src/atom_buildup.C,127 AtomBuildup::AtomBuildup(3,27 AtomBuildup::AtomBuildup(10,159 AtomBuildup::~AtomBuildup(16,237 int AtomBuildup::run(34,827 src/atom_constraint.C,446 AtomConstraint::AtomConstraint(3,30 AtomConstraint::AtomConstraint(9,123 double AtomConstraint::computeStress(20,466 double AtomConstraint::computeStress(42,1258 jVector AtomConstraint::dStress(55,1683 int AtomConstraint::Output(75,2294 int AtomConstraint::Read(81,2371 int AtomConstraint::OutputBinary(87,2440 void AtomConstraint::notifyValid(93,2523 int AtomConstraint::ReadBinary(106,2830 void AtomConstraint::notifyRemove(113,2906 src/atom_registry.C,0 src/bin_envelope_constraint.C,520 BinEnvelopeConstraint::BinEnvelopeConstraint(5,138 BinEnvelopeConstraint::~BinEnvelopeConstraint(16,396 void BinEnvelopeConstraint::PreSetup(21,450 void BinEnvelopeConstraint::PostSetup(32,778 BinEnvelopeConstraint::computeStress(40,836 BinEnvelopeConstraint::computeStress(76,1898 jVector BinEnvelopeConstraint::dStress(84,2065 int BinEnvelopeConstraint::Output(124,3159 int BinEnvelopeConstraint::Read(130,3232 int BinEnvelopeConstraint::OutputBinary(136,3356 int BinEnvelopeConstraint::ReadBinary(142,3478 src/constraint.C,743 Constraint::Constraint(4,90 Constraint::~Constraint(16,409 double Constraint::stress(21,492 double Constraint::stress(105,2201 void Constraint::setManager(113,2394 const Molecule& Constraint::getMolecule(131,2813 const ConstraintManager& Constraint::getManager(134,2892 bool Constraint::isOff(138,2966 void Constraint::switchOff(141,3016 void Constraint::notifyValid(239,5435 void Constraint::notifyOff(253,5880 void Constraint::notifyRemove(290,6884 bool Constraint::isValid(302,7131 bool Constraint::assertValidity(305,7185 DynString Constraint::Label(416,10251 void Constraint::addAtomSupport(420,10322 void Constraint::addConstraintSupport(433,10722 int Constraint::Input(446,11125 int Constraint::InputBinary(481,12231 src/constraint_manager.C,1572 ConstraintManager::ConstraintManager(4,66 ConstraintManager::~ConstraintManager(24,522 ConstraintManager::TranslateModel(51,1259 ConstraintManager::RandomPerturb(71,1612 void ConstraintManager::setPosition(87,1972 void ConstraintManager::setMolecule(115,2704 ConstraintManager::molecule_center(138,3141 jVector ConstraintManager::getStressList(152,3359 double ConstraintManager::stress(165,3654 double ConstraintManager::stress(170,3738 double ConstraintManager::stress(175,3873 jVector ConstraintManager::dStress(186,4072 jVector ConstraintManager::dStress(205,4655 int ConstraintManager::Number(212,4767 ostream& ConstraintManager::PrintGraph(220,4896 int ConstraintManager::add(226,5005 void ConstraintManager::remove(263,6021 DLList ConstraintManager::getParents(277,6473 DLList ConstraintManager::getAssocAtoms(299,6985 ConstraintManager::TurnAtomsOff(365,8810 ConstraintManager::TurnAtomOn(377,9049 ConstraintManager::TurnConstraintOn(392,9402 ConstraintManager::clearAllConstraints(424,10071 void ConstraintManager::clearConstraints(430,10223 ConstraintManager::getConstraint(447,10604 bool ConstraintManager::isDynamic(460,10911 bool ConstraintManager::makeStatic(463,10974 bool ConstraintManager::makeDynamic(479,11173 ConstraintManager::AbsDistResiduals(499,11478 void ConstraintManager::InvalidateEnvelope(528,12100 void ConstraintManager::TurnEnvelopeOn(531,12193 ConstraintManager::constraintON 541,12356 int ConstraintManager::numAtomsON(545,12536 void ConstraintManager::InvalidateAtoms(554,12691 src/constraint_registry.C,145 int ConstraintRegistry::getIntType(6,80 Constraint * ConstraintRegistry::getConstraint(24,627 int ConstraintRegistry::readConstraints(66,1914 src/cycle_all.C,105 CycleAll::CycleAll(5,76 CycleAll::CycleAll(9,149 CycleAll::~CycleAll(22,496 int CycleAll::run(29,696 src/cycl-test-jd.C,13 main(12,212 src/dens-trans.C,15 int main(4,42 src/distance_constraint.C,502 DistanceConstraint::DistanceConstraint(3,34 DistanceConstraint::DistanceConstraint(13,308 void DistanceConstraint::PreSetup(25,667 double DistanceConstraint::computeStress(36,991 double DistanceConstraint::computeStress(56,1954 jVector DistanceConstraint::dStress(171,5185 double DistanceConstraint::computeAbsRes(227,6744 int DistanceConstraint::Output(235,6932 int DistanceConstraint::Read(242,7085 int DistanceConstraint::OutputBinary(250,7294 int DistanceConstraint::ReadBinary(256,7409 src/dist.C,15 int main(5,45 src/env_diff.C,15 int main(6,47 src/envelope.C,971 Envelope::Envelope(3,23 Envelope::Envelope(20,271 Envelope::~Envelope(52,825 void Envelope::Env_Setup1(63,964 void Envelope::Env_Setup2(70,1206 void Envelope::Center(111,1930 Envelope::gradient(135,2500 Envelope::gradient(150,2864 Envelope::gradient(164,3310 Envelope::operator(178,3552 Envelope::operator(190,3884 Envelope::operator(203,4256 int Envelope::Output(215,4496 int Envelope::Build(248,5149 void Envelope::DiffReport(352,7693 int Envelope::Read(418,9644 int Envelope::OutputBinary(424,9788 int Envelope::ReadBinary(431,9918 Envelope::CalcGradient(440,10064 Envelope::Get_Eigenvectors(502,11236 Envelope::Calc_Eigenvectors(510,11359 Envelope::Upsize 569,12864 Envelope::Blur 714,16638 Envelope::NormalizeMax(813,19109 Envelope::QueryDensity(849,19788 int Envelope::WriteVRML(859,20022 int Envelope::WriteVRMLgr(910,21267 int Envelope::WriteDensity(988,23427 int Envelope::WriteAvsTxt(1003,23679 int Envelope::ReadAvsTxt(1032,24475 src/envelope_constraint.C,897 EnvelopeConstraint::EnvelopeConstraint(4,86 EnvelopeConstraint::~EnvelopeConstraint(22,538 void EnvelopeConstraint::PreSetup(36,739 void EnvelopeConstraint::PostSetup(57,1222 void EnvelopeConstraint::AlignPrincComp(85,2025 void EnvelopeConstraint::MoveModelbyGrad(134,2945 void EnvelopeConstraint::AlignModeltoCOM(169,4060 EnvelopeConstraint::computeStress(212,5048 EnvelopeConstraint::computeStress(227,5211 jVector EnvelopeConstraint::dStress(237,5318 double EnvelopeConstraint::getDensity(246,5468 jVector EnvelopeConstraint::getGradient(276,6315 EnvelopeConstraint::FindEnvelopeEigenvectors(326,7584 EnvelopeConstraint::FindModelTranslationToCOM(333,7733 EnvelopeConstraint::FindModelRotation(354,8266 int EnvelopeConstraint::Output(441,10176 int EnvelopeConstraint::Read(451,10354 int EnvelopeConstraint::OutputBinary(460,10489 int EnvelopeConstraint::ReadBinary(466,10608 src/Env-test.C,15 int main 4,44 src/err_eval.C,71 int main(17,299 void print_usage(310,7750 void print_help(321,8054 src/globals.C,2006 double gwNumerics::ls_succ_tolerance 6,124 double gwNumerics::ls_dist_tolerance 7,234 double gwNumerics::ls_deriv_tolerance 8,336 double gwNumerics::MaxAbsDistRes 10,448 double gwNumerics::AveAbsDistRes 11,493 double gwNumerics::MinDistVariance 12,531 bool gwNumerics::UseOnlyMoved 19,995 bool gwNumerics::LocalPerturb 20,1033 int gwNumerics::MaxNCuts 21,1071 int gwNumerics::NumLP 22,1107 int gwNumerics::NumNotLP 23,1142 int gwRelaxAtom::max_iterations 32,1401 bool AnimFrame::Enabled 37,1542 DynString SatisfyMolecule::BaseFN 43,1681 DynString SatisfyMolecule::AnimFN 44,1725 DynString SatisfyMolecule::FinalFN 45,1769 int jdIterator::MaxIterations 51,1919 int AtomBuildup::MaxIterations 56,2060 int AtomBuildup::MaxFinalIterations 57,2097 double jdOcc_Count::cube_width 62,2245 int StopEval::LookBack 68,2387 bool StopEval::Enable 69,2426 bool StopEval::SolveOnly 70,2456 bool StopEval::VerboseOn 71,2490 bool StopEval::Quiet 72,2529 bool StopEval::Rtp 73,2564 double Molecule::grid_delta 78,2700 double Molecule::grid_max_radius 79,2777 DynString Constraint::Identifier 88,3058 DynString AtomConstraint::Identifier 94,3210 DynString DistanceConstraint::Identifier 100,3408 DynString EnvelopeConstraint::Identifier 105,3566 int EnvelopeConstraint::num_evelopes 106,3622 double EnvelopeConstraint::density_threshold 107,3664 double EnvelopeConstraint::rotation_threshold 108,3762 double EnvelopeConstraint::translation_threshold 109,3828 int EnvelopeConstraint::blur_kernelSize 110,3896 DynString BinEnvelopeConstraint::Identifier 112,3993 DynString PositionConstraint::Identifier 118,4169 const char * AtomRegistry::names 139,4806 const double AtomRegistry::radius[144,4909 const double AtomRegistry::covalent_distance[148,4998 const char * ResidueRegistry::names 166,5809 const char * ResidueRegistry::code_1 174,6135 const char * ResidueRegistry::code_3 181,6323 const int ResidueRegistry::numAtoms 188,6575 const int ResidueRegistry::numBonds 213,7835 src/grape.C,73 int main(17,299 void print_usage(471,11937 void print_help(484,12405 src/grid-tst.C,70 jVector t2;15,215 main(17,228 void info 49,828 void info2 71,1426 src/gw_numerics.C,389 gwNumerics::gwNumerics(3,26 gwNumerics::~gwNumerics(7,58 void gwNumerics::SolveVector(12,92 gwNumerics::SetHCPosition287,2534 void gwNumerics::addVDWSegments216,6586 void gwNumerics::addLPERTSegments(308,9465 double gwNumerics::LinearThreshold(466,15357 bool gwNumerics::CubicLineSearch(482,15971 Segment gwNumerics::LineIntersectSphere(551,17925 gwNumerics::bfgs_step(921,29452 src/gw_relax_atom.C,127 gwRelaxAtom::gwRelaxAtom(4,53 gwRelaxAtom::gwRelaxAtom(10,166 gwRelaxAtom::~gwRelaxAtom(18,383 int gwRelaxAtom::run(23,480 src/jd_anim_frame.C,186 int AnimFrame::FrameNum 3,28 AnimFrame::AnimFrame(5,76 AnimFrame::AnimFrame(14,230 AnimFrame::~AnimFrame(26,484 void AnimFrame::Set_Output_Stream(37,672 int AnimFrame::run(68,1356 src/jd_err_eval.C,89 jdErr_Eval::jdErr_Eval(3,26 jdErr_Eval::~jdErr_Eval(12,242 int jdErr_Eval::run(16,277 src/jd_iterator.C,120 jdIterator::jdIterator(3,26 jdIterator::jdIterator(10,154 jdIterator::~jdIterator(16,230 int jdIterator::run(34,810 src/jd_occ_count.C,93 jdOcc_Count::jdOcc_Count(3,27 jdOcc_Count::~jdOcc_Count(8,104 int jdOcc_Count::run(12,142 src/jd_rand_eval.C,94 jdRand_Eval::jdRand_Eval(3,27 jdRand_Eval::~jdRand_Eval(12,218 int jdRand_Eval::run(16,255 src/jd_relax_subset.C,127 RelaxSubset::RelaxSubset(3,30 RelaxSubset::RelaxSubset(11,214 RelaxSubset::~RelaxSubset(30,743 int RelaxSubset::run(40,998 src/jd_stop_eval.C,477 int StopEval::NumCalls=27,771 int StopEval::NumLprAdj 28,798 int StopEval::NumLprLim 29,827 int StopEval::LastLprAdj 30,857 int StopEval::BestIter 31,887 DLList StopEval::TotalStressList;33,916 StopEval::StopEval(35,961 StopEval::StopEval(43,1128 StopEval::~StopEval(55,1343 int StopEval::check_low_error(62,1443 int StopEval::check_stress_max_tot(77,1826 void StopEval::cycle_header 101,2352 int StopEval::run(109,2624 void StopEval::writebest(379,11651 src/line-test.C,11 main(6,73 src/molecule.C,823 Molecule::Molecule(3,23 Molecule::Molecule(6,82 Molecule::Molecule(18,335 Molecule::Molecule(27,495 Molecule::~Molecule(33,573 void Molecule::Allocate(36,616 void Molecule::Deallocate(51,874 void Molecule::Reallocate(62,1008 void Molecule::Copy(77,1327 void Molecule::Bounds(92,1648 const Molecule& Molecule::operator 138,2482 jVector Molecule::getCOM(141,2573 double Molecule::MSD(154,2731 int Molecule::Output(211,4080 int Molecule::Input(218,4229 int Molecule::OutputBinary(236,4477 int Molecule::InputBinary(246,4708 istream& Molecule::DynRead(259,4952 int Molecule::setRandom(275,5240 int Molecule::readFasta(302,5884 int Molecule::readXmol(373,7619 void Molecule::writeXmol(413,8647 void Molecule::writeXmolData(420,8836 void Molecule::writeXmolData(432,9223 void Molecule::skipXmol(444,9545 src/molio.C,11 main(4,24 src/mol-test-jd.C,13 main(10,190 src/mol-tst.C,12 main(9,163 src/ocount.C,71 int main(17,346 void print_usage(188,4545 void print_help(197,4809 src/position_constraint.C,452 PositionConstraint::PositionConstraint(3,34 PositionConstraint::PositionConstraint(20,581 void PositionConstraint::PreSetup(39,1038 double PositionConstraint::computeStress(52,1442 double PositionConstraint::computeStress(70,1924 jVector PositionConstraint::dStress(95,2624 int PositionConstraint::Output(137,3722 int PositionConstraint::Read(144,3899 int PositionConstraint::OutputBinary(151,4042 int PositionConstraint::ReadBinary(157,4157 src/process.C,301 Process::Process(4,56 Process::~Process(18,307 void Process::assertOrder(29,455 void Process::runChildrenRepeatFirst(98,2260 void Process::runChildren(117,2522 void Process::cleanQueue(136,2901 int Process::runChild(143,3008 int Process::runNextChild(154,3166 void Process::addChild(160,3252 src/process-tst.C,301 class RunSum RunSum3,22 RunSum(RunSum::RunSum6,68 int run(RunSum::run7,100 int Sum(RunSum::Sum16,264 class AddIntegers AddIntegers21,330 AddIntegers(AddIntegers::AddIntegers24,381 int run(AddIntegers::run33,605 private:AddIntegers::private42,792 main(45,811 src/rand_eval.C,71 int main(17,299 void print_usage(246,5887 void print_help(260,6324 src/residue.C,159 void Residue::AddBond(5,45 void Residue::AddAtom(13,287 int Residue::Setup(31,736 const Residue& Residue::operator 396,15336 void Residue::Copy(399,15424 src/seg-test-jd2.C,11 main(4,47 src/seg-test-jd.C,11 main(4,47 include/atom_buildup.h,72 #define __ATOM_BUILDUP_H__15,307 class AtomBuildup AtomBuildup28,576 include/atom_constraint.h,200 #define __ATOM_CONSTRAINT_H__14,361 class AtomConstraint AtomConstraint21,462 ~AtomConstraint(AtomConstraint::~AtomConstraint29,640 double computeStress(AtomConstraint::computeStress31,664 include/atom.h,1027 #define __ATOM_H_20,600 #define UNINITIALIZED_ATOM_ID 28,730 #define MAX_NUM_BONDS 29,763 class AtomAtom33,817 bool Bonded Atom::Bonded41,919 inline Atom::Atom(114,2275 inline const Atom& Atom::operator 127,2506 inline void Atom::AddBond(141,2775 inline bool Atom::Bonded 145,2852 inline const int& Atom::ID(149,2938 inline int& Atom::ID(151,2988 inline const DynString& Atom::Label(154,3027 inline DynString& Atom::Label(156,3089 inline const DynString& Atom::Type(159,3140 inline DynString& Atom::Type(161,3200 inline const double& Atom::VDW(164,3249 inline double& Atom::VDW(166,3312 inline const int& Atom::ResNum(169,3364 inline int& Atom::ResNum(171,3431 inline const