scaledCharge framework/base/Atom.h /^ Real scaledCharge;$/;" m struct:ProtoMol::Atom scaledMass framework/base/Atom.h /^ Real scaledMass;$/;" m struct:ProtoMol::Atom scope framework/forces/Force.h /^ static const std::string scope;$/;" m class:ProtoMol::Force scope framework/frontend/HelpTextFactory.h /^ std::string scope;$/;" m struct:ProtoMol::HelpText scope framework/frontend/Output.h /^ static const std::string scope;$/;" m class:ProtoMol::Output scope framework/integrators/Integrator.h /^ static const std::string scope;$/;" m class:ProtoMol::Integrator scope framework/topology/GenericTopology.h /^ static const std::string scope;$/;" m class:ProtoMol::GenericTopology sd framework/imd/vmdsock.h /^ int sd; \/\/< socket file descriptor $/;" m struct:ProtoMol::IMD:: search framework/frontend/HelpTextFactory.cpp /^ string HelpTextFactory::search(const string& id){$/;" f class:ProtoMol::HelpTextFactory second framework/base/simpleTypes.h /^ unsigned int first,second;$/;" m struct:ProtoMol::PairIntSorted second framework/topology/CellListEnumerator_periodicBoundaries.h /^ struct CellPair {int first; int second;};$/;" m struct:ProtoMol::CellListEnumerator::CellPair second framework/topology/CellListEnumerator_standard.h /^ struct CellPair {int first; int second;};$/;" m struct:ProtoMol::CellListEnumerator::CellPair segID framework/base/PDB.h /^ std::string segID; \/\/\/< seg_id $/;" m struct:ProtoMol::PDB::Atom seg_id framework/base/PSF.h /^ std::string seg_id; \/\/\/< segment identifier$/;" m struct:ProtoMol::PSF::Atom send framework/parallel/Parallel-FD.cpp /^ void Parallel::send(Real *, int, int) {}$/;" f class:ProtoMol::Parallel send framework/parallel/Parallel-FD.cpp /^ void Parallel::send(Real *data, int num, int address) {$/;" f class:ProtoMol::Parallel send framework/parallel/Parallel-FD.cpp /^ void Parallel::send(Vector3DBlock *, int) {}$/;" f class:ProtoMol::Parallel send framework/parallel/Parallel-FD.cpp /^ void Parallel::send(Vector3DBlock *vect, int address) {$/;" f class:ProtoMol::Parallel send framework/parallel/Parallel.cpp /^ void Parallel::send(Real *, int, int) {}$/;" f class:ProtoMol::Parallel send framework/parallel/Parallel.cpp /^ void Parallel::send(Real *data, int num, int address) {$/;" f class:ProtoMol::Parallel send framework/parallel/Parallel.cpp /^ void Parallel::send(Vector3DBlock *, int) {}$/;" f class:ProtoMol::Parallel send framework/parallel/Parallel.cpp /^ void Parallel::send(Vector3DBlock *vect, int address) {$/;" f class:ProtoMol::Parallel send_coords framework/imd/IMDElf.cpp /^ int IMDElf::send_coords(const Vector3DBlock &c) {$/;" f class:ProtoMol::IMDElf sendrecv framework/parallel/Parallel-FD.cpp /^ void Parallel::sendrecv(Real *, int, int, Real *, int, int) {}$/;" f class:ProtoMol::Parallel sendrecv framework/parallel/Parallel-FD.cpp /^ void Parallel::sendrecv(Real *senddata, int sendnum, int sendaddr, Real *recvdata, int recvnum, int recvaddr) {$/;" f class:ProtoMol::Parallel sendrecv framework/parallel/Parallel.cpp /^ void Parallel::sendrecv(Real *, int, int, Real *, int, int) {}$/;" f class:ProtoMol::Parallel sendrecv framework/parallel/Parallel.cpp /^ void Parallel::sendrecv(Real *senddata, int sendnum, int sendaddr, Real *recvdata, int recvnum, int recvaddr) {$/;" f class:ProtoMol::Parallel sendrecv_replace framework/parallel/Parallel-FD.cpp /^ void Parallel::sendrecv_replace(Real *, int, int, int) {}$/;" f class:ProtoMol::Parallel sendrecv_replace framework/parallel/Parallel-FD.cpp /^ void Parallel::sendrecv_replace(Real *data, int num, int sendaddr, int recvaddr) {$/;" f class:ProtoMol::Parallel sendrecv_replace framework/parallel/Parallel-FD.cpp /^ void Parallel::sendrecv_replace(Vector3DBlock *, int, int) {}$/;" f class:ProtoMol::Parallel sendrecv_replace framework/parallel/Parallel-FD.cpp /^ void Parallel::sendrecv_replace(Vector3DBlock *vect, int sendaddr, int recvaddr) {$/;" f class:ProtoMol::Parallel sendrecv_replace framework/parallel/Parallel.cpp /^ void Parallel::sendrecv_replace(Real *, int, int, int) {}$/;" f class:ProtoMol::Parallel sendrecv_replace framework/parallel/Parallel.cpp /^ void Parallel::sendrecv_replace(Real *data, int num, int sendaddr, int recvaddr) {$/;" f class:ProtoMol::Parallel sendrecv_replace framework/parallel/Parallel.cpp /^ void Parallel::sendrecv_replace(Vector3DBlock *, int, int) {}$/;" f class:ProtoMol::Parallel sendrecv_replace framework/parallel/Parallel.cpp /^ void Parallel::sendrecv_replace(Vector3DBlock *vect, int sendaddr, int recvaddr) {$/;" f class:ProtoMol::Parallel set compilerTests/pngTest.cpp /^ void set(unsigned int i, unsigned int j,unsigned char a){p[(h-i-1)*w*3+j*3] = a;p[(h-i-1)*w*3+j*3+1] = a;p[(h-i-1)*w*3+j*3+2] = a;};$/;" f class:PPM set compilerTests/pngTest.cpp /^ void set(unsigned int i, unsigned int j,unsigned char r,unsigned char g,unsigned char b){p[(h-i-1)*w*3+j*3] = r;p[(h-i-1)*w*3+j*3+1] = g;p[(h-i-1)*w*3+j*3+2] = b;};$/;" f class:PPM set framework/base/BSpline.cpp /^ void BSpline::set(Real w){$/;" f class:ProtoMol::BSpline set framework/base/Configuration.cpp /^ bool Configuration::set(const string& keyword, Value v){$/;" f class:ProtoMol::Configuration set framework/base/Configuration.cpp /^ bool Configuration::set(const string& keyword, const string& v){$/;" f class:ProtoMol::Configuration set framework/base/Configuration.cpp /^ bool Configuration::set(const string& keyword, const vector >& values){$/;" f class:ProtoMol::Configuration set framework/base/Configuration.cpp /^ bool Configuration::set(const vector >& values){$/;" f class:ProtoMol::Configuration set framework/base/Hermite.cpp /^ void Hermite::set(Real w){$/;" f class:ProtoMol::Hermite set framework/base/Lagrange.cpp /^ void Lagrange::set(Real w){$/;" f class:ProtoMol::Lagrange set framework/base/PGM.h /^ void set(unsigned int x, unsigned int y,unsigned char a){p[(h-y-1)*w+x] = a;}$/;" f class:ProtoMol::PGM set framework/base/PGM.h /^ void set(unsigned int x, unsigned int y,unsigned char r,unsigned char g,unsigned char b){p[(h-y-1)*w+x] = static_cast((static_cast(r)+static_cast(g)+static_cast(b))\/3);}$/;" f class:ProtoMol::PGM set framework/base/PPM.h /^ void set(unsigned int x, unsigned int y,unsigned char a){p[(h-y-1)*w*3+x*3] = a;p[(h-y-1)*w*3+x*3+1] = a;p[(h-y-1)*w*3+x*3+2] = a;}$/;" f class:ProtoMol::PPM set framework/base/PPM.h /^ void set(unsigned int x, unsigned int y,unsigned char r,unsigned char g,unsigned char b){p[(h-y-1)*w*3+x*3] = r;p[(h-y-1)*w*3+x*3+1] = g;p[(h-y-1)*w*3+x*3+2] = b;}$/;" f class:ProtoMol::PPM set framework/base/Timer.cpp /^ void TimeRep::set(double realTime, double userTime, double sysTime)$/;" f class:ProtoMol::TimeRep set framework/base/Value.cpp /^ bool Value::set(Value v){$/;" f class:ProtoMol::Value set framework/base/Value.h /^ bool set(const char* v){return set(std::string(v));}$/;" f class:ProtoMol::Value::PlaceHolder set framework/base/Value.h /^ virtual bool set(Real v) { ok = ValueTrait::convert(v,holder) && ValueTrait::check(Constraint(),holder); return ok;}$/;" f class:ProtoMol::Value::Holder set framework/base/Value.h /^ virtual bool set(bool v) { ok = ValueTrait::convert(v,holder) && ValueTrait::check(Constraint(),holder); return ok;}$/;" f class:ProtoMol::Value::Holder set framework/base/Value.h /^ virtual bool set(const Value& val) {$/;" f class:ProtoMol::Value::Holder set framework/base/Value.h /^ virtual bool set(const Vector3D & v) { ok = ValueTrait::convert(v,holder) && ValueTrait::check(Constraint(),holder); return ok;}$/;" f class:ProtoMol::Value::Holder set framework/base/Value.h /^ virtual bool set(const std::string & v) { ok = ValueTrait::convert(v,holder) && ValueTrait::check(Constraint(),holder); return ok;}$/;" f class:ProtoMol::Value::Holder set framework/base/Value.h /^ virtual bool set(const std::vector & v) { ok = ValueTrait::convert(v,holder) && ValueTrait::check(Constraint(),holder); return ok;}$/;" f class:ProtoMol::Value::Holder set framework/base/Value.h /^ virtual bool set(int v) { ok = ValueTrait::convert(v,holder) && ValueTrait::check(Constraint(),holder); return ok;}$/;" f class:ProtoMol::Value::Holder set framework/base/Value.h /^ virtual bool set(unsigned int v) { ok = ValueTrait::convert(v,holder) && ValueTrait::check(Constraint(),holder); return ok;}$/;" f class:ProtoMol::Value::Holder set framework/base/Value.h /^ bool set(const T& value){$/;" f class:ProtoMol::Value set framework/topology/BankLennardJonesParameterTable.h /^ void set(int i, int j, int type1, int type2, const LennardJonesParameters& paramsij ) {$/;" f struct:ProtoMol::BankLennardJonesParameterTable set framework/topology/LennardJonesParameterTable.cpp /^ void LennardJonesParameterTable::set(int type1, int type2, const LennardJonesParameters ¶ms) {$/;" f class:ProtoMol::LennardJonesParameterTable set framework/topology/PeriodicBoundaryConditions.cpp /^ void PeriodicBoundaryConditions::set(const Vector3D &e1 ,const Vector3D &e2 ,$/;" f class:ProtoMol::PeriodicBoundaryConditions set framework/topology/VacuumBoundaryConditions.h /^ void set(const Vector3D &,const Vector3D &,const Vector3D &,const Vector3D &) const{};$/;" f class:ProtoMol::VacuumBoundaryConditions setAbort framework/base/Report.cpp /^ void MyStreamer::setAbort(bool flag){$/;" f class:ProtoMol::Report::MyStreamer setAlias framework/base/Makeable.cpp /^ string Makeable::setAlias(const string& id){$/;" f class:ProtoMol::Makeable setAllNodes framework/base/Report.cpp /^ void MyStreamer::setAllNodes(bool flag){$/;" f class:ProtoMol::Report::MyStreamer setAngle framework/topology/AngleInfo.cpp /^ void AngleInfo::setAngle(Real angle) {$/;" f class:ProtoMol::AngleInfo setAtomID framework/topology/AngleInfo.cpp /^ void AngleInfo::setAtomID(unsigned int ID) {$/;" f class:ProtoMol::AngleInfo setAutofit framework/io/XFigWriter.cpp /^ bool XFigWriter::setAutofit(bool autofit){$/;" f class:ProtoMol::XFigWriter setAxes framework/io/XFigWriter.cpp /^ bool XFigWriter::setAxes(bool axes){$/;" f class:ProtoMol::XFigWriter setBarrier framework/parallel/Parallel.h /^ static void setBarrier(bool b) {myUseBarrier = b;}$/;" f class:ProtoMol::Parallel setCache framework/frontend/Output.cpp /^ void Output::setCache(const OutputCache* cache){$/;" f class:ProtoMol::Output setCellSize framework/topology/CubicCellManager.cpp /^ void CubicCellManager::setCellSize(Real newSize) {$/;" f class:ProtoMol::CubicCellManager setCharmmType framework/io/PARReader.h /^ inline void PARReader::setCharmmType(PAR::CharmmTypeEnum