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OpenMM
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OpenMM
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This class represents a molecular system. More...
Inherits _object.
Public Member Functions | |
| def | __del__ |
| del(OpenMM::System self) More... | |
| def | getNumParticles |
| getNumParticles(System self) -> int More... | |
| def | addParticle |
| addParticle(System self, double mass) -> int More... | |
| def | getParticleMass |
| getParticleMass(System self, int index) -> double More... | |
| def | setParticleMass |
| setParticleMass(System self, int index, double mass) More... | |
| def | setVirtualSite |
| setVirtualSite(System self, int index, VirtualSite virtualSite) More... | |
| def | isVirtualSite |
| isVirtualSite(System self, int index) -> bool More... | |
| def | getVirtualSite |
| getVirtualSite(System self, int index) -> VirtualSite More... | |
| def | getNumConstraints |
| getNumConstraints(System self) -> int More... | |
| def | addConstraint |
| addConstraint(System self, int particle1, int particle2, double distance) -> int More... | |
| def | getConstraintParameters |
| getConstraintParameters(System self, int index) More... | |
| def | setConstraintParameters |
| setConstraintParameters(System self, int index, int particle1, int particle2, double distance) More... | |
| def | addForce |
| addForce(System self, Force force) -> int More... | |
| def | getNumForces |
| getNumForces(System self) -> int More... | |
| def | getForce |
| getForce(System self, int index) -> Force getForce(System self, int index) -> Force More... | |
| def | getDefaultPeriodicBoxVectors |
| getDefaultPeriodicBoxVectors(System self) More... | |
| def | setDefaultPeriodicBoxVectors |
| setDefaultPeriodicBoxVectors(System self, Vec3 const & a, Vec3 const & b, Vec3 const & c) More... | |
| def | __getstate__ |
| def | __setstate__ |
| def | getForces |
| Get the list of Forces in this System. More... | |
| def | __init__ |
| init(OpenMM::System self) -> System init(OpenMM::System self, System other) -> System More... | |
Public Attributes | |
| this | |
This class represents a molecular system.
The definition of a System involves four elements:
The particles and constraints are defined directly by the System object, while forces are defined by objects that extend the Force class. After creating a System, call addParticle() once for each particle, addConstraint() for each constraint, and addForce() for each Force.
In addition, particles may be designated as "virtual sites". These are particles whose positions are computed automatically based on the positions of other particles. To define a virtual site, call setVirtualSite(), passing in a VirtualSite object that defines the rules for computing its position.
| def __del__ | ( | self | ) |
del(OpenMM::System self)
References simtk.openmm.openmm.stripUnits().
| def __init__ | ( | self, | |
| args | |||
| ) |
init(OpenMM::System self) -> System init(OpenMM::System self, System other) -> System
Create a new System.
References simtk.openmm.openmm.stripUnits(), ios.this, ostream.this, istream.this, iostream.this, pairii.this, vectord.this, vectorddd.this, vectori.this, vectorii.this, vectorpairii.this, vectorstring.this, mapstringstring.this, mapstringdouble.this, mapii.this, seti.this, AmoebaAngleForce.this, AmoebaBondForce.this, AmoebaGeneralizedKirkwoodForce.this, AmoebaInPlaneAngleForce.this, AmoebaMultipoleForce.this, AmoebaOutOfPlaneBendForce.this, AmoebaPiTorsionForce.this, AmoebaStretchBendForce.this, AmoebaTorsionTorsionForce.this, AmoebaVdwForce.this, AmoebaWcaDispersionForce.this, AndersenThermostat.this, BrownianIntegrator.this, CMAPTorsionForce.this, CMMotionRemover.this, Context.this, Continuous1DFunction.this, Continuous2DFunction.this, Continuous3DFunction.this, CustomAngleForce.this, CustomBondForce.this, CustomCompoundBondForce.this, CustomExternalForce.this, CustomGBForce.this, CustomHbondForce.this, CustomIntegrator.this, CustomNonbondedForce.this, CustomTorsionForce.this, Discrete1DFunction.this, Discrete2DFunction.this, Discrete3DFunction.this, DrudeForce.this, DrudeLangevinIntegrator.this, DrudeSCFIntegrator.this, GBSAOBCForce.this, GBVIForce.this, HarmonicAngleForce.this, HarmonicBondForce.this, LangevinIntegrator.this, LocalCoordinatesSite.this, MonteCarloAnisotropicBarostat.this, MonteCarloBarostat.this, NonbondedForce.this, OpenMMException.this, OutOfPlaneSite.this, PeriodicTorsionForce.this, RBTorsionForce.this, RPMDIntegrator.this, and System.this.
| def __getstate__ | ( | self | ) |
| def __setstate__ | ( | self, | |
| serializationString | |||
| ) |
| def addConstraint | ( | self, | |
| args | |||
| ) |
addConstraint(System self, int particle1, int particle2, double distance) -> int
Add a constraint to the System. Particles whose mass is 0 cannot participate in constraints.
| particle1 | the index of the first particle involved in the constraint |
| particle2 | the index of the second particle involved in the constraint |
| distance | the required distance between the two particles, measured in nm |
References simtk.openmm.openmm.stripUnits().
| def addForce | ( | self, | |
| args | |||
| ) |
| def addParticle | ( | self, | |
| args | |||
| ) |
addParticle(System self, double mass) -> int
Add a particle to the System. If the mass is 0, Integrators will ignore the particle and not modify its position or velocity. This is most often used for virtual sites, but can also be used as a way to prevent a particle from moving.
