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OpenMM
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OpenMM
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This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model. More...
Inheritance diagram for AmoebaGeneralizedKirkwoodForce:Public Member Functions | |
| def | getNumParticles |
| getNumParticles(AmoebaGeneralizedKirkwoodForce self) -> int | |
| def | addParticle |
| addParticle(AmoebaGeneralizedKirkwoodForce self, double charge, double radius, double scalingFactor) -> int | |
| def | getParticleParameters |
| getParticleParameters(AmoebaGeneralizedKirkwoodForce self, int index) | |
| def | setParticleParameters |
| setParticleParameters(AmoebaGeneralizedKirkwoodForce self, int index, double charge, double radius, double scalingFactor) | |
| def | getSolventDielectric |
| getSolventDielectric(AmoebaGeneralizedKirkwoodForce self) -> double | |
| def | setSolventDielectric |
| setSolventDielectric(AmoebaGeneralizedKirkwoodForce self, double dielectric) | |
| def | getSoluteDielectric |
| getSoluteDielectric(AmoebaGeneralizedKirkwoodForce self) -> double | |
| def | setSoluteDielectric |
| setSoluteDielectric(AmoebaGeneralizedKirkwoodForce self, double dielectric) | |
| def | getIncludeCavityTerm |
| getIncludeCavityTerm(AmoebaGeneralizedKirkwoodForce self) -> int | |
| def | setIncludeCavityTerm |
| setIncludeCavityTerm(AmoebaGeneralizedKirkwoodForce self, int includeCavityTerm) | |
| def | getProbeRadius |
| getProbeRadius(AmoebaGeneralizedKirkwoodForce self) -> double | |
| def | setProbeRadius |
| setProbeRadius(AmoebaGeneralizedKirkwoodForce self, double probeRadius) | |
| def | getSurfaceAreaFactor |
| getSurfaceAreaFactor(AmoebaGeneralizedKirkwoodForce self) -> double | |
| def | setSurfaceAreaFactor |
| setSurfaceAreaFactor(AmoebaGeneralizedKirkwoodForce self, double surfaceAreaFactor) | |
| def | updateParametersInContext |
| updateParametersInContext(AmoebaGeneralizedKirkwoodForce self, Context context) | |
| def | __init__ |
| init(OpenMM::AmoebaGeneralizedKirkwoodForce self) -> AmoebaGeneralizedKirkwoodForce init(OpenMM::AmoebaGeneralizedKirkwoodForce self, AmoebaGeneralizedKirkwoodForce other) -> AmoebaGeneralizedKirkwoodForce | |
| def | __del__ |
| del(OpenMM::AmoebaGeneralizedKirkwoodForce self) | |
| Public Member Functions inherited from Force | |
| def | __init__ |
| def | __del__ |
| del(OpenMM::Force self) | |
| def | getForceGroup |
| getForceGroup(Force self) -> int | |
| def | setForceGroup |
| setForceGroup(Force self, int group) | |
| def | __copy__ |
| def | __deepcopy__ |
Public Attributes | |
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This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model.
To use this class, create an AmoebaGeneralizedKirkwoodForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define parameters must be equal to the number of particles in the System, or else an exception will be thrown when you try to create a Context. After a particle has been added, you can modify its force field parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().
| def __init__ | ( | self, | |
| args | |||
| ) |
init(OpenMM::AmoebaGeneralizedKirkwoodForce self) -> AmoebaGeneralizedKirkwoodForce init(OpenMM::AmoebaGeneralizedKirkwoodForce self, AmoebaGeneralizedKirkwoodForce other) -> AmoebaGeneralizedKirkwoodForce
| def __del__ | ( | self | ) |
del(OpenMM::AmoebaGeneralizedKirkwoodForce self)
| def addParticle | ( | self, | |
| args | |||
| ) |
addParticle(AmoebaGeneralizedKirkwoodForce self, double charge, double radius, double scalingFactor) -> int
Add the parameters for a particle. This should be called once for each particle in the System. When it is called for the i'th time, it specifies the parameters for the i'th particle.
