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OpenMM
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OpenMM
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Classes | |
| class | AmoebaAngleForce |
| This class implements an interaction between triplets of particles that varies with the angle between them. More... | |
| class | AmoebaBondForce |
| This class implements an interaction between pairs of particles that varies with the distance between them. More... | |
| class | AmoebaGeneralizedKirkwoodForce |
| This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model. 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 | AmoebaMultipoleForce |
| This class implements the Amoeba multipole interaction. More... | |
| class | AmoebaOutOfPlaneBendForce |
| This class implements the Amoeba out-of-plane bend interaction. More... | |
| class | AmoebaPiTorsionForce |
| This class implements the Amoeba pi-torsion interaction. More... | |
| class | AmoebaStretchBendForce |
| This class implements the Amoeba stretch-bend interaction. More... | |
| class | AmoebaTorsionTorsionForce |
| This class implements the Amoeba torsion-torsion interaction. More... | |
| class | AmoebaVdwForce |
| This class implements a buffered 14-7 potential used to model van der Waals forces. 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 | AndersenThermostat |
| This class uses the Andersen method to maintain constant temperature. More... | |
| class | BrownianIntegrator |
| This is an Integrator which simulates a System using Brownian dynamics. More... | |
| class | CMAPTorsionForce |
| This class implements an interaction between pairs of dihedral angles. More... | |
| class | CMMotionRemover |
| This class prevents the center of mass of a System from drifting. More... | |
| class | Context |
| A Context stores the complete state of a simulation. More... | |
| class | Continuous1DFunction |
| This is a TabulatedFunction that computes a continuous one dimensional function. More... | |
| class | Continuous2DFunction |
| This is a TabulatedFunction that computes a continuous two dimensional function. More... | |
| class | Continuous3DFunction |
| This is a TabulatedFunction that computes a continuous three dimensional function. More... | |
| class | CustomAngleForce |
| This class implements interactions between sets of three particles that depend on the angle between them. More... | |
| class | CustomBondForce |
| This class implements bonded interactions between pairs of particles. More... | |
| class | CustomCompoundBondForce |
| This class supports a wide variety of bonded interactions. More... | |
| class | CustomExternalForce |
| This class implements an "external" force on particles. More... | |
| class | CustomGBForce |
| This class implements complex, multiple stage nonbonded interactions between particles. More... | |
| class | CustomHbondForce |
| This class supports a wide variety of energy functions used to represent hydrogen bonding. More... | |
| class | CustomIntegrator |
| This is an Integrator that can be used to implemented arbitrary, user defined integration algorithms. More... | |
| class | CustomManyParticleForce |
| This class supports a wide variety of nonbonded N-particle interactions, where N is user specified. More... | |
| class | CustomNonbondedForce |
| This class implements nonbonded interactions between particles. More... | |
| class | CustomTorsionForce |
| This class implements interactions between sets of four particles that depend on the torsion angle between them. More... | |
| class | Discrete1DFunction |
| This is a TabulatedFunction that computes a discrete one dimensional function f(x). More... | |
| class | Discrete2DFunction |
| This is a TabulatedFunction that computes a discrete two dimensional function f(x,y). More... | |
| class | Discrete3DFunction |
| This is a TabulatedFunction that computes a discrete three dimensional function f(x,y,z). More... | |
| class | DrudeForce |
| This class implements forces that are specific to Drude oscillators. More... | |
| class | DrudeLangevinIntegrator |
| This Integrator simulates systems that include Drude particles. More... | |
| class | DrudeSCFIntegrator |
| This is a leap-frog Verlet Integrator that simulates systems with Drude particles. More... | |
| class | Force |
| Force objects apply forces to the particles in a System, or alter their behavior in other ways. More... | |
| class | GBSAOBCForce |
| This class implements an implicit solvation force using the GBSA-OBC model. More... | |
| class | GBVIForce |
| This class implements an implicit solvation force using the GB/VI model. More... | |
| class | HarmonicAngleForce |
| This class implements an interaction between groups of three particles that varies harmonically with the angle between them. More... | |
| class | HarmonicBondForce |
| This class implements an interaction between pairs of particles that varies harmonically with the distance between them. More... | |
| class | Integrator |
| An Integrator defines a method for simulating a System by integrating the equations of motion. More... | |
| class | LangevinIntegrator |
| This is an Integrator which simulates a System using Langevin dynamics. 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 | 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 | MonteCarloAnisotropicBarostat |
| This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure. 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 | MonteCarloMembraneBarostat |
| This is a Monte Carlo barostat designed specifically for membrane simulations. 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 | OpenMMException |
| This class is used for all exceptions thrown by OpenMM. More... | |
| class | OutOfPlaneSite |
| This is a VirtualSite that computes the particle location based on three other particles' locations. More... | |
| class | PeriodicTorsionForce |
| This class implements an interaction between groups of four particles that varies periodically with the torsion angle between them. More... | |
| class | Platform |
| A Platform defines an implementation of all the kernels needed to perform some calculation. 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 | RPMDIntegrator |
| This is an Integrator which simulates a System using ring polymer molecular dynamics (RPMD). More... | |
| class | RPMDMonteCarloBarostat |
| This class is very similar to MonteCarloBarostat, but it is specifically designed for use with RPMDIntegrator. More... | |
| class | SerializationNode |
| A SerializationNode stores information about an object during serialization or deserialization. | |
| class | SerializationProxy |
| A SerializationProxy is an object that knows how to serialize and deserialize objects of a particular type. | |
| class | State |
| A State object records a snapshot of the current state of a simulation at a point in time. More... | |
| class | SwigPyIterator |
| class | System |
| This class represents a molecular system. More... | |
| class | TabulatedFunction |
| A TabulatedFunction uses a set of tabulated values to define a mathematical function. More... | |
| class | ThreeParticleAverageSite |
| This is a VirtualSite that computes the particle location as a weighted average of three other particle's locations. More... | |
| class | TwoParticleAverageSite |
| This is a VirtualSite that computes the particle location as a weighted average of two other particle's locations. More... | |
| class | VariableLangevinIntegrator |
| This is an error contolled, variable time step Integrator that simulates a System using Langevin dynamics. More... | |
| class | VariableVerletIntegrator |
| This is an error contolled, variable time step Integrator that simulates a System using the leap-frog Verlet algorithm. More... | |
| class | VerletIntegrator |
| This is an Integrator which simulates a System using the leap-frog Verlet algorithm. More... | |
| class | VirtualSite |
| A VirtualSite describes the rules for computing a particle's position based on other particles. More... | |
| class | XmlSerializer |
| XmlSerializer is used for serializing objects as XML, and for reconstructing them again. More... | |
Functions | |
| 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 | 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_getPluginLoadFailures |
| Platform_getPluginLoadFailures() -> vectorstring. 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 | MonteCarloMembraneBarostat_Pressure |
| MonteCarloMembraneBarostat_Pressure() -> std::string const &. More... | |
| def | MonteCarloMembraneBarostat_SurfaceTension |
| MonteCarloMembraneBarostat_SurfaceTension() -> std::string const &. More... | |
| def | MonteCarloBarostat_Pressure |
| MonteCarloBarostat_Pressure() -> std::string const &. More... | |
| def | LocalEnergyMinimizer_minimize |
| LocalEnergyMinimizer_minimize(Context context, double tolerance=10, int maxIterations=0) 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 | RPMDMonteCarloBarostat_Pressure |
| RPMDMonteCarloBarostat_Pressure() -> std::string const &. 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 | 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 | AndersenThermostat_Temperature |
| AndersenThermostat_Temperature() -> std::string const &. More... | |
| def | AndersenThermostat_CollisionFrequency |
| AndersenThermostat_CollisionFrequency() -> std::string const &. More... | |
