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OpenMM
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OpenMM
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This class implements an interaction between triplets of particles that varies with the angle between them. More...
Inheritance diagram for AmoebaAngleForce:Public Member Functions | |
| def | getNumAngles |
| getNumAngles(AmoebaAngleForce self) -> int More... | |
| def | setAmoebaGlobalAngleCubic |
| setAmoebaGlobalAngleCubic(AmoebaAngleForce self, double cubicK) More... | |
| def | getAmoebaGlobalAngleCubic |
| getAmoebaGlobalAngleCubic(AmoebaAngleForce self) -> double More... | |
| def | setAmoebaGlobalAngleQuartic |
| setAmoebaGlobalAngleQuartic(AmoebaAngleForce self, double quarticK) More... | |
| def | getAmoebaGlobalAngleQuartic |
| getAmoebaGlobalAngleQuartic(AmoebaAngleForce self) -> double More... | |
| def | setAmoebaGlobalAnglePentic |
| setAmoebaGlobalAnglePentic(AmoebaAngleForce self, double penticK) More... | |
| def | getAmoebaGlobalAnglePentic |
| getAmoebaGlobalAnglePentic(AmoebaAngleForce self) -> double More... | |
| def | setAmoebaGlobalAngleSextic |
| setAmoebaGlobalAngleSextic(AmoebaAngleForce self, double sexticK) More... | |
| def | getAmoebaGlobalAngleSextic |
| getAmoebaGlobalAngleSextic(AmoebaAngleForce self) -> double More... | |
| def | addAngle |
| addAngle(AmoebaAngleForce self, int particle1, int particle2, int particle3, double length, double quadraticK) -> int More... | |
| def | getAngleParameters |
| getAngleParameters(AmoebaAngleForce self, int index) More... | |
| def | setAngleParameters |
| setAngleParameters(AmoebaAngleForce self, int index, int particle1, int particle2, int particle3, double length, double quadraticK) More... | |
| def | updateParametersInContext |
| updateParametersInContext(AmoebaAngleForce self, Context context) More... | |
| def | usesPeriodicBoundaryConditions |
| usesPeriodicBoundaryConditions(AmoebaAngleForce self) -> bool More... | |
| def | __init__ |
| init(OpenMM::AmoebaAngleForce self) -> AmoebaAngleForce init(OpenMM::AmoebaAngleForce self, AmoebaAngleForce other) -> AmoebaAngleForce More... | |
| def | __del__ |
| del(OpenMM::AmoebaAngleForce self) More... | |
| Public Member Functions inherited from Force | |
| def | __init__ |
| def | __del__ |
| del(OpenMM::Force self) More... | |
| def | getForceGroup |
| getForceGroup(Force self) -> int More... | |
| def | setForceGroup |
| setForceGroup(Force self, int group) More... | |
| def | usesPeriodicBoundaryConditions |
| usesPeriodicBoundaryConditions(Force self) -> bool More... | |
| def | __copy__ |
| def | __deepcopy__ |
Public Attributes | |
| this | |
This class implements an interaction between triplets of particles that varies with the angle between them.
The interaction is defined by a 6th order polynomial. Only the quadratic term is set per-angle. The coefficients of the higher order terms each have a single value that is set globally.
To use it, create an AmoebaAngleForce object then call addAngle() once for each angle. After an angle has been added, you can modify its force field parameters by calling setAngleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().
| def __init__ | ( | self, | |
| args | |||
| ) |
init(OpenMM::AmoebaAngleForce self) -> AmoebaAngleForce init(OpenMM::AmoebaAngleForce self, AmoebaAngleForce other) -> AmoebaAngleForce
Create an AmoebaAngleForce.
References simtk.openmm.openmm.stripUnits().
| def __del__ | ( | self | ) |
del(OpenMM::AmoebaAngleForce self)
References simtk.openmm.openmm.stripUnits().
| def addAngle | ( | self, | |
| args | |||
| ) |
addAngle(AmoebaAngleForce self, int particle1, int particle2, int particle3, double length, double quadraticK) -> int
Add an angle term to the force field.
| particle1 | the index of the first particle connected by the angle |
| particle2 | the index of the second particle connected by the angle |
| particle3 | the index of the third particle connected by the angle |
| length | the angle measured in degrees |
| quadratic | k the quadratic force constant for the angle, measured in kJ/mol/radian^2 |
References simtk.openmm.openmm.stripUnits().
