SimTK::RNA Member List

This is the complete list of members for SimTK::RNA, including all inherited members.

addCompoundSynonym(const Name &)	SimTK::Compound
addFirstBondCenter(const Compound::BondCenterName &centerName, const Compound::AtomPathName &atomName)	SimTK::Compound
addLeftHandedBondCenter(const Compound::BondCenterName &centerName, const Compound::AtomName &atomName, Angle bondAngle1, Angle bondAngle2)	SimTK::Compound
addPlanarBondCenter(const Compound::BondCenterName &centerName, const Compound::AtomName &atomName, Angle bondAngle1, Angle bondAngle2)	SimTK::Compound
addRightHandedBondCenter(const Compound::BondCenterName &centerName, const Compound::AtomName &atomName, Angle bondAngle1, Angle bondAngle2)	SimTK::Compound
addRingClosingBond(const Compound::BondCenterPathName &centerName1, const Compound::BondCenterPathName &centerName2, mdunits::Length bondLength, Angle dihedral=180 *Deg2Rad, BondMobility::Mobility mobility=BondMobility::Default)	SimTK::Compound
addRingClosingBond(const Compound::BondCenterPathName &centerName1, const Compound::BondCenterPathName &centerName2)	SimTK::Compound
addSecondBondCenter(const Compound::BondCenterName &centerName, const Compound::AtomName &atomName, Angle bondAngle1)	SimTK::Compound
appendResidue(const Compound::Name &resName, const BiopolymerResidue &residue)	SimTK::Biopolymer
appendResidue(const Compound::Name &resName, const BiopolymerResidue &residue, BondMobility::Mobility mobility)	SimTK::Biopolymer
assignBiotypes()	SimTK::Biopolymer
assignResidueBiotypes(ResidueInfo::Index, Ordinality::Residue)	SimTK::Biopolymer
AtomName typedef	SimTK::Compound
AtomPathName typedef	SimTK::Compound
AtomTargetLocations typedef	SimTK::Compound
Biopolymer()	SimTK::Biopolymer
bondAtom(const Compound::SingleAtom &c, const BondCenterPathName &parentBondName, mdunits::Length distance, Angle dihedral=0, BondMobility::Mobility=BondMobility::Default)	SimTK::Compound
bondAtom(const Compound::SingleAtom &c, const BondCenterPathName &parentBondName)	SimTK::Compound
BondCenterName typedef	SimTK::Compound
BondCenterPathName typedef	SimTK::Compound
bondCompound(const Compound::Name &n, const Compound &c, const BondCenterPathName &parentBondName, mdunits::Length distance, Angle dihedral=180 *Deg2Rad, BondMobility::Mobility mobility=BondMobility::Default)	SimTK::Compound
bondCompound(const Compound::Name &n, const Compound &c, const BondCenterPathName &parentBondName)	SimTK::Compound
bondCompound(const Compound::Name &n, const Compound &c, const BondCenterPathName &parentBondName, BondMobility::Mobility mobility)	SimTK::Compound
calcAtomAccelerationInGroundFrame(const State &state, Compound::AtomIndex atomId) const	SimTK::Compound
calcAtomLocationInCompoundFrame(const State &state, Compound::AtomIndex atomId) const	SimTK::Compound
calcAtomLocationInGroundFrame(const State &state, Compound::AtomIndex atomId) const	SimTK::Compound
calcAtomVelocityInGroundFrame(const State &state, Compound::AtomIndex atomId) const	SimTK::Compound
calcDefaultAtomFrameInCompoundFrame(Compound::AtomIndex) const	SimTK::Compound
calcDefaultAtomLocationInCompoundFrame(const AtomPathName &atomName) const	SimTK::Compound
calcDefaultAtomLocationInGroundFrame(const AtomPathName &atomName) const	SimTK::Compound
calcDefaultDihedralAngle(const DihedralName &dihedralName) const	SimTK::Compound
calcDihedralAngle(const State &state, const DihedralName &dihedralName) const	SimTK::Compound
