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simtk.openmm.openmm Namespace Reference

Classes

class  SwigPyIterator
 
class  State
 A State object records a snapshot of the current state of a simulation at a point in time. More...
 
class  Force
 Force objects apply forces to the particles in a System, or alter their behavior in other ways. More...
 
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  Integrator
 An Integrator defines a method for simulating a System by integrating the equations of motion. 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  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  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  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  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  LangevinIntegrator
 This is an Integrator which simulates a System using Langevin dynamics. 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  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  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  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  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  System
 This class represents a molecular system. 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  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 AndersenThermostat_Temperature
 AndersenThermostat_Temperature() -> std::string const &. More...
 
def AndersenThermostat_CollisionFrequency
 AndersenThermostat_CollisionFrequency() -> 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 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 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 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 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...
 

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)
 
 Force_swigregister = _openmm.Force_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
 
 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
 
 Integrator_swigregister = _openmm.Integrator_swigregister
 
 BrownianIntegrator_swigregister = _openmm.BrownianIntegrator_swigregister
 
 CMAPTorsionForce_swigregister = _openmm.CMAPTorsionForce_swigregister
 
 CMMotionRemover_swigregister = _openmm.CMMotionRemover_swigregister
 
 Context_swigregister = _openmm.Context_swigregister
 
 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
 
 CustomNonbondedForce_swigregister = _openmm.CustomNonbondedForce_swigregister
 
 CustomTorsionForce_swigregister = _openmm.CustomTorsionForce_swigregister
 
 DrudeForce_swigregister = _openmm.DrudeForce_swigregister
 
 DrudeLangevinIntegrator_swigregister = _openmm.DrudeLangevinIntegrator_swigregister
 
 DrudeSCFIntegrator_swigregister = _openmm.DrudeSCFIntegrator_swigregister
 
 GBSAOBCForce_swigregister = _openmm.GBSAOBCForce_swigregister
 
 GBVIForce_swigregister = _openmm.GBVIForce_swigregister
 
 HarmonicAngleForce_swigregister = _openmm.HarmonicAngleForce_swigregister
 
 HarmonicBondForce_swigregister = _openmm.HarmonicBondForce_swigregister
 
 LangevinIntegrator_swigregister = _openmm.LangevinIntegrator_swigregister
 
 LocalEnergyMinimizer_swigregister = _openmm.LocalEnergyMinimizer_swigregister
 
 MonteCarloAnisotropicBarostat_swigregister = _openmm.MonteCarloAnisotropicBarostat_swigregister
 
 MonteCarloBarostat_swigregister = _openmm.MonteCarloBarostat_swigregister
 
 NonbondedForce_swigregister = _openmm.NonbondedForce_swigregister
 
 OpenMMException_swigregister = _openmm.OpenMMException_swigregister
 
 VirtualSite_swigregister = _openmm.VirtualSite_swigregister
 
 OutOfPlaneSite_swigregister = _openmm.OutOfPlaneSite_swigregister
 
 PeriodicTorsionForce_swigregister = _openmm.PeriodicTorsionForce_swigregister
 
 Platform_swigregister = _openmm.Platform_swigregister
 
 RBTorsionForce_swigregister = _openmm.RBTorsionForce_swigregister
 
 RPMDIntegrator_swigregister = _openmm.RPMDIntegrator_swigregister
 
 SerializationNode_swigregister = _openmm.SerializationNode_swigregister
 
 SerializationProxy_swigregister = _openmm.SerializationProxy_swigregister
 
 System_swigregister = _openmm.System_swigregister
 
 ThreeParticleAverageSite_swigregister = _openmm.ThreeParticleAverageSite_swigregister
 
 TwoParticleAverageSite_swigregister = _openmm.TwoParticleAverageSite_swigregister
 
 VariableLangevinIntegrator_swigregister = _openmm.VariableLangevinIntegrator_swigregister
 
 VariableVerletIntegrator_swigregister = _openmm.VariableVerletIntegrator_swigregister
 
 VerletIntegrator_swigregister = _openmm.VerletIntegrator_swigregister
 
 XmlSerializer_swigregister = _openmm.XmlSerializer_swigregister
 
list __all__ = [k for k in locals().keys() if not (k.endswith('_swigregister') or k.startswith('_'))]
 

Function Documentation

def simtk.openmm.openmm.AndersenThermostat_CollisionFrequency ( )

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 ( )

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)
def simtk.openmm.openmm.ends (   args)
def simtk.openmm.openmm.flush (   args)
def simtk.openmm.openmm.ios_base_sync_with_stdio (   __sync = True)
def simtk.openmm.openmm.ios_base_xalloc ( )
def simtk.openmm.openmm.LocalEnergyMinimizer_minimize (   args)

minimize(Context context, double tolerance=1, int maxIterations=0) minimize(Context context, double tolerance=1) LocalEnergyMinimizer_minimize(Context context)

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.