| mass | the mass of the particle (in atomic mass units) |
References simtk.openmm.openmm.stripUnits().
| def getConstraintParameters | ( | self, | |
| args | |||
| ) |
getConstraintParameters(System self, int index)
Get the parameters defining a distance constraint.
| index | the index of the constraint for which to get parameters |
| particle1 | the index of the first particle involved in the constraint |
| particle2 | the index of the second particle involved in the constraint |
| distance | the required distance between the two particles, measured in nm |
References simtk.openmm.openmm.stripUnits().
| def getDefaultPeriodicBoxVectors | ( | self | ) |
getDefaultPeriodicBoxVectors(System self)
Get the default values of the vectors defining the axes of the periodic box (measured in nm). Any newly created Context will have its box vectors set to these. They will affect any Force added to the System that uses periodic boundary conditions.
Currently, only rectangular boxes are supported. This means that a, b, and c must be aligned with the x, y, and z axes respectively. Future releases may support arbitrary triclinic boxes.
| a | on exit, this contains the vector defining the first edge of the periodic box |
| b | on exit, this contains the vector defining the second edge of the periodic box |
| c | on exit, this contains the vector defining the third edge of the periodic box |
References simtk.openmm.openmm.stripUnits().
| def getForce | ( | self, | |
| args | |||
| ) |
getForce(System self, int index) -> Force getForce(System self, int index) -> Force
Get a writable reference to one of the Forces in this System.
| index | the index of the Force to get |
References simtk.openmm.openmm.stripUnits().
Referenced by System.getForces().
| def getForces | ( | self | ) |
Get the list of Forces in this System.
References System.getForce(), and System.getNumForces().
| def getNumConstraints | ( | self | ) |
getNumConstraints(System self) -> int
Get the number of distance constraints in this System.
References simtk.openmm.openmm.stripUnits().
| def getNumForces | ( | self | ) |
getNumForces(System self) -> int
Get the number of Force objects that have been added to the System.
References simtk.openmm.openmm.stripUnits().
Referenced by System.getForces().
| def getNumParticles | ( | self | ) |
getNumParticles(System self) -> int
Get the number of particles in this System.
References simtk.openmm.openmm.stripUnits().
| def getParticleMass | ( | self, | |
| args | |||
| ) |
getParticleMass(System self, int index) -> double
Get the mass (in atomic mass units) of a particle. If the mass is 0, Integrators will ignore the particle and not modify its position or velocity. This is most often used for virtual sites, but can also be used as a way to prevent a particle from moving.
| index | the index of the particle for which to get the mass |
References simtk.openmm.openmm.stripUnits().
| def getVirtualSite | ( | self, | |
| args | |||
| ) |
getVirtualSite(System self, int index) -> VirtualSite
Get VirtualSite object for a particle. If the particle is not a virtual site, this throws an exception.
| index | the index of the particle to get |
References simtk.openmm.openmm.stripUnits().
| def isVirtualSite | ( | self, | |
| args | |||
| ) |
isVirtualSite(System self, int index) -> bool
Get whether a particle is a VirtualSite.
| index | the index of the particle to check |
References simtk.openmm.openmm.stripUnits().
| def setConstraintParameters | ( | self, | |
| args | |||
| ) |
setConstraintParameters(System self, int index, int particle1, int particle2, double distance)
Set the parameters defining a distance constraint. Particles whose mass is 0 cannot participate in constraints.
| index | the index of the constraint for which to set parameters |
| particle1 | the index of the first particle involved in the constraint |
| particle2 | the index of the second particle involved in the constraint |
| distance | the required distance between the two particles, measured in nm |
References simtk.openmm.openmm.stripUnits().
| def setDefaultPeriodicBoxVectors | ( | self, | |
| args | |||
| ) |
setDefaultPeriodicBoxVectors(System self, Vec3 const & a, Vec3 const & b, Vec3 const & c)
Set the default values of the vectors defining the axes of the periodic box (measured in nm). Any newly created Context will have its box vectors set to these. They will affect any Force added to the System that uses periodic boundary conditions.
Currently, only rectangular boxes are supported. This means that a, b, and c must be aligned with the x, y, and z axes respectively. Future releases may support arbitrary triclinic boxes.
| a | the vector defining the first edge of the periodic box |
| b | the vector defining the second edge of the periodic box |
| c | the vector defining the third edge of the periodic box |
References simtk.openmm.openmm.stripUnits().
| def setParticleMass | ( | self, | |
| args | |||
| ) |
setParticleMass(System self, int index, double mass)
Set the mass (in atomic mass units) of a particle. If the mass is 0, Integrators will ignore the particle and not modify its position or velocity. This is most often used for virtual sites, but can also be used as a way to prevent a particle from moving.
| index | the index of the particle for which to set the mass |
| mass | the mass of the particle |
References simtk.openmm.openmm.stripUnits().
| def setVirtualSite | ( | self, | |
| args | |||
| ) |
setVirtualSite(System self, int index, VirtualSite virtualSite)
Set a particle to be a virtual site. The VirtualSite object should have been created on the heap with the "new" operator. The System takes over ownership of it, and deletes it when the System itself is deleted.
| index | the index of the particle that should be treated as a virtual site |
| virtualSite | a pointer to the VirtualSite object describing it |
| this |
Referenced by System.__init__().
1.8.5 
