|
| class | SwigPyIterator |
| |
| class | State |
| | A State object records a snapshot of the current state of a simulation at a point in time. More...
|
| |
| class | Integrator |
| | An Integrator defines a method for simulating a System by integrating the equations of motion. More...
|
| |
| class | DrudeLangevinIntegrator |
| | This Integrator simulates systems that include Drude particles. More...
|
| |
| class | Force |
| | Force objects apply forces to the particles in a System, or alter their behavior in other ways. More...
|
| |
| class | CustomBondForce |
| | This class implements bonded interactions between pairs of particles. More...
|
| |
| class | AmoebaVdwForce |
| | This class implements a buffered 14-7 potential used to model van der Waals forces. More...
|
| |
| class | BrownianIntegrator |
| | This is an Integrator which simulates a System using Brownian dynamics. More...
|
| |
| class | CustomCompoundBondForce |
| | This class supports a wide variety of bonded interactions. More...
|
| |
| class | LangevinIntegrator |
| | This is an Integrator which simulates a System using Langevin dynamics. More...
|
| |
| class | AmoebaInPlaneAngleForce |
| | This class implements an interaction at trigonal centers corresponding to the projected in-plane angle bend energy between four particles. More...
|
| |
| class | CustomGBForce |
| | This class implements complex, multiple stage nonbonded interactions between particles. More...
|
| |
| class | AmoebaOutOfPlaneBendForce |
| | This class implements the Amoeba out-of-plane bend interaction. More...
|
| |
| class | NonbondedForce |
| | This class implements nonbonded interactions between particles, including a Coulomb force to represent electrostatics and a Lennard-Jones force to represent van der Waals interactions. More...
|
| |
| class | RBTorsionForce |
| | This class implements an interaction between groups of four particles that varies with the torsion angle between them according to the Ryckaert-Bellemans potential. More...
|
| |
| class | AmoebaBondForce |
| | This class implements an interaction between pairs of particles that varies with the distance between them. More...
|
| |
| class | VirtualSite |
| | A VirtualSite describes the rules for computing a particle's position based on other particles. More...
|
| |
| class | OutOfPlaneSite |
| | This is a VirtualSite that computes the particle location based on three other particles' locations. More...
|
| |
| class | RPMDIntegrator |
| | This is an Integrator which simulates a System using ring polymer molecular dynamics (RPMD). More...
|
| |
| class | XmlSerializer |
| | XmlSerializer is used for serializing objects as XML, and for reconstructing them again. More...
|
| |
| class | CMMotionRemover |
| | This class prevents the center of mass of a System from drifting. More...
|
| |
| class | AmoebaGeneralizedKirkwoodForce |
| | This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model. More...
|
| |
| class | TabulatedFunction |
| | A TabulatedFunction uses a set of tabulated values to define a mathematical function. More...
|
| |
| class | Discrete1DFunction |
| | This is a TabulatedFunction that computes a discrete one dimensional function f(x). More...
|
| |
| class | LocalCoordinatesSite |
| | This is a VirtualSite that uses the locations of three other particles to compute a local coordinate system, then places the virtual site at a fixed location in that coordinate system. More...
|
| |
| class | CustomExternalForce |
| | This class implements an "external" force on particles. More...
|
| |
| class | DrudeForce |
| | This class implements forces that are specific to Drude oscillators. More...
|
| |
| class | Discrete3DFunction |
| | This is a TabulatedFunction that computes a discrete three dimensional function f(x,y,z). More...
|
| |
| class | GBSAOBCForce |
| | This class implements an implicit solvation force using the GBSA-OBC model. More...
|
| |
| class | AmoebaAngleForce |
| | This class implements an interaction between triplets of particles that varies with the angle between them. More...
|
| |
| class | System |
| | This class represents a molecular system. More...
|
| |
| class | AmoebaWcaDispersionForce |
| | This class implements a nonbonded interaction between pairs of particles typically used along with AmoebaGeneralizedKirkwoodForce as part of an implicit solvent model. More...
|
| |
| class | Context |
| | A Context stores the complete state of a simulation. More...
|
| |
| class | ThreeParticleAverageSite |
| | This is a VirtualSite that computes the particle location as a weighted average of three other particle's locations. More...
|
| |
| class | AndersenThermostat |
| | This class uses the Andersen method to maintain constant temperature. More...
|
| |
| class | MonteCarloMembraneBarostat |
| | This is a Monte Carlo barostat designed specifically for membrane simulations. More...
|
| |
| class | OpenMMException |
| | This class is used for all exceptions thrown by OpenMM. More...
|
| |
| class | CustomManyParticleForce |
| | This class supports a wide variety of nonbonded N-particle interactions, where N is user specified. More...
|
| |
| class | VariableLangevinIntegrator |
| | This is an error contolled, variable time step Integrator that simulates a System using Langevin dynamics. More...
|
| |
| class | SerializationProxy |
| | A SerializationProxy is an object that knows how to serialize and deserialize objects of a particular type.
|
| |
| class | HarmonicBondForce |
| | This class implements an interaction between pairs of particles that varies harmonically with the distance between them. More...
|
| |
| class | VerletIntegrator |
| | This is an Integrator which simulates a System using the leap-frog Verlet algorithm. More...
|
| |
| class | MonteCarloAnisotropicBarostat |
| | This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure. More...
|
| |
| class | Continuous2DFunction |
| | This is a TabulatedFunction that computes a continuous two dimensional function. More...
|
| |
| class | LocalEnergyMinimizer |
| | Given a Context, this class searches for a new set of particle positions that represent a local minimum of the potential energy. More...
|
| |
| class | CustomIntegrator |
| | This is an Integrator that can be used to implemented arbitrary, user defined integration algorithms. More...
|
| |
| class | Discrete2DFunction |
| | This is a TabulatedFunction that computes a discrete two dimensional function f(x,y). More...
|
| |
| class | TwoParticleAverageSite |
| | This is a VirtualSite that computes the particle location as a weighted average of two other particle's locations. More...
|
| |
| class | AmoebaStretchBendForce |
| | This class implements the Amoeba stretch-bend interaction. More...
|
| |
| class | GBVIForce |
| | This class implements an implicit solvation force using the GB/VI model. More...
|
| |
| class | CMAPTorsionForce |
| | This class implements an interaction between pairs of dihedral angles. More...
|
| |
| class | VariableVerletIntegrator |
| | This is an error contolled, variable time step Integrator that simulates a System using the leap-frog Verlet algorithm. More...
|
| |
| class | CustomTorsionForce |
| | This class implements interactions between sets of four particles that depend on the torsion angle between them. More...
|
| |
| class | PeriodicTorsionForce |
| | This class implements an interaction between groups of four particles that varies periodically with the torsion angle between them. More...
|
| |
| class | AmoebaPiTorsionForce |
| | This class implements the Amoeba pi-torsion interaction. More...
|
| |
| class | AmoebaMultipoleForce |
| | This class implements the Amoeba multipole interaction. More...
|
| |
| class | CustomHbondForce |
| | This class supports a wide variety of energy functions used to represent hydrogen bonding. More...