double& Atom::cov_dist(174,3487 inline double& Atom::cov_dist(176,3559 inline const bool& Atom::Moved(179,3620 inline bool& Atom::Moved(181,3677 inline int Atom::Compare(194,3969 inline int Atom::Output(197,4038 inline int Atom::Input(201,4220 inline int Atom::OutputBinary(204,4326 inline int Atom::InputBinary(208,4443 include/atom_registry.h,153 #define __ATOM_REGISTRY__11,199 #define num_known_atom_species 20,336 class AtomRegistryAtomRegistry37,657 inline int AtomRegistry::SetType(54,1070 include/bin_envelope_constraint.h,161 #define __BIN_ENVELOPE_CONSTRAINT_H__14,401 class BinEnvelopeConstraint BinEnvelopeConstraint23,582 jVector dStress(BinEnvelopeConstraint::dStress36,1037 include/constraint.h,703 #define __CONSTRAINT_H__13,299 #define UNINITIALIZED_CONSTRAINT_ID 27,558 class ConstraintConstraint31,625 int ID(Constraint::ID41,840 DynString Type(Constraint::Type44,907 int IntType(Constraint::IntType47,980 double stress(Constraint::stress72,2108 const IntVec& constraintSupport(Constraint::constraintSupport90,3067 int arity(Constraint::arity93,3222 virtual int Output(Constraint::Output99,3381 virtual int OutputBinary(Constraint::OutputBinary112,3966 const Molecule& getMolecule(Constraint::getMolecule122,4197 DynString Label(Constraint::Label193,6699 virtual void PostSetup(Constraint::PostSetup284,10110 #define __CONSTRAINT_DEFINED__325,11310 include/constraint_manager.h,1251 #define __CONSTRAINT_MANAGER_H__16,545 class ConstraintManagerConstraintManager45,1077 int Number(ConstraintManager::Number55,1253 const Molecule& getMolecule(ConstraintManager::getMolecule72,1467 void setAtom(ConstraintManager::setAtom117,2872 void TurnAtomsOff(ConstraintManager::TurnAtomsOff121,3016 virtual double CombineStress(ConstraintManager::CombineStress142,3464 double stress(ConstraintManager::stress168,4236 bool isDynamic(isDynamic230,6224 inline const Molecule& ConstraintManager::getMolecule(274,7361 inline void ConstraintManager::readNewMoleculeXmol(276,7524 inline const Atom& ConstraintManager::getAtom(277,7626 inline const jVector& ConstraintManager::getPosition(278,7702 inline double ConstraintManager::getRadius(279,7785 inline const Atom& ConstraintManager::operator 280,7862 inline const jVector& ConstraintManager::operator 281,7949 inline DLList ConstraintManager::approx_neighbor_i(282,8043 inline DLList ConstraintManager::neighbor_i(284,8183 inline int ConstraintManager::numAtoms(286,8309 inline void ConstraintManager::resetMoved(287,8380 inline void ConstraintManager::registerEnvelope(289,8488 inline EnvelopeConstraint* ConstraintManager::getEnvelope(291,8617 include/constraint_registry.h,91 #define __CONSTRAINT_REGISTRY__21,749 class ConstraintRegistryConstraintRegistry35,1070 include/cycle_all.h,97 #define __CYCLE_ALL_H__16,350 class CycleAll CycleAll21,438 private:CycleAll::private32,599 include/distance_constraint.h,219 #define __DISTANCE_CONSTRAINT_H__13,316 class DistanceConstraint DistanceConstraint20,444 ~DistanceConstraint(DistanceConstraint::~DistanceConstraint36,1001 jVector dStress(DistanceConstraint::dStress38,1029 include/envelope_constraint.h,207 #define __ENVELOPE_CONSTRAINT_H__15,487 class EnvelopeConstraint EnvelopeConstraint29,720 jVector dStress(EnvelopeConstraint::dStress43,940 inline int EnvelopeConstraint::WriteVRML_OrigData(162,4165 include/envelope.h,233 #define __ENVELOPE_H__13,291 #define MAX_ENV_DEN 15,315 #define MIN_ENV_DEN 16,338 #define ENV_DEN_RANGE 17,361 #define DEFAULT_CUBE_WIDTH 29,576 class EnvelopeEnvelope32,609 const double operator(Envelope::operator46,825 include/error_handler.h,113 #define __ERROR_HANDLER_H__2,28 #define DIE(DIE7,97 #define WARN(WARN14,257 #define WARN_IF(WARN_IF19,380 include/globals.h,0 include/gw_numerics.h,196 #define __GW_NUMERICS_H__17,496 class gwNumericsgwNumerics33,826 static void gwNumerics::reset_LP_Count(gwNumerics::gwNumerics::reset_LP_Count191,6313 private:gwNumerics::private236,7584 include/gw_relax_atom.h,119 #define __GW_RELAX_ATOM_H__17,620 class gwRelaxAtom gwRelaxAtom25,766 int getIndex(gwRelaxAtom::getIndex45,1155 include/jd_anim_frame.h,65 #define __ANIMFRAME_H__15,280 class AnimFrame AnimFrame25,452 include/jd_err_eval.h,69 #define __JD_ERR_EVAL_H__15,263 class jdErr_Eval jdErr_Eval25,447 include/jd_iterator.h,69 #define __JD_ITERATOR_H__15,303 class jdIterator jdIterator28,571 include/jd_occ_count.h,109 #define __JD_OCC_COUNT_H__15,266 class jdOcc_Count jdOcc_Count28,540 private:jdOcc_Count::private40,759 include/jd_rand_eval.h,72 #define __JD_RAND_EVAL_H__16,366 class jdRand_Eval jdRand_Eval26,551 include/jd_relax_subset.h,125 #define __RELAX_SUBSET_H__14,319 class RelaxSubset RelaxSubset21,462 void setFraction(RelaxSubset::setFraction40,1061 include/jd_stop_eval.h,62 #define __STOPEVAL_H__16,321 class StopEval StopEval28,544 include/molecule.h,727 #define __MOLECULE_H__13,319 class MoleculeMolecule32,697 int Number(Molecule::Number49,1026 inline int Molecule::NumRes(199,5227 inline const Atom& Molecule::getAtom(202,5278 inline const Grid& Molecule::getGrid(205,5346 inline void Molecule::setAtom(208,5412 inline const Atom& Molecule::operator 211,5479 { return A[212,5534 inline Atom& Molecule::operator 214,5552 inline const jVector& Molecule::operator(217,5613 inline const jVector& Molecule::getPosition(220,5706 inline double Molecule::VDW(223,5799 inline void Molecule::setPosition(226,5865 inline DLList Molecule::approx_neighbor_i(229,5966 inline DLList Molecule::neighbor_i(232,6105 inline const IntVec& Molecule::GetBonds 235,6230 include/position_constraint.h,217 #define __POSITION_CONSTRAINT_H__14,363 class PositionConstraint PositionConstraint20,466 ~PositionConstraint(PositionConstraint::~PositionConstraint34,877 jVector dStress(PositionConstraint::dStress36,905 include/process.h,320 #define __PROCESS_H__15,453 class ProcessProcess24,610 virtual void reset(Process::reset36,859 int numChildren(Process::numChildren82,2256 inline int Process::numChildren(150,3768 inline int Process::numQueued(153,3826 inline double Process::getPriority(156,3888 inline void Process::setPriority(159,3953 include/residue.h,634 #define __RESIDUE_H_12,246 #define UNINITIALIZED_RES_ID 23,425 class ResidueResidue27,484 const int& ID(Residue::ID42,704 inline const IntVec& Residue::GetAtomList(136,2989 inline const int& Residue::ID(139,3061 inline int& Residue::ID(141,3114 inline const DynString& Residue::Type(144,3156 inline DynString& Residue::Type(146,3219 inline const DynString& Residue::Label(149,3271 inline DynString& Residue::Label(151,3336 inline int Residue::Compare(154,3390 inline int Residue::Output(157,3465 inline int Residue::Input(161,3588 inline int Residue::OutputBinary(164,3654 inline int Residue::InputBinary(168,3774 include/residue_registry.h,229 #define __RESIDUE_REGISTRY__8,187 #define num_known_residue_species 17,321 class ResidueRegistryResidueRegistry20,360 inline int ResidueRegistry::CheckType_code_1(91,2689 