AmoebaTorsionTorsionForce Class Reference
This class implements the Amoeba torsion-torsion interaction To use it, create a TorsionTorsionForce object then call addTorsionTorsion() once for each torsionTorsion. More...
Public Member Functions | |
| def | getNumTorsionTorsions |
| getNumTorsionTorsions(self) -> int | |
| def | getNumTorsionTorsionGrids |
| getNumTorsionTorsionGrids(self) -> int | |
| def | addTorsionTorsion |
| addTorsionTorsion(self, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) -> int | |
| def | getTorsionTorsionParameters |
| getTorsionTorsionParameters(self, int index) | |
| def | setTorsionTorsionParameters |
| setTorsionTorsionParameters(self, int index, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) | |
| def | getTorsionTorsionGrid |
| getTorsionTorsionGrid(self, int index) -> vectorddd | |
| def | setTorsionTorsionGrid |
| setTorsionTorsionGrid(self, int index, vectorddd grid) | |
| def | __init__ |
| __init__(self) -> AmoebaTorsionTorsionForce __init__(self, AmoebaTorsionTorsionForce other) -> AmoebaTorsionTorsionForce | |
| def | __del__ |
| __del__(self) | |
Public Attributes | |
| this | |
Detailed Description
This class implements the Amoeba torsion-torsion interaction To use it, create a TorsionTorsionForce object then call addTorsionTorsion() once for each torsionTorsion.
After a torsionTorsion has been added, you can modify its force field parameters by calling setTorsionTorsionParameters().
Member Function Documentation
| def __del__ | ( | self | ) |
__del__(self)
Reimplemented from Force.
| def __init__ | ( | self, | ||
| args | ||||
| ) |
__init__(self) -> AmoebaTorsionTorsionForce __init__(self, AmoebaTorsionTorsionForce other) -> AmoebaTorsionTorsionForce
Create a Amoeba TorsionTorsionForce.
| def addTorsionTorsion | ( | self, | ||
| args | ||||
| ) |
addTorsionTorsion(self, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) -> int
Add a torsionTorsion term to the force field.
- Parameters:
-
particle1 the index of the first particle connected by the torsionTorsion particle2 the index of the second particle connected by the torsionTorsion particle3 the index of the third particle connected by the torsionTorsion particle4 the index of the fourth particle connected by the torsionTorsion particle5 the index of the fifth particle connected by the torsionTorsion chiralCheckAtomIndex the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check gridIndex the index to the grid to be used
| def getNumTorsionTorsionGrids | ( | self | ) |
getNumTorsionTorsionGrids(self) -> int
Get the number of torsionTorsion grids
| def getNumTorsionTorsions | ( | self | ) |
getNumTorsionTorsions(self) -> int
Get the number of torsionTorsion terms in the potential function
| def getTorsionTorsionGrid | ( | self, | ||
| args | ||||
| ) |
getTorsionTorsionGrid(self, int index) -> vectorddd
Get the torsion-torsion grid at the specified index
- Parameters:
-
gridIndex the grid index
| def getTorsionTorsionParameters | ( | self, | ||
| args | ||||
| ) |
getTorsionTorsionParameters(self, int index)
Get the force field parameters for a torsionTorsion term.
- Parameters:
-
index the index of the torsionTorsion for which to get parameters particle1 the index of the first particle connected by the torsionTorsion particle2 the index of the second particle connected by the torsionTorsion particle3 the index of the third particle connected by the torsionTorsion particle4 the index of the fourth particle connected by the torsionTorsion particle5 the index of the fifth particle connected by the torsionTorsion chiralCheckAtomIndex the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check gridIndex the grid index
| def setTorsionTorsionGrid | ( | self, | ||
| args | ||||
| ) |
setTorsionTorsionGrid(self, int index, vectorddd grid)
Set the torsion-torsion grid at the specified index
- Parameters:
-
index the index of the torsionTorsion for which to get parameters grid grid grid[x][y][0] = x value grid[x][y][1] = y value grid[x][y][2] = function value grid[x][y][3] = dfdx value grid[x][y][4] = dfdy value grid[x][y][5] = dfd(xy) value
| def setTorsionTorsionParameters | ( | self, | ||
| args | ||||
| ) |
setTorsionTorsionParameters(self, int index, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex)
Set the force field parameters for a torsionTorsion term.
- Parameters:
-
index the index of the torsionTorsion for which to set parameters particle1 the index of the first particle connected by the torsionTorsion particle2 the index of the second particle connected by the torsionTorsion particle3 the index of the third particle connected by the torsionTorsion particle4 the index of the fourth particle connected by the torsionTorsion particle5 the index of the fifth particle connected by the torsionTorsion chiralCheckAtomIndex the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check gridIndex the grid index
Member Data Documentation
The documentation for this class was generated from the following file:
- openmm.py