charmmType){$/;" f class:ProtoMol::PARReader setCharmmType framework/io/PARWriter.cpp /^ void PARWriter::setCharmmType(PAR::CharmmTypeEnum charmmType){$/;" f class:ProtoMol::PARWriter setColor framework/io/XFigWriter.cpp /^ bool XFigWriter::setColor(bool color){$/;" f class:ProtoMol::XFigWriter setComment framework/io/Writer.cpp /^ void Writer::setComment(const std::string& comment){$/;" f class:ProtoMol::Writer setCoords framework/io/XYZTrajectoryWriter.cpp /^ void XYZTrajectoryWriter::setCoords(const Vector3DBlock& coords){$/;" f class:ProtoMol::XYZTrajectoryWriter setExclusionAtom framework/topology/AngleInfo.cpp /^ void AngleInfo::setExclusionAtom() {$/;" f class:ProtoMol::AngleInfo setFilename framework/frontend/InputPosVel.cpp /^ void InputPosVel::setFilename(const string& filename){$/;" f class:ProtoMol::InputPosVel setFilename framework/io/File.h /^ inline void File::setFilename(const std::string& filename){$/;" f class:ProtoMol::File setFirststep framework/io/DCDTrajectoryWriter.cpp /^ void DCDTrajectoryWriter::setFirststep(unsigned int firststep){$/;" f class:ProtoMol::DCDTrajectoryWriter setForce framework/imd/HapticSystemForce.cpp /^ void HapticSystemForce::setForce(Vector3DBlock* forces){$/;" f class:ProtoMol::HapticSystemForce setFromZ framework/io/XFigWriter.cpp /^ Real XFigWriter::setFromZ(Real fromZ){$/;" f class:ProtoMol::XFigWriter setIAmMaster framework/base/Report.h /^ void setIAmMaster(bool master){myIAmMaster = master;}$/;" f class:ProtoMol::Report::MyStreamer setInnerAtom framework/topology/AngleInfo.cpp /^ void AngleInfo::setInnerAtom(){$/;" f class:ProtoMol::AngleInfo setLegend framework/io/XFigWriter.cpp /^ bool XFigWriter::setLegend(bool legend){$/;" f class:ProtoMol::XFigWriter setLevel framework/base/Report.h /^ void setLevel(short level) {myLevel=level;}$/;" f class:ProtoMol::Report::MyStreamer setLittleEndian framework/io/DCDTrajectoryWriter.cpp /^ void DCDTrajectoryWriter::setLittleEndian(bool littleEndian){$/;" f class:ProtoMol::DCDTrajectoryWriter setLittleEndian framework/io/XYZBinWriter.cpp /^ void XYZBinWriter::setLittleEndian(bool littleEndian){$/;" f class:ProtoMol::XYZBinWriter setMaxPackages framework/parallel/Parallel-FD.cpp /^ void Parallel::setMaxPackages(int n) {$/;" f class:ProtoMol::Parallel setMaxPackages framework/parallel/Parallel.cpp /^ void Parallel::setMaxPackages(int n) {$/;" f class:ProtoMol::Parallel setMode framework/parallel/Parallel-FD.cpp /^ void Parallel::setMode(ParallelType mode){$/;" f class:ProtoMol::Parallel setMode framework/parallel/Parallel.cpp /^ void Parallel::setMode(ParallelType mode){$/;" f class:ProtoMol::Parallel setMyNumIterMOLLYStepsize framework/integrators/BSplineMOLLYIntegrator.cpp /^ void BSplineMOLLYIntegrator::setMyNumIterMOLLYStepsize(){$/;" f class:ProtoMol::BSplineMOLLYIntegrator setNames framework/io/XYZTrajectoryWriter.cpp /^ void XYZTrajectoryWriter::setNames(const XYZ& xyz){$/;" f class:ProtoMol::XYZTrajectoryWriter setNames framework/io/XYZTrajectoryWriter.cpp /^ void XYZTrajectoryWriter::setNames(const std::vector& atoms,const std::vector& atomTypes){$/;" f class:ProtoMol::XYZTrajectoryWriter setNames framework/io/XYZTrajectoryWriter.cpp /^ void XYZTrajectoryWriter::setNames(const std::vector& names){$/;" f class:ProtoMol::XYZTrajectoryWriter setNodeNum framework/io/TempFileReader.cpp /^ void TempFileReader::setNodeNum(int num) {$/;" f class:ProtoMol::TempFileReader setNumSteps tools/rem/sequential/replica.cc /^void Replica::setNumSteps(int numSteps) {$/;" f class:Replica setOrder framework/base/BSpline.cpp /^ void BSpline::setOrder(unsigned int order){$/;" f class:ProtoMol::BSpline setOrder framework/base/Hermite.cpp /^ void Hermite::setOrder(unsigned int order){$/;" f class:ProtoMol::Hermite setOrder framework/base/Lagrange.cpp /^ void Lagrange::setOrder(unsigned int order){$/;" f class:ProtoMol::Lagrange setParallel framework/base/TimerStatistic.h /^ static void setParallel(bool b) {myIsParallel=b;}$/;" f class:ProtoMol::TimerStatistic setParameter framework/forces/Force.h /^ void setParameter(std::string& errMsg, const std::string& key, T val){$/;" f class:ProtoMol::Force setParameter framework/forces/Force.h /^ void setParameter(std::string& errMsg, unsigned int index, T val){$/;" f class:ProtoMol::Force setParameters framework/forces/Force.cpp /^ void Force::setParameters(string& errMsg, vector values){$/;" f class:ProtoMol::Force setParameters tools/rem/sequential/replica.cc /^void Replica::setParameters(const vector& parameters) {$/;" f class:Replica setParametersBySwapping framework/forces/Force.h /^ void setParametersBySwapping(T* obj, std::string& errMsg, std::vector values){$/;" f class:ProtoMol::Force setPipeSize framework/parallel/Parallel-FD.cpp /^ void Parallel::setPipeSize(int n){$/;" f class:ProtoMol::Parallel setPipeSize framework/parallel/Parallel.cpp /^ void Parallel::setPipeSize(int n){$/;" f class:ProtoMol::Parallel setPointer framework/topology/AngleInfo.cpp /^ void AngleInfo::setPointer(unsigned int atom) {$/;" f class:ProtoMol::AngleInfo setProtomolAbort framework/base/systemutilities.cpp /^ void setProtomolAbort(void (*abortFunction)()){$/;" f namespace:ProtoMol setProtomolEndSerial framework/base/systemutilities.cpp /^ void setProtomolEndSerial(void (*endSerialFunction)(bool)){$/;" f namespace:ProtoMol setProtomolExit framework/base/systemutilities.cpp /^ void setProtomolExit(void (*exitFunction)()){$/;" f namespace:ProtoMol setProtomolStartSerial framework/base/systemutilities.cpp /^ void setProtomolStartSerial(void (*startSerialFunction)(bool)){$/;" f namespace:ProtoMol setRadius framework/io/XFigWriter.cpp /^ Real XFigWriter::setRadius(Real radius){$/;" f class:ProtoMol::XFigWriter setReportLevel framework/base/Report.h /^ void setReportLevel(short level) {myReportLevel=level;}$/;" f class:ProtoMol::Report::MyStreamer setSize framework/io/XYZBinWriter.cpp /^ void XYZBinWriter::setSize(unsigned int size){$/;" f class:ProtoMol::XYZBinWriter setStream framework/base/Report.cpp /^ ostream* MyStreamer::setStream(ostream* a) {$/;" f class:ProtoMol::Report::MyStreamer setTargetTemperature tools/rem/sequential/replica.cc /^void Replica::setTargetTemperature (double targetTemp) {$/;" f class:Replica setText framework/base/Configuration.cpp /^ bool Configuration::setText(const std::string& keyword, const string& text){$/;" f class:ProtoMol::Configuration setTimestep framework/integrators/STSIntegrator.h /^ inline Real STSIntegrator::setTimestep( Real newTimestep ) {$/;" f class:ProtoMol::STSIntegrator setTimestep framework/io/DCDTrajectoryWriter.cpp /^ void DCDTrajectoryWriter::setTimestep(Real timestep){$/;" f class:ProtoMol::DCDTrajectoryWriter setToZ framework/io/XFigWriter.cpp /^ Real XFigWriter::setToZ(Real toZ){$/;" f class:ProtoMol::XFigWriter setTransformation framework/io/XFigWriter.cpp /^ Matrix3by3 XFigWriter::setTransformation(const Matrix3by3& mat){$/;" f class:ProtoMol::XFigWriter setVisited framework/topology/AngleInfo.cpp /^ void AngleInfo::setVisited() {$/;" f class:ProtoMol::AngleInfo set_angles framework/topology/topologyutilities.cpp /^ void set_angles (Stack *nodeStack,vector *angles, bool lastIsInnerAtom, Real wholeAngle) {$/;" f namespace:ProtoMol setf framework/base/Report.cpp /^ void MyStreamer::setf(std::ios::fmtflags flag){$/;" f class:ProtoMol::Report::MyStreamer setf framework/base/Report.cpp /^ void MyStreamer::setf(std::ios::fmtflags flag, std::ios::fmtflags mask){$/;" f class:ProtoMol::Report::MyStreamer setupConfig tools/rem/sequential/replica.cc /^void Replica::setupConfig() {$/;" f class:Replica setupFirstConfig tools/rem/sequential/replica.cc /^void Replica::setupFirstConfig() {$/;" f class:Replica shadowMod framework/integrators/ShadowHMCIntegrator.h /^ ModifierShadow *shadowMod;$/;" m class:ProtoMol::ShadowHMCIntegrator shift framework/base/systemutilities.h /^ inline void shift(Real &a, Real &b, Real &c, const Real d) { $/;" f namespace:ProtoMol shortRangeTerm framework/forces/NonbondedMultiGridSystemForce.h /^ smooth>::shortRangeTerm(const RealTopologyType* realTopo, $/;" f class:ProtoMol::NonbondedMultiGridSystemForce shrink framework/base/systemutilities.h /^ void shrink(T& t){$/;" f namespace:ProtoMol sigma framework/base/PAR.h /^ Real sigma; \/\/\/< minimum radius divided by 2$/;" m struct:ProtoMol::PAR::Nonbonded sigma14 framework/base/PAR.h /^ Real sigma14; \/\/\/< VDW parameter minimum radius divided by 2$/;" m struct:ProtoMol::PAR::Nonbonded sign framework/base/mathutilities.h /^ inline Real sign(Real a, Real b){$/;" f namespace:ProtoMol sign framework/base/mathutilities.h /^ inline int sign(T a) {$/;" f namespace:ProtoMol simType framework/base/XSC.h /^ std::string simType;$/;" m struct:ProtoMol::XSC sincos framework/base/mathutilities.cpp /^ void sincos(Real alpha, Real& sinAlpha, Real& cosAlpha){$/;" f namespace:ProtoMol size compilerTests/pngTest.cpp /^ unsigned int size() const{return 3*w*h;}$/;" f class:PPM size framework/base/Array_Fastest.h /^ size_type size() const { return m_nArrayElements; }$/;" f class:ProtoMol::Array size framework/base/Array_Fastest.h /^ size_type size() const { return m_NDimensions*m_SubArrayLen; }$/;" f class:ProtoMol::RefArray size framework/base/Array_Fastest.h /^ size_type size() const { return m_NDimensions; } $/;" f class:ProtoMol::RefArray size framework/base/Array_Fastest.h /^ size_type size(size_t Dim) const $/;" f class:ProtoMol::Array size framework/base/Array_Fastest.h /^ size_type size(size_t Dim) const $/;" f class:ProtoMol::RefArray size framework/base/Array_Fastest.h /^ size_type size(size_t Dim) const$/;" f class:ProtoMol::RefArray size framework/base/Array_NoPartialSpecialization.h /^ size_type size() const { return m_pNDimensions[0]; } $/;" f class:ProtoMol::Array::RefArray size framework/base/Array_NoPartialSpecialization.h /^ size_type size() const { return m_pNDimensions[0]*m_pSubArrayLen[0]; }$/;" f class:ProtoMol::Array::RefArray size framework/base/Array_NoPartialSpecialization.h /^ size_type size(unsigned int Dim) const $/;" f class:ProtoMol::Array::RefArray size framework/base/Array_NoPartialSpecialization.h /^ size_type size() const { return m_nArrayElements; }$/;" f class:ProtoMol::Array size framework/base/Array_NoPartialSpecialization.h /^ size_type size(unsigned int Dim) const $/;" f class:ProtoMol::Array size framework/base/Molecule.h /^ size_t size(){return atoms.size();}$/;" f struct:ProtoMol::Molecule size