- s -

• serialize() : XmlSerializer
• setAcceptorParameters() : CustomHbondForce
• setAngleParameters() : HarmonicAngleForce , CustomAngleForce
• setBondParameters() : HarmonicBondForce , CustomBondForce , CustomCompoundBondForce , GBVIForce
• setBornRadiusScalingMethod() : GBVIForce
• setComputedValueParameters() : CustomGBForce
• setConstraintParameters() : System
• setConstraintTolerance() : Integrator
• setCutoffDistance() : GBSAOBCForce , GBVIForce , NonbondedForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce
• setDefaultPeriodicBoxVectors() : System
• setDonorParameters() : CustomHbondForce
• setEnergyFunction() : CustomAngleForce , CustomBondForce , CustomCompoundBondForce , CustomExternalForce , CustomHbondForce , CustomNonbondedForce , CustomTorsionForce
• setEnergyTermParameters() : CustomGBForce
• setErrorTolerance() : VariableLangevinIntegrator , VariableVerletIntegrator
• setEwaldErrorTolerance() : NonbondedForce
• setExceptionParameters() : NonbondedForce
• setExclusionParticles() : CustomGBForce , CustomHbondForce , CustomNonbondedForce
• setForceGroup() : Force
• setFrequency() : CMMotionRemover , MonteCarloBarostat
• setFriction() : BrownianIntegrator , LangevinIntegrator , VariableLangevinIntegrator
• setFunctionParameters() : CustomCompoundBondForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce
• setGlobalParameterDefaultValue() : CustomAngleForce , CustomBondForce , CustomCompoundBondForce , CustomExternalForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce , CustomTorsionForce
• setGlobalParameterName() : CustomAngleForce , CustomBondForce , CustomCompoundBondForce , CustomExternalForce , CustomGBForce , CustomHbondForce , CustomNonbondedForce , CustomTorsionForce
• setGlobalVariable() : CustomIntegrator
• setGlobalVariableByName() : CustomIntegrator
• setKineticEnergyExpression() : CustomIntegrator
• setMapParameters() : CMAPTorsionForce
• setNonbondedMethod() : CustomGBForce , CustomHbondForce , CustomNonbondedForce , GBSAOBCForce , GBVIForce , NonbondedForce
• setParameter() : Context , ContextImpl
• setParticleMass() : System
• setParticleParameters() : GBVIForce , CustomExternalForce , CustomGBForce , CustomNonbondedForce , GBSAOBCForce , NonbondedForce
• setParticles() : VirtualSite
• setPerAcceptorParameterName() : CustomHbondForce
• setPerAngleParameterName() : CustomAngleForce
• setPerBondParameterName() : CustomBondForce , CustomCompoundBondForce
• setPerDofVariable() : CustomIntegrator
• setPerDofVariableByName() : CustomIntegrator
• setPerDonorParameterName() : CustomHbondForce
• setPeriodicBoxVectors() : Context , ContextImpl
• setPerParticleParameterName() : CustomGBForce , CustomNonbondedForce , CustomExternalForce
• setPerTorsionParameterName() : CustomTorsionForce
• setPlatformData() : ContextImpl
• setPositions() : Context , ContextImpl
• setPropertyDefaultValue() : Platform
• setPropertyValue() : Platform
• setQuinticLowerLimitFactor() : GBVIForce
• setQuinticUpperBornRadiusLimit() : GBVIForce
• setRandomNumberSeed() : LangevinIntegrator , AndersenThermostat , CustomIntegrator , MonteCarloBarostat , BrownianIntegrator , VariableLangevinIntegrator
• setReactionFieldDielectric() : NonbondedForce
• setReciprocalSpaceForceGroup() : NonbondedForce
• setSoluteDielectric() : GBSAOBCForce , GBVIForce
• setSolventDielectric() : GBSAOBCForce , GBVIForce
• setStepSize() : Integrator
• setTemperature() : BrownianIntegrator , LangevinIntegrator , MonteCarloBarostat , VariableLangevinIntegrator
• setTime() : Context , ContextImpl
• setTorsionParameters() : CustomTorsionForce , RBTorsionForce , PeriodicTorsionForce , CMAPTorsionForce
• setUseDispersionCorrection() : NonbondedForce
• setVelocities() : ContextImpl , Context
• setVelocitiesToTemperature() : Context
• setVirtualSite() : System
• State() : State
• stateChanged() : Integrator , CustomIntegrator
• step() : LangevinIntegrator , VerletIntegrator , VariableLangevinIntegrator , Integrator , BrownianIntegrator , VariableVerletIntegrator , CustomIntegrator
• stepTo() : VariableVerletIntegrator , VariableLangevinIntegrator
• supportsDoublePrecision() : Platform
• supportsKernels() : Platform
• System() : System