CustomTorsionForce Class Reference
This class implements interactions between sets of four particles that depend on the torsion angle between them. More...
Public Member Functions | |
| def | getNumTorsions |
| getNumTorsions(self) -> int | |
| def | getNumPerTorsionParameters |
| getNumPerTorsionParameters(self) -> int | |
| def | getNumGlobalParameters |
| getNumGlobalParameters(self) -> int | |
| def | getEnergyFunction |
| getEnergyFunction(self) -> string | |
| def | setEnergyFunction |
| setEnergyFunction(self, string energy) | |
| def | addPerTorsionParameter |
| addPerTorsionParameter(self, string name) -> int | |
| def | getPerTorsionParameterName |
| getPerTorsionParameterName(self, int index) -> string | |
| def | setPerTorsionParameterName |
| setPerTorsionParameterName(self, int index, string name) | |
| def | addGlobalParameter |
| addGlobalParameter(self, string name, double defaultValue) -> int | |
| def | getGlobalParameterName |
| getGlobalParameterName(self, int index) -> string | |
| def | setGlobalParameterName |
| setGlobalParameterName(self, int index, string name) | |
| def | getGlobalParameterDefaultValue |
| getGlobalParameterDefaultValue(self, int index) -> double | |
| def | setGlobalParameterDefaultValue |
| setGlobalParameterDefaultValue(self, int index, double defaultValue) | |
| def | addTorsion |
| addTorsion(self, int particle1, int particle2, int particle3, int particle4, vectord parameters) -> int | |
| def | getTorsionParameters |
| getTorsionParameters(self, int index) | |
| def | setTorsionParameters |
| setTorsionParameters(self, int index, int particle1, int particle2, int particle3, int particle4, vectord parameters) | |
| def | __init__ |
| __init__(self, string energy) -> CustomTorsionForce __init__(self, CustomTorsionForce other) -> CustomTorsionForce | |
| def | __del__ |
| __del__(self) | |
Public Attributes | |
| this | |
Detailed Description
This class implements interactions between sets of four particles that depend on the torsion angle between them.
Unlike PeriodicTorsionForce, 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-torsion parameters.
To use this class, create a CustomTorsionForce 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 torsion angle formed by the particles, as well as on any parameters you choose. Then call addPerTorsionParameter() to define per-torsion parameters, and addGlobalParameter() to define global parameters. The values of per-torsion 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 addTorsion() once for each torsion. After an torsion has been added, you can modify its parameters by calling setTorsionParameters().
As an example, the following code creates a CustomTorsionForce that implements a harmonic potential:
CustomTorsionForce* force = new CustomTorsionForce("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->addPerTorsionParameter("k");
force->addPerTorsionParameter("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. All trigonometric functions are defined in radians, and log is the natural logarithm. step(x) = 0 if x is less than 0, 1 otherwise.
Member Function Documentation
| def __del__ | ( | self | ) |
__del__(self)
Reimplemented from Force.
| def __init__ | ( | self, | ||
| args | ||||
| ) |
__init__(self, string energy) -> CustomTorsionForce __init__(self, CustomTorsionForce other) -> CustomTorsionForce
Create a CustomTorsionForce.
- Parameters:
-
energy an algebraic expression giving the interaction energy between three particles as a function of theta, the torsion angle between them
| def addGlobalParameter | ( | self, | ||
| args | ||||
| ) |
addGlobalParameter(self, string name, double defaultValue) -> int
Add a new global parameter that the interaction may depend on.
- Parameters:
-
name the name of the parameter defaultValue the default value of the parameter
| def addPerTorsionParameter | ( | self, | ||
| args | ||||
| ) |
addPerTorsionParameter(self, string name) -> int
Add a new per-torsion parameter that the interaction may depend on.
- Parameters:
-
name the name of the parameter
| def addTorsion | ( | self, | ||
| args | ||||
| ) |
addTorsion(self, int particle1, int particle2, int particle3, int particle4, vectord parameters) -> int
Add a torsion term to the force field.
- Parameters:
-
particle1 the index of the first particle connected by the torsion particle2 the index of the second particle connected by the torsion particle3 the index of the third particle connected by the torsion particle4 the index of the fourth particle connected by the torsion parameters the list of parameters for the new torsion
| def getEnergyFunction | ( | self | ) |
getEnergyFunction(self) -> string
Get the algebraic expression that gives the interaction energy for each torsion
| def getGlobalParameterDefaultValue | ( | self, | ||
| args | ||||
| ) |
getGlobalParameterDefaultValue(self, int index) -> double
Get the default value of a global parameter.
- Parameters:
-
index the index of the parameter for which to get the default value
| def getGlobalParameterName | ( | self, | ||
| args | ||||
| ) |
getGlobalParameterName(self, int index) -> string
Get the name of a global parameter.
- Parameters:
-
index the index of the parameter for which to get the name
| def getNumGlobalParameters | ( | self | ) |
getNumGlobalParameters(self) -> int
Get the number of global parameters that the interaction depends on.
| def getNumPerTorsionParameters | ( | self | ) |
getNumPerTorsionParameters(self) -> int
Get the number of per-torsion parameters that the interaction depends on.
| def getNumTorsions | ( | self | ) |
getNumTorsions(self) -> int
Get the number of torsions for which force field parameters have been defined.
| def getPerTorsionParameterName | ( | self, | ||
| args | ||||
| ) |
getPerTorsionParameterName(self, int index) -> string
Get the name of a per-torsion parameter.
- Parameters:
-
index the index of the parameter for which to get the name
| def getTorsionParameters | ( | self, | ||
| args | ||||
| ) |
getTorsionParameters(self, int index)
Get the force field parameters for a torsion term.
- Parameters:
-
index the index of the torsion for which to get parameters particle1 the index of the first particle connected by the torsion particle2 the index of the second particle connected by the torsion particle3 the index of the third particle connected by the torsion particle4 the index of the fourth particle connected by the torsion parameters the list of parameters for the torsion
| def setEnergyFunction | ( | self, | ||
| args | ||||
| ) |
setEnergyFunction(self, string energy)
Set the algebraic expression that gives the interaction energy for each torsion
| def setGlobalParameterDefaultValue | ( | self, | ||
| args | ||||
| ) |
setGlobalParameterDefaultValue(self, int index, double defaultValue)
Set the default value of a global parameter.
- Parameters:
-
index the index of the parameter for which to set the default value name the default value of the parameter
| def setGlobalParameterName | ( | self, | ||
| args | ||||
| ) |
setGlobalParameterName(self, int index, string name)
Set the name of a global parameter.
- Parameters:
-
index the index of the parameter for which to set the name name the name of the parameter
| def setPerTorsionParameterName | ( | self, | ||
| args | ||||
| ) |
setPerTorsionParameterName(self, int index, string name)
Set the name of a per-torsion parameter.
- Parameters:
-
index the index of the parameter for which to set the name name the name of the parameter
| def setTorsionParameters | ( | self, | ||
| args | ||||
| ) |
setTorsionParameters(self, int index, int particle1, int particle2, int particle3, int particle4, vectord parameters)
Set the force field parameters for a torsion term.
- Parameters:
-
index the index of the torsion for which to set parameters particle1 the index of the first particle connected by the torsion particle2 the index of the second particle connected by the torsion particle3 the index of the third particle connected by the torsion particle4 the index of the fourth particle connected by the torsion parameters the list of parameters for the torsion
Member Data Documentation
The documentation for this class was generated from the following file:
- openmm.py