| charge | the charge of the particle, measured in units of the proton charge |
| radius | the atomic radius of the particle, measured in nm |
| scalingFactor | the scaling factor for the particle |
| def getIncludeCavityTerm | ( | self | ) |
getIncludeCavityTerm(AmoebaGeneralizedKirkwoodForce self) -> int
Get the flag signaling whether the cavity term should be included
| def getNumParticles | ( | self | ) |
getNumParticles(AmoebaGeneralizedKirkwoodForce self) -> int
Get the number of particles in the system.
| def getParticleParameters | ( | self, | |
| args | |||
| ) |
getParticleParameters(AmoebaGeneralizedKirkwoodForce self, int index)
Get the force field parameters for a particle.
| index | the index of the particle for which to get parameters |
| charge | the charge of the particle, measured in units of the proton charge |
| radius | the atomic radius of the particle, measured in nm |
| scalingFactor | the scaling factor for the particle |
| def getProbeRadius | ( | self | ) |
getProbeRadius(AmoebaGeneralizedKirkwoodForce self) -> double
Get the probe radius (nm) used in SASA contribution
| def getSoluteDielectric | ( | self | ) |
getSoluteDielectric(AmoebaGeneralizedKirkwoodForce self) -> double
Get the dielectric constant for the solute.
| def getSolventDielectric | ( | self | ) |
getSolventDielectric(AmoebaGeneralizedKirkwoodForce self) -> double
Get the dielectric constant for the solvent.
| def getSurfaceAreaFactor | ( | self | ) |
getSurfaceAreaFactor(AmoebaGeneralizedKirkwoodForce self) -> double
Get the surface area factor kJ/(nm*nm) used in SASA contribution
| def setIncludeCavityTerm | ( | self, | |
| args | |||
| ) |
setIncludeCavityTerm(AmoebaGeneralizedKirkwoodForce self, int includeCavityTerm)
Set the flag signaling whether the cavity term should be included
| def setParticleParameters | ( | self, | |
| args | |||
| ) |
setParticleParameters(AmoebaGeneralizedKirkwoodForce self, int index, double charge, double radius, double scalingFactor)
Set the force field parameters for a particle.
| index | the index of the particle for which to set parameters |
| charge | the charge of the particle, measured in units of the proton charge |
| radius | the atomic radius of the particle, measured in nm |
| scalingFactor | the scaling factor for the particle |
| def setProbeRadius | ( | self, | |
| args | |||
| ) |
setProbeRadius(AmoebaGeneralizedKirkwoodForce self, double probeRadius)
Set the probe radius (nm) used in SASA contribution
| def setSoluteDielectric | ( | self, | |
| args | |||
| ) |
setSoluteDielectric(AmoebaGeneralizedKirkwoodForce self, double dielectric)
Set the dielectric constant for the solute.
| def setSolventDielectric | ( | self, | |
| args | |||
| ) |
setSolventDielectric(AmoebaGeneralizedKirkwoodForce self, double dielectric)
Set the dielectric constant for the solvent.
| def setSurfaceAreaFactor | ( | self, | |
| args | |||
| ) |
setSurfaceAreaFactor(AmoebaGeneralizedKirkwoodForce self, double surfaceAreaFactor)
Set the surface area factor kJ/(nm*nm) used in SASA contribution
| def updateParametersInContext | ( | self, | |
| args | |||
| ) |
updateParametersInContext(AmoebaGeneralizedKirkwoodForce self, Context context)
Update the per-particle parameters in a Context to match those stored in this Force object. This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInState() to copy them over to the Context.
The only information this method updates is the values of per-particle parameters. All other aspects of the Force (the probe radius, the surface area factor, etc.) are unaffected and can only be changed by reinitializing the Context.
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1.8.2 