Variables | |
| tuple | _openmm = swig_import_helper() |
| int | _newclass = 0 |
| ios_base_swigregister = _openmm.ios_base_swigregister | |
| cvar = _openmm.cvar | |
| ios_base_sync_with_stdio = _openmm.ios_base_sync_with_stdio | |
| ios_base_xalloc = _openmm.ios_base_xalloc | |
| ios_swigregister = _openmm.ios_swigregister | |
| ostream_swigregister = _openmm.ostream_swigregister | |
| cin = cvar.cin | |
| cout = cvar.cout | |
| cerr = cvar.cerr | |
| clog = cvar.clog | |
| istream_swigregister = _openmm.istream_swigregister | |
| iostream_swigregister = _openmm.iostream_swigregister | |
| endl_cb_ptr = _openmm.endl_cb_ptr | |
| endl = _openmm.endl | |
| ends_cb_ptr = _openmm.ends_cb_ptr | |
| ends = _openmm.ends | |
| flush_cb_ptr = _openmm.flush_cb_ptr | |
| flush = _openmm.flush | |
| SwigPyIterator_swigregister = _openmm.SwigPyIterator_swigregister | |
| pairii_swigregister = _openmm.pairii_swigregister | |
| vectord_swigregister = _openmm.vectord_swigregister | |
| vectorddd_swigregister = _openmm.vectorddd_swigregister | |
| vectori_swigregister = _openmm.vectori_swigregister | |
| vectorii_swigregister = _openmm.vectorii_swigregister | |
| vectorpairii_swigregister = _openmm.vectorpairii_swigregister | |
| vectorstring_swigregister = _openmm.vectorstring_swigregister | |
| mapstringstring_swigregister = _openmm.mapstringstring_swigregister | |
| mapstringdouble_swigregister = _openmm.mapstringdouble_swigregister | |
| mapii_swigregister = _openmm.mapii_swigregister | |
| seti_swigregister = _openmm.seti_swigregister | |
| tuple | RMIN_PER_SIGMA = math.pow(2, 1/6.0) |
| tuple | RVDW_PER_SIGMA = math.pow(2, 1/6.0) |
| tuple | _string_types = (basestring,) |
| TabulatedFunction_swigregister = _openmm.TabulatedFunction_swigregister | |
| NmPerAngstrom = cvar.NmPerAngstrom | |
| AngstromsPerNm = cvar.AngstromsPerNm | |
| PsPerFs = cvar.PsPerFs | |
| FsPerPs = cvar.FsPerPs | |
| KJPerKcal = cvar.KJPerKcal | |
| KcalPerKJ = cvar.KcalPerKJ | |
| RadiansPerDegree = cvar.RadiansPerDegree | |
| DegreesPerRadian = cvar.DegreesPerRadian | |
| SigmaPerVdwRadius = cvar.SigmaPerVdwRadius | |
| VdwRadiusPerSigma = cvar.VdwRadiusPerSigma | |
| Discrete2DFunction_swigregister = _openmm.Discrete2DFunction_swigregister | |
| Integrator_swigregister = _openmm.Integrator_swigregister | |
| LangevinIntegrator_swigregister = _openmm.LangevinIntegrator_swigregister | |
| Force_swigregister = _openmm.Force_swigregister | |
| CustomGBForce_swigregister = _openmm.CustomGBForce_swigregister | |
| CustomNonbondedForce_swigregister = _openmm.CustomNonbondedForce_swigregister | |
| VariableLangevinIntegrator_swigregister = _openmm.VariableLangevinIntegrator_swigregister | |
| AmoebaWcaDispersionForce_swigregister = _openmm.AmoebaWcaDispersionForce_swigregister | |
| RPMDIntegrator_swigregister = _openmm.RPMDIntegrator_swigregister | |
| AmoebaInPlaneAngleForce_swigregister = _openmm.AmoebaInPlaneAngleForce_swigregister | |
| VirtualSite_swigregister = _openmm.VirtualSite_swigregister | |
| ThreeParticleAverageSite_swigregister = _openmm.ThreeParticleAverageSite_swigregister | |
| OutOfPlaneSite_swigregister = _openmm.OutOfPlaneSite_swigregister | |
| Platform_swigregister = _openmm.Platform_swigregister | |
| VerletIntegrator_swigregister = _openmm.VerletIntegrator_swigregister | |
| DrudeSCFIntegrator_swigregister = _openmm.DrudeSCFIntegrator_swigregister | |
| MonteCarloMembraneBarostat_swigregister = _openmm.MonteCarloMembraneBarostat_swigregister | |
| MonteCarloBarostat_swigregister = _openmm.MonteCarloBarostat_swigregister | |
| AmoebaTorsionTorsionForce_swigregister = _openmm.AmoebaTorsionTorsionForce_swigregister | |
| AmoebaBondForce_swigregister = _openmm.AmoebaBondForce_swigregister | |
| LocalEnergyMinimizer_swigregister = _openmm.LocalEnergyMinimizer_swigregister | |
| Context_swigregister = _openmm.Context_swigregister | |
| XmlSerializer_swigregister = _openmm.XmlSerializer_swigregister | |
| VariableVerletIntegrator_swigregister = _openmm.VariableVerletIntegrator_swigregister | |
| AmoebaPiTorsionForce_swigregister = _openmm.AmoebaPiTorsionForce_swigregister | |
| CustomCompoundBondForce_swigregister = _openmm.CustomCompoundBondForce_swigregister | |
| Continuous3DFunction_swigregister = _openmm.Continuous3DFunction_swigregister | |
| Discrete3DFunction_swigregister = _openmm.Discrete3DFunction_swigregister | |
| CustomExternalForce_swigregister = _openmm.CustomExternalForce_swigregister | |
| DrudeForce_swigregister = _openmm.DrudeForce_swigregister | |
| CustomManyParticleForce_swigregister = _openmm.CustomManyParticleForce_swigregister | |
| GBVIForce_swigregister = _openmm.GBVIForce_swigregister | |
| TwoParticleAverageSite_swigregister = _openmm.TwoParticleAverageSite_swigregister | |
| GBSAOBCForce_swigregister = _openmm.GBSAOBCForce_swigregister | |
| NonbondedForce_swigregister = _openmm.NonbondedForce_swigregister | |
| AmoebaGeneralizedKirkwoodForce_swigregister = _openmm.AmoebaGeneralizedKirkwoodForce_swigregister | |
| Discrete1DFunction_swigregister = _openmm.Discrete1DFunction_swigregister | |
| Continuous1DFunction_swigregister = _openmm.Continuous1DFunction_swigregister | |
| BrownianIntegrator_swigregister = _openmm.BrownianIntegrator_swigregister | |
| OpenMMException_swigregister = _openmm.OpenMMException_swigregister | |
| LocalCoordinatesSite_swigregister = _openmm.LocalCoordinatesSite_swigregister | |
| RBTorsionForce_swigregister = _openmm.RBTorsionForce_swigregister | |
| RPMDMonteCarloBarostat_swigregister = _openmm.RPMDMonteCarloBarostat_swigregister | |
| SerializationNode_swigregister = _openmm.SerializationNode_swigregister | |
| MonteCarloAnisotropicBarostat_swigregister = _openmm.MonteCarloAnisotropicBarostat_swigregister | |
| AmoebaOutOfPlaneBendForce_swigregister = _openmm.AmoebaOutOfPlaneBendForce_swigregister | |
| CustomHbondForce_swigregister = _openmm.CustomHbondForce_swigregister | |
| CMMotionRemover_swigregister = _openmm.CMMotionRemover_swigregister | |
| CustomIntegrator_swigregister = _openmm.CustomIntegrator_swigregister | |
| System_swigregister = _openmm.System_swigregister | |
| HarmonicAngleForce_swigregister = _openmm.HarmonicAngleForce_swigregister | |
| SerializationProxy_swigregister = _openmm.SerializationProxy_swigregister | |
| AmoebaMultipoleForce_swigregister = _openmm.AmoebaMultipoleForce_swigregister | |
| CustomAngleForce_swigregister = _openmm.CustomAngleForce_swigregister | |
| AmoebaAngleForce_swigregister = _openmm.AmoebaAngleForce_swigregister | |
| AmoebaVdwForce_swigregister = _openmm.AmoebaVdwForce_swigregister | |
| DrudeLangevinIntegrator_swigregister = _openmm.DrudeLangevinIntegrator_swigregister | |
| AndersenThermostat_swigregister = _openmm.AndersenThermostat_swigregister | |
| HarmonicBondForce_swigregister = _openmm.HarmonicBondForce_swigregister | |
| CMAPTorsionForce_swigregister = _openmm.CMAPTorsionForce_swigregister | |
| CustomBondForce_swigregister = _openmm.CustomBondForce_swigregister | |
| Continuous2DFunction_swigregister = _openmm.Continuous2DFunction_swigregister | |
| AmoebaStretchBendForce_swigregister = _openmm.AmoebaStretchBendForce_swigregister | |
| CustomTorsionForce_swigregister = _openmm.CustomTorsionForce_swigregister | |
| PeriodicTorsionForce_swigregister = _openmm.PeriodicTorsionForce_swigregister | |
| list | __all__ = [k for k in locals().keys() if not (k.endswith('_swigregister') or k.startswith('_'))] |
| def simtk.openmm.openmm.AndersenThermostat_CollisionFrequency | ( | args | ) |
AndersenThermostat_CollisionFrequency() -> std::string const &.
This is the name of the parameter which store the current collision frequency (in 1/ps).
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.AndersenThermostat_Temperature | ( | args | ) |
AndersenThermostat_Temperature() -> std::string const &.
This is the name of the parameter which stores the current temperature of the heat bath (in Kelvin).
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.endl | ( | args | ) |
References simtk.openmm.openmm.endl.
| def simtk.openmm.openmm.ends | ( | args | ) |
References simtk.openmm.openmm.ends.
| def simtk.openmm.openmm.flush | ( | args | ) |
References simtk.openmm.openmm.flush.
| def simtk.openmm.openmm.ios_base_sync_with_stdio | ( | __sync = True | ) |
References simtk.openmm.openmm.ios_base_sync_with_stdio.
| def simtk.openmm.openmm.ios_base_xalloc | ( | ) |
References simtk.openmm.openmm.ios_base_xalloc.
| def simtk.openmm.openmm.LocalEnergyMinimizer_minimize | ( | args | ) |
LocalEnergyMinimizer_minimize(Context context, double tolerance=10, int maxIterations=0)
Search for a new set of particle positions that represent a local potential energy minimum. On exit, the Context will have been updated with the new positions.
| context | a Context specifying the System to minimize and the initial particle positions |
| tolerance | this specifies how precisely the energy minimum must be located. Minimization will be halted once the root-mean-square value of all force components reaches this tolerance. The default value is 10. |
| maxIterations | the maximum number of iterations to perform. If this is 0, minimation is continued until the results converge without regard to how many iterations it takes. The default value is 0. |
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.MonteCarloAnisotropicBarostat_PressureX | ( | args | ) |
MonteCarloAnisotropicBarostat_PressureX() -> std::string const &.
