CMAPTorsionForce Class Reference
This class implements an interaction between pairs of dihedral angles. More...
Public Member Functions | |
| def | getNumMaps |
| getNumMaps(self) -> int | |
| def | getNumTorsions |
| getNumTorsions(self) -> int | |
| def | addMap |
| addMap(self, int size, vectord energy) -> int | |
| def | getMapParameters |
| getMapParameters(self, int index) | |
| def | setMapParameters |
| setMapParameters(self, int index, int size, vectord energy) | |
| def | addTorsion |
| addTorsion(self, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4) -> int | |
| def | getTorsionParameters |
| getTorsionParameters(self, int index) | |
| def | setTorsionParameters |
| setTorsionParameters(self, int index, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4) | |
| def | __init__ |
| __init__(self) -> CMAPTorsionForce __init__(self, CMAPTorsionForce other) -> CMAPTorsionForce | |
| def | __del__ |
| __del__(self) | |
Public Attributes | |
| this | |
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.
Member Function Documentation
| def __del__ | ( | self | ) |
__del__(self)
Reimplemented from Force.
| def __init__ | ( | self, | ||
| args | ||||
| ) |
__init__(self) -> CMAPTorsionForce __init__(self, CMAPTorsionForce other) -> CMAPTorsionForce
Create a CMAPTorsionForce.
| def addMap | ( | self, | ||
| args | ||||
| ) |
addMap(self, int size, vectord energy) -> int
Create a new map that can be used for torsion pairs.
- Parameters:
-
size the size of the map along each dimension energy 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 addTorsion | ( | self, | ||
| args | ||||
| ) |
addTorsion(self, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4) -> int
Add a CMAP torsion term to the force field.
- Parameters:
-
map the index of the map to use for this term a1 the index of the first particle forming the first torsion a2 the index of the second particle forming the first torsion a3 the index of the third particle forming the first torsion a4 the index of the fourth particle forming the first torsion b1 the index of the first particle forming the second torsion b2 the index of the second particle forming the second torsion b3 the index of the third particle forming the second torsion b4 the index of the fourth particle forming the second torsion
| def getMapParameters | ( | self, | ||
| args | ||||
| ) |
getMapParameters(self, int index)
Get the energy values of a map.
- Parameters:
-
index the index of the map for which to get energy values size the size of the map along each dimension energy 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, | ||
| args | ||||
| ) |
getTorsionParameters(self, int index)
Get the force field parameters for a CMAP torsion term.
- Parameters:
-
index the index of the torsion for which to get parameters map the index of the map to use for this term a1 the index of the first particle forming the first torsion a2 the index of the second particle forming the first torsion a3 the index of the third particle forming the first torsion a4 the index of the fourth particle forming the first torsion b1 the index of the first particle forming the second torsion b2 the index of the second particle forming the second torsion b3 the index of the third particle forming the second torsion b4 the index of the fourth particle forming the second torsion
| def setMapParameters | ( | self, | ||
| args | ||||
| ) |
setMapParameters(self, int index, int size, vectord energy)
Set the energy values of a map.
- Parameters:
-
index the index of the map for which to set energy values size the size of the map along each dimension energy 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, | ||
| args | ||||
| ) |
setTorsionParameters(self, int index, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4)
Set the force field parameters for a CMAP torsion term.
- Parameters:
-
index the index of the torsion for which to set parameters map the index of the map to use for this term a1 the index of the first particle forming the first torsion a2 the index of the second particle forming the first torsion a3 the index of the third particle forming the first torsion a4 the index of the fourth particle forming the first torsion b1 the index of the first particle forming the second torsion b2 the index of the second particle forming the second torsion b3 the index of the third particle forming the second torsion b4 the index of the fourth particle forming the second torsion
Member Data Documentation
The documentation for this class was generated from the following file:
- openmm.py