calcRNABaseNormal(const State &state, int residueNumber, int bodyOrGroundFrame, const SimbodyMatterSubsystem &matter) const	SimTK::RNA	[inline]
clearHandle()	SimTK::PIMPLHandle< Compound, CompoundRep >
Compound()	SimTK::Compound
Compound(const Name &name)	SimTK::Compound	[explicit]
Compound(CompoundRep *ip)	SimTK::Compound	[explicit, protected]
CompoundSystem class	SimTK::Compound	[friend]
convertInboardBondCenterToOutboard()	SimTK::Compound
copyAssign(const Compound &source)	SimTK::PIMPLHandle< Compound, CompoundRep >
createAtomTargets(const class PdbStructure &targetStructure) const	SimTK::Biopolymer	[virtual]
createAtomTargets(const class PdbChain &targetChain) const	SimTK::Biopolymer	[virtual]
SimTK::Molecule::createAtomTargets(const class PdbResidue &targetResidue) const	SimTK::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)	SimTK::Compound
defineDihedralAngle(const Compound::DihedralName &angleName, const Compound::BondCenterPathName &bond1, const Compound::BondCenterPathName &bond2, Angle offset=0 *Deg2Rad)	SimTK::Compound
DihedralName typedef	SimTK::Compound
disown(Compound &newOwner)	SimTK::PIMPLHandle< Compound, CompoundRep >
DistortPlanarBonds enum value	SimTK::Compound
fitDefaultConfiguration(const AtomTargetLocations &atomTargets, SimTK::Real targetRms)	SimTK::Compound
FlipPlanarBonds enum value	SimTK::Compound
getAtomBiotypeIndex(Compound::AtomIndex) const	SimTK::Compound
getAtomElement(Compound::AtomIndex) const	SimTK::Compound
getAtomElement(const Compound::AtomName &) const	SimTK::Compound
getAtomIndex(const Compound::AtomPathName &) const	SimTK::Compound
getAtomLocationInMobilizedBodyFrame(Compound::AtomIndex) const	SimTK::Compound
getAtomMobilizedBodyIndex(Compound::AtomIndex) const	SimTK::Compound
getAtomName(Compound::AtomIndex) const	SimTK::Compound
getBondAtomIndex(Compound::BondIndex bondIndex, int which) const	SimTK::Compound
getCompoundName() const	SimTK::Compound
getDuMMAtomIndex(Compound::AtomIndex) const	SimTK::Compound
getImpl() const	SimTK::PIMPLHandle< Compound, CompoundRep >
getImplHandleCount() const	SimTK::PIMPLHandle< Compound, CompoundRep >
getNResidues() const	SimTK::Biopolymer	[inline]
getNumAtoms() const	SimTK::Compound
getNumBondCenters() const	SimTK::Compound
getNumBondCenters(Compound::AtomIndex atomIndex) const	SimTK::Compound
getNumBonds() const	SimTK::Compound
getNumResidues() const	SimTK::Biopolymer
getPdbChainId() const	SimTK::Compound
getPdbResidueName() const	SimTK::Compound
getPdbResidueNumber() const	SimTK::Compound
getResidue(ResidueInfo::Index residueIndex) const	SimTK::Biopolymer
getResidue(Compound::Name residueName) const	SimTK::Biopolymer
getResidueAtomLocationInMobilizedBodyFrame(ResidueInfo::Index res, ResidueInfo::AtomIndex a) const	SimTK::Biopolymer	[inline]
getResidueAtomMobilizedBodyIndex(ResidueInfo::Index res, ResidueInfo::AtomIndex a) const	SimTK::Biopolymer	[inline]
getResidueName(ResidueInfo::Index residueIndex) const	SimTK::Biopolymer
getSubcompound(const Compound::Name &subcompoundName) const	SimTK::Compound
getSubcompoundFrameInParentFrame(const Compound::Name &subcompoundName) const	SimTK::Compound
getTopLevelTransform() const	SimTK::Compound
getTransformAndResidual(const Compound::AtomTargetLocations &atomTargets) const	SimTK::Compound
HandleBase typedef	SimTK::PIMPLHandle< Compound, CompoundRep >
hasAtom(const AtomPathName &name) const	SimTK::Compound
hasBondCenter(const BondCenterPathName &bondCenter) const	SimTK::Compound
hasSameImplementation(const Compound &other) const	SimTK::PIMPLHandle< Compound, CompoundRep >	[protected]
