ForceField Class
The Class for Force Field
Constructor
ForceField
()
Item Index
Methods
Methods
getConformers
-
mol
Get coordinates for all conformers and attach data to molecule.
Parameters:
-
molMolecule
Returns:
Returns true on success
getCoordinates
-
mol
Get coordinates for current conformer and attach data to molecule.
Parameters:
-
molMolecule
Returns:
Returns true on success
getLineSearchType
()
Number
Get the LineSearchType
Returns:
The current LineSearchType
prepareAtomTypes
()
Boolean
Get the force atom types. The atom types will be added to the atoms data.
Returns:
Returns true on success
preparePartialCharges
()
Boolean
Get the force field formal charges. The formal charges will be added to the atoms of mol as data.
Returns:
Returns true on success
randomRotorSearch
-
conformers -
[steps=2500]
Generate conformers for the molecule (randomly rotating torsions).
The initial starting structure here is important, this structure should be minimized for the best results. randomRotorSearch works by randomly rotating around the rotatable bonds in a molecule.
Parameters:
-
conformersNumberNumber of random conformers to consider.
-
[steps=2500]Number optionalNumber of steps during geometry optimization.
Returns:
Returns this
randomRotorSearchInitialize
-
conformers -
[steps=2500]
Generate conformers for the molecule by randomly rotating torsions. To be used in combination with randomRotorSearchNexConformer().
Parameters:
-
conformersNumberNumber of random conformers to consider.
-
[steps=2500]Number optionalNumber of steps during geometry optimization.
Returns:
Returns this
Example:
ff.randomRotorSearchInitialize(300);
while (ff.randomRotorSearchNexConformer(300)) {
// do some updating (show last generated conformer, ...)
}randomRotorSearchNextConformer
-
[steps=2500]
Evaluate the next conformer
Parameters:
-
[steps=2500]Number optionalNumber of steps during geometry optimization.
Returns:
Returns true if there are more conformers
setLineSearchType
-
type
Generate conformers for the molecule (randomly rotating torsions).
Parameters:
-
typeNumberThe LineSearchType to be used.
Returns:
Returns this
Example:
ff.setLineSearchType(ob.LineSearchType.Newton2Num)setup
-
mol
Setup the forcefield for mol (assigns atom types, charges, etc.). Keep current constraints.
Parameters:
-
molMoleculeThe molecule to be set up
Returns:
Returns the result
systematicRotorSearch
-
[steps=2500]
Generate conformers for the molecule (systematicaly rotating torsions).
The initial starting structure here is important, this structure should be minimized for the best results. systematicRotorSearch works by rotating around the rotatable bond in a molecule. This rotating generates multiple conformers. The energy for all these conformers is then evaluated and the lowest energy conformer is selected.
Parameters:
-
[steps=2500]Number optionalNumber of steps during geometry optimization.
Returns:
Returns this
systematicRotorSearchInitialize
-
[steps=2500]
Generate conformers for the molecule by systematicaly rotating torsions. To be used in combination with systematicRotorSearchNexConformer().
Parameters:
-
[steps=2500]Number optionalNumber of steps during geometry optimization.
Returns:
The number of conformers
Example:
ff.systematicRotorSearchInitialize(300);
while (ff.systematicRotorSearchNextConformer(300)) {
// do some updating (show last generated conformer, ...)
}systematicRotorSearchNextConformer
-
[steps=2500]
Evaluate the next conformer.
Parameters:
-
[steps=2500]Number optionalNumber of steps during geometry optimization.
Returns:
Returns true if there are more conformers
weightedRotorSearch
-
conformers -
[steps=2500]
Generate conformers for the molecule (randomly rotating torsions).
Parameters:
-
conformersNumberNumber of random conformers to consider.
-
[steps=2500]Number optionalNumber of steps during geometry optimization.
Returns:
Returns this