, including all inherited members.
| addAtom(DuMM::ChargedAtomTypeIndex chargedAtomTypeIx) | DuMMForceFieldSubsystem | |
| addBond(DuMM::AtomIndex atom1Ix, DuMM::AtomIndex atom2Ix) | DuMMForceFieldSubsystem | |
| adoptSubsystemGuts(Subsystem::Guts *g) | Subsystem | |
| Amber99ForceSubsystem(MolecularMechanicsSystem &system) | Amber99ForceSubsystem | [inline, explicit] |
| attachAtomToBody(DuMM::AtomIndex atomIx, MobilizedBodyIndex body, const Vec3 &station=Vec3(0)) | DuMMForceFieldSubsystem | |
| attachClusterToBody(DuMM::ClusterIndex clusterIx, MobilizedBodyIndex body, const Transform &=Transform()) | DuMMForceFieldSubsystem | |
| calcClusterMassProperties(DuMM::ClusterIndex clusterIx, const Transform &=Transform()) const | DuMMForceFieldSubsystem | |
| createCluster(const char *clusterName) | DuMMForceFieldSubsystem | |
| defineAmberImproperTorsion(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKJ, Real phase1InDegrees) | DuMMForceFieldSubsystem | |
| defineAmberImproperTorsion(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKJ, Real phase1InDegrees, int periodicity2, Real amp2InKJ, Real phase2InDegrees) | DuMMForceFieldSubsystem | |
| defineAmberImproperTorsion(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKJ, Real phase1InDegrees, int periodicity2, Real amp2InKJ, Real phase2InDegrees, int periodicity3, Real amp3InKJ, Real phase3InDegrees) | DuMMForceFieldSubsystem | |
| defineAmberImproperTorsion_KA(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees) | DuMMForceFieldSubsystem | [inline] |
| defineAmberImproperTorsion_KA(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees, int periodicity2, Real amp2InKcal, Real phase2InDegrees) | DuMMForceFieldSubsystem | [inline] |
| defineAmberImproperTorsion_KA(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees, int periodicity2, Real amp2InKcal, Real phase2InDegrees, int periodicity3, Real amp3InKcal, Real phase3InDegrees) | DuMMForceFieldSubsystem | [inline] |
| defineAtomClass(DuMM::AtomClassIndex atomClassIx, const char *atomClassName, int elementNumber, int expectedValence, Real vdwRadiusInNm, Real vdwWellDepthInKJ) | DuMMForceFieldSubsystem | [inline] |
| defineAtomClass_KA(DuMM::AtomClassIndex atomClassIx, const char *atomClassName, int element, int valence, Real vdwRadiusInAng, Real vdwWellDepthInKcal) | DuMMForceFieldSubsystem | [inline] |
| defineAtomClass_KA(int atomClassIx, const char *atomClassName, int element, int valence, Real vdwRadiusInAng, Real vdwWellDepthInKcal) | DuMMForceFieldSubsystem | [inline] |
| defineBondBend(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, Real stiffnessInKJPerRadSq, Real nominalAngleInDeg) | DuMMForceFieldSubsystem | |
| defineBondBend_KA(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, Real stiffnessInKcalPerRadSq, Real nominalAngleInDeg) | DuMMForceFieldSubsystem | [inline] |
| defineBondBend_KA(int class1, int class2, int class3, Real stiffnessInKcalPerRadSq, Real nominalAngleInDeg) | DuMMForceFieldSubsystem | [inline] |
| defineBondStretch(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, Real stiffnessInKJperNmSq, Real nominalLengthInNm) | DuMMForceFieldSubsystem | |
| defineBondStretch_KA(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, Real stiffnessInKcalPerAngSq, Real nominalLengthInAng) | DuMMForceFieldSubsystem | [inline] |
| defineBondStretch_KA(int class1, int class2, Real stiffnessInKcalPerAngSq, Real nominalLengthInAng) | DuMMForceFieldSubsystem | [inline] |
| defineBondTorsion(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKJ, Real phase1InDegrees) | DuMMForceFieldSubsystem | |
| defineBondTorsion(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKJ, Real phase1InDegrees, int periodicity2, Real amp2InKJ, Real phase2InDegrees) | DuMMForceFieldSubsystem | |
| defineBondTorsion(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKJ, Real phase1InDegrees, int periodicity2, Real amp2InKJ, Real phase2InDegrees, int periodicity3, Real amp3InKJ, Real phase3InDegrees) | DuMMForceFieldSubsystem | |
