, including all inherited members.
| addCompoundSynonym(const Name &) | Compound | |
| addFirstBondCenter(const Compound::BondCenterName ¢erName, const Compound::AtomPathName &atomName) | Compound | |
| addLeftHandedBondCenter(const Compound::BondCenterName ¢erName, const Compound::AtomName &atomName, Angle bondAngle1, Angle bondAngle2) | Compound | |
| addPlanarBondCenter(const Compound::BondCenterName ¢erName, const Compound::AtomName &atomName, Angle bondAngle1, Angle bondAngle2) | Compound | |
| addRightHandedBondCenter(const Compound::BondCenterName ¢erName, const Compound::AtomName &atomName, Angle bondAngle1, Angle bondAngle2) | Compound | |
| addRingClosingBond(const Compound::BondCenterPathName ¢erName1, const Compound::BondCenterPathName ¢erName2, mdunits::Length bondLength, Angle dihedral=180 *Deg2Rad, BondMobility::Mobility mobility=BondMobility::Default) | Compound | |
| addRingClosingBond(const Compound::BondCenterPathName ¢erName1, const Compound::BondCenterPathName ¢erName2) | Compound | |
| addSecondBondCenter(const Compound::BondCenterName ¢erName, const Compound::AtomName &atomName, Angle bondAngle1) | Compound | |
| appendResidue(const Compound::Name &resName, const BiopolymerResidue &residue) | Biopolymer | |
| appendResidue(const Compound::Name &resName, const BiopolymerResidue &residue, BondMobility::Mobility mobility) | Biopolymer | |
| assignBiotypes() | Biopolymer | |
| assignResidueBiotypes(ResidueInfo::Index, Ordinality::Residue) | Biopolymer | |
| AtomName typedef | Compound | |
| AtomPathName typedef | Compound | |
| AtomTargetLocations typedef | Compound | |
| Biopolymer() | Biopolymer | |
| bondAtom(const Compound::SingleAtom &c, const BondCenterPathName &parentBondName, mdunits::Length distance, Angle dihedral=0, BondMobility::Mobility=BondMobility::Default) | Compound | |
| bondAtom(const Compound::SingleAtom &c, const BondCenterPathName &parentBondName) | Compound | |
| BondCenterName typedef | Compound | |
| BondCenterPathName typedef | Compound | |
| bondCompound(const Compound::Name &n, const Compound &c, const BondCenterPathName &parentBondName, mdunits::Length distance, Angle dihedral=180 *Deg2Rad, BondMobility::Mobility mobility=BondMobility::Default) | Compound | |
| bondCompound(const Compound::Name &n, const Compound &c, const BondCenterPathName &parentBondName) | Compound | |
| bondCompound(const Compound::Name &n, const Compound &c, const BondCenterPathName &parentBondName, BondMobility::Mobility mobility) | Compound | |
| calcAtomAccelerationInGroundFrame(const State &state, Compound::AtomIndex atomId) const | Compound | |
| calcAtomLocationInCompoundFrame(const State &state, Compound::AtomIndex atomId) const | Compound | |
| calcAtomLocationInGroundFrame(const State &state, Compound::AtomIndex atomId) const | Compound | |
| calcAtomVelocityInGroundFrame(const State &state, Compound::AtomIndex atomId) const | Compound | |
| calcDefaultAtomFrameInCompoundFrame(Compound::AtomIndex) const | Compound | |
| calcDefaultAtomLocationInCompoundFrame(const AtomPathName &atomName) const | Compound | |
| calcDefaultAtomLocationInGroundFrame(const AtomPathName &atomName) const | Compound | |
| calcDefaultDihedralAngle(const DihedralName &dihedralName) const | Compound | |
| calcDihedralAngle(const State &state, const DihedralName &dihedralName) const | Compound | |
| calcRNABaseNormal(const State &state, int residueNumber, int bodyOrGroundFrame, const SimbodyMatterSubsystem &matter) const | RNA | [inline] |
| clearHandle() | PIMPLHandle< Compound, CompoundRep > | |
