CMAPTorsionForce Class Reference

This class implements an interaction between pairs of dihedral angles. More...

Inheritance diagram for CMAPTorsionForce:

List of all members.

Public Member Functions
def	getNumMaps
	getNumMaps(self) -> int
def	getNumTorsions
	getNumTorsions(self) -> int
def	addMap
	addMap(self, size, energy) -> int
def	getMapParameters
	Get the energy values of a map.
def	setMapParameters
	Set the energy values of a map.
def	addTorsion
	addTorsion(self, map, a1, a2, a3, a4, b1, b2, b3, b4) -> int
def	getTorsionParameters
	Get the force field parameters for a CMAP torsion term.
def	setTorsionParameters
	Set the force field parameters for a CMAP torsion term.
def	updateParametersInContext
	Update the map and torsion parameters in a Context to match those stored in this Force object.
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(self) -> bool
def	__init__
	__init__(self) -> CMAPTorsionForce __init__(self, other) -> CMAPTorsionForce
Public Attributes
	this

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Detailed Description

This class implements an interaction between pairs of dihedral angles.

The interaction energy is defined by an "energy correction map" (CMAP), which is simply a set of tabulated energy values on a regular grid of (phi, psi) angles. Natural cubic spline interpolation is used to compute forces and energies at arbitrary values of the two angles.

To use this class, first create one or more energy correction maps by calling addMap(). For each one, you provide an array of energies at uniformly spaced values of the two angles. Next, add interactions by calling addTorsion(). For each one, you specify the sequence of particles used to calculate each of the two dihedral angles, and the index of the map used to calculate their interaction energy.

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Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

__init__(self) -> CMAPTorsionForce __init__(self, other) -> CMAPTorsionForce

Create a CMAPTorsionForce.

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Member Function Documentation

def addMap	(		self,
			size,
			energy
	)

addMap(self, size, energy) -> int

Create a new map that can be used for torsion pairs.

Parameters:

size	(int) the size of the map along each dimension
energy	(vector< double >) the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.

Returns:

(int) the index of the map that was added

def addTorsion	(		self,
			map,
			a1,
			a2,
			a3,
			a4,
			b1,
			b2,
			b3,
			b4
	)

addTorsion(self, map, a1, a2, a3, a4, b1, b2, b3, b4) -> int

Add a CMAP torsion term to the force field.

Parameters:

map	(int) the index of the map to use for this term
a1	(int) the index of the first particle forming the first torsion
a2	(int) the index of the second particle forming the first torsion
a3	(int) the index of the third particle forming the first torsion
a4	(int) the index of the fourth particle forming the first torsion
b1	(int) the index of the first particle forming the second torsion
b2	(int) the index of the second particle forming the second torsion
b3	(int) the index of the third particle forming the second torsion
b4	(int) the index of the fourth particle forming the second torsion

Returns:

(int) the index of the torsion that was added

def getMapParameters	(		self,
			index
	)

Get the energy values of a map.

Parameters:

index

(int) the index of the map for which to get energy values

Returns:

(int) the size of the map along each dimension

(vector< double >) the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.

def getNumMaps

(

self

)

getNumMaps(self) -> int

Get the number of maps that have been defined.

def getNumTorsions

(

self

)

getNumTorsions(self) -> int

Get the number of CMAP torsion terms in the potential function

def getTorsionParameters	(		self,
			index
	)

Get the force field parameters for a CMAP torsion term.

Parameters:

index

(int) the index of the torsion for which to get parameters

Returns:

(int) the index of the map to use for this term

(int) the index of the first particle forming the first torsion

(int) the index of the second particle forming the first torsion

(int) the index of the third particle forming the first torsion

(int) the index of the fourth particle forming the first torsion

(int) the index of the first particle forming the second torsion

(int) the index of the second particle forming the second torsion

(int) the index of the third particle forming the second torsion

(int) the index of the fourth particle forming the second torsion

def setMapParameters	(		self,
			index,
			size,
			energy
	)

Set the energy values of a map.

Parameters:

index	(int) the index of the map for which to set energy values
size	(int) the size of the map along each dimension
energy	(vector< double >) the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.

def setTorsionParameters	(		self,
			index,
			map,
			a1,
			a2,
			a3,
			a4,
			b1,
			b2,
			b3,
			b4
	)

Set the force field parameters for a CMAP torsion term.

Parameters:

index	(int) the index of the torsion for which to set parameters
map	(int) the index of the map to use for this term
a1	(int) the index of the first particle forming the first torsion
a2	(int) the index of the second particle forming the first torsion
a3	(int) the index of the third particle forming the first torsion
a4	(int) the index of the fourth particle forming the first torsion
b1	(int) the index of the first particle forming the second torsion
b2	(int) the index of the second particle forming the second torsion
b3	(int) the index of the third particle forming the second torsion
b4	(int) the index of the fourth particle forming the second torsion

def updateParametersInContext	(		self,
			context
	)

Update the map and 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 setMapParameters() and setTorsionParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.

The only information that can be updated with this method is the energy values for a map, and the map index for a torsion. The size of a map and the set of particles involved in a torsion cannot be changed. Also, new bonds and torsions cannot be added.

def usesPeriodicBoundaryConditions

(

self

)

usesPeriodicBoundaryConditions(self) -> bool

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

Returns:

(bool) false

Reimplemented from Force.

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Member Data Documentation

this

Reimplemented from Force.

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The documentation for this class was generated from the following file:

• openmm.py