| defineBondTorsion_KA(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees) | DuMMForceFieldSubsystem | [inline] |
| defineBondTorsion_KA(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees, int periodicity2, Real amp2InKcal, Real phase2InDegrees) | DuMMForceFieldSubsystem | [inline] |
| defineBondTorsion_KA(DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees, int periodicity2, Real amp2InKcal, Real phase2InDegrees, int periodicity3, Real amp3InKcal, Real phase3InDegrees) | DuMMForceFieldSubsystem | [inline] |
| defineBondTorsion_KA(int class1, int class2, int class3, int class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees) | DuMMForceFieldSubsystem | [inline] |
| defineBondTorsion_KA(int class1, int class2, int class3, int class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees, int periodicity2, Real amp2InKcal, Real phase2InDegrees) | DuMMForceFieldSubsystem | [inline] |
| defineBondTorsion_KA(int class1, int class2, int class3, int class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees, int periodicity2, Real amp2InKcal, Real phase2InDegrees, int periodicity3, Real amp3InKcal, Real phase3InDegrees) | DuMMForceFieldSubsystem | [inline] |
| defineChargedAtomType(DuMM::ChargedAtomTypeIndex atomTypeIx, const char *atomTypeName, DuMM::AtomClassIndex atomClassIx, Real partialChargeInE) | DuMMForceFieldSubsystem | [inline] |
| defineChargedAtomType_KA(DuMM::ChargedAtomTypeIndex atomTypeIx, const char *atomTypeName, DuMM::AtomClassIndex atomClassIx, Real partialChargeInE) | DuMMForceFieldSubsystem | [inline] |
| defineChargedAtomType_KA(int atomTypeIx, const char *atomTypeName, int atomClassIx, Real partialChargeInE) | DuMMForceFieldSubsystem | [inline] |
| defineIncompleteAtomClass(DuMM::AtomClassIndex classIx, const char *name, int elementNumber, int valence) | DuMMForceFieldSubsystem | [protected] |
| defineIncompleteAtomClass_KA(DuMM::AtomClassIndex classIx, const char *name, int elementNumber, int valence) | DuMMForceFieldSubsystem | [inline, protected] |
| defineIncompleteChargedAtomType(DuMM::ChargedAtomTypeIndex typeIx, const char *name, DuMM::AtomClassIndex classIx) | DuMMForceFieldSubsystem | [protected] |
| defineIncompleteChargedAtomType_KA(DuMM::ChargedAtomTypeIndex typeIx, const char *name, DuMM::AtomClassIndex classIx) | DuMMForceFieldSubsystem | [inline, protected] |
| DuMMForceFieldSubsystem | DuMMForceFieldSubsystem | [protected] |
| DuMMForceFieldSubsystem() | DuMMForceFieldSubsystem | |
| DuMMForceFieldSubsystem(MolecularMechanicsSystem &) | DuMMForceFieldSubsystem | [explicit] |
| dump() const | DuMMForceFieldSubsystem | |
| dumpCForceFieldParameters(std::ostream &os, const String &methodName="loadParameters") const | DuMMForceFieldSubsystem | |
| ForceSubsystem | DuMMForceFieldSubsystem | [protected] |
| SimTK::ForceSubsystem::ForceSubsystem() | ForceSubsystem | [inline] |
| generateBiotypeChargedAtomTypeSelfCode(std::ostream &os) const | DuMMForceFieldSubsystem | |
| getAtomBody(DuMM::AtomIndex atomIx) const | DuMMForceFieldSubsystem | |
| getAtomClassIndex(const String &atomClassName) const | DuMMForceFieldSubsystem | |
| getAtomClassIndex(DuMM::AtomIndex atomIx) const | DuMMForceFieldSubsystem | |
| getAtomDefaultColor(DuMM::AtomIndex atomIx) const | DuMMForceFieldSubsystem | |
| getAtomElement(DuMM::AtomIndex atomIx) const | DuMMForceFieldSubsystem | |
| getAtomMass(DuMM::AtomIndex atomIx) const | DuMMForceFieldSubsystem | |
| getAtomRadius(DuMM::AtomIndex atomIx) const | DuMMForceFieldSubsystem | |
| getAtomStationInCluster(DuMM::AtomIndex atomIx, DuMM::ClusterIndex clusterIx) const | DuMMForceFieldSubsystem | |
| getAtomStationOnBody(DuMM::AtomIndex atomIx) const | DuMMForceFieldSubsystem | |
| getBiotypeChargedAtomType(BiotypeIndex biotypeIx) const | DuMMForceFieldSubsystem | |
| getBondAtom(DuMM::BondIndex bond, int which) const | DuMMForceFieldSubsystem | |