framework/base/PDB.h /^ size_t size() const {return coords.size();}$/;" f struct:ProtoMol::PDB size framework/base/PGM.h /^ unsigned int size() const{return w*h;}$/;" f class:ProtoMol::PGM size framework/base/PPM.h /^ unsigned int size() const{return 3*w*h;}$/;" f class:ProtoMol::PPM size framework/base/Value.h /^ virtual unsigned int size() const{ return ValueTrait::size(holder);}$/;" f class:ProtoMol::Value::Holder size framework/base/Value.h /^ inline unsigned int Value::size() const{$/;" f class:ProtoMol::Value size framework/base/ValueType.h /^ static unsigned int size(RepType){ return 1;}$/;" f struct:ProtoMol::ValueTraits size framework/base/ValueType.h /^ static unsigned int size(const RepType& v){ return v.size();}$/;" f struct:ProtoMol::ValueTraits size framework/base/ValueType.h /^ static unsigned int size(const RepType&){ return 3;}$/;" f struct:ProtoMol::ValueTraits size framework/base/Vector3DBlock.h /^ size_type size() const {return vec.size();} $/;" f class:ProtoMol::Vector3DBlock size framework/base/XYZ.h /^ size_t size() const {return coords.size();}$/;" f struct:ProtoMol::XYZ size framework/integrators/Integrator.h /^ inline int Integrator::size() const{$/;" f class:ProtoMol::Integrator size framework/topology/ArrayCellListStructure.h /^ size_type size() const { return mySize;}$/;" f class:ProtoMol::ArrayCellListStructure size framework/topology/LennardJonesParameterTable.h /^ int size() const {return myCurrentSize;}$/;" f class:ProtoMol::LennardJonesParameterTable size_t framework/base/Array_Fastest.h /^ ArraySize(const size_t (&Dimensions)[N-1],size_t dim)$/;" m class:ProtoMol::ArraySize size_t framework/base/Array_Fastest.h /^ bool resize(const size_t (&Dimensions)[N], const T & Init=T(), bool PreserveElems=false)$/;" m class:ProtoMol::Array size_t framework/base/Array_Fastest.h /^ explicit Array(const size_t (&Dimensions)[N], const T & Init=T())$/;" m class:ProtoMol::Array size_type framework/base/Array_Fastest.h /^ typedef size_t size_type;$/;" t class:ProtoMol::Array size_type framework/base/Array_Fastest.h /^ typedef size_t size_type;$/;" t class:ProtoMol::RefArray size_type framework/base/Array_NoPartialSpecialization.h /^ typedef size_t size_type;$/;" t class:ProtoMol::Array::RefArray size_type framework/base/Array_NoPartialSpecialization.h /^ typedef size_t size_type;$/;" t class:ProtoMol::Array size_type framework/base/Vector3DBlock.h /^ typedef std::vector::size_type size_type; $/;" t class:ProtoMol::Vector3DBlock size_type framework/topology/ArrayCellListStructure.h /^ typedef TContainer::size_type size_type; $/;" t class:ProtoMol::ArrayCellListStructure slaveComm framework/parallel/Parallel-FD.cpp /^ static MPI_Comm slaveComm = MPI_COMM_NULL; \/\/ Not data member to avoid dependcies$/;" v file: slaveComm framework/parallel/Parallel.cpp /^ static MPI_Comm slaveComm = MPI_COMM_NULL; \/\/ Not data member to avoid dependcies$/;" v file: smooth framework/forces/CoulombForce.h /^ static Real smooth(Real r,Real \/*c*\/,Real cr) {r=r*r*cr*cr;return (0.0078125*cr*(315.0-r*(420.0-r*(378.0-r*(180.0-r*35.0)))));}$/;" f class:ProtoMol::CoulombForce::C4 smooth framework/forces/CoulombForce.h /^ static Real smooth(Real r,Real \/*c*\/,Real cr) {r=r*r*cr*cr;return (0.0625*cr*(35.0-r*(35.0-r*(21.0-5.0*r))));}$/;" f class:ProtoMol::CoulombForce::C3 smooth framework/forces/CoulombForce.h /^ static Real smooth(Real r,Real \/*c*\/,Real cr) {r=r*r*cr*cr;return (cr*(1.875-r*(1.25-0.375*r)));}$/;" f class:ProtoMol::CoulombForce::C2 smooth framework/forces/CoulombForce.h /^ static Real smooth(Real r,Real \/*c*\/,Real cr) {return (cr*(1.5-0.5*r*r*cr*cr));}$/;" f class:ProtoMol::CoulombForce::C1 smooth0 framework/forces/CoulombForce.h /^ static Real smooth0(Real \/*c*\/,Real cr) {return (1.5*cr);}$/;" f class:ProtoMol::CoulombForce::C1 smooth0 framework/forces/CoulombForce.h /^ static Real smooth0(Real \/*c*\/,Real cr) {return (1.875*cr);}$/;" f class:ProtoMol::CoulombForce::C2 smooth0 framework/forces/CoulombForce.h /^ static Real smooth0(Real \/*c*\/,Real cr) {return (2.1875*cr);}$/;" f class:ProtoMol::CoulombForce::C3 smooth0 framework/forces/CoulombForce.h /^ static Real smooth0(Real \/*c*\/,Real cr) {return (2.4609375*cr);}$/;" f class:ProtoMol::CoulombForce::C4 smoothKernel framework/forces/CoulombForce.h /^ static Real smoothKernel(Real r,Real c,Real cr) {return (r ForceFactoryDetails::splitForceString(const string& id) const{$/;" f class:ProtoMol::ForceFactoryDetails splitForceStringSorted framework/frontend/ForceFactoryDetails.cpp /^ vector ForceFactoryDetails::splitForceStringSorted(const string& id) const{$/;" f class:ProtoMol::ForceFactoryDetails splitRangeArea framework/base/mathutilities.cpp /^ void splitRangeArea(unsigned int p, unsigned int from, unsigned int to, $/;" f namespace:ProtoMol splitRangeQuadratic framework/base/mathutilities.cpp /^ void splitRangeQuadratic(unsigned int p, unsigned int from, unsigned int to, $/;" f namespace:ProtoMol splitString framework/base/stringutilities.cpp /^ vector splitString(const string& id){$/;" f namespace:ProtoMol springConstant framework/topology/Bond.h /^ Real springConstant;$/;" m class:ProtoMol::Bond square framework/base/mathutilities.h /^ inline Real square(Real x) {return x*x;}$/;" f namespace:ProtoMol stageNumber framework/base/Atom.h /^ int stageNumber;$/;" m struct:ProtoMol::Atom start framework/base/Cycles.h /^ void start(){if( myRunningFlag) return;myRunningFlag = true ; myStartTime = Private::getticks();}$/;" f class:ProtoMol::Cycles start framework/base/Timer.cpp /^ void Timer::start()$/;" f class:ProtoMol::Timer stateA framework/frontend/OutputState.h /^ std::vector< orderParam > stateA;$/;" m class:ProtoMol::OutputState stateB framework/frontend/OutputState.h /^ std::vector< orderParam > stateB;$/;" m class:ProtoMol::OutputState std framework/base/sstream_local.h /^namespace std$/;" n stop framework/base/Cycles.h /^ void stop() {if(!myRunningFlag) return;myEndTime = Private::getticks(); myRunningFlag = false; }$/;" f class:ProtoMol::Cycles stop framework/base/Timer.cpp /^ void Timer::stop()$/;" f class:ProtoMol::Timer str framework/base/BSplineType.cpp /^ const string BSplineEnum::str[static_cast(LAST)-static_cast(FIRST)] = {$/;" m class:ProtoMol::BSplineEnum file: str framework/base/BSplineType.h /^ static const std::string str[];$/;" m class:ProtoMol::BSplineEnum str framework/base/ConstraintValueType.cpp /^ const string ConstraintValueEnum::str[static_cast(LAST) - static_cast(FIRST)] = {$/;" m class:ProtoMol::ConstraintValueEnum file: str framework/base/ConstraintValueType.h /^ static const std::string str[];$/;" m class:ProtoMol::ConstraintValueEnum str framework/base/ValueType.cpp /^ const string ValueEnum::str[static_cast(LAST) - static_cast(FIRST)] = {$/;" m class:ProtoMol::ValueEnum file: str framework/base/ValueType.h /^ std::string str;$/;" m struct:ProtoMol::ValueEnum::Enum2ValueType str framework/base/ValueType.h /^ static const std::string str[];$/;" m class:ProtoMol::ValueEnum str framework/base/sstream_local.h /^ std::string str() const$/;" f class:std::stringbuf str framework/base/sstream_local.h /^ std::string str() const$/;" f class:std::stringstreambase str framework/base/sstream_local.h /^ void str(const std::string& s)$/;" f class:std::stringbuf str framework/base/sstream_local.h /^ void str(const std::string& s)$/;" f class:std::stringstreambase str framework/frontend/InputPosVelType.cpp /^ const string InputPosVelEnum::str[static_cast(LAST) - static_cast(FIRST)] = {$/;" m class:ProtoMol::InputPosVelEnum file: str framework/frontend/InputPosVelType.h /^ static const std::string str[];$/;" m class:ProtoMol::InputPosVelEnum str framework/integrators/PaulTrapIntegrator.cpp /^ const string ThermostatEnum::str[static_cast(LAST)-static_cast(FIRST)] = {$/;" m class:ProtoMol::ThermostatEnum file: str framework/integrators/PaulTrapIntegrator.h /^ static const std::string str[];$/;" m class:ProtoMol::ThermostatEnum str framework/parallel/ParallelType.cpp /^ const string ParallelEnum::str[static_cast(LAST)-static_cast(FIRST)] = {$/;" m class:ProtoMol::ParallelEnum file: str framework/parallel/ParallelType.h /^ static const std::string str[];$/;" m class:ProtoMol::ParallelEnum str framework/topology/ExclusionType.cpp /^ const string ExclusionEnum::str[static_cast(LAST) - static_cast(FIRST)] = {$/;" m class:ProtoMol::ExclusionEnum file: str framework/topology/ExclusionType.h /^ static const std::string str[];$/;" m class:ProtoMol::ExclusionEnum strReplace tools/rem/sequential/replica.cc /^bool Replica::strReplace(string &str, const string& oldStr, const string& newStr) {$/;" f class:Replica stringbuf framework/base/sstream_local.h /^ explicit stringbuf(const std::string &s, int which=ios::in|ios::out) :$/;" f class:std::stringbuf stringbuf framework/base/sstream_local.h /^ explicit stringbuf(int which=ios::in|ios::out) :$/;" f class:std::stringbuf stringbuf framework/base/sstream_local.h /^ class stringbuf : public streambuf$/;" c namespace:std stringstream framework/base/sstream_local.h /^ stringstream(const std::string &s, int which=ios::in|ios::out) :$/;" f class:std::stringstream stringstream framework/base/sstream_local.h /^ stringstream(int which=ios::in|ios::out) :$/;" f class:std::stringstream stringstream framework/base/sstream_local.h /^ class stringstream : public stringstreambase, public iostream {$/;" c namespace:std stringstreambase framework/base/sstream_local.h /^ stringstreambase(const std::string& s, int which) :$/;" f class:std::stringstreambase stringstreambase framework/base/sstream_local.h /^ stringstreambase(int which) :$/;" f class:std::stringstreambase stringstreambase framework/base/sstream_local.h /^ class stringstreambase : virtual public ios {$/;" c namespace:std subtract framework/base/Vector3D.h /^ Vector3D subtract(const Vector3D& b) const {return (*this)-b;}$/;" f struct:ProtoMol::Vector3D sum framework/base/Vector3DBlock.cpp /^ Vector3D Vector3DBlock::sum() const{$/;" f class:ProtoMol::Vector3DBlock sumItems framework/base/mathutilities.h /^ Real sumItems;$/;" m class:ProtoMol::WindowAve sumQ framework/base/MultiGrid.h /^ inline Real MultiGrid::sumQ(int level){$/;" f class:ProtoMol::MultiGrid sumV framework/base/MultiGrid.h /^ inline Real MultiGrid::sumV(int level){$/;" f class:ProtoMol::MultiGrid surfaceDipoleTerm framework/forces/NonbondedFullEwaldSystemForce.h /^ TSwitchingFunction>::surfaceDipoleTerm(const RealTopologyType* realTopo,$/;" f