inline int ResidueRegistry::SetType_code_1(100,2901 include/satisfy_molecule.h,398 #define __SATISFY_MOLECULE_H__18,686 class SatisfyMolecule SatisfyMolecule23,772 virtual ~SatisfyMolecule(SatisfyMolecule::~SatisfyMolecule26,838 void setMolecule(SatisfyMolecule::setMolecule33,1070 const Molecule& getMolecule(SatisfyMolecule::getMolecule35,1138 SatisfyMolecule(SatisfyMolecule::SatisfyMolecule47,1467 SatisfyMolecule(SatisfyMolecule::SatisfyMolecule48,1522 include/top_process.h,0 include/segments.inc,746 #define _SEGMENTS_H_11,450 class SegmentSegment19,544 Segment(Segment::Segment23,569 Segment(Segment::Segment25,627 ~Segment(Segment::~Segment35,764 class Segments Segments86,1962 Segments(Segments::Segments93,2023 ~Segments(Segments::~Segments94,2054 double GetNum Segments::GetNum96,2097 Segment GetSeg Segments::GetSeg100,2149 void Add(Segments::Add104,2203 void Add(Segments::Add109,2327 void QSortReduce(Segments::QSortReduce113,2410 Segment QSortReduceViol(Segments::QSortReduceViol142,3168 Segment Pop(Segments::Pop191,4550 int Number(Segments::Number194,4606 void Clear(Segments::Clear197,4652 bool Overlap Segments::Overlap202,4695 Segment Join(Segments::Join211,5043 src/aux/abitset.C,1250 uint ABitSet::default_size 9,125 static const char all_set[10,159 b2c0(13,229 b2c1(18,271 b2i(23,317 ABitSet::ABitSet(28,354 ABitSet::ABitSet(35,440 ABitSet::ABitSet(44,544 ABitSet::~ABitSet(52,675 ABitSet::operator=60,752 ABitSet::Resize(80,994 ABitSet::DefaultSize(99,1217 ABitSet::DefaultSize(109,1329 ABitSet::operator[115,1384 if 117,1421 ABitSet::Clear(133,1572 ABitSet::Invert(142,1658 ABitSet::Set(151,1744 ABitSet::Clear(163,1875 ABitSet::Invert(175,2009 ABitSet::IsAllSet(187,2145 ABitSet::IsAllClear(198,2337 ABitSet::SetAll(209,2518 ABitSet::ClearAll(215,2576 ABitSet::InvertAll(221,2635 ABitSet::Count(229,2729 ABitSet res(*this)284,3603 ABitSet res(*this)291,3704 ABitSet res(*this)298,3805 ABitSet res(*this)305,3906 ABitSet::Increment(310,3955 ABitSet::Decrement(330,4240 ABitSet::Compare(350,4525 operator << (ostream& os,367,4757 ABitSet::Iterator::Iterator(376,4906 ABitSet::Iterator::~Iterator(383,4993 ABitSet::Iterator::Reset(388,5034 ABitSet::Iterator::operator 400,5162 --i;408,5256 return i < abs.num;410,5276 ++i;416,5340 return i < abs.num;418,5360 ABitSet::Iterator::find_next(422,5389 ABitSet::Iterator::find_prev(429,5473 OutputBinary(436,5561 InputBinary(448,5738 src/aux/amat-tst.C,13 main(14,265 src/aux/dynstring.C,1634 const int DynString::BlockSize 11,199 const int DynString::BlockSize 13,282 char * DynString::Bad 16,341 DynString DynString::Empty 18,399 int DynString::Delimiter[20,433 void SetDSDelim(34,1010 void AddDSDelim(45,1238 void RemDSDelim(47,1312 DynString GetDSDelim(51,1388 int DynString::DestResize(69,1692 int DynString::NonDestResize(81,1984 const DynString& DynString::Cat(97,2371 const DynString& DynString::Cat(106,2562 int DynString::Set(117,2839 int DynString::Set(136,3189 int DynString::Set(154,3545 int DynString::Chop(175,3863 DynString::DynString(186,4058 DynString::DynString(192,4155 DynString::DynString(198,4259 DynString::DynString(204,4354 DynString::DynString(213,4513 DynString::DynString(222,4682 DynString::~DynString(231,4854 DynString DynString::Sub(236,4917 int DynString::IsSub(266,5424 int DynString::Replace(281,5742 DynString IntToDS(351,7222 const DynString& DynString::operator 362,7410 const DynString& DynString::operator 369,7548 const DynString& DynString::operator 372,7668 const DynString& DynString::operator 383,7921 const char& DynString::operator 392,8100 if(394,8153 return innards[396,8237 char& DynString::operator 399,8265 char* DynString::GetDataCopy(412,8514 int DynString::InputBinary(421,8673 int DynString::OutputBinary(443,9081 int DynString::GetChar(451,9219 int DynString::Read(460,9356 int DynString::Split(496,10068 int DynString::Output(733,15340 int DynString::Input(742,15481 DynString Reproduce(745,15539 const DynString& DynString::Pad(755,15751 istream& DynString::ReadLine(761,15872 void DynString::EatLine(770,16072 src/aux/graph-tst.C,17 int main(23,410 src/aux/grid.C,830 Grid::Grid(9,62 Grid::Grid(16,158 Grid::Grid(25,350 Grid::Grid(34,507 Grid::~Grid(56,976 void Grid::Initialize(61,1006 void Grid::setupNeighborLists(125,3045 void Grid::ReGrid 158,3730 void Grid::ReSize(172,4054 bool Grid::GNoverlap(189,4360 bool Grid::JVoverlap(201,4647 void Grid::setPosition 208,4782 DLList Grid::neighbor_d(246,6008 DLList Grid::neighbor_d(298,8013 DLList Grid::neighbor_p(342,9860 DLList Grid::neighbor_p(394,12029 DLList Grid::approx_neighbor_p(438,14036 DLList Grid::approx_neighbor_p(491,16149 DLList Grid::neighbor_i(535,18102 DLList Grid::neighbor_i(588,20243 DLList Grid::approx_neighbor_i(633,22226 DLList Grid::approx_neighbor_i(683,24245 double Grid::min_neighbor_d(726,26102 void Grid::clear(728,26197 src/aux/intvec.C,213 const int IntVec::DefCreationLength 13,219 int IntVec::CreationLength 14,260 char IntVec::IODelimiter 15,308 int * i 19,377 if(!I || L<1 || !(i 20,394 return i;22,474 int IntVec::dynread(25,493 src/aux/jvector.C,1158 int jVector::CreationLength 15,263 char jVector::IODelimiter 16,305 jVector jVector::Zero;18,339 double * d 22,401 if(!V || L<1 || !(d 23,419 return d;26,556 double jVector::sum(29,571 double jVector::sumsqr(38,702 double jVector::variance(47,841 double jVector::max(56,1021 int jVector::argmax(64,1158 double jVector::min(73,1317 int jVector::argmin(81,1454 double jVector::median(91,1616 double jVector::mean(100,1855 double jVector::nrm(103,1909 double jVector::mag(110,2038 jVector operator - (jVector x,117,2260 jVector operator + (jVector x,121,2459 double operator 124,2546 jVector operator % (jVector x,134,2807 const jVector& jVector::operator 138,2932 jVector operator 140,3033 jVector operator 141,3091 jVector operator / (jVector y,145,3276 jVector operator % (jVector x,149,3446 double JVAngle(152,3507 double euclid(155,3607 int jVector::Input(165,3874 int jVector::Output(176,4011 int jVector::dynread(186,4152 ostream& VBPrintLine(226,5074 ostream& VBPrintPoint(245,5648 ostream& VBPrintCircle(264,6116 int jVector::InputBinary(281,6588 int jVector::OutputBinary(304,6931 double Covariance(326,7215 src/aux/matrix.C,880 Matrix::Matrix(9,256 Matrix::Matrix(14,309 Matrix::Matrix(20,423 Matrix::~Matrix(28,589 Matrix &Matrix::operator=33,641 double &Matrix::operator(46,926 const double &Matrix::operator(53,1121 double &Matrix::operator(60,1328 const double &Matrix::operator(75,1603 void Matrix::setSize(89,1889 void Matrix::zero(97,2030 void Matrix::identity(104,2211 void Matrix::swapRows(116,2478 void Matrix::swapCols(121,2617 Matrix Matrix::subMatrix(135,3113 Matrix Matrix::transpose(151,3521 double Matrix::Sum(159,3728 double Matrix::SumAbsoluteValue(170,3907 Matrix Matrix::operator*182,4106 if 191,4375 return result;198,4638 if 202,4708 return result;209,4974 Matrix