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OpenMM
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OpenMM
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This class implements interactions between sets of three particles that depend on the angle between them. More...
Inheritance diagram for CustomAngleForce:Public Member Functions | |
| def | getNumAngles |
| getNumAngles(CustomAngleForce self) -> int More... | |
| def | getNumPerAngleParameters |
| getNumPerAngleParameters(CustomAngleForce self) -> int More... | |
| def | getNumGlobalParameters |
| getNumGlobalParameters(CustomAngleForce self) -> int More... | |
| def | getEnergyFunction |
| getEnergyFunction(CustomAngleForce self) -> std::string const & More... | |
| def | setEnergyFunction |
| setEnergyFunction(CustomAngleForce self, std::string const & energy) More... | |
| def | addPerAngleParameter |
| addPerAngleParameter(CustomAngleForce self, std::string const & name) -> int More... | |
| def | getPerAngleParameterName |
| getPerAngleParameterName(CustomAngleForce self, int index) -> std::string const & More... | |
| def | setPerAngleParameterName |
| setPerAngleParameterName(CustomAngleForce self, int index, std::string const & name) More... | |
| def | addGlobalParameter |
| addGlobalParameter(CustomAngleForce self, std::string const & name, double defaultValue) -> int More... | |
| def | getGlobalParameterName |
| getGlobalParameterName(CustomAngleForce self, int index) -> std::string const & More... | |
| def | setGlobalParameterName |
| setGlobalParameterName(CustomAngleForce self, int index, std::string const & name) More... | |
| def | getGlobalParameterDefaultValue |
| getGlobalParameterDefaultValue(CustomAngleForce self, int index) -> double More... | |
| def | setGlobalParameterDefaultValue |
| setGlobalParameterDefaultValue(CustomAngleForce self, int index, double defaultValue) More... | |
| def | addAngle |
| addAngle(CustomAngleForce self, int particle1, int particle2, int particle3, vectord parameters) -> int More... | |
| def | getAngleParameters |
| getAngleParameters(CustomAngleForce self, int index) More... | |
| def | setAngleParameters |
| setAngleParameters(CustomAngleForce self, int index, int particle1, int particle2, int particle3, vectord parameters) More... | |
| def | updateParametersInContext |
| updateParametersInContext(CustomAngleForce self, Context context) More... | |
| def | __init__ |
| init(OpenMM::CustomAngleForce self, std::string const & energy) -> CustomAngleForce init(OpenMM::CustomAngleForce self, CustomAngleForce other) -> CustomAngleForce More... | |
| def | __del__ |
| del(OpenMM::CustomAngleForce 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 | __copy__ |
| def | __deepcopy__ |
Public Attributes | |
| this | |
This class implements interactions between sets of three particles that depend on the angle between them.
Unlike HarmonicAngleForce, the functional form of the interaction is completely customizable, and may involve arbitrary algebraic expressions. In addition to the angle formed by the particles, it may depend on arbitrary global and per-angle parameters.
To use this class, create a CustomAngleForce object, passing an algebraic expression to the constructor that defines the interaction energy between each set of particles. The expression may depend on theta, the angle formed by the particles, as well as on any parameters you choose. Then call addPerAngleParameter() to define per-angle parameters, and addGlobalParameter() to define global parameters. The values of per-angle parameters are specified as part of the system definition, while values of global parameters may be modified during a simulation by calling Context::setParameter(). Finally, call addAngle() once for each angle. After an angle has been added, you can modify its parameters by calling setAngleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().
As an example, the following code creates a CustomAngleForce that implements a harmonic potential:
CustomAngleForce* force = new CustomAngleForce("0.5*k*(theta-theta0)^2");
This force depends on two parameters: the spring constant k and equilibrium angle theta0. The following code defines these parameters:
force->addPerAngleParameter("k");
force->addPerAngleParameter("theta0");
Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta. All trigonometric functions are defined in radians, and log is the natural logarithm. step(x) = 0 if x is less than 0, 1 otherwise. delta(x) = 1 if x is 0, 0 otherwise.
| def __init__ | ( | self, | |
| args | |||
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init(OpenMM::CustomAngleForce self, std::string const & energy) -> CustomAngleForce init(OpenMM::CustomAngleForce self, CustomAngleForce other) -> CustomAngleForce
Create a CustomAngleForce.
| energy | an algebraic expression giving the interaction energy between three particles as a function of theta, the angle between them |
References simtk.openmm.openmm.stripUnits().
| def __del__ | ( | self | ) |
del(OpenMM::CustomAngleForce self)
References simtk.openmm.openmm.stripUnits().