class:ProtoMol::NonbondedFullEwaldSystemForce surfaceDipoleTerm framework/forces/NonbondedPMEwaldSystemForce.h /^ TSwitchingFunction>::surfaceDipoleTerm(const RealTopologyType* realTopo,$/;" f class:ProtoMol::NonbondedPMEwaldSystemForce swap framework/base/Array_Fastest.h /^ void swap(Array & A)$/;" f class:ProtoMol::Array swap framework/base/Array_NoPartialSpecialization.h /^ void swap(Array & A)$/;" f class:ProtoMol::Array swap framework/base/Value.cpp /^ Value & Value::swap(Value & rhs){$/;" f class:ProtoMol::Value swap framework/base/Vector3DBlock.h /^ void swap(Vector3DBlock& x) { vec.swap(x.vec);} $/;" f class:ProtoMol::Vector3DBlock swap framework/base/Vector3DBlock.h /^inline void swap(ProtoMol::Vector3DBlock& a, ProtoMol::Vector3DBlock& b) {a.swap(b);}$/;" f swap framework/frontend/InputValue.h /^ InputValue & swap(InputValue & rhs){$/;" f class:ProtoMol::InputValue swap4 framework/imd/imd.cpp /^ static void swap4(char *data, int ndata) {$/;" f namespace:ProtoMol::IMD file: swapBytes framework/base/systemutilities.h /^ void swapBytes(T& t){$/;" f namespace:ProtoMol swap_header framework/imd/imd.cpp /^ static void swap_header(IMDheader *header) {$/;" f namespace:ProtoMol::IMD file: swcoef framework/topology/CnSwitchingFunction.cpp /^ Real CnSwitchingFunction::swcoef[][MAXEQNN] = {$/;" m class:ProtoMol::CnSwitchingFunction file: swcoef framework/topology/CnSwitchingFunction.h /^ static Real swcoef[][MAXEQNN],$/;" m class:ProtoMol::CnSwitchingFunction switchingFunction framework/forces/CoulombEwaldRealTableForce.h /^ TSwitchingFunction switchingFunction;$/;" m class:ProtoMol::CoulombEwaldRealTableForce switchingFunction framework/forces/CoulombTableForce.h /^ TSwitchingFunction switchingFunction;$/;" m class:ProtoMol::CoulombTableForce switchingFunction framework/forces/ElectricFieldSystemForce.h /^ TSwitchingFunction switchingFunction;$/;" m class:ProtoMol::ElectricFieldSystemForce switchingFunction framework/forces/LennardJonesTableForce.h /^ TSwitchingFunction switchingFunction;$/;" m class:ProtoMol::LennardJonesTableForce switchingFunction framework/forces/NonbondedFullEwaldSystemForce.h /^ TSwitchingFunction switchingFunction;$/;" m class:ProtoMol::NonbondedFullEwaldSystemForce switchingFunction framework/forces/NonbondedPMEwaldSystemForce.h /^ TSwitchingFunction switchingFunction;$/;" m class:ProtoMol::NonbondedPMEwaldSystemForce switchingFunction framework/forces/OneAtomPair.h /^ TSwitchingFunction switchingFunction;$/;" m class:ProtoMol::OneAtomPair switchingFunction framework/forces/OneAtomPairFull.h /^ TSwitchingFunction switchingFunction;$/;" m class:ProtoMol::OneAtomPairFull switchingFunction framework/forces/OneMollyPair.h /^ TSwitchingFunction switchingFunction;$/;" m class:ProtoMol::OneMollyPair switchingFunctionFirst framework/forces/OneAtomPairTwo.h /^ TSwitchingFunctionFirst switchingFunctionFirst;$/;" m class:ProtoMol::OneAtomPairTwo switchingFunctionFirst framework/forces/OneAtomPairTwoFull.h /^ TSwitchingFunctionFirst switchingFunctionFirst;$/;" m class:ProtoMol::OneAtomPairTwoFull switchingFunctionFirst framework/forces/OneMollyPairTwo.h /^ TSwitchingFunctionFirst switchingFunctionFirst;$/;" m class:ProtoMol::OneMollyPairTwo switchingFunctionSecond framework/forces/OneAtomPairTwo.h /^ TSwitchingFunctionSecond switchingFunctionSecond;$/;" m class:ProtoMol::OneAtomPairTwo switchingFunctionSecond framework/forces/OneAtomPairTwoFull.h /^ TSwitchingFunctionSecond switchingFunctionSecond;$/;" m class:ProtoMol::OneAtomPairTwoFull switchingFunctionSecond framework/forces/OneMollyPairTwo.h /^ TSwitchingFunctionSecond switchingFunctionSecond;$/;" m class:ProtoMol::OneMollyPairTwo symbol framework/base/PDB.h /^ std::string symbol; \/\/\/< element_symbol $/;" m struct:ProtoMol::PDB::Atom symbolName framework/base/AtomType.h /^ std::string symbolName; \/\/\/< The symbol untity name of this atom type.$/;" m struct:ProtoMol::AtomType sync framework/base/sstream_local.h /^inline int std::stringbuf::sync()$/;" f class:std::stringbuf sync framework/parallel/Parallel-FD.cpp /^ void Parallel::sync(){$/;" f class:ProtoMol::Parallel sync framework/parallel/Parallel.cpp /^ void Parallel::sync(){$/;" f class:ProtoMol::Parallel syncSlave framework/parallel/Parallel-FD.cpp /^ void Parallel::syncSlave(){$/;" f class:ProtoMol::Parallel syncSlave framework/parallel/Parallel.cpp /^ void Parallel::syncSlave(){$/;" f class:ProtoMol::Parallel tailString framework/base/stringutilities.cpp /^ string tailString(const string& word){$/;" f namespace:ProtoMol tempFactor framework/base/PDB.h /^ Real tempFactor; \/\/\/< temp_factor $/;" m struct:ProtoMol::PDB::Atom temperature framework/frontend/OutputCache.cpp /^ Real OutputCache::temperature() const{$/;" f class:ProtoMol::OutputCache temperature framework/topology/topologyutilities.cpp /^ Real temperature(Real kineticEnergy, $/;" f namespace:ProtoMol temperature framework/topology/topologyutilities.cpp /^ Real temperature(const GenericTopology* topology,$/;" f namespace:ProtoMol temperatureForAtomType framework/topology/topologyutilities.cpp /^ Real temperatureForAtomType(const GenericTopology* topology, $/;" f namespace:ProtoMol temperatureForNonWater framework/frontend/OutputCache.cpp /^ Real OutputCache::temperatureForNonWater() const {$/;" f class:ProtoMol::OutputCache temperatureForNonWater framework/topology/topologyutilities.cpp /^ Real temperatureForNonWater(const GenericTopology* topology,$/;" f namespace:ProtoMol temperatureForWater framework/frontend/OutputCache.cpp /^ Real OutputCache::temperatureForWater() const {$/;" f class:ProtoMol::OutputCache temperatureForWater framework/topology/topologyutilities.cpp /^ Real temperatureForWater(const GenericTopology* topology,$/;" f namespace:ProtoMol ters framework/base/PDB.h /^ std::vector ters;$/;" m struct:ProtoMol::PDB text framework/base/Parameter.h /^ std::string text;$/;" m struct:ProtoMol::Parameter text framework/base/simpleTypes.h /^ std::string text;$/;" m struct:ProtoMol::Text text framework/frontend/HelpTextFactory.h /^ std::string text;$/;" m struct:ProtoMol::HelpText the_beginning framework/topology/CellListEnumerator_periodicBoundaries.h /^ CubicCellManager::CellListStructure::const_iterator i,j,the_beginning,the_end;$/;" m class:ProtoMol::CellListEnumerator the_beginning framework/topology/CellListEnumerator_standard.h /^ CubicCellManager::CellListStructure::const_iterator i,j,the_beginning,the_end;$/;" m class:ProtoMol::CellListEnumerator the_counter framework/topology/CellListEnumerator_periodicBoundaries.h /^ int the_first, the_last, the_counter;$/;" m class:ProtoMol::CellListEnumerator the_counter framework/topology/CellListEnumerator_standard.h /^ int the_first, the_last, the_counter;$/;" m class:ProtoMol::CellListEnumerator the_end framework/topology/CellListEnumerator_periodicBoundaries.h /^ CubicCellManager::CellListStructure::const_iterator i,j,the_beginning,the_end;$/;" m class:ProtoMol::CellListEnumerator the_end framework/topology/CellListEnumerator_standard.h /^ CubicCellManager::CellListStructure::const_iterator i,j,the_beginning,the_end;$/;" m class:ProtoMol::CellListEnumerator the_first framework/topology/CellListEnumerator_periodicBoundaries.h /^ int the_first, the_last, the_counter;$/;" m class:ProtoMol::CellListEnumerator the_first framework/topology/CellListEnumerator_standard.h /^ int the_first, the_last, the_counter;$/;" m class:ProtoMol::CellListEnumerator the_last framework/topology/CellListEnumerator_periodicBoundaries.h /^ int the_first, the_last, the_counter;$/;" m class:ProtoMol::CellListEnumerator the_last framework/topology/CellListEnumerator_standard.h /^ int the_first, the_last, the_counter;$/;" m class:ProtoMol::CellListEnumerator theta framework/base/BSpline.h /^ Real* theta; \/\/\/< Bk$/;" m class:ProtoMol::BSpline theta framework/base/Hermite.h /^ Real* theta;$/;" m class:ProtoMol::Hermite theta framework/base/Lagrange.h /^ Real* theta; \/\/\/< lk$/;" m class:ProtoMol::Lagrange ticks framework/base/Cycles.h /^ typedef LARGE_INTEGER ticks;$/;" t namespace:ProtoMol::Private ticks framework/base/Cycles.h /^ typedef ULONG64 ticks;$/;" t namespace:ProtoMol::Private ticks framework/base/Cycles.h /^ typedef struct timespec ticks;$/;" t namespace:ProtoMol::Private ticks framework/base/Cycles.h /^ typedef timebasestruct_t ticks;$/;" t namespace:ProtoMol::Private ticks framework/base/Cycles.h /^ typedef unsigned int ticks;$/;" t namespace:ProtoMol::Private ticks framework/base/Cycles.h /^ typedef unsigned long long ticks;$/;" t namespace:ProtoMol::Private ticks framework/base/Cycles.h /^ typedef unsigned long ticks;$/;" t namespace:ProtoMol::Private ticks framework/base/Cycles.h /^ typedef Private::ticks ticks;$/;" t class:ProtoMol::Cycles ticks framework/base/Cycles.h /^ typedef hrtime_t ticks;$/;" t namespace:ProtoMol::Private ticks framework/base/Cycles.h /^ typedef long long ticks;$/;" t namespace:ProtoMol::Private ticks framework/base/Cycles.h /^ typedef unsigned long long ticks;$/;" t namespace:ProtoMol::Private time framework/frontend/OutputCache.cpp /^ Real OutputCache::time() const{$/;" f class:ProtoMol::OutputCache time framework/topology/GenericTopology.h /^ mutable Real time;$/;" m class:ProtoMol::GenericTopology timeout framework/imd/IMDElf.h /^ int timeout;$/;" m class:ProtoMol::IMDElf timer framework/base/TimerStatistic.cpp /^ Timer TimerStatistic::timer[static_cast(LAST)-static_cast(FIRST)];$/;" m class:ProtoMol::TimerStatistic file: timer framework/base/TimerStatistic.h /^ static Timer timer[];$/;" m class:ProtoMol::TimerStatistic toBool framework/base/stringutilities.cpp /^ bool toBool(const string& word){$/;" f namespace:ProtoMol toBool framework/base/stringutilities.cpp /^ bool toBool(const string& word, bool &b){$/;" f namespace:ProtoMol toInt framework/base/stringutilities.cpp /^ bool toInt(const string& word, int &i){$/;" f namespace:ProtoMol toInt framework/base/stringutilities.cpp /^ int toInt(const string& word){$/;" f namespace:ProtoMol toReal framework/base/stringutilities.cpp /^ Real toReal(const string& word){$/;" f namespace:ProtoMol toReal framework/base/stringutilities.cpp /^ bool toReal(const string& word, Real &r){$/;" f namespace:ProtoMol toString framework/base/stringutilities.cpp /^ string toString(Real x){$/;" f namespace:ProtoMol toString framework/base/stringutilities.cpp /^ string toString(Real x,unsigned int n, unsigned int m){$/;" f namespace:ProtoMol toString