|
| |
| class | CustomNonbondedForce |
| | This class implements nonbonded interactions between particles. More...
|
| |
| class | SerializationNode |
| | A SerializationNode stores information about an object during serialization or deserialization.
|
| |
| class | HarmonicAngleForce |
| | This class implements an interaction between groups of three particles that varies harmonically with the angle between them. More...
|
| |
| class | DrudeSCFIntegrator |
| | This is a leap-frog Verlet Integrator that simulates systems with Drude particles. More...
|
| |
| class | MonteCarloBarostat |
| | This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure. More...
|
| |
| class | Continuous1DFunction |
| | This is a TabulatedFunction that computes a continuous one dimensional function. More...
|
| |
| class | CustomAngleForce |
| | This class implements interactions between sets of three particles that depend on the angle between them. More...
|
| |
| class | Platform |
| | A Platform defines an implementation of all the kernels needed to perform some calculation. More...
|
| |
| class | Continuous3DFunction |
| | This is a TabulatedFunction that computes a continuous three dimensional function. More...
|
| |
| class | AmoebaTorsionTorsionForce |
| | This class implements the Amoeba torsion-torsion interaction. More...
|
| |
|
| def | swig_import_helper |
| |
| def | ios_base_sync_with_stdio |
| |
| def | ios_base_xalloc |
| |
| def | endl |
| |
| def | ends |
| |
| def | flush |
| |
| def | stripUnits |
| | getState(self, quantity) -> value with no units More...
|
| |
| def | XmlSerializer_serializeSystem |
| | XmlSerializer_serializeSystem(System object) -> std::string. More...
|
| |
| def | XmlSerializer_deserializeSystem |
| | XmlSerializer_deserializeSystem(char const * inputString) -> System. More...
|
| |
| def | XmlSerializer__serializeForce |
| | XmlSerializer__serializeForce(Force object) -> std::string. More...
|
| |
| def | XmlSerializer__deserializeForce |
| | XmlSerializer__deserializeForce(char const * inputString) -> Force. More...
|
| |
| def | XmlSerializer__serializeIntegrator |
| | XmlSerializer__serializeIntegrator(Integrator object) -> std::string. More...
|
| |
| def | XmlSerializer__deserializeIntegrator |
| | XmlSerializer__deserializeIntegrator(char const * inputString) -> Integrator. More...
|
| |
| def | XmlSerializer__serializeStateAsLists |
| | XmlSerializer__serializeStateAsLists(std::vector< Vec3,std::allocator< Vec3 > > const & pos, std::vector< Vec3,std::allocator< Vec3 > > const & vel, std::vector< Vec3,std::allocator< Vec3 > > const & forces, double kineticEnergy, double potentialEnergy, double time, std::vector< Vec3,std::allocator< Vec3 > > const & boxVectors, mapstringdouble params, int types) -> std::string. More...
|
| |
| def | XmlSerializer__deserializeStringIntoLists |
| | XmlSerializer__deserializeStringIntoLists(std::string const & stateAsString) -> PyObject *. More...
|
| |
| def | AndersenThermostat_Temperature |
| | AndersenThermostat_Temperature() -> std::string const &. More...
|
| |
| def | AndersenThermostat_CollisionFrequency |
| | AndersenThermostat_CollisionFrequency() -> std::string const &. More...
|
| |
| def | MonteCarloMembraneBarostat_Pressure |
| | MonteCarloMembraneBarostat_Pressure() -> std::string const &. More...
|
| |
| def | MonteCarloMembraneBarostat_SurfaceTension |
| | MonteCarloMembraneBarostat_SurfaceTension() -> std::string const &. More...
|
| |
| def | SerializationProxy_registerProxy |
| | SerializationProxy_registerProxy(std::type_info const & type, SerializationProxy proxy) More...
|
| |
| def | SerializationProxy_getProxy |
| | getProxy(std::string const & typeName) -> SerializationProxy SerializationProxy_getProxy(std::type_info const & type) -> SerializationProxy More...
|
| |
| def | MonteCarloAnisotropicBarostat_PressureX |
| | MonteCarloAnisotropicBarostat_PressureX() -> std::string const &. More...
|
| |
| def | MonteCarloAnisotropicBarostat_PressureY |
| | MonteCarloAnisotropicBarostat_PressureY() -> std::string const &. More...
|
| |
| def | MonteCarloAnisotropicBarostat_PressureZ |
| | MonteCarloAnisotropicBarostat_PressureZ() -> std::string const &. More...
|
| |
| def | LocalEnergyMinimizer_minimize |
| | minimize(Context context, double tolerance=1, int maxIterations=0) minimize(Context context, double tolerance=1) LocalEnergyMinimizer_minimize(Context context) More...
|
| |
| def | MonteCarloBarostat_Pressure |
| | MonteCarloBarostat_Pressure() -> std::string const &. More...
|
| |
| def | Platform_registerPlatform |
| | Platform_registerPlatform(Platform platform) More...
|
| |
| def | Platform_getNumPlatforms |
| | Platform_getNumPlatforms() -> int. More...
|
| |
| def | Platform_getPlatform |
| | Platform_getPlatform(int index) -> Platform. More...
|
| |
| def | Platform_getPlatformByName |
| | Platform_getPlatformByName(std::string const & name) -> Platform. More...
|
| |
| def | Platform_findPlatform |
| | Platform_findPlatform(vectorstring kernelNames) -> Platform. More...
|
| |
| def | Platform_loadPluginLibrary |
| | Platform_loadPluginLibrary(std::string const & file) More...
|
| |
| def | Platform_loadPluginsFromDirectory |
| | Platform_loadPluginsFromDirectory(std::string const & directory) -> vectorstring. More...
|
| |
| def | Platform_getDefaultPluginsDirectory |
| | Platform_getDefaultPluginsDirectory() -> std::string const &. More...
|
| |
| def | Platform_getOpenMMVersion |
| | Platform_getOpenMMVersion() -> std::string const &. More...
