AmoebaTorsionTorsionForce Class Reference

This class implements the Amoeba torsion-torsion interaction. More...

Inheritance diagram for AmoebaTorsionTorsionForce:

List of all members.

Public Member Functions
def	getNumTorsionTorsions
	getNumTorsionTorsions(self) -> int
def	getNumTorsionTorsionGrids
	getNumTorsionTorsionGrids(self) -> int
def	addTorsionTorsion
	addTorsionTorsion(self, particle1, particle2, particle3, particle4, particle5, chiralCheckAtomIndex, gridIndex) -> int
def	getTorsionTorsionParameters
	Get the force field parameters for a torsion-torsion term.
def	setTorsionTorsionParameters
	Set the force field parameters for a torsion-torsion term.
def	getTorsionTorsionGrid
	getTorsionTorsionGrid(self, index) -> vectorddd
def	setTorsionTorsionGrid
	Set the torsion-torsion grid at the specified index.
def	usesPeriodicBoundaryConditions
	usesPeriodicBoundaryConditions(self) -> bool
def	__init__
	__init__(self) -> AmoebaTorsionTorsionForce __init__(self, other) -> AmoebaTorsionTorsionForce
Public Attributes
	this

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Detailed Description

This class implements the Amoeba torsion-torsion interaction.

To use it, create an AmoebaTorsionTorsionForce object then call addTorsionTorsion() once for each torsion-torsion. After a torsion-torsion has been added, you can modify its force field parameters by calling setTorsionTorsionParameters().

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Constructor & Destructor Documentation

def __init__	(		self,
			args
	)

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

Create an AmoebaTorsionTorsionForce.

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Member Function Documentation

def addTorsionTorsion	(		self,
			particle1,
			particle2,
			particle3,
			particle4,
			particle5,
			chiralCheckAtomIndex,
			gridIndex
	)

addTorsionTorsion(self, particle1, particle2, particle3, particle4, particle5, chiralCheckAtomIndex, gridIndex) -> int

Add a torsion-torsion term to the force field.

Parameters:

particle1	(int) the index of the first particle connected by the torsion-torsion
particle2	(int) the index of the second particle connected by the torsion-torsion
particle3	(int) the index of the third particle connected by the torsion-torsion
particle4	(int) the index of the fourth particle connected by the torsion-torsion
particle5	(int) the index of the fifth particle connected by the torsion-torsion
chiralCheckAtomIndex	(int) the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
gridIndex	(int) the index to the grid to be used

Returns:

(int) the index of the torsion-torsion that was added

def getNumTorsionTorsionGrids

(

self

)

getNumTorsionTorsionGrids(self) -> int

Get the number of torsion-torsion grids

def getNumTorsionTorsions

(

self

)

getNumTorsionTorsions(self) -> int

Get the number of torsion-torsion terms in the potential function

def getTorsionTorsionGrid	(		self,
			index
	)

getTorsionTorsionGrid(self, index) -> vectorddd

Get the torsion-torsion grid at the specified index

Parameters:

index

(int) the grid index

Returns:

(vector< std::vector< std::vector< double > > >) grid return grid reference

def getTorsionTorsionParameters	(		self,
			index
	)

Get the force field parameters for a torsion-torsion term.

Parameters:

index

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

Returns:

(int) the index of the first particle connected by the torsion-torsion

(int) the index of the second particle connected by the torsion-torsion

(int) the index of the third particle connected by the torsion-torsion

(int) the index of the fourth particle connected by the torsion-torsion

(int) the index of the fifth particle connected by the torsion-torsion

(int) the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check

(int) the grid index

def setTorsionTorsionGrid	(		self,
			index,
			grid
	)

Set the torsion-torsion grid at the specified index.

Parameters:

index	(int) the index of the torsion-torsion for which to get parameters
grid	(vector< std::vector< std::vector< double > > >) either 3 or 6 values may be specified per grid point. If the derivatives are omitted, they are calculated automatically by fitting a 2D spline to the energies. grid[x][y][0] = x value grid[x][y][1] = y value grid[x][y][2] = energy grid[x][y][3] = dEdx value grid[x][y][4] = dEdy value grid[x][y][5] = dEd(xy) value

def setTorsionTorsionParameters	(		self,
			index,
			particle1,
			particle2,
			particle3,
			particle4,
			particle5,
			chiralCheckAtomIndex,
			gridIndex
	)

Set the force field parameters for a torsion-torsion term.

Parameters:

index	(int) the index of the torsion-torsion for which to set parameters
particle1	(int) the index of the first particle connected by the torsion-torsion
particle2	(int) the index of the second particle connected by the torsion-torsion
particle3	(int) the index of the third particle connected by the torsion-torsion
particle4	(int) the index of the fourth particle connected by the torsion-torsion
particle5	(int) the index of the fifth particle connected by the torsion-torsion
chiralCheckAtomIndex	(int) the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
gridIndex	(int) the grid index

def usesPeriodicBoundaryConditions

(

self

)

usesPeriodicBoundaryConditions(self) -> bool

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

Returns:

(bool) true if nonbondedMethod uses PBC and false otherwise

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