| Compound() | Compound | |
| Compound(const Name &name) | Compound | [explicit] |
| Compound(CompoundRep *ip) | Compound | [explicit, protected] |
| CompoundSystem class | Compound | [friend] |
| convertInboardBondCenterToOutboard() | Compound | |
| copyAssign(const Compound &source) | PIMPLHandle< Compound, CompoundRep > | |
| createAtomTargets(const class PdbStructure &targetStructure) const | Biopolymer | [virtual] |
| createAtomTargets(const class PdbChain &targetChain) const | Biopolymer | [virtual] |
| SimTK::Molecule::createAtomTargets(const class PdbResidue &targetResidue) const | Compound | [virtual] |
| defineDihedralAngle(const Compound::DihedralName &angleName, const Compound::AtomPathName &atom1, const Compound::AtomPathName &atom2, const Compound::AtomPathName &atom3, const Compound::AtomPathName &atom4, Angle offset=0 *Deg2Rad) | Compound | |
| defineDihedralAngle(const Compound::DihedralName &angleName, const Compound::BondCenterPathName &bond1, const Compound::BondCenterPathName &bond2, Angle offset=0 *Deg2Rad) | Compound | |
| DihedralName typedef | Compound | |
| disown(Compound &newOwner) | PIMPLHandle< Compound, CompoundRep > | |
| DistortPlanarBonds enum value | Compound | |
| fitDefaultConfiguration(const AtomTargetLocations &atomTargets, SimTK::Real targetRms) | Compound | |
| getAtomBiotypeIndex(Compound::AtomIndex) const | Compound | |
| getAtomElement(Compound::AtomIndex) const | Compound | |
| getAtomElement(const Compound::AtomName &) const | Compound | |
| getAtomIndex(const Compound::AtomPathName &) const | Compound | |
| getAtomLocationInMobilizedBodyFrame(Compound::AtomIndex) const | Compound | |
| getAtomMobilizedBodyIndex(Compound::AtomIndex) const | Compound | |
| getAtomName(Compound::AtomIndex) const | Compound | |
| getBondAtomIndex(Compound::BondIndex bondIndex, int which) const | Compound | |
| getCompoundName() const | Compound | |
| getDuMMAtomIndex(Compound::AtomIndex) const | Compound | |
| getImpl() const | PIMPLHandle< Compound, CompoundRep > | [inline] |
| getImplHandleCount() const | PIMPLHandle< Compound, CompoundRep > | |
| getNResidues() const | Biopolymer | [inline] |
| getNumAtoms() const | Compound | |
| getNumBondCenters() const | Compound | |
| getNumBondCenters(Compound::AtomIndex atomIndex) const | Compound | |
| getNumBonds() const | Compound | |
| getNumResidues() const | Biopolymer | |
| getPdbChainId() const | Compound | |
| getPdbResidueName() const | Compound | |
| getPdbResidueNumber() const | Compound | |
| getResidue(ResidueInfo::Index residueIndex) const | Biopolymer | |
| getResidue(Compound::Name residueName) const | Biopolymer | |
| getResidueAtomLocationInMobilizedBodyFrame(ResidueInfo::Index res, ResidueInfo::AtomIndex a) const | Biopolymer | [inline] |
| getResidueAtomMobilizedBodyIndex(ResidueInfo::Index res, ResidueInfo::AtomIndex a) const | Biopolymer | [inline] |
| getResidueName(ResidueInfo::Index residueIndex) const | Biopolymer | |
| getSubcompound(const Compound::Name &subcompoundName) const | Compound | |
| getSubcompoundFrameInParentFrame(const Compound::Name &subcompoundName) const | Compound | |
| getTopLevelTransform() const | Compound | |
| getTransformAndResidual(const Compound::AtomTargetLocations &atomTargets) const | Compound | |
| HandleBase typedef | PIMPLHandle< Compound, CompoundRep > | |
| hasAtom(const AtomPathName &name) const | Compound | |
| hasBondCenter(const BondCenterPathName &bondCenter) const | Compound | |
