OpenMM
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

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().


Constructor & Destructor Documentation

def __init__ (   self,
  args 
)

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

Create an AmoebaTorsionTorsionForce.


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

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.


Member Data Documentation

Reimplemented from Force.


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