inheritAtomNames(const Compound::Name &)	SimTK::Compound
inheritBondCenterNames(const Compound::Name &)	SimTK::Compound
inheritCompoundSynonyms(const Compound &otherCompound)	SimTK::Compound
isEmptyHandle() const	SimTK::PIMPLHandle< Compound, CompoundRep >
isOwnerHandle() const	SimTK::PIMPLHandle< Compound, CompoundRep >
isSameHandle(const Compound &other) const	SimTK::PIMPLHandle< Compound, CompoundRep >
KeepPlanarBonds enum value	SimTK::Compound
Match_Exact enum value	SimTK::Compound
Match_Idealized enum value	SimTK::Compound
Match_TopologyOnly enum value	SimTK::Compound
matchDefaultAtomChirality(const AtomTargetLocations &atomTargets, Angle planarityTolerance=90.0 *Deg2Rad, bool flipAll=true)	SimTK::Compound
matchDefaultBondAngles(const AtomTargetLocations &atomTargets)	SimTK::Compound
matchDefaultBondLengths(const AtomTargetLocations &atomTargets)	SimTK::Compound
matchDefaultConfiguration(const AtomTargetLocations &atomTargets, MatchStratagem matchStratagem=Match_Exact)	SimTK::Compound	[inline]
matchDefaultDihedralAngles(const AtomTargetLocations &atomTargets, PlanarBondMatchingPolicy policy=FlipPlanarBonds)	SimTK::Compound
matchDefaultTopLevelTransform(const AtomTargetLocations &atomTargets)	SimTK::Compound
MatchStratagem enum name	SimTK::Compound
Molecule()	SimTK::Molecule
Molecule(CompoundRep *rep)	SimTK::Molecule	[explicit, protected]
Name typedef	SimTK::Compound
nameAtom(const Compound::AtomName &newName, const AtomPathName &oldName)	SimTK::Compound
nameAtom(const Compound::AtomName &newName, const AtomPathName &oldName, BiotypeIndex biotype)	SimTK::Compound
nameBondCenter(const Compound::BondCenterName &newName, const BondCenterPathName &oldName)	SimTK::Compound
operator=(const PIMPLHandle &source)	SimTK::PIMPLHandle< Compound, CompoundRep >	[protected]
ParentHandle typedef	SimTK::PIMPLHandle< Compound, CompoundRep >
PIMPLHandle(CompoundRep *p=0)	SimTK::PIMPLHandle< Compound, CompoundRep >	[protected]
PIMPLHandle(const PIMPLHandle &source)	SimTK::PIMPLHandle< Compound, CompoundRep >	[protected]
PlanarBondMatchingPolicy enum name	SimTK::Compound
populateDefaultPdbChain(class PdbChain &, int &defaultNextResidueNumber, const Transform &transform=Transform()) const	SimTK::Compound
populatePdbChain(const State &state, class PdbChain &, int &defaultNextResidueNumber, const Transform &transform=Transform()) const	SimTK::Compound
referenceAssign(const Compound &source)	SimTK::PIMPLHandle< Compound, CompoundRep >
renumberPdbResidues(int firstPdbResidueNumber)	SimTK::Biopolymer
RNA(const PdbStructure &pdbStructure)	SimTK::RNA	[inline, explicit]
RNA(const PdbChain &pdbChain)	SimTK::RNA	[inline, explicit]
RNA(const Sequence &seq, bool useCappingHydroxyls=true)	SimTK::RNA	[inline, explicit]
Sequence typedef	SimTK::Biopolymer
setAtomBiotype(const Compound::AtomPathName &atomName, const String &biotypeResidueName, const String &biotypeAtomName, SimTK::Ordinality::Residue ordinality=SimTK::Ordinality::Any)	SimTK::Compound	[inline]
setBaseAtom(const Compound::AtomName &name, const Element &element, const Transform &location=Vec3(0))	SimTK::Compound
setBaseAtom(const Compound::AtomName &name, const Biotype &biotype, const Transform &location=Vec3(0))	SimTK::Compound
setBaseAtom(const Compound::SingleAtom &c, const Transform &=Transform())	SimTK::Compound
setBaseCompound(const Compound::Name &n, const Compound &c, const Transform &location=Transform())	SimTK::Compound
