, 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 | |
| AliphaticCarbon(AtomName atomName="C") | AliphaticCarbon | [inline] |
| AtomName typedef | Compound | |
| AtomPathName typedef | Compound | |
| AtomTargetLocations typedef | Compound | |
| 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 | |
| clearHandle() | PIMPLHandle | [inline] |
| Compound() | Compound | |
| Compound(const Name &name) | Compound | [explicit] |
| Compound(CompoundRep *ip) | Compound | [explicit, protected] |
| CompoundSystem class | Compound | [friend] |
| convertInboardBondCenterToOutboard() | Compound | |
| copyAssign(const HANDLE &source) | PIMPLHandle | [inline] |
| createAtomTargets(const class PdbStructure &targetStructure) const | Compound | |
| createAtomTargets(const class PdbChain &targetChain) const | Compound | |
| createAtomTargets(const class PdbResidue &targetResidue) const | Compound | |
| 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(HANDLE &newOwner) | PIMPLHandle | [inline] |
| 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 | [inline] |
| getImplHandleCount() const | PIMPLHandle | [inline] |
| getNAtoms() const | Compound | |
| getNBondCenters() const | Compound | |
| getNBondCenters(Compound::AtomIndex atomIndex) const | Compound | |
| getNBonds() const | Compound | |
| getNSubcompounds() const | Compound | |
| getPdbChainId() const | Compound | |
| getPdbResidueName() const | Compound | |
| getPdbResidueNumber() const | Compound | |
| getSubcompound(Compound::Index) const | Compound | |
| 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 | |
| hasAtom(const AtomPathName &name) const | Compound | |
| hasBondCenter(const BondCenterPathName &bondCenter) const | Compound | |
| hasSameImplementation(const HANDLE &other) const | PIMPLHandle | [inline, protected] |
| hasSubcompound(const Name &name) const | Compound | |
| inheritAtomNames(const Compound::Name &) | Compound | |
| inheritBondCenterNames(const Compound::Name &) | Compound | |
| isEmptyHandle() const | PIMPLHandle | [inline] |
| isOwnerHandle() const | PIMPLHandle | [inline] |
| isSameHandle(const HANDLE &other) const | PIMPLHandle | [inline] |
| matchDefaultAtomChirality(const AtomTargetLocations &atomTargets) | Compound | |
| matchDefaultBondAngles(const AtomTargetLocations &atomTargets) | Compound | |
| matchDefaultBondLengths(const AtomTargetLocations &atomTargets) | Compound | |
| matchDefaultConfiguration(const AtomTargetLocations &atomTargets) | Compound | |
| matchDefaultDihedralAngles(const AtomTargetLocations &atomTargets) | Compound | |
| matchDefaultTopLevelTransform(const AtomTargetLocations &atomTargets) | Compound | |
| Name typedef | Compound | |
| nameAtom(const Compound::AtomName &newName, const AtomPathName &oldName) | Compound | |
| nameAtom(const Compound::AtomName &newName, const AtomPathName &oldName, BiotypeIndex biotype) | Compound | |
| nameBondCenter(Compound::BondCenterName newName, BondCenterPathName oldName) | Compound | |
| operator=(const PIMPLHandle &source) | PIMPLHandle | [inline, protected] |
| ParentHandle typedef | PIMPLHandle | |
| PIMPLHandle(IMPL *p=0) | PIMPLHandle | [inline, explicit, protected] |
| PIMPLHandle(const PIMPLHandle &source) | PIMPLHandle | [inline, protected] |
| 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 | |
| QuadrivalentAtom(const Compound::AtomName &atomName, const Element &element) | QuadrivalentAtom | [inline] |
| QuadrivalentAtom(const Compound::AtomName &atomName, const Element &element, Angle bond12Angle, Angle bond13Angle, Angle bond14Angle, Angle dihedral3, Angle dihedral4) | QuadrivalentAtom | [inline] |
| referenceAssign(const HANDLE &source) | PIMPLHandle | [inline] |
| 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 Vec3 &location=Vec3(0)) | Compound | |
| setBaseAtom(const Compound::AtomName &name, const Biotype &biotype, const Vec3 &location=Vec3(0)) | Compound | |
| setBaseAtom(const Compound::SingleAtom &c, const Transform &=Transform()) | Compound | |
| setBaseCompound(const Compound::Name &n, const Compound &c, const Transform &=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 | |
| setCompoundSystem(CompoundSystem &system, Compound::Index) | 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, Compound::AtomName atom1, Compound::AtomName atom2, Compound::AtomName atom3, 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(IMPL *p) | PIMPLHandle | [inline, protected] |
| setInboardBondCenter(const Compound::BondCenterName ¢erName) | Compound | |
| setPdbChainId(char chainId) | Compound | |
| setPdbResidueName(const String &resName) | Compound | |
| setPdbResidueNumber(int resNum) | Compound | |
| setTopLevelTransform(const Transform &transform) | Compound | |
| SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE(Compound, Index) | 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 | |
| SingleAtom(const Compound::AtomName &atomName, const Element &element) | Compound::SingleAtom | [inline] |
| updImpl() | PIMPLHandle | [inline] |
| updSubcompound(Compound::Index) | Compound | |
| updSubcompound(const Compound::Name &subcompoundName) | Compound | |
| writeDefaultPdb(std::ostream &os, const Transform &transform=Transform()) const | Compound | |
| writeDefaultPdb(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, char *outFileName, const Transform &transform=Transform()) const | Compound | |
| writePdb(const State &state, std::ostream &os, int &nextAtomSerialNumber, const Transform &transform=Transform()) const | Compound | |
| ~PIMPLHandle() | PIMPLHandle | [inline, protected] |