|
| |
| def simtk.openmm.openmm.stripUnits |
( |
|
args | ) |
|
getState(self, quantity) -> value with no units
Examples
import simtk
x = 5 print x
5
x = stripUnits((5*simtk.unit.nanometer,)) x
(5,)
arg1 = 5*simtk.unit.angstrom x = stripUnits((arg1,)) x
(0.5,)
arg1 = 5 x = stripUnits((arg1,)) x
(5,)
arg1 = (1*simtk.unit.angstrom, 5*simtk.unit.angstrom) x = stripUnits((arg1,)) x
((0.10000000000000001, 0.5),)
arg1 = (1*simtk.unit.angstrom,
... 5*simtk.unit.kilojoule_per_mole, ... 1*simtk.unit.kilocalorie_per_mole)
y = stripUnits((arg1,)) y
((0.10000000000000001, 5, 4.1840000000000002),)
Referenced by Integrator.__del__(), DrudeLangevinIntegrator.__del__(), Force.__del__(), CustomBondForce.__del__(), AmoebaVdwForce.__del__(), BrownianIntegrator.__del__(), CustomCompoundBondForce.__del__(), LangevinIntegrator.__del__(), AmoebaInPlaneAngleForce.__del__(), CustomGBForce.__del__(), AmoebaOutOfPlaneBendForce.__del__(), NonbondedForce.__del__(), RBTorsionForce.__del__(), AmoebaBondForce.__del__(), VirtualSite.__del__(), OutOfPlaneSite.__del__(), RPMDIntegrator.__del__(), XmlSerializer.__del__(), CMMotionRemover.__del__(), AmoebaGeneralizedKirkwoodForce.__del__(), TabulatedFunction.__del__(), Discrete1DFunction.__del__(), LocalCoordinatesSite.__del__(), CustomExternalForce.__del__(), DrudeForce.__del__(), Discrete3DFunction.__del__(), GBSAOBCForce.__del__(), AmoebaAngleForce.__del__(), System.__del__(), AmoebaWcaDispersionForce.__del__(), Context.__del__(), ThreeParticleAverageSite.__del__(), AndersenThermostat.__del__(), MonteCarloMembraneBarostat.__del__(), OpenMMException.__del__(), CustomManyParticleForce.__del__(), VariableLangevinIntegrator.__del__(), HarmonicBondForce.__del__(), VerletIntegrator.__del__(), MonteCarloAnisotropicBarostat.__del__(), Continuous2DFunction.__del__(), LocalEnergyMinimizer.__del__(), CustomIntegrator.__del__(), Discrete2DFunction.__del__(), TwoParticleAverageSite.__del__(), AmoebaStretchBendForce.__del__(), GBVIForce.__del__(), CMAPTorsionForce.__del__(), VariableVerletIntegrator.__del__(), CustomTorsionForce.__del__(), PeriodicTorsionForce.__del__(), AmoebaPiTorsionForce.__del__(), AmoebaMultipoleForce.__del__(), CustomHbondForce.__del__(), CustomNonbondedForce.__del__(), HarmonicAngleForce.__del__(), DrudeSCFIntegrator.__del__(), MonteCarloBarostat.__del__(), Continuous1DFunction.__del__(), CustomAngleForce.__del__(), Platform.__del__(), Continuous3DFunction.__del__(), AmoebaTorsionTorsionForce.__del__(), DrudeLangevinIntegrator.__init__(), CustomBondForce.__init__(), AmoebaVdwForce.__init__(), BrownianIntegrator.__init__(), CustomCompoundBondForce.__init__(), LangevinIntegrator.__init__(), AmoebaInPlaneAngleForce.__init__(), CustomGBForce.__init__(), AmoebaOutOfPlaneBendForce.__init__(), NonbondedForce.__init__(), RBTorsionForce.__init__(), AmoebaBondForce.__init__(), OutOfPlaneSite.__init__(), RPMDIntegrator.__init__(), CMMotionRemover.__init__(), AmoebaGeneralizedKirkwoodForce.__init__(), Discrete1DFunction.__init__(), LocalCoordinatesSite.__init__(), CustomExternalForce.__init__(), DrudeForce.__init__(), Discrete3DFunction.__init__(), GBSAOBCForce.__init__(), AmoebaAngleForce.__init__(), System.__init__(), AmoebaWcaDispersionForce.__init__(), Context.__init__(), ThreeParticleAverageSite.__init__(), AndersenThermostat.__init__(), MonteCarloMembraneBarostat.__init__(), OpenMMException.__init__(), CustomManyParticleForce.__init__(), VariableLangevinIntegrator.__init__(), HarmonicBondForce.__init__(), VerletIntegrator.__init__(), MonteCarloAnisotropicBarostat.__init__(), Continuous2DFunction.__init__(), CustomIntegrator.__init__(), Discrete2DFunction.__init__(), TwoParticleAverageSite.__init__(), AmoebaStretchBendForce.__init__(), GBVIForce.__init__(), CMAPTorsionForce.__init__(), VariableVerletIntegrator.__init__(), CustomTorsionForce.__init__(), PeriodicTorsionForce.__init__(), AmoebaPiTorsionForce.__init__(), AmoebaMultipoleForce.__init__(), CustomHbondForce.__init__(), CustomNonbondedForce.__init__(), HarmonicAngleForce.__init__(), DrudeSCFIntegrator.__init__(), MonteCarloBarostat.__init__(), Continuous1DFunction.__init__(), CustomAngleForce.__init__(), Continuous3DFunction.__init__(), AmoebaTorsionTorsionForce.__init__(), CustomHbondForce.addAcceptor(), AmoebaInPlaneAngleForce.addAngle(), AmoebaAngleForce.addAngle(), HarmonicAngleForce.addAngle(), CustomAngleForce.addAngle(), CustomBondForce.addBond(), CustomCompoundBondForce.addBond(), AmoebaBondForce.addBond(), HarmonicBondForce.addBond(), GBVIForce.addBond(), CustomGBForce.addComputedValue(), CustomIntegrator.addComputeGlobal(), CustomIntegrator.addComputePerDof(), CustomIntegrator.addComputeSum(), CustomIntegrator.addConstrainPositions(), System.addConstraint(), CustomIntegrator.addConstrainVelocities(), CustomHbondForce.addDonor(), CustomGBForce.addEnergyTerm(), NonbondedForce.addException(), CustomGBForce.addExclusion(), CustomManyParticleForce.addExclusion(), CustomHbondForce.addExclusion(), CustomNonbondedForce.addExclusion(), CustomCompoundBondForce.addFunction(), CustomGBForce.addFunction(), CustomHbondForce.addFunction(), CustomNonbondedForce.addFunction(), CustomBondForce.addGlobalParameter(), CustomCompoundBondForce.addGlobalParameter(), CustomGBForce.addGlobalParameter(), CustomExternalForce.addGlobalParameter(), CustomManyParticleForce.addGlobalParameter(), CustomTorsionForce.addGlobalParameter(), CustomHbondForce.addGlobalParameter(), CustomNonbondedForce.addGlobalParameter(), CustomAngleForce.addGlobalParameter(), CustomIntegrator.addGlobalVariable(), CustomNonbondedForce.addInteractionGroup(), CMAPTorsionForce.addMap(), AmoebaMultipoleForce.addMultipole(), AmoebaOutOfPlaneBendForce.addOutOfPlaneBend(), AmoebaVdwForce.addParticle(), CustomGBForce.addParticle(), NonbondedForce.addParticle(