| def addAngle | ( | self, | |
| args | |||
| ) |
addAngle(CustomAngleForce self, int particle1, int particle2, int particle3, vectord parameters) -> 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 |
| parameters | the list of parameters for the new angle |
References simtk.openmm.openmm.stripUnits().
| def addGlobalParameter | ( | self, | |
| args | |||
| ) |
addGlobalParameter(CustomAngleForce self, std::string const & name, double defaultValue) -> int
Add a new global parameter that the interaction may depend on.
| name | the name of the parameter |
| defaultValue | the default value of the parameter |
References simtk.openmm.openmm.stripUnits().
| def addPerAngleParameter | ( | self, | |
| args | |||
| ) |
addPerAngleParameter(CustomAngleForce self, std::string const & name) -> int
Add a new per-angle parameter that the interaction may depend on.
| name | the name of the parameter |
References simtk.openmm.openmm.stripUnits().
| def getAngleParameters | ( | self, | |
| args | |||
| ) |
getAngleParameters(CustomAngleForce 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 |
| parameters | the list of parameters for the angle |
References simtk.openmm.openmm.stripUnits().
| def getEnergyFunction | ( | self | ) |
getEnergyFunction(CustomAngleForce self) -> std::string const &
Get the algebraic expression that gives the interaction energy for each angle
References simtk.openmm.openmm.stripUnits().
| def getGlobalParameterDefaultValue | ( | self, | |
| args | |||
| ) |
getGlobalParameterDefaultValue(CustomAngleForce self, int index) -> double
Get the default value of a global parameter.
| index | the index of the parameter for which to get the default value |
References simtk.openmm.openmm.stripUnits().
| def getGlobalParameterName | ( | self, | |
| args | |||
| ) |
getGlobalParameterName(CustomAngleForce self, int index) -> std::string const &
Get the name of a global parameter.
| index | the index of the parameter for which to get the name |
References simtk.openmm.openmm.stripUnits().
| def getNumAngles | ( | self | ) |
getNumAngles(CustomAngleForce self) -> int
Get the number of angles for which force field parameters have been defined.
References simtk.openmm.openmm.stripUnits().
| def getNumGlobalParameters | ( | self | ) |
getNumGlobalParameters(CustomAngleForce self) -> int
Get the number of global parameters that the interaction depends on.
References simtk.openmm.openmm.stripUnits().
| def getNumPerAngleParameters | ( | self | ) |
getNumPerAngleParameters(CustomAngleForce self) -> int
Get the number of per-angle parameters that the interaction depends on.
References simtk.openmm.openmm.stripUnits().
| def getPerAngleParameterName | ( | self, | |
| args | |||
| ) |
getPerAngleParameterName(CustomAngleForce self, int index) -> std::string const &
Get the name of a per-angle parameter.
| index | the index of the parameter for which to get the name |
References simtk.openmm.openmm.stripUnits().
| def setAngleParameters | ( | self, | |
| args | |||
| ) |
setAngleParameters(CustomAngleForce self, int index, int particle1, int particle2, int particle3, vectord parameters)
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 |
| parameters | the list of parameters for the angle |
References simtk.openmm.openmm.stripUnits().
| def setEnergyFunction | ( | self, | |
| args | |||
| ) |
setEnergyFunction(CustomAngleForce self, std::string const & energy)
Set the algebraic expression that gives the interaction energy for each angle
References simtk.openmm.openmm.stripUnits().
| def setGlobalParameterDefaultValue | ( | self, | |
| args | |||
| ) |
setGlobalParameterDefaultValue(CustomAngleForce self, int index, double defaultValue)
Set the default value of a global parameter.
| index | the index of the parameter for which to set the default value |
| name | the default value of the parameter |
References simtk.openmm.openmm.stripUnits().
| def setGlobalParameterName | ( | self, | |
| args | |||
| ) |
setGlobalParameterName(CustomAngleForce self, int index, std::string const & name)
Set the name of a global parameter.
| index | the index of the parameter for which to set the name |
| name | the name of the parameter |
References simtk.openmm.openmm.stripUnits().
| def setPerAngleParameterName | ( | self, | |
| args | |||
| ) |
setPerAngleParameterName(CustomAngleForce self, int index, std::string const & name)
Set the name of a per-angle parameter.
| index | the index of the parameter for which to set the name |
| name | the name of the parameter |
References simtk.openmm.openmm.stripUnits().
| def updateParametersInContext | ( | self, | |
| args | |||
| ) |
updateParametersInContext(CustomAngleForce 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 updateParametersInState() to copy them over to the Context.
This method has several limitations. The only information it updates is the values of per-angle parameters. All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing the Context. The set of particles involved in a angle cannot be changed, nor can new angles be added.
References simtk.openmm.openmm.stripUnits().
| this |
1.8.6