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- add() : Modeller
- addAcceptor() : CustomHbondForce
- addAngle() : AmoebaInPlaneAngleForce , HarmonicAngleForce , CustomAngleForce , AmoebaAngleForce
- addAtom() : Topology
- addBond() : AmoebaBondForce , HarmonicBondForce , CustomBondForce , GBVIForce , CustomCompoundBondForce , Topology
- 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() : CustomNonbondedForce , CustomHbondForce , CustomGBForce , CustomManyParticleForce
- addExtraParticles() : Modeller
- addForce() : System
- addFunction() : CustomNonbondedForce , CustomHbondForce , CustomGBForce , CustomCompoundBondForce
- addGlobalParameter() : CustomAngleForce , CustomExternalForce , CustomTorsionForce , CustomNonbondedForce , CustomHbondForce , CustomBondForce , CustomGBForce , CustomCompoundBondForce , CustomManyParticleForce
- addGlobalVariable() : CustomIntegrator
- addHydrogens() : Modeller
- addInteractionGroup() : CustomNonbondedForce
- addMap() : CMAPTorsionForce
- addMultipole() : AmoebaMultipoleForce
- addOutOfPlaneBend() : AmoebaOutOfPlaneBendForce
- addParticle() : AmoebaWcaDispersionForce , System , CustomExternalForce , AmoebaGeneralizedKirkwoodForce , CustomNonbondedForce , NonbondedForce , CustomGBForce , GBVIForce , DrudeForce , AmoebaVdwForce , GBSAOBCForce , CustomManyParticleForce
- 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() : CustomHbondForce , CustomNonbondedForce , CustomManyParticleForce , CustomCompoundBondForce , CustomGBForce
- addTorsion() : PeriodicTorsionForce , CustomTorsionForce , RBTorsionForce , CMAPTorsionForce
- addTorsionTorsion() : AmoebaTorsionTorsionForce
- addUpdateContextState() : CustomIntegrator
- applyConstraints() : Context
- applyVelocityConstraints() : Context
- atomic_number() : Element
- atoms() : Topology , Chain , Residue