| getCacheEntry(const State &, int index) const | Subsystem | |
| getChargedAtomTypeIndex(const String &chargedTypeName) const | DuMMForceFieldSubsystem | |
| getClusterBody(DuMM::ClusterIndex clusterIx) const | DuMMForceFieldSubsystem | |
| getClusterPlacementInCluster(DuMM::ClusterIndex childClusterIndex, DuMM::ClusterIndex parentClusterIndex) const | DuMMForceFieldSubsystem | |
| getClusterPlacementOnBody(DuMM::ClusterIndex clusterIx) const | DuMMForceFieldSubsystem | |
| getDiscreteVariable(const State &, int index) const | Subsystem | |
| getElementDefaultColor(int atomicNumber) const | DuMMForceFieldSubsystem | |
| getForceEvaluationCount() const | DuMMForceFieldSubsystem | |
| getMultipliers(const State &) const | Subsystem | |
| getMultipliersStart(const State &) const | Subsystem | |
| getMySubsystemIndex() const | Subsystem | |
| getName() const | Subsystem | |
| getNAtoms() const | DuMMForceFieldSubsystem | |
| getNBonds() const | DuMMForceFieldSubsystem | |
| getNextUnusedAtomClassIndex() const | DuMMForceFieldSubsystem | |
| getNextUnusedChargedAtomTypeIndex() const | DuMMForceFieldSubsystem | |
| getNMultipliers(const State &) const | Subsystem | |
| getNQ(const State &) const | Subsystem | |
| getNQErr(const State &) const | Subsystem | |
| getNU(const State &) const | Subsystem | |
| getNUDotErr(const State &) const | Subsystem | |
| getNUErr(const State &) const | Subsystem | |
| getNZ(const State &) const | Subsystem | |
| getQ(const State &) const | Subsystem | |
| getQDot(const State &) const | Subsystem | |
| getQDotDot(const State &) const | Subsystem | |
| getQErr(const State &) const | Subsystem | |
| getQErrStart(const State &) const | Subsystem | |
| getQStart(const State &) const | Subsystem | |
| getStage(const State &) const | Subsystem | |
| getSubsystemGuts() const | Subsystem | [inline] |
| getSystem() const | Subsystem | |
| getU(const State &) const | Subsystem | |
| getUDot(const State &) const | Subsystem | |
| getUDotErr(const State &) const | Subsystem | |
| getUDotErrStart(const State &) const | Subsystem | |
| getUErr(const State &) const | Subsystem | |
| getUErrStart(const State &) const | Subsystem | |
| getUseMultithreadedComputation() | DuMMForceFieldSubsystem | |
| getUStart(const State &) const | Subsystem | |
| getVdwGlobalScaleFactor() const | DuMMForceFieldSubsystem | |
| getVdwMixingRule() const | DuMMForceFieldSubsystem | |
| getVdwMixingRuleName(VdwMixingRule) const | DuMMForceFieldSubsystem | |
| getVdwRadius(DuMM::AtomClassIndex atomClassIx) const | DuMMForceFieldSubsystem | |
| getVdwWellDepth(DuMM::AtomClassIndex atomClassIx) const | DuMMForceFieldSubsystem | |
| getVersion() const | Subsystem | |
| getZ(const State &) const | Subsystem | |
| getZDot(const State &) const | Subsystem | |
| getZStart(const State &) const | Subsystem | |
| Guts class | Subsystem | [friend] |
| HalgrenHHG enum value | DuMMForceFieldSubsystem | |
| hasAtomClass(DuMM::AtomClassIndex) const | DuMMForceFieldSubsystem | |
| hasAtomClass(const String &atomClassName) const | DuMMForceFieldSubsystem | |
| hasChargedAtomType(DuMM::ChargedAtomTypeIndex) const | DuMMForceFieldSubsystem | |
| hasChargedAtomType(const String &chargedTypeName) const | DuMMForceFieldSubsystem | |
| hasGuts() const | Subsystem | [inline] |
| invalidateSubsystemTopologyCache() const | Subsystem | |
| isEmptyHandle() const | Subsystem | |
| isInSameSystem(const Subsystem &otherSubsystem) const | Subsystem | |
| isInSystem() const | Subsystem | |
| isOwnerHandle() const | Subsystem | |
| isSameSubsystem(const Subsystem &otherSubsystem) const | Subsystem | |
| isValidAtomClass(DuMM::AtomClassIndex) const | DuMMForceFieldSubsystem | [protected] |
| Jorgensen enum value | DuMMForceFieldSubsystem | |
| Kong enum value | DuMMForceFieldSubsystem | |
| loadAmber99Parameters() | DuMMForceFieldSubsystem | |
| loadTestMoleculeParameters() | DuMMForceFieldSubsystem | |
| LorentzBerthelot enum value | DuMMForceFieldSubsystem | |