This is the name of the parameter which stores the current pressure acting on the X-axis (in bar).
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.MonteCarloAnisotropicBarostat_PressureY | ( | args | ) |
MonteCarloAnisotropicBarostat_PressureY() -> std::string const &.
This is the name of the parameter which stores the current pressure acting on the Y-axis (in bar).
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.MonteCarloAnisotropicBarostat_PressureZ | ( | args | ) |
MonteCarloAnisotropicBarostat_PressureZ() -> std::string const &.
This is the name of the parameter which stores the current pressure acting on the Z-axis (in bar).
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.MonteCarloBarostat_Pressure | ( | args | ) |
MonteCarloBarostat_Pressure() -> std::string const &.
This is the name of the parameter which stores the current pressure acting on the system (in bar).
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.MonteCarloMembraneBarostat_Pressure | ( | args | ) |
MonteCarloMembraneBarostat_Pressure() -> std::string const &.
This is the name of the parameter which stores the current pressure acting on the system (in bar).
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.MonteCarloMembraneBarostat_SurfaceTension | ( | args | ) |
MonteCarloMembraneBarostat_SurfaceTension() -> std::string const &.
This is the name of the parameter which stores the current surface tension acting on the system (in bar*nm).
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.Platform_findPlatform | ( | args | ) |
Platform_findPlatform(vectorstring kernelNames) -> Platform.
Find a Platform which can be used to perform a calculation.
| kernelNames | the names of all kernels which will be needed for the calculation |
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.Platform_getDefaultPluginsDirectory | ( | args | ) |
Platform_getDefaultPluginsDirectory() -> std::string const &.
Get the default directory from which to load plugins. If the environment variable OPENMM_PLUGIN_DIR is set, this returns its value. Otherwise, it returns a platform specific default location.
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.Platform_getNumPlatforms | ( | args | ) |
Platform_getNumPlatforms() -> int.
Get the number of Platforms that have been registered.
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.Platform_getOpenMMVersion | ( | args | ) |
Platform_getOpenMMVersion() -> std::string const &.
Get a string containing the version number of the OpenMM library.
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.Platform_getPlatform | ( | args | ) |
Platform_getPlatform(int index) -> Platform.
Get a registered Platform by index.
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.Platform_getPlatformByName | ( | args | ) |
Platform_getPlatformByName(std::string const & name) -> Platform.
Get the registered Platform with a particular name. If no Platform with that name has been registered, this throws an exception.
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.Platform_getPluginLoadFailures | ( | args | ) |
Platform_getPluginLoadFailures() -> vectorstring.
Get any failures caused during the last call to loadPluginsFromDirectory
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.Platform_loadPluginLibrary | ( | args | ) |
Platform_loadPluginLibrary(std::string const & file)
Load a dynamic library (DLL) which contains an OpenMM plugin. Typically, each Platform is distributed as a separate dynamic library. This method can then be called at runtime to load each available library. Each library should contain an initializer function to register any Platforms and KernelFactories that it contains.
If the file does not exist or cannot be loaded, an exception is thrown.
| file | the path to the dynamic library file. This is interpreted using the operating system's rules for loading libraries. Typically it may be either an absolute path or relative to a set of standard locations. |
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.Platform_loadPluginsFromDirectory | ( | args | ) |
Platform_loadPluginsFromDirectory(std::string const & directory) -> vectorstring.
Load multiple dynamic libraries (DLLs) which contain OpenMM plugins from a single directory. This method loops over every file contained in the specified directory and calls loadPluginLibrary() for each one. If an error occurs while trying to load a particular file, that file is simply ignored. You can retrieve a list of all such errors by calling getPluginLoadFailures().
| directory | the path to the directory containing libraries to load |
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.Platform_registerPlatform | ( | args | ) |
Platform_registerPlatform(Platform platform)
Register a new Platform.
| def simtk.openmm.openmm.RPMDMonteCarloBarostat_Pressure | ( | args | ) |
RPMDMonteCarloBarostat_Pressure() -> std::string const &.
This is the name of the parameter which stores the current pressure acting on the system (in bar).
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.SerializationProxy_getProxy | ( | args | ) |
getProxy(std::string const & typeName) -> SerializationProxy SerializationProxy_getProxy(std::type_info const & type) -> SerializationProxy
Get the SerializationProxy to use for objects of a particular type, specified by type_info.
| type | the type_info of the object type to get a proxy for |
References simtk.openmm.openmm.stripUnits().
| def simtk.openmm.openmm.SerializationProxy_registerProxy | ( | args | ) |
SerializationProxy_registerProxy(std::type_info const & type, SerializationProxy proxy)
Register a SerializationProxy to be used for objects of a particular type.
| type | the type_info for the object type |
| proxy | the proxy to use for objects of the specified type |
References simtk.openmm.openmm.stripUnits().
| 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 TabulatedFunction.__del__(), Discrete2DFunction.__del__(), Integrator.__del__(), LangevinIntegrator.__del__(), Force.__del__(), CustomGBForce.__del__(), CustomNonbondedForce.__del__(), VariableLangevinIntegrator.__del__(), AmoebaWcaDispersionForce.__del__(), RPMDIntegrator.__del__(), AmoebaInPlaneAngleForce.__del__(), VirtualSite.__del__(), ThreeParticleAverageSite.__del__(), OutOfPlaneSite.__del__(), Platform.__del__(), VerletIntegrator.__del__(), DrudeSCFIntegrator.__del__(), MonteCarloMembraneBarostat.__del__(), MonteCarloBarostat.__del__(), AmoebaTorsionTorsionForce.__del__(), AmoebaBondForce.__del__(), LocalEnergyMinimizer.__del__(), Context.__del__(), XmlSerializer.__del__(), VariableVerletIntegrator.__del__(), AmoebaPiTorsionForce.__del__(), CustomCompoundBondForce.__del__(), Continuous3DFunction.__del__(), Discrete3DFunction.__del__(), CustomExternalForce.__del__(), DrudeForce.__del__(), CustomManyParticleForce.__del__(), GBVIForce.__del__(), TwoParticleAverageSite.__del__(), GBSAOBCForce.__del__(), NonbondedForce.__del__(), AmoebaGeneralizedKirkwoodForce.__del__(), Discrete1DFunction.__del__(), Continuous1DFunction.__del__(), BrownianIntegrator.__del__(), OpenMMException.__del__(), LocalCoordinatesSite.__del__(), RBTorsionForce.__del__(), RPMDMonteCarloBarostat.__del__(), MonteCarloAnisotropicBarostat.__del__(), AmoebaOutOfPlaneBendForce.__del__(), CustomHbondForce.__del__(), CMMotionRemover.__del__(), CustomIntegrator.__del__(), System.__del__(), HarmonicAngleForce.__del__(), AmoebaMultipoleForce.__del__(), CustomAngleForce.__del__(), AmoebaAngleForce.__del__(), AmoebaVdwForce.__del__(), DrudeLangevinIntegrator.__del__(), AndersenThermostat.__del__(), HarmonicBondForce.__del__(), CMAPTorsionForce.__del__(), CustomBondForce.__del__(), Continuous2DFunction.__del__(), AmoebaStretchBendForce.