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OpenMM
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OpenMM
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This class implements interactions between sets of four particles that depend on the torsion angle between them. More...
Inheritance diagram for CustomTorsionForce:Public Member Functions | |
| def | getNumTorsions |
| getNumTorsions(self) -> int | |
| def | getNumPerTorsionParameters |
| getNumPerTorsionParameters(self) -> int | |
| def | getNumGlobalParameters |
| getNumGlobalParameters(self) -> int | |
| def | getEnergyFunction |
| getEnergyFunction(self) -> std::string const & | |
| def | setEnergyFunction |
| Set the algebraic expression that gives the interaction energy for each torsion. | |
| def | addPerTorsionParameter |
| addPerTorsionParameter(self, name) -> int | |
| def | getPerTorsionParameterName |
| getPerTorsionParameterName(self, index) -> std::string const & | |
| def | setPerTorsionParameterName |
| Set the name of a per-torsion parameter. | |
| def | addGlobalParameter |
| addGlobalParameter(self, name, defaultValue) -> int | |
| def | getGlobalParameterName |
| getGlobalParameterName(self, index) -> std::string const & | |
| def | setGlobalParameterName |
| Set the name of a global parameter. | |
| def | getGlobalParameterDefaultValue |
| getGlobalParameterDefaultValue(self, index) -> double | |
| def | setGlobalParameterDefaultValue |
| Set the default value of a global parameter. | |
| def | addTorsion |
| addTorsion(self, particle1, particle2, particle3, particle4, parameters) -> int addTorsion(self, particle1, particle2, particle3, particle4) -> int | |
| def | getTorsionParameters |
| Get the force field parameters for a torsion term. | |
| def | setTorsionParameters |
| Set the force field parameters for a torsion term. | |
| def | updateParametersInContext |
| Update the per-torsion parameters in a Context to match those stored in this Force object. | |
| def | usesPeriodicBoundaryConditions |
| usesPeriodicBoundaryConditions(self) -> bool | |
| def | __init__ |
| __init__(self, energy) -> CustomTorsionForce __init__(self, other) -> CustomTorsionForce | |
Public Attributes | |
| this | |
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(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().
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, floor, ceil, step, delta, select. 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. select(x,y,z) = z if x = 0, y otherwise.
| def __init__ | ( | self, | |
| args | |||
| ) |
__init__(self, energy) -> CustomTorsionForce __init__(self, other) -> CustomTorsionForce
Create a CustomTorsionForce.
| energy | (string) an algebraic expression giving the interaction energy between three particles as a function of theta, the torsion angle between them |
| def addGlobalParameter | ( | self, | |
| name, | |||
| defaultValue | |||
| ) |
addGlobalParameter(self, name, defaultValue) -> int
Add a new global parameter that the interaction may depend on.
| name | (string) the name of the parameter |
| defaultValue | (double) the default value of the parameter |
| def addPerTorsionParameter | ( | self, | |
| name | |||
| ) |
addPerTorsionParameter(self, name) -> int
Add a new per-torsion parameter that the interaction may depend on.
| name | (string) the name of the parameter |
| def addTorsion | ( | self, | |
| args | |||
| ) |
addTorsion(self, particle1, particle2, particle3, particle4, parameters) -> int addTorsion(self, particle1, particle2, particle3, particle4) -> int
Add a torsion term to the force field.
| particle1 | (int) the index of the first particle connected by the torsion |
| particle2 | (int) the index of the second particle connected by the torsion |
| particle3 | (int) the index of the third particle connected by the torsion |
| particle4 | (int) the index of the fourth particle connected by the torsion |
| parameters | (vector< double >) the list of parameters for the new torsion |
| def getEnergyFunction | ( | self | ) |
getEnergyFunction(self) -> std::string const &
Get the algebraic expression that gives the interaction energy for each torsion
| def getGlobalParameterDefaultValue | ( | self, | |
| index | |||
| ) |
getGlobalParameterDefaultValue(self, index) -> double
Get the default value of a global parameter.
| index | (int) the index of the parameter for which to get the default value |
| def getGlobalParameterName | ( | self, | |
| index | |||
| ) |
getGlobalParameterName(self, index) -> std::string const &
Get the name of a global parameter.
| index | (int) 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, | |
| index | |||
| ) |
getPerTorsionParameterName(self, index) -> std::string const &
Get the name of a per-torsion parameter.
| index | (int) the index of the parameter for which to get the name |
| def getTorsionParameters | ( | self, | |
| index | |||
| ) |
Get the force field parameters for a torsion term.
| index | (int) the index of the torsion for which to get parameters |
| def setEnergyFunction | ( | self, | |
| energy | |||
| ) |
Set the algebraic expression that gives the interaction energy for each torsion.
| def setGlobalParameterDefaultValue | ( | self, | |
| index, | |||
| defaultValue | |||
| ) |
Set the default value of a global parameter.
| index | (int) the index of the parameter for which to set the default value |
| defaultValue | (double) the default value of the parameter |
| def setGlobalParameterName | ( | self, | |
| index, | |||
| name | |||
| ) |
Set the name of a global parameter.
| index | (int) the index of the parameter for which to set the name |
| name | (string) the name of the parameter |
| def setPerTorsionParameterName | ( | self, | |
| index, | |||
| name | |||
| ) |
Set the name of a per-torsion parameter.
| index | (int) the index of the parameter for which to set the name |
| name | (string) the name of the parameter |
| def setTorsionParameters | ( | self, | |
| args | |||
| ) |
Set the force field parameters for a torsion term.
| index | (int) the index of the torsion for which to set parameters |
| particle1 | (int) the index of the first particle connected by the torsion |
| particle2 | (int) the index of the second particle connected by the torsion |
| particle3 | (int) the index of the third particle connected by the torsion |
| particle4 | (int) the index of the fourth particle connected by the torsion |
| parameters | (vector< double >) the list of parameters for the torsion |
| def updateParametersInContext | ( | self, | |
| context | |||
| ) |
Update the per-torsion 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 setTorsionParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.
This method has several limitations. The only information it updates is the values of per-torsion 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 torsion cannot be changed, nor can new torsions be added.
| def usesPeriodicBoundaryConditions | ( | self | ) |
usesPeriodicBoundaryConditions(self) -> bool
Returns whether or not this force makes use of periodic boundary conditions.
Reimplemented from Force.
1.7.6.1