Matrix::operator*212,4994 void Matrix::findEigenVectors(230,5581 double Matrix::det(332,8525 double Matrix::tr(368,9351 ostream & Matrix::PrettyPrint(388,9690 Matrix operator*407,10264 src/aux/qs-tst.C,16 int main(8,101 src/aux/queue-tst.C,11 main(3,20 src/aux/randomgenerator.C,397 void RanBaseClass::Seed(11,193 RanBaseClass::RanBaseClass(107,2835 RanBaseClass::~RanBaseClass(113,2907 double RanBaseClass::GetReal(116,2943 RanDbl::RanDbl(130,3271 double RanDbl::Get(133,3355 double RanDbl::Get(136,3425 RanInt::RanInt(139,3537 int RanInt::Get(147,3704 int RanInt::Get(150,3795 char RanChar::Get(153,3922 char RanLetter::Get(159,4032 DynString RanWord::Get(168,4204 src/aux/stl-tst.C,80 struct eqstreqstr9,117 bool operator eqstr::operator11,134 main(18,254 src/aux/utils.C,67 static const char sccs_ident[3,20 const int bit_count_array[5,89 include/aux/abbrev.h,308 #define _ABBREV_H_9,170 typedef unsigned int uint;uint11,190 typedef short int sint;sint12,217 typedef long int lint;lint13,241 typedef unsigned short int usint;usint14,264 typedef unsigned long int ulint;ulint15,298 typedef unsigned char uchar;uchar16,331 typedef class ABitSet ABS;ABS17,360 include/aux/abitset.h,319 #define __ABITSET_H__DEF__2,27 class ABitSetABitSet18,305 bool IsAllSet(ABitSet::IsAllSet59,902 bool IsSet(ABitSet::IsSet66,1039 bool In(ABitSet::In73,1151 void Add(ABitSet::Add75,1202 void Remove(ABitSet::Remove77,1236 int Compare(ABitSet::Compare101,1812 int Count(ABitSet::Count104,1889 include/aux/ajiobin.h,663 #define __AJIOBIN_H__DEF__9,219 OutputBinary 114,2112 OutputBinary 120,2207 OutputBinary 126,2320 OutputBinary 132,2429 OutputBinary 138,2522 OutputBinary 144,2633 OutputBinary 150,2730 OutputBinary 156,2845 OutputBinary 162,2940 OutputBinary 168,3053 OutputBinary 176,3201 OutputBinary 182,3296 OutputBinary 188,3393 OutputBinary 194,3492 InputBinary 284,5268 InputBinary 289,5357 InputBinary 294,5464 InputBinary 299,5567 InputBinary 304,5654 InputBinary 309,5759 InputBinary 314,5850 InputBinary 319,5959 InputBinary 324,6048 InputBinary 329,6155 InputBinary 337,6279 InputBinary 342,6368 InputBinary 347,6459 InputBinary 352,6552 include/aux/amatrix.h,301 #define __AMATRIX_H__DEF__2,27 class AMatrixAMatrix64,1319 void calculate_gj_inverse(AMatrix::calculate_gj_inverse119,2477 AMatrix UniqueCopy(AMatrix::UniqueCopy168,3779 int Cols(AMatrix::Cols303,7468 int Compare(AMatrix::Compare306,7548 AMatrix operator AMatrix::operator433,11459 include/aux/bits.h,88 #define _BITS_H_2,17 inline uint reverse_bits(9,99 inline ostream& print_bits(25,375 include/aux/compoper.h,178 #define __COMPOPERATOR_DEF__2,29 #define MAKECOMPARISONS_NO_COMPARE(MAKECOMPARISONS_NO_COMPARE14,252 #define MAKECOMPARISONS_WITH_COMPARE(MAKECOMPARISONS_WITH_COMPARE28,772 include/aux/ddgraph.h,568 #define _DDGRAPH_H_31,1391 enum GraphStatusGraphStatus47,1650 NoVertices 49,1669 VertexBad 50,1690 VertexInG 51,1710 VertexNotInG 52,1730 VertexAddFailure 53,1753 NoEdges 54,1779 EdgeBad 55,1798 EdgeInG 56,1817 EdgeNotInG 57,1836 EdgeAddFailure 58,1857 const DynString V_BEGIN_DELIM 61,1884 const DynString V_END_DELIM 62,1921 const DynString E_BEGIN_DELIM 63,1956 const DynString E_END_DELIM 64,1993 class ddGraphddGraph71,2172 int NumVertices(ddGraph::NumVertices91,2583 MAKE_IO_STREAM_OPERATORS(MAKE_IO_STREAM_OPERATORS168,5150 include/aux/ddvertex.h,322 #define _DDVERTEX_H_2,21 class ddEdgeddEdge26,502 ~ddEdge(ddEdge::~ddEdge30,547 int Compare(ddEdge::Compare36,688 int Output(ddEdge::Output41,833 int InputBinary(ddEdge::InputBinary44,897 int OutputBinary(ddEdge::OutputBinary46,957 class ddVertexddVertex62,1387 ddVertex(ddVertex73,1594 include/aux/dllist.h,546 #define _DLLIST_H_11,250 class DLListNodeDLListNode28,559 DLListNode(DLListNode::DLListNode36,726 DLListNode(DLListNode::DLListNode38,771 ~DLListNode(DLListNode::~DLListNode42,874 private:DLListNode::private53,1126 class DLListRep DLListRep58,1208 private:DLListRep::private73,1506 class DLListDLList79,1576 int IsEmpty(DLList::IsEmpty91,1749 int Number(DLList::Number99,1926 DLList UniqueCopy(DLList::UniqueCopy163,3920 DLList::ConstIterator GetConstIterator(DLList::GetConstIterator170,4088 include/aux/dynstring.h,843 #define _DYNSTRING_H_10,198 class DynStringDynString25,450 int IsBad(DynString::IsBad41,743 int DestResizeToFit(DynString::DestResizeToFit45,842 int NonDestResizeToFit(DynString::NonDestResizeToFit47,923 int Resize(DynString::Resize49,1010 void Clear(DynString::Clear83,2300 DynString Sub(DynString::Sub95,2615 int IsSub(DynString::IsSub100,2773 void ToLower(DynString::ToLower110,3143 double ToDbl(DynString::ToDbl114,3262 int ToInt(DynString::ToInt116,3313 int Compare(DynString::Compare122,3437 const char* GetData(DynString::GetData128,3647 char* GetDataCopy(DynString::GetDataCopy130,3699 int Bytes(DynString::Bytes138,3891 int Blocks(DynString::Blocks141,3981 int Split(DynString::Split194,5806 int Output(DynString::Output204,6142 typedef DynString DS;DS247,7417 include/aux/graph_weights.h,460 #define __GRAPH_WEIGHTS_H__2,28 class UnitWeightUnitWeight7,104 UnitWeight(UnitWeight::UnitWeight11,137 UnitWeight(UnitWeight::UnitWeight12,155 UnitWeight(UnitWeight::UnitWeight13,179 UnitWeight(UnitWeight::UnitWeight14,200 int Output(UnitWeight::Output24,442 int Input(UnitWeight::Input26,505 int OutputBinary(UnitWeight::OutputBinary28,545 int InputBinary(UnitWeight::InputBinary30,598 private:UnitWeight::private36,768 include/aux/grid.h,972 #define __GRID_H__12,257 typedef long GridNumber;GridNumber21,379 typedef hash_multimap, equal_to > hashmap_type;hashmap_type22,406 typedef jVector* pointList;pointList23,496 class Grid Grid25,527 double getBounds(Grid::getBounds58,1267 double getDistance(Grid::getDistance78,1848 int addPoint Grid::addPoint150,5052 int deletePoint Grid::deletePoint156,5337 double calcDistance3(Grid::calcDistance3221,7577 inline double Grid::calcDistance3(247,8550 inline const jVector& Grid::getPosition(250,8735 inline double Grid::getDistance(254,8887 inline double Grid::getDistance(257,9014 inline double Grid::getBounds(261,9142 inline double Grid::getDelta(264,9208 inline int Grid::getNumPoints(267,9270 inline const pointList Grid::getPoints 270,9337 inline const GridNumber* Grid::getGrids 273,9413 inline GridNumber Grid::getGrid(276,9505 inline GridNumber Grid::getGridDimension(281,9665 include/aux/idgen.h,471 #define _IDGEN_H_18,559 class IdGenIdGen24,621 int Max(IdGen::Max32,721 inline IdGen::IdGen(74,1824 inline IdGen::~IdGen(77,1886 inline int IdGen::Max(80,1926 inline int IdGen::Peek(83,1979 inline int IdGen::Get(90,2085 inline void IdGen::Free(103,2253 inline void IdGen::Reset(111,2402 inline int IdGen::NumberIssued(117,2477 inline int IdGen::NumberFree(120,2545 inline int IdGen::NumberUsed(123,2613 inline ostream& operator << (ostream& os,126,2695 include/aux/intvec.h,138 #define _INTVEC_H_10,195 class IntVecIntVec20,349 int Length(IntVec::Length40,771 int OutputBinary(IntVec::OutputBinary83,2007 include/aux/ipqueue.h,205 #define _INTPQUEUE_H_2,22 const int IPQDEFLEN 9,109 class IntPriorityQueueIntPriorityQueue15,255 int IsEmpty(IntPriorityQueue::IsEmpty32,843 ostream& PrintTop(IntPriorityQueue::PrintTop88,2639 include/aux/jsmisc.h,349 #define _JS_MISC_H_11,227 typedef unsigned int uint;uint15,269 typedef short int sint;sint16,296 typedef long int lint;lint17,320 typedef unsigned short int usint;usint18,343 typedef unsigned long int ulint;ulint19,377 typedef unsigned char uchar;uchar20,410 typedef class ABitSet ABS;ABS21,439 #define PI 24,478 #define INF 28,530 include/aux/jvector.h,875 #define _JVECTOR_H_12,265 const int DEFAULTLEN 25,475 class jVectorjVector27,502 int Resize(jVector::Resize34,606 int Copy(jVector::Copy48,870 const double& get(jVector::get60,1110 void set(jVector::set62,1162 const jVector& set(jVector::set65,1212 const jVector& zero(jVector::zero68,1346 jVector(jVector::jVector72,1437 jVector(jVector::jVector75,1516 jVector(jVector::jVector77,1569 ~jVector(jVector::~jVector80,1642 const jVector& transpose(jVector::transpose82,1672 int Vertical(jVector::Vertical83,1736 int Length(jVector::Length84,1776 double sum(jVector::sum87,1857 double mag(jVector::mag109,2324 int Compare(jVector::Compare203,4536 int Output(jVector::Output244,6036 int OutputBinary(jVector::OutputBinary263,6798 inline int binsearch(299,7889 int dcomp(319,8227 void JVqsort(329,8425 include/aux/kadjmat.h,192 #define _KADJMAT_H_2,20 class KAdjMatKAdjMat21,531 int Connect(KAdjMat::Connect38,979 int Disconnect(KAdjMat::Disconnect47,1198 const ABitSet& operator KAdjMat::operator67,1847 include/aux/matrix.h,236 #define MATRIX_H_9,370 class Matrix Matrix23,757 const double &operator(Matrix::operator36,1030 int getCols(Matrix::getCols42,1264 Matrix subMatrix(Matrix::subMatrix47,1411 inline ostream &operator<<(ostream &os,94,2762 include/aux/queue.h,210 #define _QUEUE_H_11,216 class Queue Queue16,275 void Add(Queue::Add19,318 void Add(Queue::Add21,364 T Remove(Queue::Remove23,422 const T& Peek(Queue::Peek25,470 T& Peek(Queue::Peek26,518 include/aux/randomgenerator.h,874 #define _RANDOMGENERATOR_H_11,220 static class zz62,2117 z(z::z65,2150 ~z(z::~z66,2188 } z;71,2334 class RanBaseClassRanBaseClass73,2342 double GetReal(RanBaseClass::GetReal85,2538 class RanDbl RanDbl89,2621 ~RanDbl(RanDbl::~RanDbl93,2720 double Get(RanDbl::Get94,2735 class RanInt RanInt100,2841 ~RanInt(RanInt::~RanInt109,3119 int Get(RanInt::Get110,3134 class RanChar RanChar119,3341 RanChar(RanChar::RanChar122,3389 ~RanChar(RanChar::~RanChar123,3404 char Get(RanChar::Get124,3420 class RanLetter RanLetter129,3474 RanLetter(RanLetter::RanLetter132,3524 ~RanLetter(RanLetter::~RanLetter133,3541 char Get(RanLetter::Get134,3559 class RanWord RanWord138,3594 RanWord(RanWord::RanWord141,3642 ~RanWord(RanWord::~RanWord142,3657 DynString Get(RanWord::Get143,3673 include/aux/refrep.h,242 #define __REFREP_H__DEF__2,26 class RefRepRefRep75,1978 long References(RefRep::References86,2142 RefRep::RefRep(111,2650 RefRep::Reference(120,2807 RefRep::Dereference(134,3191 RefRep::References(148,3351 RefRep::~RefRep(156,3430 include/aux/sdgraph.h,794 #define _SDGRAPH_H_9,170 int PathsVisited 31,503 typedef set SDG_SetInt;SDG_SetInt38,659 typedef set SDG_SetSetInt;SDG_SetSetInt40,734 typedef DLList SDG_IntList;SDG_IntList41,774 typedef sdGraph SDG_GraphSetInt;SDG_GraphSetInt63,1231 enum sdg_colorsdg_color65,1288 sdg_white 67,1305 sdg_gray 68,1322 sdg_black 69,1338 class sdGraphsdGraph73,1395 int NumVertices(sdGraph::NumVertices91,1830 int OutputBinary(sdGraph::OutputBinary168,4590 neighbor_iterator begin_neighbor(sdGraph::begin_neighbor206,6099 df_iterator begin_df(sdGraph::begin_df208,6208 bf_iterator begin_bf(sdGraph::begin_bf210,6299 path_iterator begin_path(sdGraph::begin_path212,6390 jVector Dijkstra(sdGraph::Dijkstra246,7229 include/aux/sdvertex.h,372 #define _SDVERTEX_H_9,173 class sdEdgesdEdge27,591 sdEdge(sdEdge::sdEdge31,647 sdEdge(sdEdge::sdEdge32,669 ~sdEdge(sdEdge::~sdEdge33,719 int Compare(sdEdge::Compare35,748 class sdVertexsdVertex49,1147 int OutDegree(sdVertex::OutDegree73,1642 int Compare(sdVertex::Compare89,2123 const sdEdge& GetOutEdge(sdVertex::GetOutEdge122,3376 include/aux/search-sort.h,535 #define _SEARCH_SORT_H_36,790 search_swap(42,848 inline void BubbleSort(51,929 inline void BubbleSortPtrs(65,1206 inline void BubbleSortR(79,1494 inline void BubbleSortPtrsR(93,1773 inline int Partition(107,2061 inline int PartitionPtrs(134,2406 inline void RecQuickSort(159,2732 inline void RecQuickSortPtrs(170,2906 inline void QuickSort(181,3097 inline void QuickSortPtrs(188,3218 inline int BinSearch(192,3332 inline int BinSearchPtr(211,3684 inline int SelectPartition(230,4040 inline double LinearSelect(263,4623 include/aux/stack.h,182 #define _STACK_H_10,171 class Stack Stack16,252 void Push(Stack::Push19,295 void Push(Stack::Push20,346 T Pop(Stack::Pop21,402 const T& Peek(Stack::Peek22,442 include/aux/streamoper.h,171 #define __STREAM_OPERATOR_DEF__2,32 #define MAKE_IO_STREAM_OPERATORS(MAKE_IO_STREAM_OPERATORS10,211 #define MAKE_BIN_STREAM_OPERATORS(MAKE_BIN_STREAM_OPERATORS16,454 include/aux/utils.h,806 #define __UTILS_H_2,19 util_swap(22,448 util_max(31,535 util_min(38,628 bound(45,721 bounded(52,865 bounds_compare(59,1005 mod_dist(70,1159 extern const int bit_count_array[85,1374 bit_count(88,1425 const double sqrt2 93,1487 const double sqrt2_2 95,1558 const double sqrt3 97,1631 const double sqrt3_2 99,1702 const double sqrt5 101,1775 const double sqrt5_2 103,1846 const double pi 105,1919 const double pi2 107,1987 const double pi_2 109,2056 const double o_sqrt2 112,2127 const double o_sqrt2_2 114,2200 const double o_sqrt3 116,2275 const double o_sqrt3_2 118,2348 const double o_pi 120,2423 const double o_pi2 122,2493 const double o_pi_2 124,2564 const double rad_to_deg 127,2637 const double deg_to_rad 129,2714 #define ERROR(ERROR133,2792 odd(139,2937 sq(147,3000 include/aux/amatrix.inc,788 AMatrix::AMatrixRep::do_new(19,407 AMatrix::AMatrixRep::do_delete(35,618 AMatrix::AMatrixRep::operator(43,749 AMatrix::AMatrix(56,982 inline AMatrix::AMatrix(60,1032 AMatrix::~AMatrix(66,1130 AMatrix::operator=72,1215 AMatrix::UniqueCopy 82,1400 AMatrix::operator(90,1536 AMatrix::operator(105,1832 AMatrix::operator[121,2130 if 124,2197 AMatrix::operator[136,2426 AMatrix::operator(152,2724 AMatrix::operator(167,3066 AMatrix::IsBadMatrix(184,3409 AMatrix::Compare(190,3503 AMatrix::operator 217,4017 AMatrix::operator 248,4539 AMatrix::operator 268,4961 AMatrix::GJInverse(287,5318 AMatrix::SVD_DiagW(304,5665 AMatrix::SVD_U(311,5791 AMatrix::SVD_V(318,5909 if 330,6107 AMatrix::Reset(361,6724 AMatrix::Set_Begin_Row(382,7109 AMatrix::Set_End_Row(393,7300 include/aux/ddgraph.inc,3755 inline ostream& PrintGStatus(1,0 inline void ddGraph::Clear(55,1243 inline void ddGraph::Copy(67,1493 inline void ddGraph::Copy(94,2281 inline