AmoebaOutOfPlaneBendForce

class simtk.openmm.openmm.AmoebaOutOfPlaneBendForce(*args)

This class implements the Amoeba out-of-plane bend interaction.

To use it, create an OutOfPlaneBendForce object then call addOutOfPlaneBend() once for each outOfPlaneBend. After an out-of-plane bend has been added, you can modify its force field parameters by calling setOutOfPlaneBendParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

__init__(self) → AmoebaOutOfPlaneBendForce

__init__(self, other) -> AmoebaOutOfPlaneBendForce

Create an AmoebaOutOfPlaneBendForce.

Methods

__init__((self) -> AmoebaOutOfPlaneBendForce) __init__(self, other) -> AmoebaOutOfPlaneBendForce
addOutOfPlaneBend((self, particle1, ...) Add an out-of-plane bend term to the force field.
getAmoebaGlobalOutOfPlaneBendCubic(...) Get the global cubic term
getAmoebaGlobalOutOfPlaneBendPentic(...) Get the global pentic term
getAmoebaGlobalOutOfPlaneBendQuartic(...) Get the global quartic term
getAmoebaGlobalOutOfPlaneBendSextic(...) Get the global sextic term
getForceGroup((self) -> int) Get the force group this Force belongs to.
getNumOutOfPlaneBends((self) -> int) Get the number of out-of-plane bend terms in the potential function
getOutOfPlaneBendParameters(self, index) Get the force field parameters for an out-of-plane bend term.
setAmoebaGlobalOutOfPlaneBendCubic(self, cubicK) Set the global cubic term
setAmoebaGlobalOutOfPlaneBendPentic(self, ...) Set the global pentic term
setAmoebaGlobalOutOfPlaneBendQuartic(self, ...) Set the global cubic term
setAmoebaGlobalOutOfPlaneBendSextic(self, ...) Set the global sextic term
setForceGroup(self, group) Set the force group this Force belongs to.
setOutOfPlaneBendParameters(self, index, ...) Set the force field parameters for an out-of-plane bend term.
setUsesPeriodicBoundaryConditions(self, periodic) Set whether this force should apply periodic boundary conditions when calculating displacements.
updateParametersInContext(self, context) Update the per-bend term parameters in a Context to match those stored in this Force object.
usesPeriodicBoundaryConditions((self) -> bool) Returns whether or not this force makes use of periodic boundary conditions.
getNumOutOfPlaneBends(self) → int

Get the number of out-of-plane bend terms in the potential function

setAmoebaGlobalOutOfPlaneBendCubic(self, cubicK)

Set the global cubic term

Parameters:cubicK (double) – the cubic force constant for the angle
getAmoebaGlobalOutOfPlaneBendCubic(self) → double

Get the global cubic term

Returns:global cubicK term
Return type:double
setAmoebaGlobalOutOfPlaneBendQuartic(self, quarticK)

Set the global cubic term

Parameters:quarticK (double) – the quartic force constant for the angle
getAmoebaGlobalOutOfPlaneBendQuartic(self) → double

Get the global quartic term

Returns:global quartic term
Return type:double
setAmoebaGlobalOutOfPlaneBendPentic(self, penticK)

Set the global pentic term

Parameters:penticK (double) – the pentic force constant for the angle
getAmoebaGlobalOutOfPlaneBendPentic(self) → double

Get the global pentic term

Returns:global penticK term
Return type:double
setAmoebaGlobalOutOfPlaneBendSextic(self, sexticK)

Set the global sextic term

Parameters:sexticK (double) – the sextic force constant for the angle
getAmoebaGlobalOutOfPlaneBendSextic(self) → double

Get the global sextic term

Returns:global sexticK term
Return type:double
addOutOfPlaneBend(self, particle1, particle2, particle3, particle4, k) → int

Add an out-of-plane bend term to the force field.

Parameters:
  • particle1 (int) – the index of the first particle connected by the outOfPlaneBend
  • particle2 (int) – the index of the second particle connected by the outOfPlaneBend
  • particle3 (int) – the index of the third particle connected by the outOfPlaneBend
  • particle4 (int) – the index of the fourth particle connected by the outOfPlaneBend
  • k (double) – the force constant for the out-of-plane bend
Returns:

the index of the out-of-plane bend that was added

Return type:

int

getOutOfPlaneBendParameters(self, index)

Get the force field parameters for an out-of-plane bend term.

Parameters:index (int) – the index of the outOfPlaneBend for which to get parameters
Returns:
  • particle1 (int) – the index of the first particle connected by the outOfPlaneBend
  • particle2 (int) – the index of the second particle connected by the outOfPlaneBend
  • particle3 (int) – the index of the third particle connected by the outOfPlaneBend
  • particle4 (int) – the index of the fourth particle connected by the outOfPlaneBend
  • k (double) – the force constant for the out-of-plane bend
setOutOfPlaneBendParameters(self, index, particle1, particle2, particle3, particle4, k)

Set the force field parameters for an out-of-plane bend term.

Parameters:
  • index (int) – the index of the outOfPlaneBend for which to set parameters
  • particle1 (int) – the index of the first particle connected by the outOfPlaneBend
  • particle2 (int) – the index of the second particle connected by the outOfPlaneBend
  • particle3 (int) – the index of the third particle connected by the outOfPlaneBend
  • particle4 (int) – the index of the fourth particle connected by the outOfPlaneBend
  • k (double) – the force constant for the out-of-plane bend
updateParametersInContext(self, context)

Update the per-bend term 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 setOutOfPlaneBendParameters() 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-bend term parameters. The set of particles involved in a term cannot be changed, nor can new terms be added.

setUsesPeriodicBoundaryConditions(self, periodic)

Set whether this force should apply periodic boundary conditions when calculating displacements. Usually this is not appropriate for bonded forces, but there are situations when it can be useful.

usesPeriodicBoundaryConditions(self) → bool

Returns whether or not this force makes use of periodic boundary conditions.

Returns:true if force uses PBC and false otherwise
Return type:bool
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__sizeof__() → int

size of object in memory, in bytes

__str__
getForceGroup(self) → int

Get the force group this Force belongs to.

setForceGroup(self, group)

Set the force group this Force belongs to.

Parameters:group (int) – the group index. Legal values are between 0 and 31 (inclusive).