GBSAOBCSoftcoreForce Class Reference
This class implements an implicit solvation force using the GBSA-OBC model. More...
Public Member Functions | |
| def | getNumParticles |
| getNumParticles(self) -> int | |
| def | addParticle |
| addParticle(self, double charge, double radius, double scalingFactor, double nonPolarScalingFactor = 1.0) -> int addParticle(self, double charge, double radius, double scalingFactor) -> int | |
| def | getParticleParameters |
| getParticleParameters(self, int index) | |
| def | setParticleParameters |
| setParticleParameters(self, int index, double charge, double radius, double scalingFactor, double nonPolarScalingFactor = 1.0) setParticleParameters(self, int index, double charge, double radius, double scalingFactor) | |
| def | getSolventDielectric |
| getSolventDielectric(self) -> double | |
| def | setSolventDielectric |
| setSolventDielectric(self, double dielectric) | |
| def | getSoluteDielectric |
| getSoluteDielectric(self) -> double | |
| def | setSoluteDielectric |
| setSoluteDielectric(self, double dielectric) | |
| def | getNonPolarPrefactor |
| getNonPolarPrefactor(self) -> double | |
| def | setNonPolarPrefactor |
| setNonPolarPrefactor(self, double inputNonPolarPrefactor) | |
| def | getNonbondedMethod |
| getNonbondedMethod(self) -> NonbondedSoftcoreMethod | |
| def | setNonbondedMethod |
| setNonbondedMethod(self, NonbondedSoftcoreMethod method) | |
| def | getCutoffDistance |
| getCutoffDistance(self) -> double | |
| def | setCutoffDistance |
| setCutoffDistance(self, double distance) | |
| def | __init__ |
| __init__(self) -> GBSAOBCSoftcoreForce __init__(self, GBSAOBCSoftcoreForce other) -> GBSAOBCSoftcoreForce | |
| def | __del__ |
| __del__(self) | |
Public Attributes | |
| this | |
Static Public Attributes | |
| NoCutoff = _openmm.GBSAOBCSoftcoreForce_NoCutoff | |
| CutoffNonPeriodic = _openmm.GBSAOBCSoftcoreForce_CutoffNonPeriodic | |
| CutoffPeriodic = _openmm.GBSAOBCSoftcoreForce_CutoffPeriodic | |
Detailed Description
This class implements an implicit solvation force using the GBSA-OBC model.
To use this class, create a GBSAOBCSoftcoreForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define GBSA parameters must be exactly 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().
If the System also contains a NonbondedForce, this force will use the cutoffs and periodic boundary conditions specified in it.
Member Function Documentation
| def __del__ | ( | self | ) |
__del__(self)
Reimplemented from Force.
| def __init__ | ( | self, | ||
| args | ||||
| ) |
__init__(self) -> GBSAOBCSoftcoreForce __init__(self, GBSAOBCSoftcoreForce other) -> GBSAOBCSoftcoreForce
| def addParticle | ( | self, | ||
| args | ||||
| ) |
addParticle(self, double charge, double radius, double scalingFactor, double nonPolarScalingFactor = 1.0) -> int addParticle(self, double charge, double radius, double scalingFactor) -> int
Add the GBSA 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.
- Parameters:
-
charge the charge of the particle, measured in units of the proton charge radius the GBSA radius of the particle, measured in nm scalingFactor the OBC scaling factor for the particle nonPolarScalingFactor the nonpolar scaling factor for the particle (default: 1.0)
| def getCutoffDistance | ( | self | ) |
getCutoffDistance(self) -> double
Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use is NoCutoff, this value will have no effect.
| def getNonbondedMethod | ( | self | ) |
getNonbondedMethod(self) -> NonbondedSoftcoreMethod
Get the method used for handling long range nonbonded interactions.
| def getNonPolarPrefactor | ( | self | ) |
getNonPolarPrefactor(self) -> double
Get the nonPolarPrefactor.
| def getNumParticles | ( | self | ) |
getNumParticles(self) -> int
Get the number of particles in the system.
| def getParticleParameters | ( | self, | ||
| args | ||||
| ) |
getParticleParameters(self, int index)
Get the force field parameters for a particle.
- Parameters:
-
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 GBSA radius of the particle, measured in nm scalingFactor the OBC scaling factor for the particle nonPolarScalingFactor the nonpolar scaling factor for the particle
| def getSoluteDielectric | ( | self | ) |
getSoluteDielectric(self) -> double
Get the dielectric constant for the solute.
| def getSolventDielectric | ( | self | ) |
getSolventDielectric(self) -> double
Get the dielectric constant for the solvent.
| def setCutoffDistance | ( | self, | ||
| args | ||||
| ) |
setCutoffDistance(self, double distance)
Set the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use is NoCutoff, this value will have no effect.
| def setNonbondedMethod | ( | self, | ||
| args | ||||
| ) |
setNonbondedMethod(self, NonbondedSoftcoreMethod method)
Set the method used for handling long range nonbonded interactions.
| def setNonPolarPrefactor | ( | self, | ||
| args | ||||
| ) |
setNonPolarPrefactor(self, double inputNonPolarPrefactor)
Set the nonPolarPrefactor; units are kJ/mol/nm^2
| def setParticleParameters | ( | self, | ||
| args | ||||
| ) |
setParticleParameters(self, int index, double charge, double radius, double scalingFactor, double nonPolarScalingFactor = 1.0) setParticleParameters(self, int index, double charge, double radius, double scalingFactor)
Set the force field parameters for a particle.
- Parameters:
-
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 GBSA radius of the particle, measured in nm scalingFactor the OBC scaling factor for the particle nonPolarScalingFactor the nonpolar scaling factor for the particle (default: 1.0)
| def setSoluteDielectric | ( | self, | ||
| args | ||||
| ) |
setSoluteDielectric(self, double dielectric)
Set the dielectric constant for the solute.
| def setSolventDielectric | ( | self, | ||
| args | ||||
| ) |
setSolventDielectric(self, double dielectric)
Set the dielectric constant for the solvent.
Member Data Documentation
CutoffNonPeriodic = _openmm.GBSAOBCSoftcoreForce_CutoffNonPeriodic [static] |
CutoffPeriodic = _openmm.GBSAOBCSoftcoreForce_CutoffPeriodic [static] |
NoCutoff = _openmm.GBSAOBCSoftcoreForce_NoCutoff [static] |
The documentation for this class was generated from the following file:
- openmm.py