Parameters
contexta Context specifying the System to minimize and the initial particle positions
tolerancethis 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 1.
maxIterationsthe 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 ( )

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 ( )

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 ( )

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 ( )

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.Platform_findPlatform (   args)

Platform_findPlatform(vectorstring kernelNames) -> Platform.

Find a Platform which can be used to perform a calculation.

Parameters
kernelNamesthe names of all kernels which will be needed for the calculation

References simtk.openmm.openmm.stripUnits().

def simtk.openmm.openmm.Platform_getDefaultPluginsDirectory ( )

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 ( )

Platform_getNumPlatforms() -> int.

Get the number of Platforms that have been registered.

References simtk.openmm.openmm.stripUnits().

def simtk.openmm.openmm.Platform_getOpenMMVersion ( )

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_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.

Parameters
filethe 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.

Parameters
directorythe 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.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.

Parameters
typethe 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.

Parameters
typethe type_info for the object type
proxythe 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 Force.__del__(), AmoebaAngleForce.__del__(), AmoebaBondForce.__del__(), AmoebaGeneralizedKirkwoodForce.__del__(), AmoebaInPlaneAngleForce.__del__(), AmoebaMultipoleForce.__del__(), AmoebaOutOfPlaneBendForce.__del__(), AmoebaPiTorsionForce.__del__(), AmoebaStretchBendForce.__del__(), AmoebaTorsionTorsionForce.__del__(), AmoebaVdwForce.__del__(), AmoebaWcaDispersionForce.__del__(), AndersenThermostat.__del__(), Integrator.__del__(), BrownianIntegrator.__del__(), CMAPTorsionForce.__del__(), CMMotionRemover.__del__(), Context.__del__(), CustomAngleForce.__del__(), CustomBondForce.__del__(), CustomCompoundBondForce.__del__(), CustomExternalForce.__del__(), CustomGBForce.__del__(), CustomHbondForce.__del__(), CustomIntegrator.__del__(), CustomNonbondedForce.__del__(), CustomTorsionForce.__del__(), DrudeForce.__del__(), DrudeLangevinIntegrator.__del__(), DrudeSCFIntegrator.__del__(), GBSAOBCForce.__del__(), GBVIForce.__del__(), HarmonicAngleForce.__del__(), HarmonicBondForce.__del__(), LangevinIntegrator.__del__(), LocalEnergyMinimizer.__del__(), MonteCarloAnisotropicBarostat.__del__(), MonteCarloBarostat.__del__(), NonbondedForce.__del__(), OpenMMException.__del__(), VirtualSite.__del__(), OutOfPlaneSite.__del__(), PeriodicTorsionForce.__del__(), Platform.__del__(), RBTorsionForce.__del__(), RPMDIntegrator.__del__(), System.__del__(), ThreeParticleAverageSite.__del__(), TwoParticleAverageSite.__del__(), VariableLangevinIntegrator.__del__(), VariableVerletIntegrator.__del__(), VerletIntegrator.__del__(), XmlSerializer.__del__(), AmoebaAngleForce.__init__(), AmoebaBondForce.__init__(), AmoebaGeneralizedKirkwoodForce.__init__(), AmoebaInPlaneAngleForce.__init__(), AmoebaMultipoleForce.__init__(), AmoebaOutOfPlaneBendForce.__init__(), AmoebaPiTorsionForce.__init__(), AmoebaStretchBendForce.__init__(), AmoebaTorsionTorsionForce.__init__(), AmoebaVdwForce.__init__(), AmoebaWcaDispersionForce.__init__(), AndersenThermostat.__init__(), BrownianIntegrator.__init__(), CMAPTorsionForce.__init__(), CMMotionRemover.__init__(), Context.__init__(), CustomAngleForce.__init__(), CustomBondForce.__init__(), CustomCompoundBondForce.__init__(), CustomExternalForce.__init__(), CustomGBForce.__init__(), CustomHbondForce.__init__(), CustomIntegrator.__init__(), CustomNonbondedForce.__init__(), CustomTorsionForce.__init__(), DrudeForce.__init__(), DrudeLangevinIntegrator.__init__(), DrudeSCFIntegrator.