- a -

• add() : Modeller
• addAcceptor() : CustomHbondForce
• addAngle() : AmoebaAngleForce , AmoebaInPlaneAngleForce , CustomAngleForce , HarmonicAngleForce
• addAtom() : Topology
• addBond() : Topology , AmoebaBondForce , CustomBondForce , CustomCompoundBondForce , GBVIForce , HarmonicBondForce
• addChain() : Topology
• addComputedValue() : CustomGBForce
• addComputeGlobal() : CustomIntegrator
• addComputePerDof() : CustomIntegrator
• addComputeSum() : CustomIntegrator
• addConstrainPositions() : CustomIntegrator
• addConstraint() : System
• addConstrainVelocities() : CustomIntegrator
• addDonor() : CustomHbondForce
• addEnergyTerm() : CustomGBForce
• addException() : NonbondedForce
• addException_usingRMin() : NonbondedForce
• addExclusion() : CustomGBForce , CustomHbondForce , CustomManyParticleForce , CustomNonbondedForce
• addExtraParticles() : Modeller
• addForce() : System
• addFunction() : CustomCompoundBondForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce
• addGlobalParameter() : CustomAngleForce , CustomBondForce , CustomCompoundBondForce , CustomExternalForce , CustomGBForce , CustomHbondForce , CustomManyParticleForce , CustomNonbondedForce , CustomTorsionForce
• addGlobalVariable() : CustomIntegrator
• addHydrogens() : Modeller
• addInteractionGroup() : CustomNonbondedForce
• addMap() : CMAPTorsionForce
• addMultipole() : AmoebaMultipoleForce
• addOutOfPlaneBend() : AmoebaOutOfPlaneBendForce
• addParticle() : AmoebaGeneralizedKirkwoodForce , AmoebaVdwForce , AmoebaWcaDispersionForce , CustomExternalForce , CustomGBForce , CustomManyParticleForce , CustomNonbondedForce , DrudeForce , GBSAOBCForce , GBVIForce , NonbondedForce , System
• addParticle_usingRVdw() : NonbondedForce
• addPerAcceptorParameter() : CustomHbondForce
• addPerAngleParameter() : CustomAngleForce
• addPerBondParameter() : CustomBondForce , CustomCompoundBondForce
• addPerDofVariable() : CustomIntegrator
• addPerDonorParameter() : CustomHbondForce
• addPerParticleParameter() : CustomExternalForce , CustomGBForce , CustomManyParticleForce , CustomNonbondedForce
• addPerTorsionParameter() : CustomTorsionForce
• addPiTorsion() : AmoebaPiTorsionForce
• addResidue() : Topology
• addScreenedPair() : DrudeForce
• addSolvent() : Modeller
• addStretchBend() : AmoebaStretchBendForce
• addTabulatedFunction() : CustomCompoundBondForce , CustomGBForce , CustomHbondForce , CustomManyParticleForce , CustomNonbondedForce
• addTorsion() : CMAPTorsionForce , CustomTorsionForce , PeriodicTorsionForce , RBTorsionForce
• addTorsionTorsion() : AmoebaTorsionTorsionForce
• addUpdateContextState() : CustomIntegrator
• applyConstraints() : Context
• applyVelocityConstraints() : Context
• atomic_number() : Element
• atoms() : Chain , Residue , Topology