| hasSameImplementation(const Compound &other) const | PIMPLHandle< Compound, CompoundRep > | [protected] |
| inheritAtomNames(const Compound::Name &) | Compound | |
| inheritBondCenterNames(const Compound::Name &) | Compound | |
| inheritCompoundSynonyms(const Compound &otherCompound) | Compound | |
| isEmptyHandle() const | PIMPLHandle< Compound, CompoundRep > | [inline] |
| isOwnerHandle() const | PIMPLHandle< Compound, CompoundRep > | |
| isSameHandle(const Compound &other) const | PIMPLHandle< Compound, CompoundRep > | |
| KeepPlanarBonds enum value | Compound | |
| Match_Exact enum value | Compound | |
| Match_Idealized enum value | Compound | |
| Match_TopologyOnly enum value | Compound | |
| matchDefaultAtomChirality(const AtomTargetLocations &atomTargets, Angle planarityTolerance=90.0 *Deg2Rad, bool flipAll=true) | Compound | |
| matchDefaultBondAngles(const AtomTargetLocations &atomTargets) | Compound | |
| matchDefaultBondLengths(const AtomTargetLocations &atomTargets) | Compound | |
| matchDefaultConfiguration(const AtomTargetLocations &atomTargets, MatchStratagem matchStratagem=Match_Exact) | Compound | [inline] |
| matchDefaultDihedralAngles(const AtomTargetLocations &atomTargets, PlanarBondMatchingPolicy policy=KeepPlanarBonds) | Compound | |
| matchDefaultTopLevelTransform(const AtomTargetLocations &atomTargets) | Compound | |
| MatchStratagem enum name | Compound | |
| Molecule() | Molecule | |
| Molecule(CompoundRep *rep) | Molecule | [explicit, protected] |
| Name typedef | Compound | |
| nameAtom(const Compound::AtomName &newName, const AtomPathName &oldName) | Compound | |
| nameAtom(const Compound::AtomName &newName, const AtomPathName &oldName, BiotypeIndex biotype) | Compound | |
| nameBondCenter(const Compound::BondCenterName &newName, const BondCenterPathName &oldName) | Compound | |
| operator=(const PIMPLHandle &source) | PIMPLHandle< Compound, CompoundRep > | [protected] |
| ParentHandle typedef | PIMPLHandle< Compound, CompoundRep > | |
| PIMPLHandle(CompoundRep *p=0) | PIMPLHandle< Compound, CompoundRep > | [explicit, protected] |
| PIMPLHandle(const PIMPLHandle &source) | PIMPLHandle< Compound, CompoundRep > | [protected] |
| PlanarBondMatchingPolicy enum name | Compound | |
| populateDefaultPdbChain(class PdbChain &, int &defaultNextResidueNumber, const Transform &transform=Transform()) const | Compound | |
| populatePdbChain(const State &state, class PdbChain &, int &defaultNextResidueNumber, const Transform &transform=Transform()) const | Compound | |
| referenceAssign(const Compound &source) | PIMPLHandle< Compound, CompoundRep > | |
| renumberPdbResidues(int firstPdbResidueNumber) | Biopolymer | |
| RNA(const PdbStructure &pdbStructure) | RNA | [inline, explicit] |
| RNA(const PdbChain &pdbChain) | RNA | [inline, explicit] |
| RNA(const Sequence &seq, bool useCappingHydroxyls=true) | RNA | [inline, explicit] |
| Sequence typedef | Biopolymer | |
| setAtomBiotype(const Compound::AtomPathName &atomName, const String &biotypeResidueName, const String &biotypeAtomName, SimTK::Ordinality::Residue ordinality=SimTK::Ordinality::Any) | Compound | [inline] |
| setBaseAtom(const Compound::AtomName &name, const Element &element, const Transform &location=Vec3(0)) | Compound | |
| setBaseAtom(const Compound::AtomName &name, const Biotype &biotype, const Transform &location=Vec3(0)) | Compound | |
| setBaseAtom(const Compound::SingleAtom &c, const Transform &=Transform()) | Compound | |
| setBaseCompound(const Compound::Name &n, const Compound &c, const Transform &location=Transform()) | Compound | |