__del__(), CustomTorsionForce.__del__(), PeriodicTorsionForce.__del__(), Discrete2DFunction.__init__(), LangevinIntegrator.__init__(), CustomGBForce.__init__(), CustomNonbondedForce.__init__(), VariableLangevinIntegrator.__init__(), AmoebaWcaDispersionForce.__init__(), RPMDIntegrator.__init__(), AmoebaInPlaneAngleForce.__init__(), ThreeParticleAverageSite.__init__(), OutOfPlaneSite.__init__(), VerletIntegrator.__init__(), DrudeSCFIntegrator.__init__(), MonteCarloMembraneBarostat.__init__(), MonteCarloBarostat.__init__(), AmoebaTorsionTorsionForce.__init__(), AmoebaBondForce.__init__(), Context.__init__(), VariableVerletIntegrator.__init__(), AmoebaPiTorsionForce.__init__(), CustomCompoundBondForce.__init__(), Continuous3DFunction.__init__(), Discrete3DFunction.__init__(), CustomExternalForce.__init__(), DrudeForce.__init__(), CustomManyParticleForce.__init__(), GBVIForce.__init__(), TwoParticleAverageSite.__init__(), GBSAOBCForce.__init__(), NonbondedForce.__init__(), AmoebaGeneralizedKirkwoodForce.__init__(), Discrete1DFunction.__init__(), Continuous1DFunction.__init__(), BrownianIntegrator.__init__(), OpenMMException.__init__(), LocalCoordinatesSite.__init__(), RBTorsionForce.__init__(), RPMDMonteCarloBarostat.__init__(), MonteCarloAnisotropicBarostat.__init__(), AmoebaOutOfPlaneBendForce.__init__(), CustomHbondForce.__init__(), CMMotionRemover.__init__(), CustomIntegrator.__init__(), System.__init__(), HarmonicAngleForce.__init__(), AmoebaMultipoleForce.__init__(), CustomAngleForce.__init__(), AmoebaAngleForce.__init__(), AmoebaVdwForce.__init__(), DrudeLangevinIntegrator.__init__(), AndersenThermostat.__init__(), HarmonicBondForce.__init__(), CMAPTorsionForce.__init__(), CustomBondForce.__init__(), Continuous2DFunction.__init__(), AmoebaStretchBendForce.__init__(), CustomTorsionForce.__init__(), PeriodicTorsionForce.__init__(), CustomHbondForce.addAcceptor(), AmoebaInPlaneAngleForce.addAngle(), HarmonicAngleForce.addAngle(), CustomAngleForce.addAngle(), AmoebaAngleForce.addAngle(), AmoebaBondForce.addBond(), CustomCompoundBondForce.addBond(), GBVIForce.addBond(), HarmonicBondForce.addBond(), CustomBondForce.addBond(), CustomGBForce.addComputedValue(), CustomIntegrator.addComputeGlobal(), CustomIntegrator.addComputePerDof(), CustomIntegrator.addComputeSum(), CustomIntegrator.addConstrainPositions(), System.addConstraint(), CustomIntegrator.addConstrainVelocities(), CustomHbondForce.addDonor(), CustomGBForce.addEnergyTerm(), NonbondedForce.addException(), CustomGBForce.addExclusion(), CustomNonbondedForce.addExclusion(), CustomManyParticleForce.addExclusion(), CustomHbondForce.addExclusion(), CustomGBForce.addFunction(), CustomNonbondedForce.addFunction(), CustomCompoundBondForce.addFunction(), CustomHbondForce.addFunction(), CustomGBForce.addGlobalParameter(), CustomNonbondedForce.addGlobalParameter(), CustomCompoundBondForce.addGlobalParameter(), CustomExternalForce.addGlobalParameter(), CustomManyParticleForce.addGlobalParameter(), CustomHbondForce.addGlobalParameter(), CustomAngleForce.addGlobalParameter(), CustomBondForce.addGlobalParameter(), CustomTorsionForce.addGlobalParameter(), CustomIntegrator.addGlobalVariable(), CustomNonbondedForce.addInteractionGroup(), CMAPTorsionForce.addMap(), AmoebaMultipoleForce.addMultipole(), AmoebaOutOfPlaneBendForce.addOutOfPlaneBend(), CustomGBForce.addParticle(), CustomNonbondedForce.addParticle(), AmoebaWcaDispersionForce.addParticle(), CustomExternalForce.addParticle(), DrudeForce.addParticle(), CustomManyParticleForce.addParticle(), GBVIForce.addParticle(), GBSAOBCForce.addParticle(), NonbondedForce.addParticle(), AmoebaGeneralizedKirkwoodForce.addParticle(), System.addParticle(), AmoebaVdwForce.addParticle(), CustomHbondForce.addPerAcceptorParameter(), CustomAngleForce.addPerAngleParameter(), CustomCompoundBondForce.addPerBondParameter(), CustomBondForce.addPerBondParameter(), CustomIntegrator.addPerDofVariable(), CustomHbondForce.addPerDonorParameter(), CustomGBForce.addPerParticleParameter(), CustomNonbondedForce.addPerParticleParameter(), CustomExternalForce.addPerParticleParameter(), CustomManyParticleForce.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(), Discrete2DFunction.Copy(), Continuous3DFunction.Copy(), Discrete3DFunction.Copy(), Discrete1DFunction.Copy(), Continuous1DFunction.Copy(), Continuous2DFunction.Copy(), NonbondedForce.createExceptionsFromBonds(), CustomNonbondedForce.createExclusionsFromBonds(), CustomManyParticleForce.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(), HarmonicAngleForce.getAngleParameters(), CustomAngleForce.getAngleParameters(), AmoebaAngleForce.getAngleParameters(), RPMDIntegrator.getApplyThermostat(), AmoebaWcaDispersionForce.getAwater(), AmoebaBondForce.getBondParameters(), CustomCompoundBondForce.getBondParameters(), GBVIForce.getBondParameters(), HarmonicBondForce.getBondParameters(), CustomBondForce.getBondParameters(), GBVIForce.getBornRadiusScalingMethod(), CustomIntegrator.getComputationStep(), CustomGBForce.getComputedValueParameters(), System.getConstraintParameters(), Integrator.getConstraintTolerance(), RPMDIntegrator.getContractions(), AmoebaMultipoleForce.getCovalentMap(), AmoebaMultipoleForce.getCovalentMaps(), AmoebaVdwForce.getCutoff(), CustomGBForce.getCutoffDistance(), CustomNonbondedForce.getCutoffDistance(), CustomManyParticleForce.getCutoffDistance(), GBVIForce.getCutoffDistance(), GBSAOBCForce.getCutoffDistance(), NonbondedForce.getCutoffDistance(), CustomHbondForce.getCutoffDistance(), AmoebaMultipoleForce.getCutoffDistance(), AndersenThermostat.getDefaultCollisionFrequency(), System.getDefaultPeriodicBoxVectors(), Platform.getDefaultPluginsDirectory(), MonteCarloMembraneBarostat.getDefaultPressure(), MonteCarloBarostat.getDefaultPressure(), RPMDMonteCarloBarostat.getDefaultPressure(), MonteCarloAnisotropicBarostat.getDefaultPressure(), MonteCarloMembraneBarostat.getDefaultSurfaceTension(), AndersenThermostat.getDefaultTemperature(), AmoebaWcaDispersionForce.getDispoff(), CustomHbondForce.getDonorParameters(), DrudeLangevinIntegrator.getDrudeFriction(), DrudeLangevinIntegrator.getDrudeTemperature(), AmoebaMultipoleForce.getElectrostaticPotential(), CustomNonbondedForce.getEnergyFunction(), CustomCompoundBondForce.getEnergyFunction(), CustomExternalForce.getEnergyFunction(), CustomManyParticleForce.getEnergyFunction(), CustomHbondForce.getEnergyFunction(), CustomAngleForce.getEnergyFunction(), CustomBondForce.getEnergyFunction(), CustomTorsionForce.getEnergyFunction(), CustomGBForce.getEnergyTermParameters(), AmoebaWcaDispersionForce.getEpsh(), AmoebaVdwForce.getEpsilonCombiningRule(), AmoebaWcaDispersionForce.getEpso(), VariableLangevinIntegrator.getErrorTolerance(), VariableVerletIntegrator.getErrorTolerance(), NonbondedForce.getEwaldErrorTolerance(), AmoebaMultipoleForce.getEwaldErrorTolerance(), NonbondedForce.getExceptionParameters(), CustomGBForce.getExclusionParticles(), CustomNonbondedForce.getExclusionParticles(), CustomManyParticleForce.getExclusionParticles(), CustomHbondForce.getExclusionParticles(), System.getForce(), Force.getForceGroup(), MonteCarloMembraneBarostat.getFrequency(), MonteCarloBarostat.getFrequency(), RPMDMonteCarloBarostat.getFrequency(), MonteCarloAnisotropicBarostat.getFrequency(), CMMotionRemover.getFrequency(), LangevinIntegrator.getFriction(), VariableLangevinIntegrator.getFriction(), RPMDIntegrator.getFriction(), BrownianIntegrator.getFriction(), DrudeLangevinIntegrator.getFriction(), Discrete2DFunction.getFunctionParameters(), CustomGBForce.getFunctionParameters(), CustomNonbondedForce.getFunctionParameters(), CustomCompoundBondForce.getFunctionParameters(), Continuous3DFunction.getFunctionParameters(), Discrete3DFunction.getFunctionParameters(), Discrete1DFunction.getFunctionParameters(), Continuous1DFunction.getFunctionParameters(), CustomHbondForce.getFunctionParameters(), Continuous2DFunction.getFunctionParameters(), CustomGBForce.getGlobalParameterDefaultValue(), CustomNonbondedForce.getGlobalParameterDefaultValue(), CustomCompoundBondForce.getGlobalParameterDefaultValue(), CustomExternalForce.getGlobalParameterDefaultValue(), CustomManyParticleForce.getGlobalParameterDefaultValue(), CustomHbondForce.getGlobalParameterDefaultValue(), CustomAngleForce.getGlobalParameterDefaultValue(), CustomBondForce.getGlobalParameterDefaultValue(), CustomTorsionForce.getGlobalParameterDefaultValue(), CustomGBForce.getGlobalParameterName(), CustomNonbondedForce.getGlobalParameterName(), CustomCompoundBondForce.getGlobalParameterName(), CustomExternalForce.getGlobalParameterName(), CustomManyParticleForce.getGlobalParameterName(), CustomHbondForce.getGlobalParameterName(), CustomAngleForce.getGlobalParameterName(), CustomBondForce.getGlobalParameterName(), CustomTorsionForce.