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OpenMM
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This class implements the Amoeba torsion-torsion interaction. More...
Inheritance diagram for AmoebaTorsionTorsionForce:Public Member Functions | |
| def | getNumTorsionTorsions |
| getNumTorsionTorsions(AmoebaTorsionTorsionForce self) -> int | |
| def | getNumTorsionTorsionGrids |
| getNumTorsionTorsionGrids(AmoebaTorsionTorsionForce self) -> int | |
| def | addTorsionTorsion |
| addTorsionTorsion(AmoebaTorsionTorsionForce self, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) -> int | |
| def | getTorsionTorsionParameters |
| getTorsionTorsionParameters(AmoebaTorsionTorsionForce self, int index) | |
| def | setTorsionTorsionParameters |
| setTorsionTorsionParameters(AmoebaTorsionTorsionForce self, int index, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) | |
| def | getTorsionTorsionGrid |
| getTorsionTorsionGrid(AmoebaTorsionTorsionForce self, int index) -> vectorddd | |
| def | setTorsionTorsionGrid |
| setTorsionTorsionGrid(AmoebaTorsionTorsionForce self, int index, vectorddd grid) | |
| def | __init__ |
| init(OpenMM::AmoebaTorsionTorsionForce self) -> AmoebaTorsionTorsionForce init(OpenMM::AmoebaTorsionTorsionForce self, AmoebaTorsionTorsionForce other) -> AmoebaTorsionTorsionForce | |
| def | __del__ |
| del(OpenMM::AmoebaTorsionTorsionForce self) | |
| Public Member Functions inherited from Force | |
| def | __init__ |
| def | __del__ |
| del(OpenMM::Force self) | |
| def | getForceGroup |
| getForceGroup(Force self) -> int | |
| def | setForceGroup |
| setForceGroup(Force self, int group) | |
| def | __copy__ |
| def | __deepcopy__ |
Public Attributes | |
| this | |
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().
| def __init__ | ( | self, | |
| args | |||
| ) |
init(OpenMM::AmoebaTorsionTorsionForce self) -> AmoebaTorsionTorsionForce init(OpenMM::AmoebaTorsionTorsionForce self, AmoebaTorsionTorsionForce other) -> AmoebaTorsionTorsionForce
Create an AmoebaTorsionTorsionForce.
| def __del__ | ( | self | ) |
del(OpenMM::AmoebaTorsionTorsionForce self)
| def addTorsionTorsion | ( | self, | |
| args | |||
| ) |
addTorsionTorsion(AmoebaTorsionTorsionForce self, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) -> int
Add a torsion-torsion term to the force field.
| particle1 | the index of the first particle connected by the torsion-torsion |
| particle2 | the index of the second particle connected by the torsion-torsion |
| particle3 | the index of the third particle connected by the torsion-torsion |
| particle4 | the index of the fourth particle connected by the torsion-torsion |
| particle5 | the index of the fifth particle connected by the torsion-torsion |
| 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(AmoebaTorsionTorsionForce self) -> int
Get the number of torsion-torsion grids
| def getNumTorsionTorsions | ( | self | ) |
getNumTorsionTorsions(AmoebaTorsionTorsionForce self) -> int
Get the number of torsion-torsion terms in the potential function
| def getTorsionTorsionGrid | ( | self, | |
| args | |||
| ) |
getTorsionTorsionGrid(AmoebaTorsionTorsionForce self, int index) -> vectorddd
Get the torsion-torsion grid at the specified index
| gridIndex | the grid index |
| def getTorsionTorsionParameters | ( | self, | |
| args | |||
| ) |
getTorsionTorsionParameters(AmoebaTorsionTorsionForce self, int index)
Get the force field parameters for a torsion-torsion term.
| index | the index of the torsion-torsion for which to get parameters |
| particle1 | the index of the first particle connected by the torsion-torsion |
| particle2 | the index of the second particle connected by the torsion-torsion |
| particle3 | the index of the third particle connected by the torsion-torsion |
| particle4 | the index of the fourth particle connected by the torsion-torsion |
| particle5 | the index of the fifth particle connected by the torsion-torsion |
| 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(AmoebaTorsionTorsionForce self, int index, vectorddd grid)
Set the torsion-torsion grid at the specified index
| index | the index of the torsion-torsion 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(AmoebaTorsionTorsionForce self, int index, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex)
Set the force field parameters for a torsion-torsion term.
| index | the index of the torsion-torsion for which to set parameters |
| particle1 | the index of the first particle connected by the torsion-torsion |
| particle2 | the index of the second particle connected by the torsion-torsion |
| particle3 | the index of the third particle connected by the torsion-torsion |
| particle4 | the index of the fourth particle connected by the torsion-torsion |
| particle5 | the index of the fifth particle connected by the torsion-torsion |
| chiralCheckAtomIndex | the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check |
| gridIndex | the grid index |
| this |
1.8.2 