setBiotypeIndex(const Compound::AtomPathName &atomName, BiotypeIndex biotype)	SimTK::Compound
setBondMobility(BondMobility::Mobility mobility, const AtomPathName &atom1, const AtomPathName &atom2)	SimTK::Compound
setBondMobility(BondMobility::Mobility mobility, Compound::BondIndex bondIndex)	SimTK::Compound
setCompoundBondMobility(BondMobility::Mobility mobility)	SimTK::Compound
setCompoundName(const Name &)	SimTK::Compound
setDefaultBondAngle(Angle angle, const AtomPathName &atom1, const AtomPathName &atom2, const AtomPathName &atom3)	SimTK::Compound
setDefaultBondLength(mdunits::Length length, const AtomPathName &atom1, const AtomPathName &atom2)	SimTK::Compound
setDefaultDihedralAngle(const DihedralName &dihedralName, Angle angleInRadians)	SimTK::Compound
setDefaultDihedralAngle(Angle angle, Compound::AtomIndex atom1, Compound::AtomIndex atom2, Compound::AtomIndex atom3, Compound::AtomIndex atom4)	SimTK::Compound
setDefaultDihedralAngle(Angle angle, const Compound::AtomName &atom1, const Compound::AtomName &atom2, const Compound::AtomName &atom3, const Compound::AtomName &atom4)	SimTK::Compound
setDefaultInboardBondLength(mdunits::Length)	SimTK::Compound
setDefaultInboardDihedralAngle(Angle)	SimTK::Compound
setDihedralAngle(State &state, const DihedralName &dihedralName, Angle)	SimTK::Compound
setDuMMAtomIndex(Compound::AtomIndex, DuMM::AtomIndex)	SimTK::Compound	[protected]
setImpl(CompoundRep *p)	SimTK::PIMPLHandle< Compound, CompoundRep >	[protected]
setInboardBondCenter(const Compound::BondCenterName &centerName)	SimTK::Compound
setMultibodySystem(MultibodySystem &system)	SimTK::Compound
setPdbChainId(char chainId)	SimTK::Compound
setPdbResidueName(const String &resName)	SimTK::Compound
setPdbResidueNumber(int resNum)	SimTK::Compound
setResidueBondMobility(ResidueInfo::Index, BondMobility::Mobility)	SimTK::Biopolymer
setRNABondMobility(BondMobility::Mobility mobility, ResidueInfo::Index startResidue, ResidueInfo::Index endResidue)	SimTK::RNA	[inline]
setTopLevelTransform(const Transform &transform)	SimTK::Compound
SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE(Compound, AtomIndex)	SimTK::Compound
SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE(Compound, LocalAtomIndex)	SimTK::Compound
SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE(Compound, BondCenterIndex)	SimTK::Compound
SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE(Compound, BondIndex)	SimTK::Compound
SimTK_INSERT_DERIVED_HANDLE_DECLARATIONS(Biopolymer, BiopolymerRep, Molecule)	SimTK::Biopolymer
SimTK::Molecule::SimTK_INSERT_DERIVED_HANDLE_DECLARATIONS(Molecule, CompoundRep, Compound)	SimTK::Molecule
updImpl()	SimTK::PIMPLHandle< Compound, CompoundRep >
updResidue(ResidueInfo::Index residueIndex)	SimTK::Biopolymer
updResidue(Compound::Name residueName)	SimTK::Biopolymer
updSubcompound(const Compound::Name &subcompoundName)	SimTK::Compound
writeDefaultPdb(std::ostream &os, const Transform &transform=Transform()) const	SimTK::Compound
writeDefaultPdb(const char *outFileName, const Transform &transform) const	SimTK::Compound
writeDefaultPdb(std::ostream &os, int &nextAtomSerialNumber, const Transform &transform=Transform()) const	SimTK::Compound
writePdb(const State &state, std::ostream &os, const Transform &transform=Transform()) const	SimTK::Compound
writePdb(const State &state, std::ostream &os, int &nextAtomSerialNumber, const Transform &transform=Transform()) const	SimTK::Compound
~PIMPLHandle()	SimTK::PIMPLHandle< Compound, CompoundRep >	[protected]