__init__(), GBSAOBCForce.__init__(), GBVIForce.__init__(), HarmonicAngleForce.__init__(), HarmonicBondForce.__init__(), LangevinIntegrator.__init__(), MonteCarloAnisotropicBarostat.__init__(), MonteCarloBarostat.__init__(), NonbondedForce.__init__(), OpenMMException.__init__(), OutOfPlaneSite.__init__(), PeriodicTorsionForce.__init__(), RBTorsionForce.__init__(), RPMDIntegrator.__init__(), System.__init__(), ThreeParticleAverageSite.__init__(), TwoParticleAverageSite.__init__(), VariableLangevinIntegrator.__init__(), VariableVerletIntegrator.__init__(), VerletIntegrator.__init__(), CustomHbondForce.addAcceptor(), AmoebaAngleForce.addAngle(), AmoebaInPlaneAngleForce.addAngle(), CustomAngleForce.addAngle(), HarmonicAngleForce.addAngle(), AmoebaBondForce.addBond(), CustomBondForce.addBond(), CustomCompoundBondForce.addBond(), GBVIForce.addBond(), HarmonicBondForce.addBond(), CustomGBForce.addComputedValue(), CustomIntegrator.addComputeGlobal(), CustomIntegrator.addComputePerDof(), CustomIntegrator.addComputeSum(), CustomIntegrator.addConstrainPositions(), System.addConstraint(), CustomIntegrator.addConstrainVelocities(), CustomHbondForce.addDonor(), CustomGBForce.addEnergyTerm(), NonbondedForce.addException(), CustomGBForce.addExclusion(), CustomHbondForce.addExclusion(), CustomNonbondedForce.addExclusion(), CustomCompoundBondForce.addFunction(), CustomGBForce.addFunction(), CustomHbondForce.addFunction(), CustomNonbondedForce.addFunction(), CustomAngleForce.addGlobalParameter(), CustomBondForce.addGlobalParameter(), CustomCompoundBondForce.addGlobalParameter(), CustomExternalForce.addGlobalParameter(), CustomGBForce.addGlobalParameter(), CustomHbondForce.addGlobalParameter(), CustomNonbondedForce.addGlobalParameter(), CustomTorsionForce.addGlobalParameter(), CustomIntegrator.addGlobalVariable(), CustomNonbondedForce.addInteractionGroup(), CMAPTorsionForce.addMap(), AmoebaMultipoleForce.addMultipole(), AmoebaOutOfPlaneBendForce.addOutOfPlaneBend(), AmoebaGeneralizedKirkwoodForce.addParticle(), AmoebaVdwForce.addParticle(), AmoebaWcaDispersionForce.addParticle(), CustomExternalForce.addParticle(), CustomGBForce.addParticle(), CustomNonbondedForce.addParticle(), DrudeForce.addParticle(), GBSAOBCForce.addParticle(), GBVIForce.addParticle(), NonbondedForce.addParticle(), System.addParticle(), CustomHbondForce.addPerAcceptorParameter(), CustomAngleForce.addPerAngleParameter(), CustomBondForce.addPerBondParameter(), CustomCompoundBondForce.addPerBondParameter(), CustomIntegrator.addPerDofVariable(), CustomHbondForce.addPerDonorParameter(), CustomExternalForce.addPerParticleParameter(), CustomGBForce.addPerParticleParameter(), CustomNonbondedForce.addPerParticleParameter(), CustomTorsionForce.addPerTorsionParameter(), AmoebaPiTorsionForce.addPiTorsion(), DrudeForce.addScreenedPair(), AmoebaStretchBendForce.addStretchBend(), CMAPTorsionForce.addTorsion(), CustomTorsionForce.addTorsion(), PeriodicTorsionForce.addTorsion(), RBTorsionForce.addTorsion(), AmoebaTorsionTorsionForce.addTorsionTorsion(), CustomIntegrator.addUpdateContextState(), simtk.openmm.openmm.AndersenThermostat_CollisionFrequency(), simtk.openmm.openmm.AndersenThermostat_Temperature(), Context.applyConstraints(), Context.applyVelocityConstraints(), AndersenThermostat.CollisionFrequency(), Context.computeVirtualSites(), NonbondedForce.createExceptionsFromBonds(), 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(), AmoebaAngleForce.getAngleParameters(), AmoebaInPlaneAngleForce.getAngleParameters(), CustomAngleForce.getAngleParameters(), HarmonicAngleForce.getAngleParameters(), RPMDIntegrator.getApplyThermostat(), AmoebaWcaDispersionForce.getAwater(), AmoebaBondForce.getBondParameters(), CustomBondForce.getBondParameters(), CustomCompoundBondForce.getBondParameters(), GBVIForce.getBondParameters(), HarmonicBondForce.getBondParameters(), GBVIForce.getBornRadiusScalingMethod(), CustomIntegrator.getComputationStep(), CustomGBForce.getComputedValueParameters(), System.getConstraintParameters(), Integrator.getConstraintTolerance(), RPMDIntegrator.getContractions(), AmoebaMultipoleForce.getCovalentMap(), AmoebaMultipoleForce.getCovalentMaps(), AmoebaVdwForce.getCutoff(), AmoebaMultipoleForce.getCutoffDistance(), CustomGBForce.getCutoffDistance(), CustomHbondForce.getCutoffDistance(), CustomNonbondedForce.getCutoffDistance(), GBSAOBCForce.getCutoffDistance(), GBVIForce.getCutoffDistance(), NonbondedForce.getCutoffDistance(), AndersenThermostat.getDefaultCollisionFrequency(), System.getDefaultPeriodicBoxVectors(), Platform.getDefaultPluginsDirectory(), MonteCarloAnisotropicBarostat.getDefaultPressure(), MonteCarloBarostat.getDefaultPressure(), AndersenThermostat.getDefaultTemperature(), AmoebaWcaDispersionForce.getDispoff(), CustomHbondForce.getDonorParameters(), DrudeLangevinIntegrator.getDrudeFriction(), DrudeLangevinIntegrator.getDrudeTemperature(), AmoebaMultipoleForce.getElectrostaticPotential(), CustomAngleForce.getEnergyFunction(), CustomBondForce.getEnergyFunction(), CustomCompoundBondForce.getEnergyFunction(), CustomExternalForce.getEnergyFunction(), CustomHbondForce.getEnergyFunction(), CustomNonbondedForce.getEnergyFunction(), CustomTorsionForce.getEnergyFunction(), CustomGBForce.getEnergyTermParameters(), AmoebaWcaDispersionForce.getEpsh(), AmoebaVdwForce.getEpsilonCombiningRule(), AmoebaWcaDispersionForce.getEpso(), VariableLangevinIntegrator.getErrorTolerance(), VariableVerletIntegrator.getErrorTolerance(), AmoebaMultipoleForce.getEwaldErrorTolerance(), NonbondedForce.getEwaldErrorTolerance(), NonbondedForce.getExceptionParameters(), CustomGBForce.getExclusionParticles(), CustomHbondForce.getExclusionParticles(), CustomNonbondedForce.getExclusionParticles(), System.getForce(), Force.getForceGroup(), CMMotionRemover.getFrequency(), MonteCarloAnisotropicBarostat.getFrequency(), MonteCarloBarostat.getFrequency(), BrownianIntegrator.getFriction(), DrudeLangevinIntegrator.getFriction(), LangevinIntegrator.getFriction(), RPMDIntegrator.getFriction(), VariableLangevinIntegrator.getFriction(), CustomCompoundBondForce.getFunctionParameters(), CustomGBForce.getFunctionParameters(), CustomHbondForce.getFunctionParameters(), CustomNonbondedForce.getFunctionParameters(), CustomAngleForce.getGlobalParameterDefaultValue(), CustomBondForce.getGlobalParameterDefaultValue(), CustomCompoundBondForce.getGlobalParameterDefaultValue(), CustomExternalForce.getGlobalParameterDefaultValue(), CustomGBForce.getGlobalParameterDefaultValue(), CustomHbondForce.getGlobalParameterDefaultValue(), CustomNonbondedForce.getGlobalParameterDefaultValue(), CustomTorsionForce.getGlobalParameterDefaultValue(), CustomAngleForce.getGlobalParameterName(), CustomBondForce.getGlobalParameterName(), CustomCompoundBondForce.getGlobalParameterName(), CustomExternalForce.getGlobalParameterName(), CustomGBForce.getGlobalParameterName(), CustomHbondForce.getGlobalParameterName(), CustomNonbondedForce.getGlobalParameterName(), CustomTorsionForce.getGlobalParameterName(), CustomIntegrator.getGlobalVariable(), CustomIntegrator.getGlobalVariableName(), AmoebaGeneralizedKirkwoodForce.getIncludeCavityTerm(), AmoebaMultipoleForce.getInducedDipoles(), Context.getIntegrator(), CustomNonbondedForce.getInteractionGroupParameters(), CustomIntegrator.getKineticEnergyExpression(), CMAPTorsionForce.getMapParameters(), DrudeSCFIntegrator.getMinimizationErrorTolerance(), AmoebaMultipoleForce.getMultipoleParameters(), AmoebaMultipoleForce.getMutualInducedMaxIterations(), AmoebaMultipoleForce.getMutualInducedTargetEpsilon(), Platform.getName(), AmoebaMultipoleForce.getNonbondedMethod(), AmoebaVdwForce.getNonbondedMethod(), CustomGBForce.getNonbondedMethod(), CustomHbondForce.getNonbondedMethod(), CustomNonbondedForce.getNonbondedMethod(), GBSAOBCForce.getNonbondedMethod(), GBVIForce.getNonbondedMethod(), NonbondedForce.getNonbondedMethod(), CustomHbondForce.getNumAcceptors(), AmoebaAngleForce.getNumAngles(), AmoebaInPlaneAngleForce.getNumAngles(), CustomAngleForce.getNumAngles(), HarmonicAngleForce.getNumAngles(), AmoebaBondForce.getNumBonds(), CustomBondForce.getNumBonds(), CustomCompoundBondForce.getNumBonds(), GBVIForce.getNumBonds(), HarmonicBondForce.getNumBonds(), CustomIntegrator.getNumComputations(), CustomGBForce.getNumComputedValues(), System.getNumConstraints(), RPMDIntegrator.getNumCopies(), CustomHbondForce.getNumDonors(), CustomGBForce.getNumEnergyTerms(), NonbondedForce.getNumExceptions(), CustomGBForce.getNumExclusions(), CustomHbondForce.getNumExclusions(), CustomNonbondedForce.getNumExclusions(), System.getNumForces(), CustomCompoundBondForce.getNumFunctions(), CustomGBForce.getNumFunctions(), CustomHbondForce.getNumFunctions(), CustomNonbondedForce.getNumFunctions(), CustomAngleForce.getNumGlobalParameters(), CustomBondForce.getNumGlobalParameters(), CustomCompoundBondForce.getNumGlobalParameters(), CustomExternalForce.getNumGlobalParameters(), CustomGBForce.getNumGlobalParameters(), CustomHbondForce.getNumGlobalParameters(), CustomNonbondedForce.getNumGlobalParameters(), CustomTorsionForce.getNumGlobalParameters(), CustomIntegrator.getNumGlobalVariables(), CustomNonbondedForce.getNumInteractionGroups(), CMAPTorsionForce.getNumMaps(), AmoebaMultipoleForce.getNumMultipoles(), AmoebaOutOfPlaneBendForce.getNumOutOfPlaneBends(), AmoebaGeneralizedKirkwoodForce.getNumParticles(), AmoebaVdwForce.getNumParticles(), AmoebaWcaDispersionForce.getNumParticles(), CustomExternalForce.getNumParticles(), CustomGBForce.getNumParticles(), CustomNonbondedForce.getNumParticles(), DrudeForce.getNumParticles(), GBSAOBCForce.getNumParticles(), GBVIForce.getNumParticles(), NonbondedForce.getNumParticles(), VirtualSite.getNumParticles(), System.getNumParticles(), CustomCompoundBondForce.getNumParticlesPerBond(), CustomHbondForce.getNumPerAcceptorParameters(), CustomAngleForce.getNumPerAngleParameters(), CustomBondForce.getNumPerBondParameters(), CustomCompoundBondForce.getNumPerBondParameters(), CustomIntegrator.getNumPerDofVariables(), CustomHbondForce.getNumPerDonorParameters(), CustomExternalForce.getNumPerParticleParameters(), CustomGBForce.getNumPerParticleParameters(), CustomNonbondedForce.getNumPerParticleParameters(), CustomTorsionForce.getNumPerTorsionParameters(), AmoebaPiTorsionForce.getNumPiTorsions(), Platform.getNumPlatforms(), DrudeForce.getNumScreenedPairs(), AmoebaStretchBendForce.getNumStretchBends(), CMAPTorsionForce.getNumTorsions(), CustomTorsionForce.getNumTorsions(), PeriodicTorsionForce.getNumTorsions(), RBTorsionForce.getNumTorsions(), AmoebaTorsionTorsionForce.getNumTorsionTorsionGrids(), AmoebaTorsionTorsionForce.getNumTorsionTorsions(), Platform.getOpenMMVersion(), AmoebaOutOfPlaneBendForce.getOutOfPlaneBendParameters(), Context.getParameter(), VirtualSite.getParticle(), AmoebaVdwForce.getParticleExclusions(), System.getParticleMass(), AmoebaGeneralizedKirkwoodForce.getParticleParameters(), AmoebaVdwForce.getParticleParameters(), AmoebaWcaDispersionForce.getParticleParameters(), CustomExternalForce.getParticleParameters(), CustomGBForce.getParticleParameters(), CustomNonbondedForce.getParticleParameters(), DrudeForce.getParticleParameters(), GBSAOBCForce.getParticleParameters(), GBVIForce.getParticleParameters(), NonbondedForce.getParticleParameters(), CustomHbondForce.getPerAcceptorParameterName(), CustomAngleForce.getPerAngleParameterName(), CustomBondForce.getPerBondParameterName(), CustomCompoundBondForce.getPerBondParameterName(), CustomIntegrator.getPerDofVariableName(), CustomHbondForce.getPerDonorParameterName(), CustomExternalForce.getPerParticleParameterName(), CustomGBForce.getPerParticleParameterName(), CustomNonbondedForce.getPerParticleParameterName(), CustomTorsionForce.getPerTorsionParameterName(), AmoebaPiTorsionForce.getPiTorsionParameters(), Context.getPlatform(), Platform.getPlatform(), Platform.getPlatformByName(), AmoebaMultipoleForce.getPmeBSplineOrder(), AmoebaMultipoleForce.getPmeGridDimensions(), AmoebaMultipoleForce.getPolarizationType(), AmoebaGeneralizedKirkwoodForce.getProbeRadius(), Platform.getPropertyDefaultValue(), Platform.getPropertyNames(), Platform.getPropertyValue(), GBVIForce.getQuinticLowerLimitFactor(), GBVIForce.getQuinticUpperBornRadiusLimit(), AndersenThermostat.getRandomNumberSeed(), BrownianIntegrator.getRandomNumberSeed(), CustomIntegrator.getRandomNumberSeed(), DrudeLangevinIntegrator.getRandomNumberSeed(), LangevinIntegrator.getRandomNumberSeed(), MonteCarloAnisotropicBarostat.getRandomNumberSeed(), MonteCarloBarostat.getRandomNumberSeed(), RPMDIntegrator.getRandomNumberSeed(), VariableLangevinIntegrator.