| MolecularMechanicsSystem class | DuMMForceFieldSubsystem | [friend] |
| operator=(const Subsystem &) | Subsystem | |
| placeAtomInCluster(DuMM::AtomIndex atomIx, DuMM::ClusterIndex clusterIx, const Vec3 &station) | DuMMForceFieldSubsystem | |
| placeClusterInCluster(DuMM::ClusterIndex childClusterIndex, DuMM::ClusterIndex parentClusterIndex, const Transform &placement) | DuMMForceFieldSubsystem | |
| populateFromTinkerParameterFile(std::istream &) | DuMMForceFieldSubsystem | |
| setAllGlobalScaleFactors(Real s) | DuMMForceFieldSubsystem | [inline] |
| setAmberImproperTorsionGlobalScaleFactor(Real) | DuMMForceFieldSubsystem | |
| setAtomClassVdwParameters(DuMM::AtomClassIndex atomClassIx, Real vdwRadiusInNm, Real vdwWellDepthInKJPerMol) | DuMMForceFieldSubsystem | [protected] |
| setAtomClassVdwParameters_KA(DuMM::AtomClassIndex atomClassIx, Real radiusInAng, Real wellDepthInKcal) | DuMMForceFieldSubsystem | [inline, protected] |
| setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex chargedAtomTypeIndex, BiotypeIndex biotypeIx) | DuMMForceFieldSubsystem | |
| setBondBendGlobalScaleFactor(Real) | DuMMForceFieldSubsystem | |
| setBondStretchGlobalScaleFactor(Real) | DuMMForceFieldSubsystem | |
| setBondTorsionGlobalScaleFactor(Real) | DuMMForceFieldSubsystem | |
| setChargedAtomTypeCharge(DuMM::ChargedAtomTypeIndex, Real charge) | DuMMForceFieldSubsystem | [protected] |
| setChargedAtomTypeCharge_KA(DuMM::ChargedAtomTypeIndex chargedAtomTypeIx, Real charge) | DuMMForceFieldSubsystem | [inline, protected] |
| setCoulomb12ScaleFactor(Real) | DuMMForceFieldSubsystem | |
| setCoulomb13ScaleFactor(Real) | DuMMForceFieldSubsystem | |
| setCoulomb14ScaleFactor(Real) | DuMMForceFieldSubsystem | |
| setCoulomb15ScaleFactor(Real) | DuMMForceFieldSubsystem | |
| setCoulombGlobalScaleFactor(Real) | DuMMForceFieldSubsystem | |
| setGbsaGlobalScaleFactor(Real) | DuMMForceFieldSubsystem | |
| setGbsaIncludeAceApproximation(bool) | DuMMForceFieldSubsystem | |
| setGbsaIncludeAceApproximationOff() | DuMMForceFieldSubsystem | [inline] |
| setGbsaIncludeAceApproximationOn() | DuMMForceFieldSubsystem | [inline] |
| setQ(State &s, const Vector &q) const | Subsystem | [inline] |
| setSystem(System &, SubsystemIndex) | Subsystem | |
| setU(State &s, const Vector &u) const | Subsystem | [inline] |
| setUseMultithreadedComputation(bool) | DuMMForceFieldSubsystem | |
| setVdw12ScaleFactor(Real) | DuMMForceFieldSubsystem | |
| setVdw13ScaleFactor(Real) | DuMMForceFieldSubsystem | |
| setVdw14ScaleFactor(Real) | DuMMForceFieldSubsystem | |
| setVdw15ScaleFactor(Real) | DuMMForceFieldSubsystem | |
| setVdwGlobalScaleFactor(Real) | DuMMForceFieldSubsystem | |
| setVdwMixingRule(VdwMixingRule) | DuMMForceFieldSubsystem | |
| setZ(State &s, const Vector &z) const | Subsystem | [inline] |
| Subsystem | DuMMForceFieldSubsystem | [protected] |
| SimTK::Subsystem::Subsystem() | Subsystem | [inline] |
| SimTK::Subsystem::Subsystem(const Subsystem &) | Subsystem | |
| SimTK::Subsystem::Subsystem(Subsystem::Guts *g) | Subsystem | [inline, explicit] |
| subsystemTopologyHasBeenRealized() const | Subsystem | |
| updCacheEntry(const State &, int index) const | Subsystem | |
| updDiscreteVariable(State &, int index) const | Subsystem | |
| updMultipliers(const State &) const | Subsystem | |
| updQ(State &) const | Subsystem | |
| updQDot(const State &) const | Subsystem | |
| updQDotDot(const State &) const | Subsystem | |
| updQErr(const State &) const | Subsystem | |
| updSubsystemGuts() | Subsystem | [inline] |
| updSystem() | Subsystem | |
| updU(State &) const | Subsystem | |
| updUDot(const State &) const | Subsystem | |
| updUDotErr(const State &) const | Subsystem | |
| updUErr(const State &) const | Subsystem | |
| updZ(State &) const | Subsystem | |
| updZDot(const State &) const | Subsystem | |
| VdwMixingRule enum name | DuMMForceFieldSubsystem | |
| WaldmanHagler enum value | DuMMForceFieldSubsystem | |
| ~Subsystem() | Subsystem | |