ddGraph::ddGraph(132,3220 inline ddGraph::ddGraph(139,3320 inline ddGraph::ddGraph(147,3460 inline ddGraph::~ddGraph(155,3600 inline int ddGraph::NumVertices(159,3680 inline int ddGraph::NumEdges(163,3777 inline int ddGraph::HasVertex(167,3871 inline int ddGraph::HasVertex(171,3989 inline int ddGraph::HasEdge(175,4102 inline int ddGraph::OutDegree(189,4517 inline int ddGraph::InDegree(197,4717 inline int ddGraph::Degree(205,4915 inline int ddGraph::NextFreeId(213,5134 inline int ddGraph::AddVertex(217,5236 inline ddVertex* ddGraph* ddGraph::GetVertex(229,5499 inline int ddGraph::GetVertexId(236,5692 inline DT& ddGraph::GetData(243,5889 inline DT& ddGraph::GetData(259,6345 inline const DT& ddGraph::GetData(267,6553 inline int ddGraph::AddEdge(275,6773 inline int ddGraph::AddEdge(295,7231 inline int ddGraph::AddEdge(313,7702 inline int ddGraph::AddEdge(317,7861 inline const WT& ddGraph::GetWeight(321,8013 inline void ddGraph::SetWeight(343,8484 inline void ddGraph::SetWeight(353,8811 inline void ddGraph::SetWeight(362,9112 inline void ddGraph::ChangeWeight(367,9277 inline void ddGraph::ChangeWeight(377,9607 inline void ddGraph::ChangeWeight(386,9907 inline const WT& ddGraph::operator 391,10078 inline void ddGraph::RemOutEdges(395,10224 inline void ddGraph::RemInEdges(404,10471 inline void ddGraph::RemEdges(413,10715 inline int ddGraph::RemVertex(422,10952 inline int ddGraph::RemEdge(458,11627 inline int ddGraph::RemEdge(473,11928 inline int ddGraph::Output(489,12271 inline int ddGraph::Input(512,12878 inline const ddGraph& ddGraph& ddGraph::operator 623,15466 inline const ddGraph& ddGraph& ddGraph::operator 627,15612 inline istream& InputBinary(632,15761 inline ostream& OutputBinary(642,15956 include/aux/ddvertex.inc,969 inline int ddEdge::Compare(2,20 inline ddVertex::ddVertex(12,311 inline ddVertex::ddVertex(18,404 inline int ddVertex::HaveSelfLoop(24,478 inline int ddVertex::OutDegree(33,704 inline int ddVertex::InDegree(37,794 inline int ddVertex::Degree(41,882 inline const double& ddVertex::GetWeightTo(45,999 inline const double& ddVertex::GetWeightFrom(53,1205 inline void ddVertex::SetWeightTo(61,1411 inline void ddVertex::SetWeightFrom(69,1637 inline void ddVertex::ChangeWeightTo(77,1863 inline void ddVertex::ChangeWeightFrom(85,2091 inline void ddVertex::PrintOutEdges(93,2319 inline void ddVertex::PrintInEdges(105,2619 inline void ddVertex::PrintEdges(117,2916 inline ostream& operator << (ostream& os,121,3036 inline int ddVertex::RemOutEdges(132,3354 inline int ddVertex::RemInEdges(155,3962 inline int ddVertex::RemEdges(173,4341 inline ddVertex::~ddVertex(177,4441 include/aux/dllist.inc,1476 inline DLListRep::DLListRep(15,378 inline DLListRep::~DLListRep(19,458 inline int DLList::IsEmpty(29,727 inline void DLList::Clear(33,823 inline int DLList::Number(37,950 inline bool DLList::AddToFront(41,1032 inline bool DLList::AddToBack(68,1525 inline bool DLList::AddToFront(96,2020 inline bool DLList::AddToBack(127,2726 inline bool DLList::Add(158,3440 inline bool DLList::Add(162,3532 inline T DLList::RemoveFromFront(176,3865 inline T DLList::RemoveFromBack(202,4505 inline T DLList::Remove(227,5128 inline const T& DLList::Get(231,5209 inline T& DLList::Get(252,5574 inline const T& DLList::PeekFront(273,5927 inline T& DLList::PeekFront(277,6026 inline const T& DLList::PeekBack(281,6113 inline T& DLList::PeekBack(285,6211 inline T DLList::RemoveLocation(290,6298 inline int DLList::operator 323,6866 inline int DLList::FindLocation(344,7377 inline T& DLList::Find(356,7609 inline const T& DLList::Find(360,7710 inline int DLList::In(364,7823 inline T DLList::Remove(368,7930 inline ostream& DLList::Print(372,8043 inline ostream& operator << (ostream& os,385,8259 inline istream& InputBinary(389,8371 inline ostream& OutputBinary(412,8778 inline const DLList& DLList::operator 435,9328 inline DLList DLList::UniqueCopy(446,9594 inline DLList::DLList(459,9821 inline DLList::DLList(463,9905 inline DLList::~DLList(470,10043 include/aux/dlliter.inc,694 class IteratorIterator8,152 void Reset(Iterator::Reset12,205 T& operator Iterator::operator13,241 void Copy(Iterator::Copy17,405 Iterator(Iterator::Iterator31,680 Iterator(Iterator::Iterator32,715 ~Iterator(Iterator::~Iterator34,783 Iterator(Iterator::Iterator36,847 class ConstIteratorConstIterator46,1011 void Reset(ConstIterator::Reset50,1069 const T& operator ConstIterator::operator51,1105 void Copy(ConstIterator::Copy55,1280 ConstIterator(ConstIterator::ConstIterator69,1570 ConstIterator(ConstIterator::ConstIterator70,1610 ~ConstIterator(ConstIterator::~ConstIterator72,1688 ConstIterator(ConstIterator::ConstIterator75,1771 include/aux/dsiter.inc,575 class DSIteratorDSIterator10,191 void Reset(DSIterator::Reset13,220 void SetString(DSIterator::SetString16,266 void SetDelim(DSIterator::SetDelim20,406 DynString operator DSIterator::operator25,551 void Copy(DSIterator::Copy45,890 DSIterator(DSIterator::DSIterator57,1128 DSIterator(DSIterator::DSIterator59,1167 DSIterator(DSIterator::DSIterator62,1221 DSIterator(DSIterator::DSIterator70,1365 ~DSIterator(DSIterator::~DSIterator78,1488 int DelimMatch(DSIterator::DelimMatch89,1705 void Position(DSIterator::Position97,1840 include/aux/intvec.inc,1043 inline int IntVec::AppendUnique(11,196 inline int IntVec::Append(27,439 inline int IntVec::Resize(39,604 inline bool IntVec::Contains(52,865 inline int IntVec::Copy(59,994 inline const IntVec& IntVec::set(68,1162 inline const IntVec& IntVec::setrange(71,1260 inline const IntVec& IntVec::zero(74,1384 inline IntVec::IntVec(77,1442 inline IntVec::IntVec(80,1508 inline IntVec::IntVec(83,1613 inline IntVec::IntVec(86,1737 inline IntVec::~IntVec(89,1808 inline int IntVec::Length(92,1852 { return L;96,1940 inline const IntVec& IntVec::operator 98,1957 inline const int& IntVec::Access(101,2047 inline int& IntVec::Access(107,2208 inline const int& IntVec::operator 113,2351 inline int& IntVec::operator 116,2428 inline int operator 119,2493 inline int operator < (const IntVec& a,154,3235 inline int operator > (const IntVec& a,166,3478 inline int IntVec::Input(178,3721 inline int IntVec::Output(189,3879 inline int IntVec::InputBinary(199,4050 inline int IntVec::OutputBinary(215,4328 inline IntVec cat(233,4577 include/aux/ipqueue.inc,1644 inline uint IntPriorityQueue::Parent(2,20 inline uint IntPriorityQueue::Left(6,119 inline uint IntPriorityQueue::Right(10,216 inline int IntPriorityQueue::IsBad(14,329 inline int IntPriorityQueue::BadId(19,446 void IntPriorityQueue::Swap(23,557 inline void IntPriorityQueue::Heapify(42,928 inline void IntPriorityQueue::BubbleUp(84,1729 inline void IntPriorityQueue::Build(111,2202 inline void IntPriorityQueue::Clear(121,2381 inline int IntPriorityQueue::Copy(134,2588 inline const IntPriorityQueue& IntPriorityQueue::operator 178,3471 inline IntPriorityQueue::IntPriorityQueue(183,3633 inline IntPriorityQueue::IntPriorityQueue(196,3861 