AmoebaGeneralizedKirkwoodForce Class Reference
This class implements an implicit solvation force using the generalized Kirkwood/OBC model. More...
Public Member Functions | |
| def | getNumParticles |
| getNumParticles(self) -> int | |
| def | addParticle |
| 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) | |
| def | getSolventDielectric |
| getSolventDielectric(self) -> double | |
| def | setSolventDielectric |
| setSolventDielectric(self, double dielectric) | |
| def | getSoluteDielectric |
| getSoluteDielectric(self) -> double | |
| def | setSoluteDielectric |
| setSoluteDielectric(self, double dielectric) | |
| def | getIncludeCavityTerm |
| getIncludeCavityTerm(self) -> int | |
| def | setIncludeCavityTerm |
| setIncludeCavityTerm(self, int includeCavityTerm) | |
| def | getProbeRadius |
| getProbeRadius(self) -> double | |
| def | setProbeRadius |
| setProbeRadius(self, double probeRadius) | |
| def | getSurfaceAreaFactor |
| getSurfaceAreaFactor(self) -> double | |
| def | setSurfaceAreaFactor |
| setSurfaceAreaFactor(self, double surfaceAreaFactor) | |
| def | __init__ |
| __init__(self) -> AmoebaGeneralizedKirkwoodForce __init__(self, AmoebaGeneralizedKirkwoodForce other) -> AmoebaGeneralizedKirkwoodForce | |
| def | __del__ |
| __del__(self) | |
Public Attributes | |
| this | |
Detailed Description
This class implements an implicit solvation force using the generalized Kirkwood/OBC model.
To use this class, create a AmoebaGeneralizedKirkwoodForce 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 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().
Member Function Documentation
| def __del__ | ( | self | ) |
__del__(self)
Reimplemented from Force.
| def __init__ | ( | self, | ||
| args | ||||
| ) |
__init__(self) -> AmoebaGeneralizedKirkwoodForce __init__(self, AmoebaGeneralizedKirkwoodForce other) -> AmoebaGeneralizedKirkwoodForce
| def addParticle | ( | self, | ||
| args | ||||
| ) |
addParticle(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.
- 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
| def getIncludeCavityTerm | ( | self | ) |
getIncludeCavityTerm(self) -> int
Get the dielectric offset (nm) used in OBC Set the dielectric offset (nm) used in OBC Get the flag signalling whether the cavity term should be included
| 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
| def getProbeRadius | ( | self | ) |
getProbeRadius(self) -> double
Get the probe radius (nm) used in SASA contribution
| 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 getSurfaceAreaFactor | ( | self | ) |
getSurfaceAreaFactor(self) -> double
Get the surface area factor kJ/(nm*nm) used in SASA contribution
| def setIncludeCavityTerm | ( | self, | ||
| args | ||||
| ) |
setIncludeCavityTerm(self, int includeCavityTerm)
Set the flag signalling whether the cavity term should be included
| def setParticleParameters | ( | self, | ||
| args | ||||
| ) |
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
| def setProbeRadius | ( | self, | ||
| args | ||||
| ) |
setProbeRadius(self, double probeRadius)
Set the probe radius (nm) used in SASA contribution
| 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.
| def setSurfaceAreaFactor | ( | self, | ||
| args | ||||
| ) |
setSurfaceAreaFactor(self, double surfaceAreaFactor)
Set the surface area factor kJ/(nm*nm) used in SASA contribution
Member Data Documentation
The documentation for this class was generated from the following file:
- openmm.py