framework/base/stringutilities.cpp /^ string toString(bool x){$/;" f namespace:ProtoMol toString framework/base/stringutilities.cpp /^ string toString(const Vector3D& c){$/;" f namespace:ProtoMol toString framework/base/stringutilities.cpp /^ string toString(const vector& v){$/;" f namespace:ProtoMol toString framework/base/stringutilities.h /^ inline const std::string & toString(const std::string& x) {return x;}$/;" f namespace:ProtoMol toString framework/base/stringutilities.h /^ inline std::string toString(T x){$/;" f namespace:ProtoMol toStringGeneric framework/base/stringutilities.cpp /^ inline string toStringGeneric(T x){$/;" f namespace:ProtoMol toUInt framework/base/stringutilities.cpp /^ bool toUInt(const string& word, unsigned int &i){$/;" f namespace:ProtoMol toUInt framework/base/stringutilities.cpp /^ unsigned int toUInt(const string& word){$/;" f namespace:ProtoMol toVector framework/base/stringutilities.cpp /^ bool toVector(const string& word, vector &v){$/;" f namespace:ProtoMol toVector framework/base/stringutilities.cpp /^ vector toVector(const string& word){$/;" f namespace:ProtoMol toVector3D framework/base/stringutilities.cpp /^ Vector3D toVector3D(const string& word){$/;" f namespace:ProtoMol toVector3D framework/base/stringutilities.cpp /^ bool toVector3D(const string& word, Vector3D &c){$/;" f namespace:ProtoMol top framework/integrators/Integrator.cpp /^ Integrator* Integrator::top(){$/;" f class:ProtoMol::Integrator top framework/integrators/Integrator.cpp /^ const Integrator* Integrator::top() const{$/;" f class:ProtoMol::Integrator totalEnergy framework/frontend/OutputCache.cpp /^ Real OutputCache::totalEnergy() const{$/;" f class:ProtoMol::OutputCache trajectory framework/base/ScalarStructure.cpp /^ bool ScalarStructure::trajectory(bool doTrajectory){$/;" f class:ProtoMol::ScalarStructure trajectory framework/base/ScalarStructure.h /^ bool trajectory() const {return myDoTrajectory;}$/;" f class:ProtoMol::ScalarStructure transpose framework/base/Matrix3by3.cpp /^ void Matrix3by3::transpose() $/;" f class:ProtoMol::Matrix3by3 transpose framework/base/Matrix3by3.cpp /^ void Matrix3by3::transpose(const Matrix3by3& tm) $/;" f class:ProtoMol::Matrix3by3 transposed framework/base/Matrix3by3.cpp /^ Matrix3by3 Matrix3by3::transposed() const $/;" f class:ProtoMol::Matrix3by3 transposed framework/base/ReducedHessAngle.cpp /^ ReducedHessAngle ReducedHessAngle::transposed()$/;" f class:ProtoMol::ReducedHessAngle trate framework/imd/IMDElf.h /^ int trate;$/;" m class:ProtoMol::IMDElf tryFormat framework/frontend/InputPosVel.cpp /^ bool InputPosVel::tryFormat(InputPosVelType::Enum type){$/;" f class:ProtoMol::InputPosVel tryFormat framework/io/AMBERReader.cpp /^ bool AMBERReader::tryFormat(){ \/\/tryFormat check file format$/;" f class:ProtoMol::AMBERReader tryFormat framework/io/CRDReader.cpp /^ bool CRDReader::tryFormat(){$/;" f class:ProtoMol::CRDReader tryFormat framework/io/ConfigurationReader.cpp /^ bool ConfigurationReader::tryFormat(){$/;" f class:ProtoMol::ConfigurationReader tryFormat framework/io/DCDTrajectoryReader.cpp /^ bool DCDTrajectoryReader::tryFormat(){$/;" f class:ProtoMol::DCDTrajectoryReader tryFormat framework/io/PARReader.cpp /^ bool PARReader::tryFormat(){$/;" f class:ProtoMol::PARReader tryFormat framework/io/PDBReader.cpp /^ bool PDBReader::tryFormat(){$/;" f class:ProtoMol::PDBReader tryFormat framework/io/PGMReader.cpp /^ bool PGMReader::tryFormat(){$/;" f class:ProtoMol::PGMReader tryFormat framework/io/PPMReader.cpp /^ bool PPMReader::tryFormat(){$/;" f class:ProtoMol::PPMReader tryFormat framework/io/PSFReader.cpp /^ bool PSFReader::tryFormat(){$/;" f class:ProtoMol::PSFReader tryFormat framework/io/REMConfigurationReader.cpp /^ bool REMConfigurationReader::tryFormat(){$/;" f class:ProtoMol::REMConfigurationReader tryFormat framework/io/TempFileReader.cpp /^ bool TempFileReader::tryFormat() {$/;" f class:ProtoMol::TempFileReader tryFormat framework/io/XYZBinReader.cpp /^ bool XYZBinReader::tryFormat(){$/;" f class:ProtoMol::XYZBinReader tryFormat framework/io/XYZReader.cpp /^ bool XYZReader::tryFormat(){$/;" f class:ProtoMol::XYZReader tryFormat framework/io/XYZTrajectoryReader.cpp /^ bool XYZTrajectoryReader::tryFormat(){$/;" f class:ProtoMol::XYZTrajectoryReader tstep framework/imd/imd.h /^ int32 tstep;$/;" m struct:ProtoMol::IMD:: type framework/base/Atom.h /^ int type;$/;" m struct:ProtoMol::Atom type framework/base/Molecule.h /^ unsigned int type, newtype;$/;" m struct:ProtoMol::Molecule type framework/base/Value.h /^ virtual const std::type_info & type() const { return typeid(ValueTrait);}$/;" f class:ProtoMol::Value::Holder type framework/base/Value.h /^ inline const std::type_info & Value::type() const{$/;" f class:ProtoMol::Value type framework/base/typeSelection.h /^ Real>::type,size>::type type;$/;" t struct:ProtoMol::TypeSelection::Float type framework/base/typeSelection.h /^ typename Private::SelectType::type>::type,size>::type type;$/;" t struct:ProtoMol::TypeSelection::Int type framework/base/typeSelection.h /^ typedef typename SelectTypeCheckHelper::type type;$/;" t struct:ProtoMol::Private::SelectTypeCheck type framework/base/typeSelection.h /^ typedef typename SelectTypeHelper::type type;$/;" t struct:ProtoMol::Private::SelectType type framework/base/typeSelection.h /^ typedef A type;$/;" t struct:ProtoMol::Private::SelectTypeCheckHelper type framework/base/typeSelection.h /^ typedef A type;$/;" t struct:ProtoMol::Private::SelectTypeHelper type framework/base/typeSelection.h /^ typedef B type;$/;" t struct:ProtoMol::Private::SelectTypeHelper type framework/imd/imd.cpp /^ int32 type;$/;" m struct:ProtoMol::IMD:: file: ub_flag framework/base/PAR.h /^ bool ub_flag; $/;" m struct:ProtoMol::PAR::Angle uncache framework/forces/CompareForce.cpp /^ void CompareForce::uncache(){$/;" f class:ProtoMol::CompareForce uncache framework/forces/Force.h /^ virtual void uncache(){};$/;" f class:ProtoMol::Force uncache framework/forces/ForceGroup.cpp /^ void ForceGroup::uncache(){$/;" f class:ProtoMol::ForceGroup uncache framework/forces/NonbondedFullEwaldSystemForce.h /^ virtual void uncache(){myCached=false;};$/;" f class:ProtoMol::NonbondedFullEwaldSystemForce uncache framework/forces/NonbondedFullSystemForce.h /^ virtual void uncache(){myCached=false;};$/;" f class:ProtoMol::NonbondedFullSystemForce uncache framework/forces/NonbondedMultiGridSystemForce.h /^ virtual void uncache(){myCached=false;};$/;" f class:ProtoMol::NonbondedMultiGridSystemForce uncache framework/forces/NonbondedPMEwaldSystemForce.h /^ virtual void uncache(){myCached=false;};$/;" f class:ProtoMol::NonbondedPMEwaldSystemForce uncache framework/forces/NonbondedSimpleFullSystemForce.h /^ virtual void uncache(){myCached=false;};$/;" f class:ProtoMol::NonbondedSimpleFullSystemForce uncache framework/forces/PaulTrapExtendedForce.h /^ virtual void uncache(){myCached=false;};$/;" f class:ProtoMol::PaulTrapExtendedForce uncache framework/forces/TimeForce.cpp /^ void TimeForce::uncache(){$/;" f class:ProtoMol::TimeForce uncache framework/frontend/OutputCache.cpp /^ void OutputCache::uncache() const{$/;" f class:ProtoMol::OutputCache uncache framework/imd/HapticSystemForce.h /^ virtual void uncache(){myCached=false;};$/;" f class:ProtoMol::HapticSystemForce uncache framework/integrators/Integrator.cpp /^ void Integrator::uncache(){$/;" f class:ProtoMol::Integrator uncache framework/topology/ArrayCellListStructure.h /^ void uncache(){valid = false;}$/;" f class:ProtoMol::ArrayCellListStructure uncacheCellList framework/topology/Topology.h /^ virtual void uncacheCellList(){cellLists.uncache();}$/;" f class:ProtoMol::Topology undefined framework/base/Value.h /^ static const Undefined* undefined; \/\/\/< Undefined value$/;" m class:ProtoMol::Value underflow framework/base/sstream_local.h /^inline int std::stringbuf::underflow()$/;" f class:std::stringbuf uniqueForceString framework/frontend/ForceFactoryDetails.cpp /^ string ForceFactoryDetails::uniqueForceString(const string& id) const{$/;" f class:ProtoMol::ForceFactoryDetails unpauseCalc framework/integrators/ModifierShadow.h /^ inline void ModifierShadow::unpauseCalc() {$/;" f class:ProtoMol::ModifierShadow unregisterAllExemplars framework/frontend/Factory.h /^ static void unregisterAllExemplars(){$/;" f class:ProtoMol::Factory unregisterAllExemplars framework/frontend/HelpTextFactory.cpp /^ void HelpTextFactory::unregisterAllExemplars(){$/;" f class:ProtoMol::HelpTextFactory unregisterExemplar framework/frontend/Factory.h /^ static bool unregisterExemplar(const std::string& id){$/;" f class:ProtoMol::Factory unregisterExemplar framework/frontend/HelpTextFactory.cpp /^ bool HelpTextFactory::unregisterExemplar(const string& id){$/;" f class:ProtoMol::HelpTextFactory unregisterKeyword framework/base/Configuration.cpp /^ void Configuration::unregisterKeyword(const std::string& keyword){$/;" f class:ProtoMol::Configuration updateB_Bx framework/integrators/BSplineMOLLYIntegrator.cpp /^ void BSplineMOLLYIntegrator::updateB_Bx() {$/;" f class:ProtoMol::BSplineMOLLYIntegrator updateB_Bx_Px_for1Kick framework/integrators/BSplineMOLLYIntegrator.cpp /^ void BSplineMOLLYIntegrator::updateB_Bx_Px_for1Kick() {$/;" f class:ProtoMol::BSplineMOLLYIntegrator updateB_Bx_Px_for1stHalfKick framework/integrators/BSplineMOLLYIntegrator.cpp /^ void BSplineMOLLYIntegrator::updateB_Bx_Px_for1stHalfKick(){$/;" f class:ProtoMol::BSplineMOLLYIntegrator updateBeta framework/integrators/ImpulseIntegrator.cpp /^ void ImpulseIntegrator::updateBeta( Real dt ) {$/;" f class:ProtoMol::ImpulseIntegrator updateBeta framework/integrators/Integrator.h /^ inline void Integrator::updateBeta( Real timestep ) {};$/;" f class:ProtoMol::Integrator updateBeta framework/integrators/LeapfrogIntegrator.cpp /^ void LeapfrogIntegrator::updateBeta( Real dt ) {$/;" f class:ProtoMol::LeapfrogIntegrator updateCache framework/frontend/ForceFactoryDetails.cpp /^ void ForceFactoryDetails::updateCache() const{$/;" f class:ProtoMol::ForceFactoryDetails updateCache framework/topology/ArrayCellListStructure.cpp /^ void ArrayCellListStructure::updateCache(){ $/;" f class:ProtoMol::ArrayCellListStructure updateCache framework/topology/CubicCellManager.cpp /^ void CubicCellManager::updateCache(CellListStructure& cellList) const{$/;" f class:ProtoMol::CubicCellManager updateCellLists framework/topology/Topology.h /^ void updateCellLists(const Vector3DBlock* positions) const{$/;" f