inline IntPriorityQueue::~IntPriorityQueue(223,4396 inline int IntPriorityQueue::IsEmpty(228,4573 inline int IntPriorityQueue::IsFull(236,4752 inline int IntPriorityQueue::Size(240,4840 inline int IntPriorityQueue::Number(244,4929 inline int IntPriorityQueue::In(248,5020 inline int IntPriorityQueue::Add(252,5141 inline int IntPriorityQueue::FixDir(317,6429 inline PT IntPriorityQueue::Peek(344,6918 inline int IntPriorityQueue::ChangeId(352,7101 inline void IntPriorityQueue::Modify(368,7448 inline void IntPriorityQueue::RelModify(390,7891 inline int IntPriorityQueue::Extreme(400,8142 inline int IntPriorityQueue::Remove(408,8275 inline const PT& IntPriorityQueue::GetPriority(442,8851 inline const PT& IntPriorityQueue::operator 449,9017 inline ostream& operator << (ostream& os,453,9134 inline ostream& IntPriorityQueue::PrintTop(466,9384 include/aux/sdgalg.inc,815 inline int sdGraph::Initialize_Single_Source(5,72 inline void sdGraph::Relax(18,319 inline jVector sdGraph::Dijkstra(35,738 inline void sdGraph::DF_Visit(69,1514 inline int sdGraph::DFTimeStamps(107,2463 inline SDG_SetSetInt sdGraph::SCC(126,2915 inline SDG_SetSetInt sdGraph::StronglyConnectedComponents(168,3801 inline sdGraph sdGraph sdGraph::SCCGraph(172,3925 inline int sdGraph::NumSCC(357,8503 include/aux/sdgiter.inc,2204 friend class base_iteratorbase_iterator11,199 int Invalid(base_iterator::Invalid20,476 base_iterator(base_iterator::base_iterator23,567 base_iterator(base_iterator::base_iterator31,740 base_iterator(base_iterator::base_iterator33,816 void Reverse(base_iterator::Reverse35,915 int bad(base_iterator::bad43,1131 virtual ~base_iterator(base_iterator::~base_iterator46,1183 virtual void reset(base_iterator::reset47,1224 virtual int operator*base_iterator::operator50,1381 friend class neighbor_iterator neighbor_iterator53,1434 neighbor_iterator(neighbor_iterator::neighbor_iterator58,1549 neighbor_iterator(neighbor_iterator::neighbor_iterator61,1673 neighbor_iterator(neighbor_iterator::neighbor_iterator65,1828 ~neighbor_iterator(neighbor_iterator::~neighbor_iterator70,1968 void reset(neighbor_iterator::reset72,2010 int operator*neighbor_iterator::operator95,2452 friend class df_iterator df_iterator109,2808 df_iterator(df_iterator::df_iterator114,2905 df_iterator(df_iterator::df_iterator119,3129 df_iterator(df_iterator::df_iterator123,3288 ~df_iterator(df_iterator::~df_iterator129,3436 void reset(df_iterator::reset144,3742 int operator*df_iterator::operator204,5077 friend class bf_iterator bf_iterator215,5292 bf_iterator(bf_iterator::bf_iterator220,5389 bf_iterator(bf_iterator::bf_iterator225,5612 bf_iterator(bf_iterator::bf_iterator229,5760 ~bf_iterator(bf_iterator::~bf_iterator235,5896 void reset(bf_iterator::reset250,6202 int operator*bf_iterator::operator311,7540 friend class path_iteratorpath_iterator324,7976 int bad(path_iterator::bad328,8046 int source(path_iterator::source331,8113 int target(path_iterator::target332,8166 int length(path_iterator::length333,8219 void copy(path_iterator::copy335,8255 path_iterator(path_iterator::path_iterator405,9970 path_iterator(path_iterator::path_iterator415,10161 ~path_iterator(path_iterator::~path_iterator424,10328 int * operator*path_iterator::operator536,12953 void reset(path_iterator::reset544,13157 path_iterator(path_iterator::path_iterator562,13404 include/aux/sdgraph.inc,3641 inline void sdGraph::Clear(14,371 inline void sdGraph::Copy(25,597 inline void sdGraph::Copy(68,1713 inline const sdGraph& sdGraph& sdGraph::operator 300,7755 inline const sdGraph& sdGraph& sdGraph::operator 304,7901 inline sdGraph::sdGraph(308,8053 inline sdGraph::sdGraph(317,8181 inline sdGraph::sdGraph(328,8429 inline sdGraph::~sdGraph(338,8619 inline int sdGraph::NumVertices(342,8698 inline int sdGraph::NumEdges(346,8794 inline int sdGraph::GetVertexIndex(350,8887 inline int sdGraph::HasVertex(354,9017 inline int sdGraph::HasEdge(358,9143 inline int sdGraph::ValidVertex(368,9399 inline int sdGraph::ValidData(372,9528 inline int sdGraph::OutDegree(376,9648 inline int sdGraph::InDegree(384,9845 inline int sdGraph::Degree(392,10039 inline const sdVertex& sdGraph& sdGraph::GetVertex(400,10245 inline sdVertex& sdGraph& sdGraph::GetVertex(408,10454 inline const sdVertex& sdGraph& sdGraph::operator 416,10672 inline sdVertex& sdGraph& sdGraph::operator 420,10798 inline const DT& sdGraph::GetData(424,10912 inline DT& sdGraph::GetData(432,11130 inline const DT& sdGraph::operator 440,11345 inline DT& sdGraph::operator 444,11460 inline const WT& sdGraph::GetWeight(448,11563 inline WT& sdGraph::GetWeight(458,11920 inline const WT& sdGraph::operator 468,12265 inline WT& sdGraph::operator 472,12404 inline sdGraph sdGraph sdGraph::SubGraph(476,12531 inline int sdGraph::Output(604,15785 inline ostream& sdGraph::PrintDotty(626,16331 inline ostream& operator << (ostream& os,661,17182 inline ostream& operator << (ostream& os, const sdGraph::AdjMatrix(665,17320 KAdjMat * sdGraph::TravMatrices(675,17555 inline SDG_IntList ** sdGraph::TravLists(706,18297 inline int sdGraph::InputBinary(769,19572 inline int sdGraph::Input(880,21927 inline int sdGraph::OutputBinary(884,22020 include/aux/sdvertex.inc,1978 inline int sdEdge::Compare(15,358 ID 26,692 NumO 27,705 NumI 28,719 OutE 29,733 InE 30,747 inline sdVertex::sdVertex(int id,63,1327 inline sdVertex::sdVertex(int id, int num_out,63,1327 inline sdVertex::~sdVertex(81,1747 inline int sdVertex::OutDegree(85,1836 inline int sdVertex::InDegree(89,1919 inline int sdVertex::Degree(93,2001 inline void sdVertex::SortEdges(97,2101 inline void sdVertex::PrintOutEdges(104,2221 inline void sdVertex::PrintInEdges(111,2412 inline void sdVertex::PrintEdges(118,2600 inline ostream& operator << (ostream& os,122,2720 inline const sdVertex& sdVertex::operator 126,2841 inline int sdVertex::Compare(170,3724 inline const sdVertex& sdVertex::GetOutNeighbor(174,3833 inline sdVertex& sdVertex::GetOutNeighbor(178,3950 inline const sdVertex& sdVertex::operator 182,4055 inline sdVertex& sdVertex::operator 186,4175 inline const sdVertex& sdVertex::GetInNeighbor(190,4283 inline sdVertex& sdVertex::GetInNeighbor(194,4398 inline const sdVertex& sdVertex::operator 198,4501 inline sdVertex& sdVertex::operator 202,4620 inline int sdVertex::GetOutEdgeIndex(206,4727 inline int sdVertex::GetOutEdgeIndex(217,4983 inline int sdVertex::GetInEdgeIndex(221,5112 inline int sdVertex::GetInEdgeIndex(232,5370 inline int sdVertex::HasEdgeTo(236,5501 inline int sdVertex::HasEdgeFrom(240,5632 inline int Connected(244,5768 inline const sdEdge& sdVertex::GetOutEdge(248,5913 inline sdEdge& sdVertex::GetOutEdge(252,6019 inline const sdEdge& sdVertex::GetInEdge(256,6114 inline sdEdge& sdVertex::GetInEdge(260,6218 inline const WT& sdVertex::GetOutWeight(264,6310 inline WT& sdVertex::GetOutWeight(268,6412 inline const WT& sdVertex::GetInWeight(272,6502 inline WT& sdVertex::GetInWeight(276,6602