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(), CustomGBForce.getNonbondedMethod(), CustomNonbondedForce.getNonbondedMethod(), CustomManyParticleForce.getNonbondedMethod(), GBVIForce.getNonbondedMethod(), GBSAOBCForce.getNonbondedMethod(), NonbondedForce.getNonbondedMethod(), CustomHbondForce.getNonbondedMethod(), AmoebaMultipoleForce.getNonbondedMethod(), AmoebaVdwForce.getNonbondedMethod(), CustomHbondForce.getNumAcceptors(), AmoebaInPlaneAngleForce.getNumAngles(), HarmonicAngleForce.getNumAngles(), CustomAngleForce.getNumAngles(), AmoebaAngleForce.getNumAngles(), AmoebaBondForce.getNumBonds(), CustomCompoundBondForce.getNumBonds(), GBVIForce.getNumBonds(), HarmonicBondForce.getNumBonds(), CustomBondForce.getNumBonds(), CustomIntegrator.getNumComputations(), CustomGBForce.getNumComputedValues(), System.getNumConstraints(), RPMDIntegrator.getNumCopies(), CustomHbondForce.getNumDonors(), CustomGBForce.getNumEnergyTerms(), NonbondedForce.getNumExceptions(), CustomGBForce.getNumExclusions(), CustomNonbondedForce.getNumExclusions(), CustomManyParticleForce.getNumExclusions(), CustomHbondForce.getNumExclusions(), System.getNumForces(), CustomGBForce.getNumFunctions(), CustomNonbondedForce.getNumFunctions(), CustomCompoundBondForce.getNumFunctions(), CustomHbondForce.getNumFunctions(), CustomGBForce.getNumGlobalParameters(), CustomNonbondedForce.getNumGlobalParameters(), CustomCompoundBondForce.getNumGlobalParameters(), CustomExternalForce.getNumGlobalParameters(), CustomManyParticleForce.getNumGlobalParameters(), CustomHbondForce.getNumGlobalParameters(), CustomAngleForce.getNumGlobalParameters(), CustomBondForce.getNumGlobalParameters(), CustomTorsionForce.getNumGlobalParameters(), CustomIntegrator.getNumGlobalVariables(), CustomNonbondedForce.getNumInteractionGroups(), CMAPTorsionForce.getNumMaps(), AmoebaMultipoleForce.getNumMultipoles(), AmoebaOutOfPlaneBendForce.getNumOutOfPlaneBends(), CustomGBForce.getNumParticles(), CustomNonbondedForce.getNumParticles(), AmoebaWcaDispersionForce.getNumParticles(), VirtualSite.getNumParticles(), CustomExternalForce.getNumParticles(), DrudeForce.getNumParticles(), CustomManyParticleForce.getNumParticles(), GBVIForce.getNumParticles(), GBSAOBCForce.getNumParticles(), NonbondedForce.getNumParticles(), AmoebaGeneralizedKirkwoodForce.getNumParticles(), System.getNumParticles(), AmoebaVdwForce.getNumParticles(), CustomCompoundBondForce.getNumParticlesPerBond(), CustomManyParticleForce.getNumParticlesPerSet(), CustomHbondForce.getNumPerAcceptorParameters(), CustomAngleForce.getNumPerAngleParameters(), CustomCompoundBondForce.getNumPerBondParameters(), CustomBondForce.getNumPerBondParameters(), CustomIntegrator.getNumPerDofVariables(), CustomHbondForce.getNumPerDonorParameters(), CustomGBForce.getNumPerParticleParameters(), CustomNonbondedForce.getNumPerParticleParameters(), CustomExternalForce.getNumPerParticleParameters(), CustomManyParticleForce.getNumPerParticleParameters(), CustomTorsionForce.getNumPerTorsionParameters(), AmoebaPiTorsionForce.getNumPiTorsions(), Platform.getNumPlatforms(), DrudeForce.getNumScreenedPairs(), AmoebaStretchBendForce.getNumStretchBends(), CustomGBForce.getNumTabulatedFunctions(), CustomNonbondedForce.getNumTabulatedFunctions(), CustomCompoundBondForce.getNumTabulatedFunctions(), CustomManyParticleForce.getNumTabulatedFunctions(), CustomHbondForce.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(), CustomGBForce.getParticleParameters(), CustomNonbondedForce.getParticleParameters(), AmoebaWcaDispersionForce.getParticleParameters(), CustomExternalForce.getParticleParameters(), DrudeForce.getParticleParameters(), CustomManyParticleForce.getParticleParameters(), GBVIForce.getParticleParameters(), GBSAOBCForce.getParticleParameters(), NonbondedForce.getParticleParameters(), AmoebaGeneralizedKirkwoodForce.getParticleParameters(), AmoebaVdwForce.getParticleParameters(), CustomHbondForce.getPerAcceptorParameterName(), CustomAngleForce.getPerAngleParameterName(), CustomCompoundBondForce.getPerBondParameterName(), CustomBondForce.getPerBondParameterName(), CustomIntegrator.getPerDofVariableByName(), CustomIntegrator.getPerDofVariableName(), CustomHbondForce.getPerDonorParameterName(), CustomManyParticleForce.getPermutationMode(), CustomGBForce.getPerParticleParameterName(), CustomNonbondedForce.getPerParticleParameterName(), CustomExternalForce.getPerParticleParameterName(), CustomManyParticleForce.getPerParticleParameterName(), CustomTorsionForce.getPerTorsionParameterName(), AmoebaPiTorsionForce.getPiTorsionParameters(), Platform.getPlatform(), Context.getPlatform(), Platform.getPlatformByName(), Platform.getPluginLoadFailures(), AmoebaMultipoleForce.getPmeBSplineOrder(), AmoebaMultipoleForce.getPmeGridDimensions(), NonbondedForce.getPMEParameters(), AmoebaMultipoleForce.getPolarizationType(), AmoebaGeneralizedKirkwoodForce.getProbeRadius(), Platform.getPropertyDefaultValue(), Platform.getPropertyNames(), Platform.getPropertyValue(), GBVIForce.getQuinticLowerLimitFactor(), GBVIForce.getQuinticUpperBornRadiusLimit(), LangevinIntegrator.getRandomNumberSeed(), VariableLangevinIntegrator.getRandomNumberSeed(), RPMDIntegrator.getRandomNumberSeed(), MonteCarloMembraneBarostat.getRandomNumberSeed(), MonteCarloBarostat.getRandomNumberSeed(), BrownianIntegrator.getRandomNumberSeed(), RPMDMonteCarloBarostat.getRandomNumberSeed(), MonteCarloAnisotropicBarostat.getRandomNumberSeed(), CustomIntegrator.getRandomNumberSeed(), DrudeLangevinIntegrator.getRandomNumberSeed(), AndersenThermostat.getRandomNumberSeed(), NonbondedForce.getReactionFieldDielectric(), NonbondedForce.getReciprocalSpaceForceGroup(), AmoebaWcaDispersionForce.getRminh(), AmoebaWcaDispersionForce.getRmino(), MonteCarloAnisotropicBarostat.getScaleX(), MonteCarloAnisotropicBarostat.getScaleY(), MonteCarloAnisotropicBarostat.getScaleZ(), DrudeForce.getScreenedPairParameters(), AmoebaWcaDispersionForce.getShctd(), AmoebaVdwForce.getSigmaCombiningRule(), AmoebaWcaDispersionForce.getSlevy(), GBVIForce.getSoluteDielectric(), GBSAOBCForce.getSoluteDielectric(), AmoebaGeneralizedKirkwoodForce.getSoluteDielectric(), GBVIForce.getSolventDielectric(), GBSAOBCForce.getSolventDielectric(), AmoebaGeneralizedKirkwoodForce.getSolventDielectric(), Platform.getSpeed(), Integrator.getStepSize(), AmoebaStretchBendForce.getStretchBendParameters(), GBSAOBCForce.getSurfaceAreaEnergy(), AmoebaGeneralizedKirkwoodForce.getSurfaceAreaFactor(), CustomNonbondedForce.getSwitchingDistance(), NonbondedForce.getSwitchingDistance(), Context.getSystem(), AmoebaMultipoleForce.getSystemMultipoleMoments(), CustomGBForce.getTabulatedFunction(), CustomNonbondedForce.getTabulatedFunction(), CustomCompoundBondForce.getTabulatedFunction(), CustomManyParticleForce.getTabulatedFunction(), CustomHbondForce.getTabulatedFunction(), CustomGBForce.getTabulatedFunctionName(), CustomNonbondedForce.getTabulatedFunctionName(), CustomCompoundBondForce.getTabulatedFunctionName(), CustomManyParticleForce.getTabulatedFunctionName(), CustomHbondForce.getTabulatedFunctionName(), LangevinIntegrator.getTemperature(), VariableLangevinIntegrator.getTemperature(), RPMDIntegrator.getTemperature(), MonteCarloMembraneBarostat.getTemperature(), MonteCarloBarostat.getTemperature(), BrownianIntegrator.getTemperature(), MonteCarloAnisotropicBarostat.getTemperature(), DrudeLangevinIntegrator.getTemperature(), RBTorsionForce.getTorsionParameters(), CMAPTorsionForce.getTorsionParameters(), CustomTorsionForce.getTorsionParameters(), PeriodicTorsionForce.getTorsionParameters(), AmoebaTorsionTorsionForce.getTorsionTorsionGrid(), AmoebaTorsionTorsionForce.getTorsionTorsionParameters(), RPMDIntegrator.getTotalEnergy(), CustomManyParticleForce.getTypeFilter(), NonbondedForce.getUseDispersionCorrection(), AmoebaVdwForce.getUseDispersionCorrection(), CustomNonbondedForce.getUseLongRangeCorrection(), CustomNonbondedForce.getUseSwitchingFunction(), NonbondedForce.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_getPluginLoadFailures(), simtk.openmm.openmm.Platform_loadPluginLibrary(), simtk.openmm.openmm.Platform_loadPluginsFromDirectory(), MonteCarloMembraneBarostat.Pressure(), MonteCarloBarostat.Pressure(), RPMDMonteCarloBarostat.Pressure(), MonteCarloAnisotropicBarostat.PressureX(), MonteCarloAnisotropicBarostat.PressureY(), MonteCarloAnisotropicBarostat.PressureZ(), Context.reinitialize(), System.removeConstraint(), System.removeForce(), simtk.openmm.openmm.RPMDMonteCarloBarostat_Pressure(), 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(), HarmonicAngleForce.setAngleParameters(), CustomAngleForce.setAngleParameters(), AmoebaAngleForce.setAngleParameters(), RPMDIntegrator.setApplyThermostat(), AmoebaWcaDispersionForce.setAwater(), AmoebaBondForce.setBondParameters(), CustomCompoundBondForce.setBondParameters(), GBVIForce.setBondParameters(), HarmonicBondForce.setBondParameters(), CustomBondForce.setBondParameters(), GBVIForce.setBornRadiusScalingMethod(), CustomGBForce.setComputedValueParameters(), System.setConstraintParameters(), Integrator.setConstraintTolerance(), AmoebaMultipoleForce.setCovalentMap(), AmoebaVdwForce.setCutoff(), CustomGBForce.setCutoffDistance(), CustomNonbondedForce.setCutoffDistance(), CustomManyParticleForce.setCutoffDistance(), GBVIForce.setCutoffDistance(), GBSAOBCForce.setCutoffDistance(), NonbondedForce.setCutoffDistance(), CustomHbondForce.setCutoffDistance(), AmoebaMultipoleForce.setCutoffDistance(), AndersenThermostat.setDefaultCollisionFrequency(), System.setDefaultPeriodicBoxVectors(), MonteCarloMembraneBarostat.setDefaultPressure(), MonteCarloBarostat.setDefaultPressure(), RPMDMonteCarloBarostat.setDefaultPressure(), MonteCarloAnisotropicBarostat.setDefaultPressure(), MonteCarloMembraneBarostat.setDefaultSurfaceTension(), AndersenThermostat.setDefaultTemperature(), AmoebaWcaDispersionForce.setDispoff(), CustomHbondForce.setDonorParameters(), DrudeLangevinIntegrator.setDrudeFriction(), DrudeLangevinIntegrator.setDrudeTemperature(), CustomNonbondedForce.setEnergyFunction(), CustomCompoundBondForce.setEnergyFunction(), CustomExternalForce.setEnergyFunction(), CustomManyParticleForce.setEnergyFunction(), CustomHbondForce.setEnergyFunction(), CustomAngleForce.setEnergyFunction(), CustomBondForce.setEnergyFunction(), CustomTorsionForce.setEnergyFunction(), CustomGBForce.setEnergyTermParameters(), AmoebaWcaDispersionForce.setEpsh(), AmoebaVdwForce.setEpsilonCombiningRule(), AmoebaWcaDispersionForce.setEpso(), VariableLangevinIntegrator.setErrorTolerance(), VariableVerletIntegrator.setErrorTolerance(), NonbondedForce.setEwaldErrorTolerance(), AmoebaMultipoleForce.setEwaldErrorTolerance(), NonbondedForce.setExceptionParameters(), CustomGBForce.setExclusionParticles(), CustomNonbondedForce.setExclusionParticles(), CustomManyParticleForce.setExclusionParticles(), CustomHbondForce.setExclusionParticles(), Force.setForceGroup(), MonteCarloMembraneBarostat.setFrequency(), MonteCarloBarostat.setFrequency(), RPMDMonteCarloBarostat.setFrequency(), MonteCarloAnisotropicBarostat.setFrequency(), CMMotionRemover.setFrequency(), LangevinIntegrator.setFriction(), VariableLangevinIntegrator.setFriction(), RPMDIntegrator.setFriction(), BrownianIntegrator.setFriction(), DrudeLangevinIntegrator.setFriction(), Discrete2DFunction.setFunctionParameters(), CustomGBForce.setFunctionParameters(), CustomNonbondedForce.setFunctionParameters(), CustomCompoundBondForce.setFunctionParameters(), Continuous3DFunction.setFunctionParameters(), Discrete3DFunction.setFunctionParameters(), Discrete1DFunction.setFunctionParameters(), Continuous1DFunction.setFunctionParameters(), CustomHbondForce.setFunctionParameters(), Continuous2DFunction.setFunctionParameters(), CustomGBForce.setGlobalParameterDefaultValue(), CustomNonbondedForce.setGlobalParameterDefaultValue(), CustomCompoundBondForce.setGlobalParameterDefaultValue(), CustomExternalForce.setGlobalParameterDefaultValue(), CustomManyParticleForce.setGlobalParameterDefaultValue(), CustomHbondForce.setGlobalParameterDefaultValue(), CustomAngleForce.setGlobalParameterDefaultValue(), CustomBondForce.setGlobalParameterDefaultValue(), CustomTorsionForce.setGlobalParameterDefaultValue(), CustomGBForce.setGlobalParameterName(), CustomNonbondedForce.setGlobalParameterName(), CustomCompoundBondForce.setGlobalParameterName(), CustomExternalForce.setGlobalParameterName(), CustomManyParticleForce.setGlobalParameterName(), CustomHbondForce.setGlobalParameterName(), CustomAngleForce.setGlobalParameterName(), CustomBondForce.setGlobalParameterName(), CustomTorsionForce.setGlobalParameterName(), CustomIntegrator.setGlobalVariable(), CustomIntegrator.setGlobalVariableByName(), AmoebaGeneralizedKirkwoodForce.setIncludeCavityTerm(), CustomNonbondedForce.setInteractionGroupParameters(), CustomIntegrator.setKineticEnergyExpression(), CMAPTorsionForce.setMapParameters(), DrudeSCFIntegrator.setMinimizationErrorTolerance(), AmoebaMultipoleForce.setMultipoleParameters(), AmoebaMultipoleForce.setMutualInducedMaxIterations(), AmoebaMultipoleForce.setMutualInducedTargetEpsilon(), CustomGBForce.setNonbondedMethod(), CustomNonbondedForce.setNonbondedMethod(), CustomManyParticleForce.setNonbondedMethod(), GBVIForce.setNonbondedMethod(), GBSAOBCForce.setNonbondedMethod(), NonbondedForce.setNonbondedMethod(), CustomHbondForce.setNonbondedMethod(), AmoebaMultipoleForce.setNonbondedMethod(), AmoebaVdwForce.setNonbondedMethod(), AmoebaOutOfPlaneBendForce.setOutOfPlaneBendParameters(), Context.setParameter(), AmoebaVdwForce.setParticleExclusions(), System.setParticleMass(), CustomGBForce.setParticleParameters(), CustomNonbondedForce.setParticleParameters(), AmoebaWcaDispersionForce.setParticleParameters(), CustomExternalForce.setParticleParameters(), DrudeForce.setParticleParameters(), CustomManyParticleForce.setParticleParameters(), GBVIForce.setParticleParameters(), GBSAOBCForce.setParticleParameters(), NonbondedForce.setParticleParameters(), AmoebaGeneralizedKirkwoodForce.setParticleParameters(), AmoebaVdwForce.setParticleParameters(), CustomHbondForce.setPerAcceptorParameterName(), CustomAngleForce.setPerAngleParameterName(), CustomCompoundBondForce.setPerBondParameterName(), CustomBondForce.setPerBondParameterName(), CustomIntegrator.setPerDofVariable(), CustomIntegrator.setPerDofVariableByName(), CustomHbondForce.setPerDonorParameterName(), Context.setPeriodicBoxVectors(), CustomManyParticleForce.setPermutationMode(), CustomGBForce.setPerParticleParameterName(), CustomNonbondedForce.setPerParticleParameterName(), CustomExternalForce.setPerParticleParameterName(), CustomManyParticleForce.