class:ProtoMol::Topology updateSize framework/base/MultiGrid.h /^ void MultiGrid::updateSize(Vector3D min, Vector3D max){$/;" f class:ProtoMol::MultiGrid updateXx framework/integrators/BSplineMOLLYIntegrator.cpp /^ void BSplineMOLLYIntegrator::updateXx() {$/;" f class:ProtoMol::BSplineMOLLYIntegrator uppercase framework/base/stringutilities.cpp /^ string uppercase (const string& word){$/;" f namespace:ProtoMol ureyBradleyConstant framework/topology/Angle.h /^ Real ureyBradleyConstant;$/;" m class:ProtoMol::Angle ureyBradleyRestLength framework/topology/Angle.h /^ Real ureyBradleyRestLength;$/;" m class:ProtoMol::Angle v compilerTests/glutTest.cpp /^static GLfloat v[8][3]; \/* Will be filled in with X,Y,Z vertexes. *\/$/;" v file: v tools/bccAnalyzer.cpp /^ Vector3D v; $/;" m class:Vector3DIdx file: v0 tools/bccAnalyzer.cpp /^ Vector3DIdx v0,c,v1;$/;" m class:PairVector3D file: v1 tools/bccAnalyzer.cpp /^ Vector3DIdx v0,c,v1;$/;" m class:PairVector3D file: valid framework/base/AbstractEnumType.h /^ bool valid() const {return (myType>T::FIRST && myTypeT::FIRST && e value framework/base/Parameter.h /^ Value value;$/;" m struct:ProtoMol::Parameter value framework/base/ValueType.h /^ enum { value = e};$/;" e enum:ProtoMol::ValueEnum::Enum2ValueType:: value framework/base/ValueType.h /^ enum { value = ValueType::BOOL};$/;" e enum:ProtoMol::ValueTraits:: value framework/base/ValueType.h /^ enum { value = ValueType::FORCE};$/;" e enum:ProtoMol::ValueTraits:: value framework/base/ValueType.h /^ enum { value = ValueType::INTEGRATOR};$/;" e enum:ProtoMol::ValueTraits:: value framework/base/ValueType.h /^ enum { value = ValueType::INT};$/;" e enum:ProtoMol::ValueTraits:: value framework/base/ValueType.h /^ enum { value = ValueType::REAL};$/;" e enum:ProtoMol::ValueTraits:: value framework/base/ValueType.h /^ enum { value = ValueType::UINT};$/;" e enum:ProtoMol::ValueTraits:: value framework/base/ValueType.h /^ enum { value = ValueType::VECTOR3D};$/;" e enum:ProtoMol::ValueTraits:: value framework/base/ValueType.h /^ enum { value = ValueType::VECTOR};$/;" e enum:ProtoMol::ValueTraits:: value framework/base/ValueType.h /^ enum {value = ValueType::STRING}; \/\/ Enum value$/;" e enum:ProtoMol::ValueTraits:: value_type framework/base/Array_Fastest.h /^ typedef T value_type;$/;" t class:ProtoMol::Array value_type framework/base/Array_Fastest.h /^ typedef T value_type;$/;" t class:ProtoMol::RefArray value_type framework/base/Array_NoPartialSpecialization.h /^ typedef T value_type;$/;" t class:ProtoMol::Array::RefArray value_type framework/base/Array_NoPartialSpecialization.h /^ typedef T value_type;$/;" t class:ProtoMol::Array value_type framework/base/Vector3DBlock.h /^ typedef std::vector::value_type value_type; $/;" t class:ProtoMol::Vector3DBlock value_type framework/topology/ArrayCellListStructure.h /^ typedef TContainer::value_type value_type;$/;" t class:ProtoMol::ArrayCellListStructure values framework/frontend/IntegratorFactoryDetails.h /^ std::vector values;$/;" m struct:ProtoMol::IntegratorFactoryDetails::IntegratorInput vdw framework/base/PAR.h /^ bool vdw; $/;" m struct:ProtoMol::PAR::Nonbonded vec framework/base/Vector3DBlock.h /^ std::vector vec; $/;" m class:ProtoMol::Vector3DBlock velocityVirial framework/topology/topologyutilities.cpp /^ ScalarStructure velocityVirial(const GenericTopology* topology,$/;" f namespace:ProtoMol view framework/frontend/OutputBSDL.cpp /^ string OutputBSDL::view(const Vector3DBlock* pos) const{$/;" f class:ProtoMol::OutputBSDL virial framework/base/ScalarStructure.cpp /^ bool ScalarStructure::virial(bool doVirial){$/;" f class:ProtoMol::ScalarStructure virial framework/base/ScalarStructure.h /^ bool virial() const {return myDoVirial;}$/;" f class:ProtoMol::ScalarStructure vmd_atoms framework/imd/IMDElf.h /^ IMD::int32* vmd_atoms;$/;" m class:ProtoMol::IMDElf vmd_forces framework/imd/IMDElf.h /^ float* vmd_forces;$/;" m class:ProtoMol::IMDElf vmdsock_accept framework/imd/vmdsock.cpp /^ void *vmdsock_accept(void * v) { return 0; }$/;" f namespace:ProtoMol::IMD vmdsock_accept framework/imd/vmdsock.cpp /^ void *vmdsock_accept(void * v) {$/;" f namespace:ProtoMol::IMD vmdsock_bind framework/imd/vmdsock.cpp /^ int vmdsock_bind(void * v, int port) { return 0; }$/;" f namespace:ProtoMol::IMD vmdsock_bind framework/imd/vmdsock.cpp /^ int vmdsock_bind(void * v, int port) {$/;" f namespace:ProtoMol::IMD vmdsock_connect framework/imd/vmdsock.cpp /^ int vmdsock_connect(void *v, const char *host, int port) { return 0; }$/;" f namespace:ProtoMol::IMD vmdsock_connect framework/imd/vmdsock.cpp /^ int vmdsock_connect(void *v, const char *host, int port) {$/;" f namespace:ProtoMol::IMD vmdsock_create framework/imd/vmdsock.cpp /^ void * vmdsock_create(void) { return 0; }$/;" f namespace:ProtoMol::IMD vmdsock_create framework/imd/vmdsock.cpp /^ void * vmdsock_create(void) {$/;" f namespace:ProtoMol::IMD vmdsock_destroy framework/imd/vmdsock.cpp /^ void vmdsock_destroy(void * v) { return; }$/;" f namespace:ProtoMol::IMD vmdsock_destroy framework/imd/vmdsock.cpp /^ void vmdsock_destroy(void * v) {$/;" f namespace:ProtoMol::IMD vmdsock_init framework/imd/vmdsock.cpp /^ int vmdsock_init(void) { return -1; }$/;" f namespace:ProtoMol::IMD vmdsock_init framework/imd/vmdsock.cpp /^ int vmdsock_init(void) {$/;" f namespace:ProtoMol::IMD vmdsock_listen framework/imd/vmdsock.cpp /^ int vmdsock_listen(void * v) { return 0; }$/;" f namespace:ProtoMol::IMD vmdsock_listen framework/imd/vmdsock.cpp /^ int vmdsock_listen(void * v) {$/;" f namespace:ProtoMol::IMD vmdsock_read framework/imd/vmdsock.cpp /^ int vmdsock_read(void * v, void *buf, int len) { return 0; }$/;" f namespace:ProtoMol::IMD vmdsock_read framework/imd/vmdsock.cpp /^ int vmdsock_read(void * v, void *buf, int len) {$/;" f namespace:ProtoMol::IMD vmdsock_selread framework/imd/vmdsock.cpp /^ int vmdsock_selread(void *v, int sec) { return 0; }$/;" f namespace:ProtoMol::IMD vmdsock_selread framework/imd/vmdsock.cpp /^ int vmdsock_selread(void *v, int sec) {$/;" f namespace:ProtoMol::IMD vmdsock_selwrite framework/imd/vmdsock.cpp /^ int vmdsock_selwrite(void *v, int sec) { return 0; }$/;" f namespace:ProtoMol::IMD vmdsock_selwrite framework/imd/vmdsock.cpp /^ int vmdsock_selwrite(void *v, int sec) {$/;" f namespace:ProtoMol::IMD vmdsock_write framework/imd/vmdsock.cpp /^ int vmdsock_write(void * v, const void *buf, int len) { return 0; }$/;" f namespace:ProtoMol::IMD vmdsock_write framework/imd/vmdsock.cpp /^ int vmdsock_write(void * v, const void *buf, int len) {$/;" f namespace:ProtoMol::IMD vmdsocket framework/imd/vmdsock.h /^ } vmdsocket;$/;" t namespace:ProtoMol::IMD volum framework/forces/MagneticDipoleForce.h /^ Real volum, expfactor, realChi, kappa;$/;" m class:ProtoMol::MagneticDipoleForce volume framework/frontend/OutputCache.cpp /^ Real OutputCache::volume() const{$/;" f class:ProtoMol::OutputCache w compilerTests/pngTest.cpp /^ unsigned int w,h;$/;" m class:PPM file: w framework/base/PGM.h /^ unsigned int w,h;$/;" m class:ProtoMol::PGM w framework/base/PPM.h /^ unsigned int w,h;$/;" m class:ProtoMol::PPM wait_imd framework/imd/IMDElf.h /^ int wait_imd;$/;" m class:ProtoMol::IMDElf walk framework/integrators/MCIntegrator.cpp /^ void MCIntegrator::walk(int steps){$/;" f class:ProtoMol::MCIntegrator warning framework/base/Report.cpp /^ MyStreamer& warning(MyStreamer& stream){$/;" f namespace:ProtoMol::Report water framework/base/Molecule.h /^ bool water;$/;" m struct:ProtoMol::Molecule waterOption framework/topology/topologyutilities.h /^ enum waterOption {IGNORE_WATER, ONLY_WATER, ALL};$/;" g namespace:ProtoMol width compilerTests/pngTest.cpp /^ unsigned int width() const{return w;}$/;" f class:PPM width framework/base/PGM.h /^ unsigned int width() const{return w;}$/;" f class:ProtoMol::PGM width framework/base/PPM.h /^ unsigned int width() const{return w;}$/;" f class:ProtoMol::PPM width framework/base/Report.cpp /^ void MyStreamer::width(int wide){$/;" f class:ProtoMol::Report::MyStreamer write framework/io/DCDTrajectoryWriter.cpp /^ bool DCDTrajectoryWriter::write(const Vector3DBlock& coords){$/;" f class:ProtoMol::DCDTrajectoryWriter write framework/io/PARWriter.cpp /^ bool PARWriter::write(const PAR& par){$/;" f class:ProtoMol::PARWriter write framework/io/PDBWriter.cpp /^ bool PDBWriter::write(const PDB& pdb){$/;" f class:ProtoMol::PDBWriter write framework/io/PDBWriter.cpp /^ bool PDBWriter::write(const Vector3DBlock& coords, const PDB& pdb){$/;" f class:ProtoMol::PDBWriter write framework/io/PDBWriter.cpp /^ bool PDBWriter::write(const Vector3DBlock& coords, const vector& atoms){$/;" f class:ProtoMol::PDBWriter write framework/io/PDBWriter.cpp /^ bool PDBWriter::write(const Vector3DBlock& coords, const vector& atoms, const vector& ters){$/;" f class:ProtoMol::PDBWriter write framework/io/PGMWriter.cpp /^ bool PGMWriter::write(const PGM& pgm){$/;" f class:ProtoMol::PGMWriter write framework/io/PGMWriter.cpp /^ bool PGMWriter::write(const PPM& ppm){$/;" f class:ProtoMol::PGMWriter write framework/io/PNGWriter.cpp /^ bool PNGWriter::write(const PGM& pgm){$/;" f class:ProtoMol::PNGWriter write framework/io/PNGWriter.cpp /^ bool PNGWriter::write(const PPM& ppm){$/;" f class:ProtoMol::PNGWriter write framework/io/PPMWriter.cpp /^ bool PPMWriter::write(const PGM& pgm){$/;" f class:ProtoMol::PPMWriter write framework/io/PPMWriter.cpp /^ bool PPMWriter::write(const PPM& ppm){$/;" f class:ProtoMol::PPMWriter write framework/io/PSFWriter.cpp /^ bool PSFWriter::write(const PSF& psf){$/;" f class:ProtoMol::PSFWriter write framework/io/XFigWriter.cpp /^ bool XFigWriter::write(const Vector3DBlock& coords, const std::vector& names){$/;" f class:ProtoMol::XFigWriter write framework/io/XFigWriter.cpp /^ bool XFigWriter::write(const XYZ& xyz){$/;" f class:ProtoMol::XFigWriter write framework/io/XYZBinWriter.cpp /^ bool XYZBinWriter::write(const Vector3DBlock& coords){$/;" f class:ProtoMol::XYZBinWriter write framework/io/XYZBinWriter.cpp /^ bool XYZBinWriter::write(const Vector3DBlock& coords, bool isLittleEndian, unsigned int size){$/;" f class:ProtoMol::XYZBinWriter write framework/io/XYZBinWriter.cpp /^ bool XYZBinWriter::write(const XYZ& xyz){$/;" f class:ProtoMol::XYZBinWriter write framework/io/XYZBinWriter.cpp /^ bool XYZBinWriter::write(const XYZ& xyz, bool isLittleEndian, unsigned int size){$/;" f class:ProtoMol::XYZBinWriter write framework/io/XYZTrajectoryWriter.cpp /^ bool XYZTrajectoryWriter::write(){$/;" f class:ProtoMol::XYZTrajectoryWriter write framework/io/XYZTrajectoryWriter.cpp /^ bool XYZTrajectoryWriter::write(const Vector3DBlock& coords){$/;" f class:ProtoMol::XYZTrajectoryWriter write framework/io/XYZTrajectoryWriter.cpp /^ bool XYZTrajectoryWriter::write(const Vector3DBlock& coords, const std::vector& atoms,$/;" f class:ProtoMol::XYZTrajectoryWriter write framework/io/XYZTrajectoryWriter.cpp /^ bool XYZTrajectoryWriter::write(const Vector3DBlock& coords, const std::vector& names){$/;" f class:ProtoMol::XYZTrajectoryWriter write framework/io/XYZTrajectoryWriter.cpp /^ bool XYZTrajectoryWriter::write(const XYZ& xyz){$/;" f class:ProtoMol::XYZTrajectoryWriter write framework/io/XYZWriter.cpp /^ bool XYZWriter::write(const Vector3DBlock& coords, $/;" f class:ProtoMol::XYZWriter write framework/io/XYZWriter.cpp /^ bool XYZWriter::write(const Vector3DBlock& coords, const std::vector& names){$/;" f class:ProtoMol::XYZWriter write framework/io/XYZWriter.cpp /^ bool XYZWriter::write(const XYZ& xyz){$/;" f class:ProtoMol::XYZWriter writeData framework/io/AMBERReader.cpp /^ void AMBERReader::writeData() {$/;" f class:ProtoMol::AMBERReader writeData framework/io/CRDReader.cpp /^ void CRDReader::writeData()$/;" f class:ProtoMol::CRDReader x framework/base/Grid.h /^ TInterpolation x;$/;" m struct:ProtoMol::Grid::Interpolation3D x framework/base/Grid.h /^ struct Int3D {int x; int y; int z;};$/;" m struct:ProtoMol::Grid::Int3D x framework/base/MultiGrid.h /^ TInterpolation x;$/;" m struct:ProtoMol::MultiGrid::Interpolation3D x framework/base/MultiGrid.h /^ struct Int3D {int x, y, z;};$/;" m struct:ProtoMol::MultiGrid::Int3D x framework/base/Vector3D.h /^ Real x,y,z;$/;" m struct:ProtoMol::Vector3D x framework/parallel/Parallel-FD.cpp /^ int x = -1;$/;" v x framework/topology/CubicCellLocation.h /^ int x;$/;" m class:ProtoMol::CubicCellLocation xFigBW1 framework/io/XFigWriter.cpp /^ static const std::string xFigBW1[xFigBWN] ={"1 3 0 1 7 0",$/;" v file: xFigBW2 framework/io/XFigWriter.cpp /^ static const std::string xFigBW2[xFigBWN] ={"0 20 0.000 1 0.0000",$/;" v file: xFigBWN framework/io/XFigWriter.cpp /^ static const int xFigBWN = 4;$/;" v file: xFigColors framework/io/XFigWriter.cpp /^ static const int xFigColors[xFigColorsN] = {0,20,13,10,31,1,2,3,4,5,6,7,8,9,11,12,14,15,16,17,18,19,21,22,23,24,25,26,27,28,29,30};$/;" v file: xFigColorsN framework/io/XFigWriter.cpp /^ static const int xFigColorsN = 32;$/;" v file: xFigXMax framework/io/XFigWriter.cpp /^ static const int xFigXMax = 12500;$/;" v file: xFigYMax framework/io/XFigWriter.cpp /^ static const int xFigYMax = 9700;$/;" v file: y framework/base/Grid.h /^ TInterpolation y;$/;" m struct:ProtoMol::Grid::Interpolation3D y framework/base/Grid.h /^ struct Int3D {int x; int y; int z;};$/;" m struct:ProtoMol::Grid::Int3D y framework/base/MultiGrid.h /^ TInterpolation y;$/;" m struct:ProtoMol::MultiGrid::Interpolation3D y framework/base/MultiGrid.h /^ struct Int3D {int x, y, z;};$/;" m struct:ProtoMol::MultiGrid::Int3D y framework/base/Vector3D.h /^ Real x,y,z;$/;" m struct:ProtoMol::Vector3D y framework/parallel/Parallel-FD.cpp /^ int y = -1;$/;" v y framework/topology/CubicCellLocation.h /^ int y;$/;" m class:ProtoMol::CubicCellLocation z framework/base/Grid.h /^ TInterpolation z;$/;" m struct:ProtoMol::Grid::Interpolation3D z framework/base/Grid.h /^ struct Int3D {int x; int y; int z;};$/;" m struct:ProtoMol::Grid::Int3D z framework/base/MultiGrid.h /^ TInterpolation z;$/;" m struct:ProtoMol::MultiGrid::Interpolation3D z framework/base/MultiGrid.h /^ struct Int3D {int x, y, z;};$/;" m struct:ProtoMol::MultiGrid::Int3D z framework/base/Vector3D.h /^ Real x,y,z;$/;" m struct:ProtoMol::Vector3D z framework/topology/CubicCellLocation.h /^ int z;$/;" m class:ProtoMol::CubicCellLocation zero framework/base/Matrix3by3.cpp /^ bool Matrix3by3::zero() const$/;" f class:ProtoMol::Matrix3by3 zero framework/base/Vector3DBlock.h /^ void zero(int n=-1) {$/;" f class:ProtoMol::Vector3DBlock zeroMatrix framework/base/Matrix3by3.cpp /^ void Matrix3by3::zeroMatrix() $/;" f class:ProtoMol::Matrix3by3 zfft2d framework/base/fft.c /^int zfft2d( int sign, int n1, int n2, zomplex *array, int ld, zomplex *save)$/;" f zfft2d_ framework/base/fft.c /^int zfft2d_(int *sign, int *x, int *y, zomplex *a, int *lda, zomplex *coeff)$/;" f zfft2di framework/base/fft.c /^zomplex *zfft2di( int n1, int n2, zomplex *save)$/;" f zfft2di_ framework/base/fft.c /^int zfft2di_(int *x, int *y,zomplex * coeff)$/;" f zfft3d framework/base/fft.c /^int zfft3d( int sign, int n1, int n2, int n3, zomplex *array, int ld1, int ld2, zomplex *save)$/;" f zfft3d_ framework/base/fft.c /^int zfft3d_(int *sign,int * x, int *y, int *z__,zomplex * a, int *la1, int *la2,zomplex * coeff)$/;" f zfft3di framework/base/fft.c /^zomplex *zfft3di( int n1, int n2, int n3, zomplex *save)$/;" f zfft3di_ framework/base/fft.c /^int zfft3di_(int *x, int *y, int *z__,zomplex * coeff)$/;" f zfftcopyin_ framework/base/fft.c /^void zfftcopyin_(int *n,int * b,int * bdim,zomplex * a,int * inc ,int * lda,int * rindex,zomplex * w,int * lpref)$/;" f zfftcopyout_ framework/base/fft.c /^void zfftcopyout_(int *n, int *b, zomplex *a, int *inc, int *lda,zomplex *w)$/;" f zfftm1big_ framework/base/fft.c /^int zfftm1big_(int *sign,int * n,int * p,zomplex * a,int * inc,int * lda,int * lpref,int * nf,int * f,zomplex *coeff,int *rindex)$/;" f zfftm1d framework/base/fft.c /^int zfftm1d( int sign, int m, int n, zomplex *array, int incI, int incJ, zomplex *save)$/;" f zfftm1d_ framework/base/fft.c /^int zfftm1d_(int *sign,int * n,int * p, zomplex* a, int *inc,int * lda, zomplex *coeff, int *lpref)$/;" f zfftm1di framework/base/fft.c /^zomplex *zfftm1di( int m, zomplex *save)$/;" f zfftm1di_ framework/base/fft.c /^int zfftm1di_(int *n,zomplex * coeff)$/;" f zfftm1rowb_ framework/base/fft.c /^int zfftm1rowb_(int *n, int *b, int *bdim,zomplex *w, int *nf, int *f, double *coeff, zomplex *a, int *inc, int *lda, $/;" f zfftm1rowf_ framework/base/fft.c /^int zfftm1rowf_(int *n, int *b, int *bdim,zomplex * w, int *nf, int *f, double *coeff, zomplex *a, int *inc, int *lda, $/;" f zfftrev_ framework/base/fft.c /^int zfftrev_(int *n, int *inc, int *nf, int *f, int * nmax , int *rindex,int * ipadok)$/;" f zomplex framework/base/FFTComplex.h /^ } zomplex;$/;" t zomplex framework/base/fft.c /^} zomplex;$/;" t file: ~AMBERReader framework/io/AMBERReader.cpp /^ AMBERReader::~AMBERReader(){$/;" f class:ProtoMol::AMBERReader ~AngleInfo framework/topology/AngleInfo.cpp /^ AngleInfo::~AngleInfo() {$/;" f class:ProtoMol::AngleInfo ~AngleSystemForceBase framework/forces/AngleSystemForceBase.h /^ virtual ~AngleSystemForceBase(){}$/;" f class:ProtoMol::AngleSystemForceBase ~Array framework/base/Array_Fastest.h /^ ~Array() $/;" f class:ProtoMol::Array ~Array framework/base/Array_NoPartialSpecialization.h /^ ~Array() $/;" f class:ProtoMol::Array ~BSpline framework/base/BSpline.cpp /^ BSpline::~BSpline(){$/;" f class:ProtoMol::BSpline ~BSplineEnum framework/base/BSplineType.h /^ virtual ~BSplineEnum(){}$/;" f class:ProtoMol::BSplineEnum ~BSplineMOLLYIntegrator framework/integrators/BSplineMOLLYIntegrator.cpp /^ BSplineMOLLYIntegrator::~BSplineMOLLYIntegrator() {$/;" f class:ProtoMol::BSplineMOLLYIntegrator ~BondSystemForceBase framework/forces/BondSystemForceBase.h /^ virtual ~BondSystemForceBase(){}$/;" f class:ProtoMol::BondSystemForceBase ~CRDReader framework/io/CRDReader.cpp /^ CRDReader::~CRDReader(){$/;" f class:ProtoMol::CRDReader ~CompareForce framework/forces/CompareForce.cpp /^ CompareForce::~CompareForce(){$/;" f class:ProtoMol::CompareForce ~ConfigurationReader framework/io/ConfigurationReader.cpp /^ ConfigurationReader::~ConfigurationReader(){$/;" f class:ProtoMol::ConfigurationReader ~ConstraintValueEnum framework/base/ConstraintValueType.h /^ virtual ~ConstraintValueEnum(){}$/;" f class:ProtoMol::ConstraintValueEnum ~DCDTrajectoryReader framework/io/DCDTrajectoryReader.cpp /^ DCDTrajectoryReader::~DCDTrajectoryReader(){$/;" f class:ProtoMol::DCDTrajectoryReader ~DMDLeapfrogIntegrator framework/integrators/DMDLeapfrogIntegrator.cpp /^ DMDLeapfrogIntegrator::~DMDLeapfrogIntegrator()$/;" f class:ProtoMol::DMDLeapfrogIntegrator ~DihedralHMCIntegrator framework/integrators/DihedralHMCIntegrator.cpp /^ DihedralHMCIntegrator::~DihedralHMCIntegrator(){$/;" f class:ProtoMol::DihedralHMCIntegrator ~DihedralSystemForceBase framework/forces/DihedralSystemForceBase.h /^ virtual ~DihedralSystemForceBase(){}$/;" f class:ProtoMol::DihedralSystemForceBase ~ElectricFieldSystemForceBase framework/forces/ElectricFieldSystemForceBase.h /^ virtual ~ElectricFieldSystemForceBase(){}$/;" f class:ProtoMol::ElectricFieldSystemForceBase ~EquilibriumMOLLYIntegrator framework/integrators/EquilibriumMOLLYIntegrator.cpp /^ EquilibriumMOLLYIntegrator::~EquilibriumMOLLYIntegrator(){$/;" f class:ProtoMol::EquilibriumMOLLYIntegrator ~ExclusionEnum framework/topology/ExclusionType.h /^ virtual ~ExclusionEnum(){}$/;" f class:ProtoMol::ExclusionEnum ~ExclusionTable framework/topology/ExclusionTable.cpp /^ ExclusionTable::~ExclusionTable(){$/;" f class:ProtoMol::ExclusionTable ~ExtendedForce framework/forces/ExtendedForce.h /^ virtual ~ExtendedForce(){}$/;" f class:ProtoMol::ExtendedForce ~FFTComplex framework/base/FFTComplex.cpp /^ FFTComplex::~FFTComplex(){$/;" f class:ProtoMol::FFTComplex ~FFTInternal framework/base/FFTComplex.cpp /^ FFTInternal::~FFTInternal(){$/;" f class:ProtoMol::FFTInternal ~Factory framework/frontend/Factory.h /^ virtual ~Factory(){$/;" f class:ProtoMol::Factory ~FactoryBase framework/frontend/Factory.h /^ virtual ~FactoryBase(){$/;" f class:ProtoMol::FactoryBase ~File framework/io/File.cpp /^ File::~File(){$/;" f class:ProtoMol::File ~Force framework/forces/Force.h /^ virtual ~Force(){}$/;" f class:ProtoMol::Force ~ForceFactoryDetails framework/frontend/ForceFactoryDetails.cpp /^ ForceFactoryDetails::~ForceFactoryDetails(){$/;" f class:ProtoMol::ForceFactoryDetails ~ForceGroup framework/forces/ForceGroup.cpp /^ ForceGroup::~ForceGroup() {$/;" f class:ProtoMol::ForceGroup ~GenericTopology framework/topology/GenericTopology.h /^ virtual ~GenericTopology(){};$/;" f class:ProtoMol::GenericTopology ~Grid framework/base/Grid.h /^ Grid::~Grid(){$/;" f class:ProtoMol::Grid ~HapticSystemForce framework/imd/HapticSystemForce.cpp /^ HapticSystemForce::~HapticSystemForce(){$/;" f class:ProtoMol::HapticSystemForce ~HarmDihedralSystemForceBase framework/forces/HarmDihedralSystemForceBase.h /^ virtual ~HarmDihedralSystemForceBase(){}$/;" f class:ProtoMol::HarmDihedralSystemForceBase ~HelpTextFactory framework/frontend/HelpTextFactory.cpp /^ HelpTextFactory::~HelpTextFactory(){}$/;" f class:ProtoMol::HelpTextFactory ~Hermite framework/base/Hermite.cpp /^ Hermite::~Hermite(){$/;" f class:ProtoMol::Hermite ~IMDElf framework/imd/IMDElf.cpp /^ IMDElf::~IMDElf() {$/;" f class:ProtoMol::IMDElf ~ImproperSystemForceBase framework/forces/ImproperSystemForceBase.h /^ virtual ~ImproperSystemForceBase(){}$/;" f class:ProtoMol::ImproperSystemForceBase ~InputPosVelEnum framework/frontend/InputPosVelType.h /^ virtual ~InputPosVelEnum(){}$/;" f class:ProtoMol::InputPosVelEnum ~InputValue framework/frontend/InputValue.h /^ virtual ~InputValue(){}$/;" f class:ProtoMol::InputValue ~Integrator framework/integrators/Integrator.cpp /^ Integrator::~Integrator(){$/;" f class:ProtoMol::Integrator ~IntegratorFactoryDetails framework/frontend/IntegratorFactoryDetails.cpp /^ IntegratorFactoryDetails::~IntegratorFactoryDetails(){$/;" f class:ProtoMol::IntegratorFactoryDetails ~Lagrange framework/base/Lagrange.cpp /^ Lagrange::~Lagrange(){$/;" f class:ProtoMol::Lagrange ~LeapfrogIntegrator framework/integrators/LeapfrogIntegrator.cpp /^ LeapfrogIntegrator::~LeapfrogIntegrator() {}$/;" f class:ProtoMol::LeapfrogIntegrator ~LennardJonesParameterTable framework/topology/LennardJonesParameterTable.cpp /^ LennardJonesParameterTable::~LennardJonesParameterTable(){$/;" f class:ProtoMol::LennardJonesParameterTable ~LookUpTableBase framework/base/LookUpTableBase.h /^ virtual ~LookUpTableBase(){$/;" f class:ProtoMol::LookUpTableBase ~MCIntegrator framework/integrators/MCIntegrator.cpp /^ MCIntegrator::~MCIntegrator(){$/;" f class:ProtoMol::MCIntegrator ~MOLLYIntegrator framework/integrators/MOLLYIntegrator.cpp /^ MOLLYIntegrator::~MOLLYIntegrator(){}$/;" f class:ProtoMol::MOLLYIntegrator ~MTSIntegrator framework/integrators/MTSIntegrator.cpp /^ MTSIntegrator::~MTSIntegrator(){$/;" f class:ProtoMol::MTSIntegrator ~Makeable framework/base/Makeable.h /^ virtual ~Makeable(){};$/;" f class:ProtoMol::Makeable ~MetaForce framework/forces/MetaForce.h /^ virtual ~MetaForce(){}$/;" f class:ProtoMol::MetaForce ~Modifier framework/integrators/Modifier.h /^ virtual ~Modifier(){}$/;" f class:ProtoMol::Modifier ~MollyForce framework/forces/MollyForce.h /^ virtual ~MollyForce(){}$/;" f class:ProtoMol::MollyForce ~MultiGrid framework/base/MultiGrid.h /^ ~MultiGrid(){$/;" f class:ProtoMol::MultiGrid ~NonbondedCutoffForceBase framework/forces/NonbondedCutoffForceBase.h /^ virtual ~NonbondedCutoffForceBase(){}$/;" f class:ProtoMol::NonbondedCutoffForceBase ~NonbondedFullEwaldSystemForce framework/forces/NonbondedFullEwaldSystemForce.h /^ TSwitchingFunction>::~NonbondedFullEwaldSystemForce(){$/;" f class:ProtoMol::NonbondedFullEwaldSystemForce ~NonbondedFullSystemForce framework/forces/NonbondedFullSystemForce.h /^ virtual ~NonbondedFullSystemForce(){};$/;" f class:ProtoMol::NonbondedFullSystemForce ~NonbondedMultiGridSystemForce framework/forces/NonbondedMultiGridSystemForce.h /^ smooth>::~NonbondedMultiGridSystemForce(){$/;" f class:ProtoMol::NonbondedMultiGridSystemForce ~NonbondedPMEwaldSystemForce framework/forces/NonbondedPMEwaldSystemForce.h /^ TSwitchingFunction>::~NonbondedPMEwaldSystemForce(){$/;" f class:ProtoMol::NonbondedPMEwaldSystemForce ~NonbondedSimpleFullSystemForce framework/forces/NonbondedSimpleFullSystemForce.h /^ virtual ~NonbondedSimpleFullSystemForce(){}; $/;" f class:ProtoMol::NonbondedSimpleFullSystemForce ~NonbondedSimpleFullSystemForceBase framework/forces/NonbondedSimpleFullSystemForceBase.h /^ virtual ~NonbondedSimpleFullSystemForceBase(){}$/;" f class:ProtoMol::NonbondedSimpleFullSystemForceBase ~OutputBSDL framework/frontend/OutputBSDL.cpp /^ OutputBSDL::~OutputBSDL(){$/;" f class:ProtoMol::OutputBSDL ~OutputCache framework/frontend/OutputCache.cpp /^ OutputCache::~OutputCache(){$/;" f class:ProtoMol::OutputCache ~OutputCollection framework/frontend/OutputCollection.cpp /^ OutputCollection::~OutputCollection(){$/;" f class:ProtoMol::OutputCollection ~OutputDCDTrajectory framework/frontend/OutputDCDTrajectory.cpp /^ OutputDCDTrajectory::~OutputDCDTrajectory(){$/;" f class:ProtoMol::OutputDCDTrajectory ~OutputDihedrals framework/frontend/OutputDihedrals.cpp /^ OutputDihedrals::~OutputDihedrals(){$/;" f class:ProtoMol::OutputDihedrals ~OutputFactoryDetails framework/frontend/OutputFactoryDetails.cpp /^ OutputFactoryDetails::~OutputFactoryDetails(){$/;" f class:ProtoMol::OutputFactoryDetails ~OutputFile framework/frontend/OutputFile.cpp /^ OutputFile::~OutputFile(){$/;" f class:ProtoMol::OutputFile ~OutputREMExchangeRate framework/frontend/OutputREMExchangeRate.cpp /^ OutputREMExchangeRate::~OutputREMExchangeRate() {}$/;" f class:ProtoMol::OutputREMExchangeRate ~OutputREMHistoryFile framework/frontend/OutputREMHistory.cpp /^ OutputREMHistoryFile::~OutputREMHistoryFile() {}$/;" f class:ProtoMol::OutputREMHistoryFile ~OutputState framework/frontend/OutputState.cpp /^ OutputState::~OutputState(){$/;" f class:ProtoMol::OutputState ~OutputTemperatures framework/frontend/OutputTemperatures.cpp /^ OutputTemperatures::~OutputTemperatures(){}$/;" f class:ProtoMol::OutputTemperatures ~OutputXYZBinTrajectoryPos framework/frontend/OutputXYZBinTrajectoryPos.cpp /^ OutputXYZBinTrajectoryPos::~OutputXYZBinTrajectoryPos(){$/;" f class:ProtoMol::OutputXYZBinTrajectoryPos ~OutputXYZBinTrajectoryVel framework/frontend/OutputXYZBinTrajectoryVel.cpp /^ OutputXYZBinTrajectoryVel::~OutputXYZBinTrajectoryVel(){$/;" f class:ProtoMol::OutputXYZBinTrajectoryVel ~OutputXYZTrajectoryForce framework/frontend/OutputXYZTrajectoryForce.cpp /^ OutputXYZTrajectoryForce::~OutputXYZTrajectoryForce(){$/;" f class:ProtoMol::OutputXYZTrajectoryForce ~OutputXYZTrajectoryPos framework/frontend/OutputXYZTrajectoryPos.cpp /^ OutputXYZTrajectoryPos::~OutputXYZTrajectoryPos(){$/;" f class:ProtoMol::OutputXYZTrajectoryPos ~OutputXYZTrajectoryVel framework/frontend/OutputXYZTrajectoryVel.cpp /^ OutputXYZTrajectoryVel::~OutputXYZTrajectoryVel(){$/;" f class:ProtoMol::OutputXYZTrajectoryVel ~PARReader framework/io/PARReader.cpp /^ PARReader::~PARReader(){$/;" f class:ProtoMol::PARReader ~PDBReader framework/io/PDBReader.cpp /^ PDBReader::~PDBReader(){$/;" f class:ProtoMol::PDBReader ~PGM framework/base/PGM.cpp /^ PGM::~PGM(){delete [] p;}$/;" f class:ProtoMol::PGM ~PGMReader framework/io/PGMReader.cpp /^ PGMReader::~PGMReader(){$/;" f class:ProtoMol::PGMReader ~PLeapfrogIntegrator framework/integrators/PLeapfrogIntegrator.cpp /^ PLeapfrogIntegrator::~PLeapfrogIntegrator() {$/;" f class:ProtoMol::PLeapfrogIntegrator ~PPM compilerTests/pngTest.cpp /^PPM::~PPM(){delete [] p;}$/;" f class:PPM ~PPM framework/base/PPM.cpp /^ PPM::~PPM(){delete [] p;}$/;" f class:ProtoMol::PPM ~PPMReader framework/io/PPMReader.cpp /^ PPMReader::~PPMReader(){$/;" f class:ProtoMol::PPMReader ~PSFReader framework/io/PSFReader.cpp /^ PSFReader::~PSFReader(){$/;" f class:ProtoMol::PSFReader ~PSFWriter framework/io/PSFWriter.cpp /^ PSFWriter::~PSFWriter(){}$/;" f class:ProtoMol::PSFWriter ~Parallel framework/parallel/Parallel-FD.cpp /^ Parallel::~Parallel(){$/;" f class:ProtoMol::Parallel ~Parallel framework/parallel/Parallel.cpp /^ Parallel::~Parallel(){$/;" f class:ProtoMol::Parallel ~ParallelEnum framework/parallel/ParallelType.h /^ virtual ~ParallelEnum(){}$/;" f class:ProtoMol::ParallelEnum ~PaulTrapExtendedForceBase framework/forces/PaulTrapExtendedForceBase.h /^ virtual ~PaulTrapExtendedForceBase(){}$/;" f class:ProtoMol::PaulTrapExtendedForceBase ~PlaceHolder framework/base/Value.h /^ virtual ~PlaceHolder(){}$/;" f class:ProtoMol::Value::PlaceHolder ~Proxy framework/base/Proxy.h /^ virtual ~Proxy(){}$/;" f class:ProtoMol::Proxy ~REMConfigurationReader framework/io/REMConfigurationReader.cpp /^ REMConfigurationReader::~REMConfigurationReader(){$/;" f class:ProtoMol::REMConfigurationReader ~Reader framework/io/Reader.cpp /^ Reader::~Reader(){}$/;" f class:ProtoMol::Reader ~ReducedHessAngle framework/base/ReducedHessAngle.h /^ ~ReducedHessAngle(){}$/;" f class:ProtoMol::ReducedHessAngle ~SemiGenericTopology framework/topology/SemiGenericTopology.h /^ virtual ~SemiGenericTopology(){};$/;" f class:ProtoMol::SemiGenericTopology ~ShadowHMCIntegrator framework/integrators/ShadowHMCIntegrator.cpp /^ ShadowHMCIntegrator::~ShadowHMCIntegrator() {}$/;" f class:ProtoMol::ShadowHMCIntegrator ~Stack framework/base/Stack.h /^ Stack::~Stack() {$/;" f class:ProtoMol::Stack ~SystemForce framework/forces/SystemForce.h /^ virtual ~SystemForce(){}$/;" f class:ProtoMol::SystemForce ~SystemTimeForce framework/forces/SystemTimeForce.h /^ virtual ~SystemTimeForce(){};$/;" f class:ProtoMol::SystemTimeForce ~TempFileReader framework/io/TempFileReader.h /^ virtual ~TempFileReader() {}$/;" f class:ProtoMol::TempFileReader ~TimeForce framework/forces/TimeForce.cpp /^ TimeForce::~TimeForce(){$/;" f class:ProtoMol::TimeForce ~Topology framework/topology/Topology.h /^ virtual ~Topology(){};$/;" f class:ProtoMol::Topology ~TopologyFactoryDetails framework/frontend/TopologyFactoryDetails.cpp /^ TopologyFactoryDetails::~TopologyFactoryDetails(){$/;" f class:ProtoMol::TopologyFactoryDetails ~UniversalSwitchingFunctionBase framework/topology/UniversalSwitchingFunctionBase.h /^ virtual ~UniversalSwitchingFunctionBase(){}$/;" f class:ProtoMol::UniversalSwitchingFunctionBase ~Value framework/base/Value.cpp /^ Value::~Value(){if(myValue != NULL) delete myValue;myValue=NULL;}$/;" f class:ProtoMol::Value ~ValueEnum framework/base/ValueType.h /^ virtual ~ValueEnum(){}$/;" f class:ProtoMol::ValueEnum ~WrapperMetaForce framework/forces/WrapperMetaForce.cpp /^ WrapperMetaForce::~WrapperMetaForce(){$/;" f class:ProtoMol::WrapperMetaForce ~Writer framework/io/Writer.cpp /^ Writer::~Writer(){}$/;" f class:ProtoMol::Writer ~XYZBinReader framework/io/XYZBinReader.cpp /^ XYZBinReader::~XYZBinReader(){$/;" f class:ProtoMol::XYZBinReader ~XYZReader framework/io/XYZReader.cpp /^ XYZReader::~XYZReader(){$/;" f class:ProtoMol::XYZReader ~XYZTrajectoryReader framework/io/XYZTrajectoryReader.cpp /^ XYZTrajectoryReader::~XYZTrajectoryReader(){$/;" f class:ProtoMol::XYZTrajectoryReader ~XYZTrajectoryWriter framework/io/XYZTrajectoryWriter.cpp /^ XYZTrajectoryWriter::~XYZTrajectoryWriter(){}$/;" f class:ProtoMol::XYZTrajectoryWriter