), AmoebaGeneralizedKirkwoodForce.addParticle(), CustomExternalForce.addParticle(), DrudeForce.addParticle(), GBSAOBCForce.addParticle(), System.addParticle(), AmoebaWcaDispersionForce.addParticle(), CustomManyParticleForce.addParticle(), GBVIForce.addParticle(), CustomNonbondedForce.addParticle(), CustomHbondForce.addPerAcceptorParameter(), CustomAngleForce.addPerAngleParameter(), CustomBondForce.addPerBondParameter(), CustomCompoundBondForce.addPerBondParameter(), CustomIntegrator.addPerDofVariable(), CustomHbondForce.addPerDonorParameter(), CustomGBForce.addPerParticleParameter(), CustomExternalForce.addPerParticleParameter(), CustomManyParticleForce.addPerParticleParameter(), CustomNonbondedForce.addPerParticleParameter(), CustomTorsionForce.addPerTorsionParameter(), AmoebaPiTorsionForce.addPiTorsion(), DrudeForce.addScreenedPair(), AmoebaStretchBendForce.addStretchBend(), RBTorsionForce.addTorsion(), CMAPTorsionForce.addTorsion(), CustomTorsionForce.addTorsion(), PeriodicTorsionForce.addTorsion(), AmoebaTorsionTorsionForce.addTorsionTorsion(), CustomIntegrator.addUpdateContextState(), simtk.openmm.openmm.AndersenThermostat_CollisionFrequency(), simtk.openmm.openmm.AndersenThermostat_Temperature(), Context.applyConstraints(), Context.applyVelocityConstraints(), AndersenThermostat.CollisionFrequency(), Context.computeVirtualSites(), TabulatedFunction.Copy(), Discrete1DFunction.Copy(), Discrete3DFunction.Copy(), Continuous2DFunction.Copy(), Discrete2DFunction.Copy(), Continuous1DFunction.Copy(), Continuous3DFunction.Copy(), NonbondedForce.createExceptionsFromBonds(), CustomManyParticleForce.createExclusionsFromBonds(), CustomNonbondedForce.createExclusionsFromBonds(), Platform.findPlatform(), CustomHbondForce.getAcceptorParameters(), AmoebaMultipoleForce.getAEwald(), AmoebaAngleForce.getAmoebaGlobalAngleCubic(), AmoebaAngleForce.getAmoebaGlobalAnglePentic(), AmoebaAngleForce.getAmoebaGlobalAngleQuartic(), AmoebaAngleForce.getAmoebaGlobalAngleSextic(), AmoebaBondForce.getAmoebaGlobalBondCubic(), AmoebaBondForce.getAmoebaGlobalBondQuartic(), AmoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleCubic(), AmoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAnglePentic(), AmoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleQuartic(), AmoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleSextic(), AmoebaOutOfPlaneBendForce.getAmoebaGlobalOutOfPlaneBendCubic(), AmoebaOutOfPlaneBendForce.getAmoebaGlobalOutOfPlaneBendPentic(), AmoebaOutOfPlaneBendForce.getAmoebaGlobalOutOfPlaneBendQuartic(), AmoebaOutOfPlaneBendForce.getAmoebaGlobalOutOfPlaneBendSextic(), AmoebaInPlaneAngleForce.getAngleParameters(), AmoebaAngleForce.getAngleParameters(), HarmonicAngleForce.getAngleParameters(), CustomAngleForce.getAngleParameters(), RPMDIntegrator.getApplyThermostat(), AmoebaWcaDispersionForce.getAwater(), CustomBondForce.getBondParameters(), CustomCompoundBondForce.getBondParameters(), AmoebaBondForce.getBondParameters(), HarmonicBondForce.getBondParameters(), GBVIForce.getBondParameters(), GBVIForce.getBornRadiusScalingMethod(), CustomIntegrator.getComputationStep(), CustomGBForce.getComputedValueParameters(), System.getConstraintParameters(), Integrator.getConstraintTolerance(), RPMDIntegrator.getContractions(), AmoebaMultipoleForce.getCovalentMap(), AmoebaMultipoleForce.getCovalentMaps(), AmoebaVdwForce.getCutoff(), CustomGBForce.getCutoffDistance(), NonbondedForce.getCutoffDistance(), GBSAOBCForce.getCutoffDistance(), CustomManyParticleForce.getCutoffDistance(), GBVIForce.getCutoffDistance(), AmoebaMultipoleForce.getCutoffDistance(), CustomHbondForce.getCutoffDistance(), CustomNonbondedForce.getCutoffDistance(), AndersenThermostat.getDefaultCollisionFrequency(), System.getDefaultPeriodicBoxVectors(), Platform.getDefaultPluginsDirectory(), MonteCarloMembraneBarostat.getDefaultPressure(), MonteCarloAnisotropicBarostat.getDefaultPressure(), MonteCarloBarostat.getDefaultPressure(), MonteCarloMembraneBarostat.getDefaultSurfaceTension(), AndersenThermostat.getDefaultTemperature(), AmoebaWcaDispersionForce.getDispoff(), CustomHbondForce.getDonorParameters(), DrudeLangevinIntegrator.getDrudeFriction(), DrudeLangevinIntegrator.getDrudeTemperature(), AmoebaMultipoleForce.getElectrostaticPotential(), CustomBondForce.getEnergyFunction(), CustomCompoundBondForce.getEnergyFunction(), CustomExternalForce.getEnergyFunction(), CustomManyParticleForce.getEnergyFunction(), CustomTorsionForce.getEnergyFunction(), CustomHbondForce.getEnergyFunction(), CustomNonbondedForce.getEnergyFunction(), CustomAngleForce.getEnergyFunction(), CustomGBForce.getEnergyTermParameters(), AmoebaWcaDispersionForce.getEpsh(), AmoebaVdwForce.getEpsilonCombiningRule(), AmoebaWcaDispersionForce.getEpso(), VariableLangevinIntegrator.getErrorTolerance(), VariableVerletIntegrator.getErrorTolerance(), NonbondedForce.getEwaldErrorTolerance(), AmoebaMultipoleForce.getEwaldErrorTolerance(), NonbondedForce.getExceptionParameters(), CustomGBForce.getExclusionParticles(), CustomManyParticleForce.getExclusionParticles(), CustomHbondForce.getExclusionParticles(), CustomNonbondedForce.getExclusionParticles(), System.getForce(), Force.getForceGroup(), CMMotionRemover.getFrequency(), MonteCarloMembraneBarostat.getFrequency(), MonteCarloAnisotropicBarostat.getFrequency(), MonteCarloBarostat.getFrequency(), DrudeLangevinIntegrator.getFriction(), BrownianIntegrator.getFriction(), LangevinIntegrator.getFriction(), RPMDIntegrator.getFriction(), VariableLangevinIntegrator.getFriction(), CustomCompoundBondForce.getFunctionParameters(), CustomGBForce.getFunctionParameters(), Discrete1DFunction.getFunctionParameters(), Discrete3DFunction.getFunctionParameters(), Continuous2DFunction.getFunctionParameters(), Discrete2DFunction.getFunctionParameters(), CustomHbondForce.getFunctionParameters(), CustomNonbondedForce.getFunctionParameters(), Continuous1DFunction.getFunctionParameters(), Continuous3DFunction.getFunctionParameters(), CustomBondForce.getGlobalParameterDefaultValue(), CustomCompoundBondForce.getGlobalParameterDefaultValue(), CustomGBForce.getGlobalParameterDefaultValue(), CustomExternalForce.getGlobalParameterDefaultValue(), CustomManyParticleForce.getGlobalParameterDefaultValue(), CustomTorsionForce.getGlobalParameterDefaultValue(), CustomHbondForce.getGlobalParameterDefaultValue(), CustomNonbondedForce.getGlobalParameterDefaultValue(), CustomAngleForce.getGlobalParameterDefaultValue(), CustomBondForce.getGlobalParameterName(), CustomCompoundBondForce.getGlobalParameterName(), CustomGBForce.getGlobalParameterName(), CustomExternalForce.getGlobalParameterName(), CustomManyParticleForce.getGlobalParameterName(), CustomTorsionForce.getGlobalParameterName(), CustomHbondForce.getGlobalParameterName(), CustomNonbondedForce.getGlobalParameterName(), CustomAngleForce.getGlobalParameterName(), CustomIntegrator.getGlobalVariable(), CustomIntegrator.getGlobalVariableByName(), CustomIntegrator.getGlobalVariableName(), AmoebaGeneralizedKirkwoodForce.getIncludeCavityTerm(), AmoebaMultipoleForce.getInducedDipoles(), Context.getIntegrator(), CustomNonbondedForce.getInteractionGroupParameters(), CustomIntegrator.getKineticEnergyExpression(), LocalCoordinatesSite.getLocalPosition(), CMAPTorsionForce.getMapParameters(), DrudeSCFIntegrator.getMinimizationErrorTolerance(), Context.getMolecules(), AmoebaMultipoleForce.getMultipoleParameters(), AmoebaMultipoleForce.getMutualInducedMaxIterations(), AmoebaMultipoleForce.getMutualInducedTargetEpsilon(), Platform.getName(), AmoebaVdwForce.getNonbondedMethod(), CustomGBForce.getNonbondedMethod(), NonbondedForce.getNonbondedMethod(), GBSAOBCForce.getNonbondedMethod(), CustomManyParticleForce.getNonbondedMethod(), GBVIForce.getNonbondedMethod(), AmoebaMultipoleForce.getNonbondedMethod(), CustomHbondForce.getNonbondedMethod(), CustomNonbondedForce.getNonbondedMethod(), CustomHbondForce.getNumAcceptors(), AmoebaInPlaneAngleForce.getNumAngles(), AmoebaAngleForce.getNumAngles(), HarmonicAngleForce.getNumAngles(), CustomAngleForce.getNumAngles(), CustomBondForce.getNumBonds(), CustomCompoundBondForce.getNumBonds(), AmoebaBondForce.getNumBonds(), HarmonicBondForce.getNumBonds(), GBVIForce.getNumBonds(), CustomIntegrator.getNumComputations(), CustomGBForce.getNumComputedValues(), System.getNumConstraints(), RPMDIntegrator.getNumCopies(), CustomHbondForce.getNumDonors(), CustomGBForce.getNumEnergyTerms(), NonbondedForce.getNumExceptions(), CustomGBForce.getNumExclusions(), CustomManyParticleForce.getNumExclusions(), CustomHbondForce.getNumExclusions(), CustomNonbondedForce.getNumExclusions(), System.getNumForces(), CustomCompoundBondForce.getNumFunctions(), CustomGBForce.getNumFunctions(), CustomHbondForce.getNumFunctions(), CustomNonbondedForce.getNumFunctions(), CustomBondForce.getNumGlobalParameters(), CustomCompoundBondForce.getNumGlobalParameters(), CustomGBForce.getNumGlobalParameters(), CustomExternalForce.getNumGlobalParameters(), CustomManyParticleForce.getNumGlobalParameters(), CustomTorsionForce.getNumGlobalParameters(), CustomHbondForce.getNumGlobalParameters(), CustomNonbondedForce.getNumGlobalParameters(), CustomAngleForce.getNumGlobalParameters(), CustomIntegrator.getNumGlobalVariables(), CustomNonbondedForce.getNumInteractionGroups(), CMAPTorsionForce.getNumMaps(), AmoebaMultipoleForce.getNumMultipoles(), AmoebaOutOfPlaneBendForce.getNumOutOfPlaneBends(), AmoebaVdwForce.getNumParticles(), CustomGBForce.getNumParticles(), NonbondedForce.getNumParticles(), VirtualSite.getNumParticles(), AmoebaGeneralizedKirkwoodForce.getNumParticles(), CustomExternalForce.getNumParticles(), DrudeForce.getNumParticles(), GBSAOBCForce.getNumParticles(), System.getNumParticles(), AmoebaWcaDispersionForce.getNumParticles(), CustomManyParticleForce.getNumParticles(), GBVIForce.getNumParticles(), CustomNonbondedForce.getNumParticles(), CustomCompoundBondForce.getNumParticlesPerBond(), CustomManyParticleForce.getNumParticlesPerSet(), CustomHbondForce.getNumPerAcceptorParameters(), CustomAngleForce.getNumPerAngleParameters(), CustomBondForce.getNumPerBondParameters(), CustomCompoundBondForce.getNumPerBondParameters(), CustomIntegrator.getNumPerDofVariables(), CustomHbondForce.getNumPerDonorParameters(), CustomGBForce.getNumPerParticleParameters(), CustomExternalForce.getNumPerParticleParameters(), CustomManyParticleForce.getNumPerParticleParameters(), CustomNonbondedForce.getNumPerParticleParameters(), CustomTorsionForce.getNumPerTorsionParameters(), AmoebaPiTorsionForce.getNumPiTorsions(), Platform.getNumPlatforms(), DrudeForce.getNumScreenedPairs(), AmoebaStretchBendForce.getNumStretchBends(), CustomCompoundBondForce.getNumTabulatedFunctions(), CustomGBForce.getNumTabulatedFunctions(), CustomManyParticleForce.getNumTabulatedFunctions(), CustomHbondForce.getNumTabulatedFunctions(), CustomNonbondedForce.getNumTabulatedFunctions(), RBTorsionForce.getNumTorsions(), CMAPTorsionForce.getNumTorsions(), CustomTorsionForce.getNumTorsions(), PeriodicTorsionForce.getNumTorsions(), AmoebaTorsionTorsionForce.getNumTorsionTorsionGrids(), AmoebaTorsionTorsionForce.getNumTorsionTorsions(), Platform.getOpenMMVersion(), LocalCoordinatesSite.getOriginWeights(), AmoebaOutOfPlaneBendForce.getOutOfPlaneBendParameters(), Context.getParameter(), VirtualSite.getParticle(), AmoebaVdwForce.getParticleExclusions(), System.getParticleMass(), AmoebaVdwForce.getParticleParameters(), CustomGBForce.getParticleParameters(), NonbondedForce.getParticleParameters(), AmoebaGeneralizedKirkwoodForce.getParticleParameters(), CustomExternalForce.getParticleParameters(), DrudeForce.getParticleParameters(), GBSAOBCForce.getParticleParameters(), AmoebaWcaDispersionForce.getParticleParameters(), CustomManyParticleForce.getParticleParameters(), GBVIForce.getParticleParameters(), CustomNonbondedForce.getParticleParameters(), CustomHbondForce.getPerAcceptorParameterName(), CustomAngleForce.getPerAngleParameterName(), CustomBondForce.getPerBondParameterName(), CustomCompoundBondForce.getPerBondParameterName(), CustomIntegrator.getPerDofVariableByName(), CustomIntegrator.getPerDofVariableName(), CustomHbondForce.getPerDonorParameterName(), CustomManyParticleForce.getPermutationMode(), CustomGBForce.getPerParticleParameterName(), CustomExternalForce.getPerParticleParameterName(), CustomManyParticleForce.getPerParticleParameterName(), CustomNonbondedForce.getPerParticleParameterName(), CustomTorsionForce.getPerTorsionParameterName(), AmoebaPiTorsionForce.getPiTorsionParameters(), Context.getPlatform(), Platform.getPlatform(), Platform.getPlatformByName(), AmoebaMultipoleForce.getPmeBSplineOrder(), AmoebaMultipoleForce.getPmeGridDimensions(), NonbondedForce.getPMEParameters(), AmoebaMultipoleForce.getPolarizationType(), AmoebaGeneralizedKirkwoodForce.getProbeRadius(), Platform.getPropertyDefaultValue(), Platform.getPropertyNames(), Platform.getPropertyValue(), GBVIForce.getQuinticLowerLimitFactor(), GBVIForce.getQuinticUpperBornRadiusLimit(), DrudeLangevinIntegrator.getRandomNumberSeed(), BrownianIntegrator.getRandomNumberSeed(), LangevinIntegrator.getRandomNumberSeed(), RPMDIntegrator.getRandomNumberSeed(), AndersenThermostat.getRandomNumberSeed(), MonteCarloMembraneBarostat.getRandomNumberSeed(), VariableLangevinIntegrator.getRandomNumberSeed(), MonteCarloAnisotropicBarostat.getRandomNumberSeed(), CustomIntegrator.getRandomNumberSeed(), MonteCarloBarostat.getRandomNumberSeed(), NonbondedForce.getReactionFieldDielectric(), NonbondedForce.getReciprocalSpaceForceGroup(), AmoebaWcaDispersionForce.getRminh(), AmoebaWcaDispersionForce.getRmino(), MonteCarloAnisotropicBarostat.getScaleX(), MonteCarloAnisotropicBarostat.getScaleY(), MonteCarloAnisotropicBarostat.getScaleZ(), DrudeForce.getScreenedPairParameters(), AmoebaWcaDispersionForce.getShctd(), AmoebaVdwForce.getSigmaCombiningRule(), AmoebaWcaDispersionForce.getSlevy(), AmoebaGeneralizedKirkwoodForce.getSoluteDielectric(), GBSAOBCForce.getSoluteDielectric(), GBVIForce.getSoluteDielectric(), AmoebaGeneralizedKirkwoodForce.getSolventDielectric(), GBSAOBCForce.getSolventDielectric(), GBVIForce.getSolventDielectric(), Platform.getSpeed(), Integrator.getStepSize(), AmoebaStretchBendForce.getStretchBendParameters(), GBSAOBCForce.getSurfaceAreaEnergy(), AmoebaGeneralizedKirkwoodForce.getSurfaceAreaFactor(), NonbondedForce.getSwitchingDistance(), CustomNonbondedForce.getSwitchingDistance(), Context.getSystem(), AmoebaMultipoleForce.getSystemMultipoleMoments(), CustomCompoundBondForce.getTabulatedFunction(), CustomGBForce.getTabulatedFunction(), CustomManyParticleForce.getTabulatedFunction(), CustomHbondForce.getTabulatedFunction(), CustomNonbondedForce.getTabulatedFunction(), CustomCompoundBondForce.getTabulatedFunctionName(), CustomGBForce.getTabulatedFunctionName(), CustomManyParticleForce.getTabulatedFunctionName(), CustomHbondForce.getTabulatedFunctionName(), CustomNonbondedForce.getTabulatedFunctionName(), DrudeLangevinIntegrator.getTemperature(), BrownianIntegrator.getTemperature(), LangevinIntegrator.getTemperature(), RPMDIntegrator.getTemperature(), MonteCarloMembraneBarostat.getTemperature(), VariableLangevinIntegrator.getTemperature(), MonteCarloAnisotropicBarostat.getTemperature(), MonteCarloBarostat.getTemperature(), RBTorsionForce.getTorsionParameters(), CMAPTorsionForce.getTorsionParameters(), CustomTorsionForce.getTorsionParameters(), PeriodicTorsionForce.getTorsionParameters(), AmoebaTorsionTorsionForce.getTorsionTorsionGrid(), AmoebaTorsionTorsionForce.getTorsionTorsionParameters(), RPMDIntegrator.getTotalEnergy(), CustomManyParticleForce.getTypeFilter(), AmoebaVdwForce.getUseDispersionCorrection(), NonbondedForce.getUseDispersionCorrection(), CustomNonbondedForce.getUseLongRangeCorrection(), NonbondedForce.getUseSwitchingFunction(), CustomNonbondedForce.getUseSwitchingFunction(), System.getVirtualSite(), ThreeParticleAverageSite.getWeight(), TwoParticleAverageSite.getWeight(), OutOfPlaneSite.getWeight12(), OutOfPlaneSite.getWeight13(), OutOfPlaneSite.getWeightCross(), LocalCoordinatesSite.getXWeights(), MonteCarloMembraneBarostat.getXYMode(), LocalCoordinatesSite.getYWeights(), MonteCarloMembraneBarostat.getZMode(), System.isVirtualSite(), Platform.loadPluginLibrary(), Platform.loadPluginsFromDirectory(), simtk.openmm.openmm.LocalEnergyMinimizer_minimize(), LocalEnergyMinimizer.minimize(), simtk.openmm.openmm.MonteCarloAnisotropicBarostat_PressureX(), simtk.openmm.openmm.MonteCarloAnisotropicBarostat_PressureY(), simtk.openmm.openmm.MonteCarloAnisotropicBarostat_PressureZ(), simtk.openmm.openmm.MonteCarloBarostat_Pressure(), simtk.openmm.openmm.MonteCarloMembraneBarostat_Pressure(), simtk.openmm.openmm.MonteCarloMembraneBarostat_SurfaceTension(), simtk.openmm.openmm.Platform_findPlatform(), simtk.openmm.openmm.Platform_getDefaultPluginsDirectory(), simtk.openmm.openmm.Platform_getNumPlatforms(), simtk.openmm.openmm.Platform_getOpenMMVersion(), simtk.openmm.openmm.Platform_getPlatform(), simtk.openmm.openmm.Platform_getPlatformByName(), simtk.openmm.openmm.Platform_loadPluginLibrary(), simtk.openmm.openmm.Platform_loadPluginsFromDirectory(), MonteCarloMembraneBarostat.Pressure(), MonteCarloBarostat.Pressure(), MonteCarloAnisotropicBarostat.PressureX(), MonteCarloAnisotropicBarostat.PressureY(), MonteCarloAnisotropicBarostat.PressureZ(), Context.reinitialize(), simtk.openmm.openmm.SerializationProxy_getProxy(), simtk.openmm.openmm.SerializationProxy_registerProxy(), CustomHbondForce.setAcceptorParameters(), AmoebaMultipoleForce.setAEwald(), AmoebaAngleForce.setAmoebaGlobalAngleCubic(), AmoebaAngleForce.setAmoebaGlobalAnglePentic(), AmoebaAngleForce.setAmoebaGlobalAngleQuartic(), AmoebaAngleForce.setAmoebaGlobalAngleSextic(), AmoebaBondForce.setAmoebaGlobalBondCubic(), AmoebaBondForce.setAmoebaGlobalBondQuartic(), AmoebaInPlaneAngleForce.setAmoebaGlobalInPlaneAngleCubic(), AmoebaInPlaneAngleForce.setAmoebaGlobalInPlaneAnglePentic(), AmoebaInPlaneAngleForce.setAmoebaGlobalInPlaneAngleQuartic(), AmoebaInPlaneAngleForce.setAmoebaGlobalInPlaneAngleSextic(), AmoebaOutOfPlaneBendForce.setAmoebaGlobalOutOfPlaneBendCubic(), AmoebaOutOfPlaneBendForce.setAmoebaGlobalOutOfPlaneBendPentic(), AmoebaOutOfPlaneBendForce.setAmoebaGlobalOutOfPlaneBendQuartic(), AmoebaOutOfPlaneBendForce.setAmoebaGlobalOutOfPlaneBendSextic(), AmoebaInPlaneAngleForce.setAngleParameters(), AmoebaAngleForce.setAngleParameters(), HarmonicAngleForce.setAngleParameters(), CustomAngleForce.setAngleParameters(), RPMDIntegrator.setApplyThermostat(), AmoebaWcaDispersionForce.setAwater(), CustomBondForce.setBondParameters(), CustomCompoundBondForce.setBondParameters(), AmoebaBondForce.setBondParameters(), HarmonicBondForce.setBondParameters(), GBVIForce.setBondParameters(), GBVIForce.setBornRadiusScalingMethod(), CustomGBForce.setComputedValueParameters(), System.setConstraintParameters(), Integrator.setConstraintTolerance(), AmoebaMultipoleForce.setCovalentMap(), AmoebaVdwForce.setCutoff(), CustomGBForce.setCutoffDistance(), NonbondedForce.setCutoffDistance(), GBSAOBCForce.setCutoffDistance(), CustomManyParticleForce.setCutoffDistance(), GBVIForce.setCutoffDistance(), AmoebaMultipoleForce.setCutoffDistance(), CustomHbondForce.setCutoffDistance(), CustomNonbondedForce.setCutoffDistance(), AndersenThermostat.setDefaultCollisionFrequency(), System.setDefaultPeriodicBoxVectors(), MonteCarloMembraneBarostat.setDefaultPressure(), MonteCarloAnisotropicBarostat.setDefaultPressure(), MonteCarloBarostat.setDefaultPressure(), MonteCarloMembraneBarostat.setDefaultSurfaceTension(), AndersenThermostat.setDefaultTemperature(), AmoebaWcaDispersionForce.setDispoff(), CustomHbondForce.setDonorParameters(), DrudeLangevinIntegrator.setDrudeFriction(), DrudeLangevinIntegrator.setDrudeTemperature(), CustomBondForce.setEnergyFunction(), CustomCompoundBondForce.setEnergyFunction(), CustomExternalForce.setEnergyFunction(), CustomManyParticleForce.setEnergyFunction(), CustomTorsionForce.setEnergyFunction(), CustomHbondForce.setEnergyFunction(), CustomNonbondedForce.setEnergyFunction(), CustomAngleForce.setEnergyFunction(), CustomGBForce.setEnergyTermParameters(), AmoebaWcaDispersionForce.setEpsh(), AmoebaVdwForce.setEpsilonCombiningRule(), AmoebaWcaDispersionForce.setEpso(), VariableLangevinIntegrator.setErrorTolerance(), VariableVerletIntegrator.setErrorTolerance(), NonbondedForce.setEwaldErrorTolerance(), AmoebaMultipoleForce.setEwaldErrorTolerance(), NonbondedForce.setExceptionParameters(), CustomGBForce.setExclusionParticles(), CustomManyParticleForce.setExclusionParticles(), CustomHbondForce.setExclusionParticles(), CustomNonbondedForce.setExclusionParticles(), Force.setForceGroup(), CMMotionRemover.setFrequency(), MonteCarloMembraneBarostat.setFrequency(), MonteCarloAnisotropicBarostat.setFrequency(), MonteCarloBarostat.setFrequency(), DrudeLangevinIntegrator.setFriction(), BrownianIntegrator.setFriction(), LangevinIntegrator.setFriction(), RPMDIntegrator.setFriction(), VariableLangevinIntegrator.setFriction(), CustomCompoundBondForce.setFunctionParameters(), CustomGBForce.setFunctionParameters(), Discrete1DFunction.setFunctionParameters(), Discrete3DFunction.setFunctionParameters(), Continuous2DFunction.setFunctionParameters(), Discrete2DFunction.setFunctionParameters(), CustomHbondForce.setFunctionParameters(), CustomNonbondedForce.setFunctionParameters(), Continuous1DFunction.setFunctionParameters(), Continuous3DFunction.setFunctionParameters(), CustomBondForce.setGlobalParameterDefaultValue(), CustomCompoundBondForce.setGlobalParameterDefaultValue(), CustomGBForce.setGlobalParameterDefaultValue(), CustomExternalForce.setGlobalParameterDefaultValue(), CustomManyParticleForce.setGlobalParameterDefaultValue(), CustomTorsionForce.setGlobalParameterDefaultValue(), CustomHbondForce.setGlobalParameterDefaultValue(), CustomNonbondedForce.setGlobalParameterDefaultValue(), CustomAngleForce.setGlobalParameterDefaultValue(), CustomBondForce.setGlobalParameterName(), CustomCompoundBondForce.setGlobalParameterName(), CustomGBForce.setGlobalParameterName(), CustomExternalForce.setGlobalParameterName(), CustomManyParticleForce.setGlobalParameterName(), CustomTorsionForce.setGlobalParameterName(), CustomHbondForce.setGlobalParameterName(), CustomNonbondedForce.setGlobalParameterName(), CustomAngleForce.setGlobalParameterName(), CustomIntegrator.setGlobalVariable(), CustomIntegrator.setGlobalVariableByName(), AmoebaGeneralizedKirkwoodForce.setIncludeCavityTerm(), CustomNonbondedForce.setInteractionGroupParameters(), CustomIntegrator.setKineticEnergyExpression(), CMAPTorsionForce.setMapParameters(), DrudeSCFIntegrator.setMinimizationErrorTolerance(), AmoebaMultipoleForce.setMultipoleParameters(), AmoebaMultipoleForce.setMutualInducedMaxIterations(), AmoebaMultipoleForce.setMutualInducedTargetEpsilon(), AmoebaVdwForce.setNonbondedMethod(), CustomGBForce.setNonbondedMethod(), NonbondedForce.setNonbondedMethod(), GBSAOBCForce.setNonbondedMethod(), CustomManyParticleForce.setNonbondedMethod(), GBVIForce.setNonbondedMethod(), AmoebaMultipoleForce.setNonbondedMethod(), CustomHbondForce.setNonbondedMethod(), CustomNonbondedForce.setNonbondedMethod(), AmoebaOutOfPlaneBendForce.setOutOfPlaneBendParameters(), Context.setParameter(), AmoebaVdwForce.setParticleExclusions(), System.setParticleMass(), AmoebaVdwForce.setParticleParameters(), CustomGBForce.setParticleParameters(), NonbondedForce.setParticleParameters(), AmoebaGeneralizedKirkwoodForce.setParticleParameters(), CustomExternalForce.setParticleParameters(), DrudeForce.setParticleParameters(), GBSAOBCForce.setParticleParameters(), AmoebaWcaDispersionForce.setParticleParameters(), CustomManyParticleForce.setParticleParameters(), GBVIForce.setParticleParameters(), CustomNonbondedForce.setParticleParameters(), CustomHbondForce.setPerAcceptorParameterName(), CustomAngleForce.setPerAngleParameterName(), CustomBondForce.setPerBondParameterName(), CustomCompoundBondForce.setPerBondParameterName(), CustomIntegrator.setPerDofVariable(), CustomIntegrator.setPerDofVariableByName(), CustomHbondForce.setPerDonorParameterName(), Context.setPeriodicBoxVectors(), CustomManyParticleForce.setPermutationMode(), CustomGBForce.setPerParticleParameterName(), CustomExternalForce.setPerParticleParameterName(), CustomManyParticleForce.setPerParticleParameterName(), CustomNonbondedForce.setPerParticleParameterName(), CustomTorsionForce.setPerTorsionParameterName(), AmoebaPiTorsionForce.setPiTorsionParameters(), AmoebaMultipoleForce.setPmeGridDimensions(), NonbondedForce.setPMEParameters(), AmoebaMultipoleForce.setPolarizationType(), RPMDIntegrator.setPositions(), Context.setPositions(), AmoebaGeneralizedKirkwoodForce.setProbeRadius(), Platform.setPropertyDefaultValue(), Platform.setPropertyValue(), GBVIForce.setQuinticLowerLimitFactor(), GBVIForce.setQuinticUpperBornRadiusLimit(), DrudeLangevinIntegrator.setRandomNumberSeed(), BrownianIntegrator.setRandomNumberSeed(), LangevinIntegrator.setRandomNumberSeed(), RPMDIntegrator.setRandomNumberSeed(), AndersenThermostat.setRandomNumberSeed(), MonteCarloMembraneBarostat.setRandomNumberSeed(), VariableLangevinIntegrator.setRandomNumberSeed(), MonteCarloAnisotropicBarostat.setRandomNumberSeed(), CustomIntegrator.setRandomNumberSeed(), MonteCarloBarostat.setRandomNumberSeed(), NonbondedForce.setReactionFieldDielectric(), NonbondedForce.setReciprocalSpaceForceGroup(), AmoebaWcaDispersionForce.setRminh(), AmoebaWcaDispersionForce.setRmino(), DrudeForce.setScreenedPairParameters(), AmoebaWcaDispersionForce.setShctd(), AmoebaVdwForce.setSigmaCombiningRule(), AmoebaWcaDispersionForce.setSlevy(), AmoebaGeneralizedKirkwoodForce.setSoluteDielectric(), GBSAOBCForce.setSoluteDielectric(), GBVIForce.setSoluteDielectric(), AmoebaGeneralizedKirkwoodForce.setSolventDielectric(), GBSAOBCForce.setSolventDielectric(), GBVIForce.setSolventDielectric(), Integrator.setStepSize(), AmoebaStretchBendForce.setStretchBendParameters(), GBSAOBCForce.setSurfaceAreaEnergy(), AmoebaGeneralizedKirkwoodForce.setSurfaceAreaFactor(), NonbondedForce.setSwitchingDistance(), CustomNonbondedForce.setSwitchingDistance(), DrudeLangevinIntegrator.setTemperature(), BrownianIntegrator.setTemperature(), LangevinIntegrator.setTemperature(), RPMDIntegrator.setTemperature(), MonteCarloMembraneBarostat.setTemperature(), VariableLangevinIntegrator.setTemperature(), MonteCarloAnisotropicBarostat.setTemperature(), MonteCarloBarostat.setTemperature(), Context.setTime(), RBTorsionForce.setTorsionParameters(), CMAPTorsionForce.setTorsionParameters(), CustomTorsionForce.setTorsionParameters(), PeriodicTorsionForce.setTorsionParameters(), AmoebaTorsionTorsionForce.setTorsionTorsionGrid(), AmoebaTorsionTorsionForce.setTorsionTorsionParameters(), CustomManyParticleForce.setTypeFilter(), AmoebaVdwForce.setUseDispersionCorrection(), NonbondedForce.setUseDispersionCorrection(), CustomNonbondedForce.setUseLongRangeCorrection(), NonbondedForce.setUseSwitchingFunction(), CustomNonbondedForce.setUseSwitchingFunction(), RPMDIntegrator.setVelocities(), Context.setVelocities(), Context.setVelocitiesToTemperature(), MonteCarloMembraneBarostat.setXYMode(), MonteCarloMembraneBarostat.setZMode(), Integrator.step(), DrudeLangevinIntegrator.step(), BrownianIntegrator.step(), LangevinIntegrator.step(), RPMDIntegrator.step(), VariableLangevinIntegrator.step(), VerletIntegrator.step(), CustomIntegrator.step(), VariableVerletIntegrator.step(), DrudeSCFIntegrator.step(), VariableLangevinIntegrator.stepTo(), VariableVerletIntegrator.stepTo(), Platform.supportsDoublePrecision(), Platform.supportsKernels(), MonteCarloMembraneBarostat.SurfaceTension(), AndersenThermostat.Temperature(), CustomBondForce.updateParametersInContext(), AmoebaVdwForce.updateParametersInContext(), CustomCompoundBondForce.updateParametersInContext(), AmoebaInPlaneAngleForce.updateParametersInContext(), CustomGBForce.updateParametersInContext(), AmoebaOutOfPlaneBendForce.updateParametersInContext(), NonbondedForce.updateParametersInContext(), RBTorsionForce.updateParametersInContext(), AmoebaBondForce.updateParametersInContext(), AmoebaGeneralizedKirkwoodForce.updateParametersInContext(), CustomExternalForce.updateParametersInContext(), DrudeForce.updateParametersInContext(), GBSAOBCForce.updateParametersInContext(), AmoebaAngleForce.updateParametersInContext(), AmoebaWcaDispersionForce.updateParametersInContext(), CustomManyParticleForce.updateParametersInContext(), HarmonicBondForce.updateParametersInContext(), AmoebaStretchBendForce.updateParametersInContext(), CustomTorsionForce.updateParametersInContext(), PeriodicTorsionForce.updateParametersInContext(), AmoebaPiTorsionForce.updateParametersInContext(), AmoebaMultipoleForce.updateParametersInContext(), CustomHbondForce.updateParametersInContext(), CustomNonbondedForce.updateParametersInContext(), HarmonicAngleForce.updateParametersInContext(), CustomAngleForce.updateParametersInContext(), and OpenMMException.what().
1.8.6 