| def getAmoebaGlobalAngleCubic | ( | self, | |
| args | |||
| ) |
getAmoebaGlobalAngleCubic(AmoebaAngleForce self) -> double
Get the global cubic term
References simtk.openmm.openmm.stripUnits().
| def getAmoebaGlobalAnglePentic | ( | self, | |
| args | |||
| ) |
getAmoebaGlobalAnglePentic(AmoebaAngleForce self) -> double
Get the global pentic term
References simtk.openmm.openmm.stripUnits().
| def getAmoebaGlobalAngleQuartic | ( | self, | |
| args | |||
| ) |
getAmoebaGlobalAngleQuartic(AmoebaAngleForce self) -> double
Get the global quartic term
References simtk.openmm.openmm.stripUnits().
| def getAmoebaGlobalAngleSextic | ( | self, | |
| args | |||
| ) |
getAmoebaGlobalAngleSextic(AmoebaAngleForce self) -> double
Get the global sextic term
References simtk.openmm.openmm.stripUnits().
| def getAngleParameters | ( | self, | |
| args | |||
| ) |
getAngleParameters(AmoebaAngleForce self, int index)
Get the force field parameters for an angle term.
| index | the index of the angle for which to get parameters |
| particle1 | the index of the first particle connected by the angle |
| particle2 | the index of the second particle connected by the angle |
| particle3 | the index of the third particle connected by the angle |
| length | the equilibrium angle, measured in degress |
| quadratic | k the quadratic force constant for the angle, measured in kJ/mol/radian^2 |
References simtk.openmm.openmm.stripUnits().
| def getNumAngles | ( | self, | |
| args | |||
| ) |
getNumAngles(AmoebaAngleForce self) -> int
Get the number of angle stretch terms in the potential function
References simtk.openmm.openmm.stripUnits().
| def setAmoebaGlobalAngleCubic | ( | self, | |
| args | |||
| ) |
setAmoebaGlobalAngleCubic(AmoebaAngleForce self, double cubicK)
Set the global cubic term
| cubicK | the cubic force constant for the angle |
References simtk.openmm.openmm.stripUnits().
| def setAmoebaGlobalAnglePentic | ( | self, | |
| args | |||
| ) |
setAmoebaGlobalAnglePentic(AmoebaAngleForce self, double penticK)
Set the global pentic term
| penticK | the pentic force constant for the angle |
References simtk.openmm.openmm.stripUnits().
| def setAmoebaGlobalAngleQuartic | ( | self, | |
| args | |||
| ) |
setAmoebaGlobalAngleQuartic(AmoebaAngleForce self, double quarticK)
Set the global quartic term
| quarticK | the quartic force constant for the angle |
References simtk.openmm.openmm.stripUnits().
| def setAmoebaGlobalAngleSextic | ( | self, | |
| args | |||
| ) |
setAmoebaGlobalAngleSextic(AmoebaAngleForce self, double sexticK)
Set the global sextic term
| sexticK | the sextic force constant for the angle |
References simtk.openmm.openmm.stripUnits().
| def setAngleParameters | ( | self, | |
| args | |||
| ) |
setAngleParameters(AmoebaAngleForce self, int index, int particle1, int particle2, int particle3, double length, double quadraticK)
Set the force field parameters for an angle term.
| index | the index of the angle for which to set parameters |
| particle1 | the index of the first particle connected by the angle |
| particle2 | the index of the second particle connected by the angle |
| particle3 | the index of the third particle connected by the angle |
| length | the equilibrium angle, measured in degrees |
| quadratic | k the quadratic force constant for the angle, measured in kJ/mol/radian^2 |
References simtk.openmm.openmm.stripUnits().
| def updateParametersInContext | ( | self, | |
| args | |||
| ) |
updateParametersInContext(AmoebaAngleForce self, Context context)
Update the per-angle 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 setAngleParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.
The only information this method updates is the values of per-angle parameters. The set of particles involved in an angle cannot be changed, nor can new angles be added.
References simtk.openmm.openmm.stripUnits().
| def usesPeriodicBoundaryConditions | ( | self, | |
| args | |||
| ) |
usesPeriodicBoundaryConditions(AmoebaAngleForce self) -> bool
Returns whether or not this force makes use of periodic boundary conditions.
References simtk.openmm.openmm.stripUnits().
| this |
1.8.8 