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(), LangevinIntegrator.setRandomNumberSeed(), VariableLangevinIntegrator.setRandomNumberSeed(), RPMDIntegrator.setRandomNumberSeed(), MonteCarloMembraneBarostat.setRandomNumberSeed(), MonteCarloBarostat.setRandomNumberSeed(), BrownianIntegrator.setRandomNumberSeed(), RPMDMonteCarloBarostat.setRandomNumberSeed(), MonteCarloAnisotropicBarostat.setRandomNumberSeed(), CustomIntegrator.setRandomNumberSeed(), DrudeLangevinIntegrator.setRandomNumberSeed(), AndersenThermostat.setRandomNumberSeed(), NonbondedForce.setReactionFieldDielectric(), NonbondedForce.setReciprocalSpaceForceGroup(), AmoebaWcaDispersionForce.setRminh(), AmoebaWcaDispersionForce.setRmino(), DrudeForce.setScreenedPairParameters(), AmoebaWcaDispersionForce.setShctd(), AmoebaVdwForce.setSigmaCombiningRule(), AmoebaWcaDispersionForce.setSlevy(), GBVIForce.setSoluteDielectric(), GBSAOBCForce.setSoluteDielectric(), AmoebaGeneralizedKirkwoodForce.setSoluteDielectric(), GBVIForce.setSolventDielectric(), GBSAOBCForce.setSolventDielectric(), AmoebaGeneralizedKirkwoodForce.setSolventDielectric(), Integrator.setStepSize(), AmoebaStretchBendForce.setStretchBendParameters(), GBSAOBCForce.setSurfaceAreaEnergy(), AmoebaGeneralizedKirkwoodForce.setSurfaceAreaFactor(), CustomNonbondedForce.setSwitchingDistance(), NonbondedForce.setSwitchingDistance(), LangevinIntegrator.setTemperature(), VariableLangevinIntegrator.setTemperature(), RPMDIntegrator.setTemperature(), MonteCarloMembraneBarostat.setTemperature(), MonteCarloBarostat.setTemperature(), BrownianIntegrator.setTemperature(), MonteCarloAnisotropicBarostat.setTemperature(), DrudeLangevinIntegrator.setTemperature(), Context.setTime(), RBTorsionForce.setTorsionParameters(), CMAPTorsionForce.setTorsionParameters(), CustomTorsionForce.setTorsionParameters(), PeriodicTorsionForce.setTorsionParameters(), AmoebaTorsionTorsionForce.setTorsionTorsionGrid(), AmoebaTorsionTorsionForce.setTorsionTorsionParameters(), CustomManyParticleForce.setTypeFilter(), NonbondedForce.setUseDispersionCorrection(), AmoebaVdwForce.setUseDispersionCorrection(), CustomNonbondedForce.setUseLongRangeCorrection(), CustomNonbondedForce.setUseSwitchingFunction(), NonbondedForce.setUseSwitchingFunction(), RPMDIntegrator.setVelocities(), Context.setVelocities(), Context.setVelocitiesToTemperature(), MonteCarloMembraneBarostat.setXYMode(), MonteCarloMembraneBarostat.setZMode(), Integrator.step(), LangevinIntegrator.step(), VariableLangevinIntegrator.step(), RPMDIntegrator.step(), VerletIntegrator.step(), DrudeSCFIntegrator.step(), VariableVerletIntegrator.step(), BrownianIntegrator.step(), CustomIntegrator.step(), DrudeLangevinIntegrator.step(), VariableLangevinIntegrator.stepTo(), VariableVerletIntegrator.stepTo(), Platform.supportsDoublePrecision(), Platform.supportsKernels(), MonteCarloMembraneBarostat.SurfaceTension(), AndersenThermostat.Temperature(), CustomGBForce.updateParametersInContext(), CustomNonbondedForce.updateParametersInContext(), AmoebaWcaDispersionForce.updateParametersInContext(), AmoebaInPlaneAngleForce.updateParametersInContext(), AmoebaBondForce.updateParametersInContext(), AmoebaPiTorsionForce.updateParametersInContext(), CustomCompoundBondForce.updateParametersInContext(), CustomExternalForce.updateParametersInContext(), DrudeForce.updateParametersInContext(), CustomManyParticleForce.updateParametersInContext(), GBSAOBCForce.updateParametersInContext(), NonbondedForce.updateParametersInContext(), AmoebaGeneralizedKirkwoodForce.updateParametersInContext(), RBTorsionForce.updateParametersInContext(), AmoebaOutOfPlaneBendForce.updateParametersInContext(), CustomHbondForce.updateParametersInContext(), HarmonicAngleForce.updateParametersInContext(), AmoebaMultipoleForce.updateParametersInContext(), CustomAngleForce.updateParametersInContext(), AmoebaAngleForce.updateParametersInContext(), AmoebaVdwForce.updateParametersInContext(), HarmonicBondForce.updateParametersInContext(), CMAPTorsionForce.updateParametersInContext(), CustomBondForce.updateParametersInContext(), AmoebaStretchBendForce.updateParametersInContext(), CustomTorsionForce.updateParametersInContext(), PeriodicTorsionForce.updateParametersInContext(), Force.usesPeriodicBoundaryConditions(), CustomGBForce.usesPeriodicBoundaryConditions(), CustomNonbondedForce.usesPeriodicBoundaryConditions(), AmoebaWcaDispersionForce.usesPeriodicBoundaryConditions(), AmoebaInPlaneAngleForce.usesPeriodicBoundaryConditions(), MonteCarloMembraneBarostat.usesPeriodicBoundaryConditions(), MonteCarloBarostat.usesPeriodicBoundaryConditions(), AmoebaTorsionTorsionForce.usesPeriodicBoundaryConditions(), AmoebaBondForce.usesPeriodicBoundaryConditions(), AmoebaPiTorsionForce.usesPeriodicBoundaryConditions(), CustomCompoundBondForce.usesPeriodicBoundaryConditions(), CustomExternalForce.usesPeriodicBoundaryConditions(), DrudeForce.usesPeriodicBoundaryConditions(), CustomManyParticleForce.usesPeriodicBoundaryConditions(), GBVIForce.usesPeriodicBoundaryConditions(), GBSAOBCForce.usesPeriodicBoundaryConditions(), NonbondedForce.usesPeriodicBoundaryConditions(), AmoebaGeneralizedKirkwoodForce.usesPeriodicBoundaryConditions(), RBTorsionForce.usesPeriodicBoundaryConditions(), RPMDMonteCarloBarostat.usesPeriodicBoundaryConditions(), MonteCarloAnisotropicBarostat.usesPeriodicBoundaryConditions(), AmoebaOutOfPlaneBendForce.usesPeriodicBoundaryConditions(), CustomHbondForce.usesPeriodicBoundaryConditions(), CMMotionRemover.usesPeriodicBoundaryConditions(), System.usesPeriodicBoundaryConditions(), HarmonicAngleForce.usesPeriodicBoundaryConditions(), AmoebaMultipoleForce.usesPeriodicBoundaryConditions(), CustomAngleForce.usesPeriodicBoundaryConditions(), AmoebaAngleForce.usesPeriodicBoundaryConditions(), AmoebaVdwForce.usesPeriodicBoundaryConditions(), AndersenThermostat.usesPeriodicBoundaryConditions(), HarmonicBondForce.usesPeriodicBoundaryConditions(), CMAPTorsionForce.usesPeriodicBoundaryConditions(), CustomBondForce.usesPeriodicBoundaryConditions(), AmoebaStretchBendForce.usesPeriodicBoundaryConditions(), CustomTorsionForce.usesPeriodicBoundaryConditions(), PeriodicTorsionForce.usesPeriodicBoundaryConditions(), and OpenMMException.what().
| def simtk.openmm.openmm.swig_import_helper | ( | ) |
| def simtk.openmm.openmm.XmlSerializer__deserializeForce | ( | args | ) |
XmlSerializer__deserializeForce(char const * inputString) -> Force.
| def simtk.openmm.openmm.XmlSerializer__deserializeIntegrator | ( | args | ) |
XmlSerializer__deserializeIntegrator(char const * inputString) -> Integrator.
| def simtk.openmm.openmm.XmlSerializer__deserializeStringIntoLists | ( | args | ) |
XmlSerializer__deserializeStringIntoLists(std::string const & stateAsString) -> PyObject *.
| def simtk.openmm.openmm.XmlSerializer__serializeForce | ( | args | ) |
XmlSerializer__serializeForce(Force object) -> std::string.
| def simtk.openmm.openmm.XmlSerializer__serializeIntegrator | ( | args | ) |
XmlSerializer__serializeIntegrator(Integrator object) -> std::string.
| def simtk.openmm.openmm.XmlSerializer__serializeStateAsLists | ( | args | ) |
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.
| def simtk.openmm.openmm.XmlSerializer_deserializeSystem | ( | args | ) |
XmlSerializer_deserializeSystem(char const * inputString) -> System.
This method exists only for backward compatibility.
| def simtk.openmm.openmm.XmlSerializer_serializeSystem | ( | args | ) |
XmlSerializer_serializeSystem(System object) -> std::string.