| setBiotypeIndex(const Compound::AtomPathName &atomName, BiotypeIndex biotype) | Compound | |
| setBondMobility(BondMobility::Mobility mobility, const AtomPathName &atom1, const AtomPathName &atom2) | Compound | |
| setBondMobility(BondMobility::Mobility mobility, Compound::BondIndex bondIndex) | Compound | |
| setCompoundBondMobility(BondMobility::Mobility mobility) | Compound | |
| setCompoundName(const Name &) | Compound | |
| setDefaultBondAngle(Angle angle, const AtomPathName &atom1, const AtomPathName &atom2, const AtomPathName &atom3) | Compound | |
| setDefaultBondLength(mdunits::Length length, const AtomPathName &atom1, const AtomPathName &atom2) | Compound | |
| setDefaultDihedralAngle(const DihedralName &dihedralName, Angle angleInRadians) | Compound | |
| setDefaultDihedralAngle(Angle angle, Compound::AtomIndex atom1, Compound::AtomIndex atom2, Compound::AtomIndex atom3, Compound::AtomIndex atom4) | Compound | |
| setDefaultDihedralAngle(Angle angle, const Compound::AtomName &atom1, const Compound::AtomName &atom2, const Compound::AtomName &atom3, const Compound::AtomName &atom4) | Compound | |
| setDefaultInboardBondLength(mdunits::Length) | Compound | |
| setDefaultInboardDihedralAngle(Angle) | Compound | |
| setDihedralAngle(State &state, const DihedralName &dihedralName, Angle) | Compound | |
| setDuMMAtomIndex(Compound::AtomIndex, DuMM::AtomIndex) | Compound | [protected] |
| setImpl(CompoundRep *p) | PIMPLHandle< Compound, CompoundRep > | [protected] |
| setInboardBondCenter(const Compound::BondCenterName ¢erName) | Compound | |
| setMultibodySystem(MultibodySystem &system) | Compound | |
| setPdbChainId(char chainId) | Compound | |
| setPdbResidueName(const String &resName) | Compound | |
| setPdbResidueNumber(int resNum) | Compound | |
| setResidueBondMobility(ResidueInfo::Index, BondMobility::Mobility) | Biopolymer | |
| setRNABondMobility(BondMobility::Mobility mobility, ResidueInfo::Index startResidue, ResidueInfo::Index endResidue) | RNA | [inline] |
| setTopLevelTransform(const Transform &transform) | Compound | |
| SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE(Compound, AtomIndex) | Compound | |
| SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE(Compound, LocalAtomIndex) | Compound | |
| SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE(Compound, BondCenterIndex) | Compound | |
| SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE(Compound, BondIndex) | Compound | |
| SimTK_INSERT_DERIVED_HANDLE_DECLARATIONS(Biopolymer, BiopolymerRep, Molecule) | Biopolymer | |
| SimTK::Molecule::SimTK_INSERT_DERIVED_HANDLE_DECLARATIONS(Molecule, CompoundRep, Compound) | Molecule | |
| updImpl() | PIMPLHandle< Compound, CompoundRep > | [inline] |
| updResidue(ResidueInfo::Index residueIndex) | Biopolymer | |
| updResidue(Compound::Name residueName) | Biopolymer | |
| updSubcompound(const Compound::Name &subcompoundName) | Compound | |
| writeDefaultPdb(std::ostream &os, const Transform &transform=Transform()) const | Compound | |
| writeDefaultPdb(const char *outFileName, const Transform &transform) const | Compound | |
| writeDefaultPdb(std::ostream &os, int &nextAtomSerialNumber, const Transform &transform=Transform()) const | Compound | |
| writePdb(const State &state, std::ostream &os, const Transform &transform=Transform()) const | Compound | |
| writePdb(const State &state, std::ostream &os, int &nextAtomSerialNumber, const Transform &transform=Transform()) const | Compound | |
| ~PIMPLHandle() | PIMPLHandle< Compound, CompoundRep > | [protected] |
