- a -

• AcetylResidue() : SimTK::AcetylResidue
• Actinium() : SimTK::Element::Actinium
• addAtom() : SimTK::ResidueInfo , SimTK::DuMMForceFieldSubsystem , SimTK::AtomSubsystem , SimTK::PdbResidue , SimTK::VanDerWaalsForce
• addBodyExclusion() : SimTK::AtomSubsystem
• addBond() : SimTK::AtomSubsystem , SimTK::DuMMForceFieldSubsystem
• addBoundarySphere() : SimTK::VanDerWaalsForce
• addCompoundSynonym() : SimTK::Compound
• addFirstBondCenter() : SimTK::Compound
• addLeftHandedBondCenter() : SimTK::Compound
• addPlanarBondCenter() : SimTK::Compound
• addRightHandedBondCenter() : SimTK::Compound
• addRingClosingBond() : SimTK::Compound
• addSecondBondCenter() : SimTK::Compound
• AdenineBase() : SimTK::AdenineBase
• Adenylate() : SimTK::RibonucleotideResidue::Adenylate
• adoptCompound() : SimTK::CompoundSystem
• Alanine() : SimTK::AminoAcidResidue::Alanine
• AlcoholOHGroup() : SimTK::AlcoholOHGroup
• AliphaticCarbon() : SimTK::AliphaticCarbon
• AliphaticHydrogen() : SimTK::AliphaticHydrogen
• Aluminum() : SimTK::Element::Aluminum
• Amber99ForceSubsystem() : SimTK::Amber99ForceSubsystem
• Americium() : SimTK::Element::Americium
• AminoAcidResidue() : SimTK::AminoAcidResidue
• Antimony() : SimTK::Element::Antimony
• appendResidue() : SimTK::Biopolymer , SimTK::PdbChain
• Arginine() : SimTK::AminoAcidResidue::Arginine
• Argon() : SimTK::Biotype , SimTK::Argon , SimTK::Element::Argon
• AromaticSixMemberedCHGroup() : SimTK::AromaticSixMemberedCHGroup
• Arsenic() : SimTK::Element::Arsenic
• Asparagine() : SimTK::AminoAcidResidue::Asparagine
• Aspartate() : SimTK::AminoAcidResidue::Aspartate
• assignBiotypes() : SimTK::Biopolymer , SimTK::BiopolymerResidue
• assignResidueBiotypes() : SimTK::Biopolymer
• Astatine() : SimTK::Element::Astatine
• atEnd() : SimTK::AtomSubsystem::PairIterator
• Atom() : SimTK::AtomSubsystem::Atom
• AtomBonding() : SimTK::CompoundModeler::AtomBonding
• AtomInfo() : SimTK::ResidueInfo::AtomInfo
• AtomsByBody() : SimTK::AtomSubsystem::AtomsByBody
• AtomSubsystem() : SimTK::AtomSubsystem
• attachAtomToBody() : SimTK::DuMMForceFieldSubsystem
• attachClusterToBody() : SimTK::DuMMForceFieldSubsystem