This method exists only for backward compatibility.
| list __all__ = [k for k in locals().keys() if not (k.endswith('_swigregister') or k.startswith('_'))] |
| int _newclass = 0 |
| tuple _openmm = swig_import_helper() |
| tuple _string_types = (basestring,) |
| AmoebaAngleForce_swigregister = _openmm.AmoebaAngleForce_swigregister |
| AmoebaBondForce_swigregister = _openmm.AmoebaBondForce_swigregister |
| AmoebaGeneralizedKirkwoodForce_swigregister = _openmm.AmoebaGeneralizedKirkwoodForce_swigregister |
| AmoebaInPlaneAngleForce_swigregister = _openmm.AmoebaInPlaneAngleForce_swigregister |
| AmoebaMultipoleForce_swigregister = _openmm.AmoebaMultipoleForce_swigregister |
| AmoebaOutOfPlaneBendForce_swigregister = _openmm.AmoebaOutOfPlaneBendForce_swigregister |
| AmoebaPiTorsionForce_swigregister = _openmm.AmoebaPiTorsionForce_swigregister |
| AmoebaStretchBendForce_swigregister = _openmm.AmoebaStretchBendForce_swigregister |
| AmoebaTorsionTorsionForce_swigregister = _openmm.AmoebaTorsionTorsionForce_swigregister |
| AmoebaVdwForce_swigregister = _openmm.AmoebaVdwForce_swigregister |
| AmoebaWcaDispersionForce_swigregister = _openmm.AmoebaWcaDispersionForce_swigregister |
| AndersenThermostat_swigregister = _openmm.AndersenThermostat_swigregister |
| AngstromsPerNm = cvar.AngstromsPerNm |
| BrownianIntegrator_swigregister = _openmm.BrownianIntegrator_swigregister |
| cerr = cvar.cerr |
| cin = cvar.cin |
| clog = cvar.clog |
| CMAPTorsionForce_swigregister = _openmm.CMAPTorsionForce_swigregister |
| CMMotionRemover_swigregister = _openmm.CMMotionRemover_swigregister |
| Context_swigregister = _openmm.Context_swigregister |
| Continuous1DFunction_swigregister = _openmm.Continuous1DFunction_swigregister |
| Continuous2DFunction_swigregister = _openmm.Continuous2DFunction_swigregister |
| Continuous3DFunction_swigregister = _openmm.Continuous3DFunction_swigregister |
| cout = cvar.cout |
| CustomAngleForce_swigregister = _openmm.CustomAngleForce_swigregister |
| CustomBondForce_swigregister = _openmm.CustomBondForce_swigregister |
| CustomCompoundBondForce_swigregister = _openmm.CustomCompoundBondForce_swigregister |
| CustomExternalForce_swigregister = _openmm.CustomExternalForce_swigregister |
| CustomGBForce_swigregister = _openmm.CustomGBForce_swigregister |
| CustomHbondForce_swigregister = _openmm.CustomHbondForce_swigregister |
| CustomIntegrator_swigregister = _openmm.CustomIntegrator_swigregister |
| CustomManyParticleForce_swigregister = _openmm.CustomManyParticleForce_swigregister |
| CustomNonbondedForce_swigregister = _openmm.CustomNonbondedForce_swigregister |
| CustomTorsionForce_swigregister = _openmm.CustomTorsionForce_swigregister |
| cvar = _openmm.cvar |
| DegreesPerRadian = cvar.DegreesPerRadian |
| Discrete1DFunction_swigregister = _openmm.Discrete1DFunction_swigregister |
| Discrete2DFunction_swigregister = _openmm.Discrete2DFunction_swigregister |
| Discrete3DFunction_swigregister = _openmm.Discrete3DFunction_swigregister |
| DrudeForce_swigregister = _openmm.DrudeForce_swigregister |
| DrudeLangevinIntegrator_swigregister = _openmm.DrudeLangevinIntegrator_swigregister |
| DrudeSCFIntegrator_swigregister = _openmm.DrudeSCFIntegrator_swigregister |
| endl = _openmm.endl |
Referenced by simtk.openmm.openmm.endl().
| endl_cb_ptr = _openmm.endl_cb_ptr |
| ends = _openmm.ends |
Referenced by simtk.openmm.openmm.ends().
| ends_cb_ptr = _openmm.ends_cb_ptr |
| flush = _openmm.flush |
Referenced by simtk.openmm.openmm.flush().
| flush_cb_ptr = _openmm.flush_cb_ptr |
| Force_swigregister = _openmm.Force_swigregister |
| FsPerPs = cvar.FsPerPs |
| GBSAOBCForce_swigregister = _openmm.GBSAOBCForce_swigregister |
| GBVIForce_swigregister = _openmm.GBVIForce_swigregister |
| HarmonicAngleForce_swigregister = _openmm.HarmonicAngleForce_swigregister |
| HarmonicBondForce_swigregister = _openmm.HarmonicBondForce_swigregister |
| Integrator_swigregister = _openmm.Integrator_swigregister |
| ios_base_swigregister = _openmm.ios_base_swigregister |
| ios_base_sync_with_stdio = _openmm.ios_base_sync_with_stdio |
Referenced by simtk.openmm.openmm.ios_base_sync_with_stdio().
| ios_base_xalloc = _openmm.ios_base_xalloc |
Referenced by simtk.openmm.openmm.ios_base_xalloc().
| ios_swigregister = _openmm.ios_swigregister |
| iostream_swigregister = _openmm.iostream_swigregister |
| istream_swigregister = _openmm.istream_swigregister |
| KcalPerKJ = cvar.KcalPerKJ |
| KJPerKcal = cvar.KJPerKcal |
| LangevinIntegrator_swigregister = _openmm.LangevinIntegrator_swigregister |
| LocalCoordinatesSite_swigregister = _openmm.LocalCoordinatesSite_swigregister |
| LocalEnergyMinimizer_swigregister = _openmm.LocalEnergyMinimizer_swigregister |
| mapii_swigregister = _openmm.mapii_swigregister |
| mapstringdouble_swigregister = _openmm.mapstringdouble_swigregister |
| mapstringstring_swigregister = _openmm.mapstringstring_swigregister |
| MonteCarloAnisotropicBarostat_swigregister = _openmm.MonteCarloAnisotropicBarostat_swigregister |
| MonteCarloBarostat_swigregister = _openmm.MonteCarloBarostat_swigregister |
| MonteCarloMembraneBarostat_swigregister = _openmm.MonteCarloMembraneBarostat_swigregister |
| NmPerAngstrom = cvar.NmPerAngstrom |
| NonbondedForce_swigregister = _openmm.NonbondedForce_swigregister |
| OpenMMException_swigregister = _openmm.OpenMMException_swigregister |
| ostream_swigregister = _openmm.ostream_swigregister |
| OutOfPlaneSite_swigregister = _openmm.OutOfPlaneSite_swigregister |
| pairii_swigregister = _openmm.pairii_swigregister |
| PeriodicTorsionForce_swigregister = _openmm.PeriodicTorsionForce_swigregister |
| Platform_swigregister = _openmm.Platform_swigregister |
| PsPerFs = cvar.PsPerFs |
| RadiansPerDegree = cvar.RadiansPerDegree |
| RBTorsionForce_swigregister = _openmm.RBTorsionForce_swigregister |
| tuple RMIN_PER_SIGMA = math.pow(2, 1/6.0) |
| RPMDIntegrator_swigregister = _openmm.RPMDIntegrator_swigregister |
| RPMDMonteCarloBarostat_swigregister = _openmm.RPMDMonteCarloBarostat_swigregister |
| tuple RVDW_PER_SIGMA = math.pow(2, 1/6.0) |
| SerializationNode_swigregister = _openmm.SerializationNode_swigregister |
| SerializationProxy_swigregister = _openmm.SerializationProxy_swigregister |
| seti_swigregister = _openmm.seti_swigregister |
| SigmaPerVdwRadius = cvar.SigmaPerVdwRadius |
| SwigPyIterator_swigregister = _openmm.SwigPyIterator_swigregister |
| System_swigregister = _openmm.System_swigregister |
| TabulatedFunction_swigregister = _openmm.TabulatedFunction_swigregister |
| ThreeParticleAverageSite_swigregister = _openmm.ThreeParticleAverageSite_swigregister |
| TwoParticleAverageSite_swigregister = _openmm.TwoParticleAverageSite_swigregister |
| VariableLangevinIntegrator_swigregister = _openmm.VariableLangevinIntegrator_swigregister |
| VariableVerletIntegrator_swigregister = _openmm.VariableVerletIntegrator_swigregister |
| VdwRadiusPerSigma = cvar.VdwRadiusPerSigma |
| vectord_swigregister = _openmm.vectord_swigregister |
| vectorddd_swigregister = _openmm.vectorddd_swigregister |
| vectori_swigregister = _openmm.vectori_swigregister |
| vectorii_swigregister = _openmm.vectorii_swigregister |
| vectorpairii_swigregister = _openmm.vectorpairii_swigregister |
| vectorstring_swigregister = _openmm.vectorstring_swigregister |
| VerletIntegrator_swigregister = _openmm.VerletIntegrator_swigregister |
| VirtualSite_swigregister = _openmm.VirtualSite_swigregister |
| XmlSerializer_swigregister = _openmm.XmlSerializer_swigregister |
1.8.8 