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(), AmoebaGeneralizedKirkwoodForce.getSurfaceAreaFactor(), CustomNonbondedForce.getSwitchingDistance(), NonbondedForce.getSwitchingDistance(), Context.getSystem(), AmoebaMultipoleForce.getSystemMultipoleMoments(), BrownianIntegrator.getTemperature(), DrudeLangevinIntegrator.getTemperature(), LangevinIntegrator.getTemperature(), MonteCarloAnisotropicBarostat.getTemperature(), MonteCarloBarostat.getTemperature(), RPMDIntegrator.getTemperature(), VariableLangevinIntegrator.getTemperature(), CMAPTorsionForce.getTorsionParameters(), CustomTorsionForce.getTorsionParameters(), PeriodicTorsionForce.getTorsionParameters(), RBTorsionForce.getTorsionParameters(), AmoebaTorsionTorsionForce.getTorsionTorsionGrid(), AmoebaTorsionTorsionForce.getTorsionTorsionParameters(), AmoebaVdwForce.getUseDispersionCorrection(), NonbondedForce.getUseDispersionCorrection(), CustomNonbondedForce.getUseLongRangeCorrection(), CustomNonbondedForce.getUseSwitchingFunction(), NonbondedForce.getUseSwitchingFunction(), System.getVirtualSite(), ThreeParticleAverageSite.getWeight(), TwoParticleAverageSite.getWeight(), OutOfPlaneSite.getWeight12(), OutOfPlaneSite.getWeight13(), OutOfPlaneSite.getWeightCross(), 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.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(), 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(), AmoebaAngleForce.setAngleParameters(), AmoebaInPlaneAngleForce.setAngleParameters(), CustomAngleForce.setAngleParameters(), HarmonicAngleForce.setAngleParameters(), RPMDIntegrator.setApplyThermostat(), AmoebaWcaDispersionForce.setAwater(), AmoebaBondForce.setBondParameters(), CustomBondForce.setBondParameters(), CustomCompoundBondForce.setBondParameters(), GBVIForce.setBondParameters(), HarmonicBondForce.setBondParameters(), GBVIForce.setBornRadiusScalingMethod(), CustomGBForce.setComputedValueParameters(), System.setConstraintParameters(), Integrator.setConstraintTolerance(), AmoebaMultipoleForce.setCovalentMap(), AmoebaVdwForce.setCutoff(), AmoebaMultipoleForce.setCutoffDistance(), CustomGBForce.setCutoffDistance(), CustomHbondForce.setCutoffDistance(), CustomNonbondedForce.setCutoffDistance(), GBSAOBCForce.setCutoffDistance(), GBVIForce.setCutoffDistance(), NonbondedForce.setCutoffDistance(), System.setDefaultPeriodicBoxVectors(), AmoebaWcaDispersionForce.setDispoff(), CustomHbondForce.setDonorParameters(), DrudeLangevinIntegrator.setDrudeFriction(), DrudeLangevinIntegrator.setDrudeTemperature(), CustomAngleForce.setEnergyFunction(), CustomBondForce.setEnergyFunction(), CustomCompoundBondForce.setEnergyFunction(), CustomExternalForce.setEnergyFunction(), CustomHbondForce.setEnergyFunction(), CustomNonbondedForce.setEnergyFunction(), CustomTorsionForce.setEnergyFunction(), CustomGBForce.setEnergyTermParameters(), AmoebaWcaDispersionForce.setEpsh(), AmoebaVdwForce.setEpsilonCombiningRule(), AmoebaWcaDispersionForce.setEpso(), VariableLangevinIntegrator.setErrorTolerance(), VariableVerletIntegrator.setErrorTolerance(), AmoebaMultipoleForce.setEwaldErrorTolerance(), NonbondedForce.setEwaldErrorTolerance(), NonbondedForce.setExceptionParameters(), CustomGBForce.setExclusionParticles(), CustomHbondForce.setExclusionParticles(), CustomNonbondedForce.setExclusionParticles(), Force.setForceGroup(), CMMotionRemover.setFrequency(), MonteCarloAnisotropicBarostat.setFrequency(), MonteCarloBarostat.setFrequency(), BrownianIntegrator.setFriction(), DrudeLangevinIntegrator.setFriction(), LangevinIntegrator.setFriction(), RPMDIntegrator.setFriction(), VariableLangevinIntegrator.setFriction(), CustomCompoundBondForce.setFunctionParameters(), CustomGBForce.setFunctionParameters(), CustomHbondForce.setFunctionParameters(), CustomNonbondedForce.setFunctionParameters(), CustomAngleForce.setGlobalParameterDefaultValue(), CustomBondForce.setGlobalParameterDefaultValue(), CustomCompoundBondForce.setGlobalParameterDefaultValue(), CustomExternalForce.setGlobalParameterDefaultValue(), CustomGBForce.setGlobalParameterDefaultValue(), CustomHbondForce.setGlobalParameterDefaultValue(), CustomNonbondedForce.setGlobalParameterDefaultValue(), CustomTorsionForce.setGlobalParameterDefaultValue(), CustomAngleForce.setGlobalParameterName(), CustomBondForce.setGlobalParameterName(), CustomCompoundBondForce.setGlobalParameterName(), CustomExternalForce.setGlobalParameterName(), CustomGBForce.setGlobalParameterName(), CustomHbondForce.setGlobalParameterName(), CustomNonbondedForce.setGlobalParameterName(), CustomTorsionForce.setGlobalParameterName(), CustomIntegrator.setGlobalVariable(), CustomIntegrator.setGlobalVariableByName(), AmoebaGeneralizedKirkwoodForce.setIncludeCavityTerm(), CustomNonbondedForce.setInteractionGroupParameters(), CustomIntegrator.setKineticEnergyExpression(), CMAPTorsionForce.setMapParameters(), DrudeSCFIntegrator.setMinimizationErrorTolerance(), AmoebaMultipoleForce.setMultipoleParameters(), AmoebaMultipoleForce.setMutualInducedMaxIterations(), AmoebaMultipoleForce.setMutualInducedTargetEpsilon(), AmoebaMultipoleForce.setNonbondedMethod(), AmoebaVdwForce.setNonbondedMethod(), CustomGBForce.setNonbondedMethod(), CustomHbondForce.setNonbondedMethod(), CustomNonbondedForce.setNonbondedMethod(), GBSAOBCForce.setNonbondedMethod(), GBVIForce.setNonbondedMethod(), NonbondedForce.setNonbondedMethod(), AmoebaOutOfPlaneBendForce.setOutOfPlaneBendParameters(), Context.setParameter(), AmoebaVdwForce.setParticleExclusions(), System.setParticleMass(), AmoebaGeneralizedKirkwoodForce.setParticleParameters(), AmoebaVdwForce.setParticleParameters(), AmoebaWcaDispersionForce.setParticleParameters(), CustomExternalForce.setParticleParameters(), CustomGBForce.setParticleParameters(), CustomNonbondedForce.setParticleParameters(), DrudeForce.setParticleParameters(), GBSAOBCForce.setParticleParameters(), GBVIForce.setParticleParameters(), NonbondedForce.setParticleParameters(), CustomHbondForce.setPerAcceptorParameterName(), CustomAngleForce.setPerAngleParameterName(), CustomBondForce.setPerBondParameterName(), CustomCompoundBondForce.setPerBondParameterName(), CustomIntegrator.setPerDofVariable(), CustomIntegrator.setPerDofVariableByName(), CustomHbondForce.setPerDonorParameterName(), Context.setPeriodicBoxVectors(), CustomExternalForce.setPerParticleParameterName(), CustomGBForce.setPerParticleParameterName(), CustomNonbondedForce.setPerParticleParameterName(), CustomTorsionForce.setPerTorsionParameterName(), AmoebaPiTorsionForce.setPiTorsionParameters(), AmoebaMultipoleForce.setPmeGridDimensions(), AmoebaMultipoleForce.setPolarizationType(), Context.setPositions(), RPMDIntegrator.setPositions(), AmoebaGeneralizedKirkwoodForce.setProbeRadius(), Platform.setPropertyDefaultValue(), Platform.setPropertyValue(), GBVIForce.setQuinticLowerLimitFactor(), GBVIForce.setQuinticUpperBornRadiusLimit(), AndersenThermostat.setRandomNumberSeed(), BrownianIntegrator.setRandomNumberSeed(), CustomIntegrator.setRandomNumberSeed(), DrudeLangevinIntegrator.setRandomNumberSeed(), LangevinIntegrator.setRandomNumberSeed(), MonteCarloAnisotropicBarostat.setRandomNumberSeed(), MonteCarloBarostat.setRandomNumberSeed(), RPMDIntegrator.setRandomNumberSeed(), VariableLangevinIntegrator.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(), AmoebaGeneralizedKirkwoodForce.setSurfaceAreaFactor(), CustomNonbondedForce.setSwitchingDistance(), NonbondedForce.setSwitchingDistance(), BrownianIntegrator.setTemperature(), DrudeLangevinIntegrator.setTemperature(), LangevinIntegrator.setTemperature(), MonteCarloAnisotropicBarostat.setTemperature(), MonteCarloBarostat.setTemperature(), RPMDIntegrator.setTemperature(), VariableLangevinIntegrator.setTemperature(), Context.setTime(), CMAPTorsionForce.setTorsionParameters(), CustomTorsionForce.setTorsionParameters(), PeriodicTorsionForce.setTorsionParameters(), RBTorsionForce.setTorsionParameters(), AmoebaTorsionTorsionForce.setTorsionTorsionGrid(), AmoebaTorsionTorsionForce.setTorsionTorsionParameters(), AmoebaVdwForce.setUseDispersionCorrection(), NonbondedForce.setUseDispersionCorrection(), CustomNonbondedForce.setUseLongRangeCorrection(), CustomNonbondedForce.setUseSwitchingFunction(), NonbondedForce.setUseSwitchingFunction(), Context.setVelocities(), RPMDIntegrator.setVelocities(), Context.setVelocitiesToTemperature(), Integrator.step(), BrownianIntegrator.step(), CustomIntegrator.step(), DrudeLangevinIntegrator.step(), DrudeSCFIntegrator.step(), LangevinIntegrator.step(), RPMDIntegrator.step(), VariableLangevinIntegrator.step(), VariableVerletIntegrator.step(), VerletIntegrator.step(), VariableLangevinIntegrator.stepTo(), VariableVerletIntegrator.stepTo(), Platform.supportsDoublePrecision(), Platform.supportsKernels(), AndersenThermostat.Temperature(), AmoebaAngleForce.updateParametersInContext(), AmoebaBondForce.updateParametersInContext(), AmoebaGeneralizedKirkwoodForce.updateParametersInContext(), AmoebaInPlaneAngleForce.updateParametersInContext(), AmoebaMultipoleForce.updateParametersInContext(), AmoebaOutOfPlaneBendForce.updateParametersInContext(), AmoebaPiTorsionForce.updateParametersInContext(), AmoebaStretchBendForce.updateParametersInContext(), AmoebaVdwForce.updateParametersInContext(), AmoebaWcaDispersionForce.updateParametersInContext(), CustomAngleForce.updateParametersInContext(), CustomBondForce.updateParametersInContext(), CustomCompoundBondForce.updateParametersInContext(), CustomExternalForce.updateParametersInContext(), CustomGBForce.updateParametersInContext(), CustomHbondForce.updateParametersInContext(), CustomNonbondedForce.updateParametersInContext(), CustomTorsionForce.updateParametersInContext(), DrudeForce.updateParametersInContext(), GBSAOBCForce.updateParametersInContext(), HarmonicAngleForce.updateParametersInContext(), HarmonicBondForce.updateParametersInContext(), NonbondedForce.updateParametersInContext(), PeriodicTorsionForce.updateParametersInContext(), RBTorsionForce.updateParametersInContext(), 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.

Deprecated:
Use deserialize() instead.
def simtk.openmm.openmm.XmlSerializer_serializeSystem (   args)

XmlSerializer_serializeSystem(System object) -> std::string.

This method exists only for backward compatibility.

Deprecated:
Use serialize() instead.

Variable Documentation

list __all__ = [k for k in locals().keys() if not (k.endswith('_swigregister') or k.startswith('_'))]
int _newclass = 0
tuple _openmm = swig_import_helper()
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
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
CustomNonbondedForce_swigregister = _openmm.CustomNonbondedForce_swigregister
CustomTorsionForce_swigregister = _openmm.CustomTorsionForce_swigregister
cvar = _openmm.cvar
DegreesPerRadian = cvar.DegreesPerRadian
DrudeForce_swigregister = _openmm.DrudeForce_swigregister
DrudeLangevinIntegrator_swigregister = _openmm.DrudeLangevinIntegrator_swigregister
DrudeSCFIntegrator_swigregister = _openmm.DrudeSCFIntegrator_swigregister
endl = _openmm.endl
endl_cb_ptr = _openmm.endl_cb_ptr
ends = _openmm.ends
ends_cb_ptr = _openmm.ends_cb_ptr
flush = _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
ios_base_xalloc = _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
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
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
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
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