Class Mmff
java.lang.Object
org.openscience.cdk.forcefield.mmff.Mmff
Facade to access Merck Molecular Force Field (MMFF) functions.
Atom Types Symbolic atom types are assigned with
Partial Charges Partial charges are assigned with
- [T. A. Halgren. J. Comput. Chem. 1996. 17]
- [T. A. Halgren. J. Comput. Chem. 1996. 17]
- [T. A. Halgren. J. Comput. Chem. 1996. 17]
- [T. A. Halgren. J. Comput. Chem. 1996. 17]
- [T. A. Halgren. J. Comput. Chem. 1996. 17]
Atom Types Symbolic atom types are assigned with
assignAtomTypes(IAtomContainer)
.
The atom type name can be accessed with IAtomType.getAtomTypeName()
.
Partial Charges Partial charges are assigned with
partialCharges(IAtomContainer)
.
Atom types must be assigned before calling this function. Effective formal
charges can also be obtained with effectiveCharges(IAtomContainer)
both charge values are accessed with IAtom.getCharge()
. Atoms of
unknown type are assigned a neutral charge - to avoid this check the return
value of assignAtomTypes(IAtomContainer)
.
IAtomContainer mol = ...;
Mmff mmff = new Mmff();
mmff.assignAtomTypes(mol);
mmff.partialCharges(mol);
mmff.clearProps(mol); // optional
- Author:
- John May
- Source code:
- main
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionboolean
Assign MMFF Symbolic atom types.void
clearProps
(IAtomContainer mol) Clear all transient properties assigned by this class.boolean
Assign the effective formal charges used by MMFF in calculating the final partial charge values.boolean
Assign the partial charges, all existing charges are cleared.
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Constructor Details
-
Mmff
public Mmff()
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-
Method Details
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assignAtomTypes
Assign MMFF Symbolic atom types. The symbolic type can be accessed withIAtomType.getAtomTypeName()
. An atom of unknown type is assigned the symbolic type'UNK'
. All atoms, including hydrogens must be explicitly represented.- Parameters:
mol
- molecule- Returns:
- all atoms had a type assigned
-
effectiveCharges
Assign the effective formal charges used by MMFF in calculating the final partial charge values. Atom types must be assigned first. All existing charges are cleared.- Parameters:
mol
- molecule- Returns:
- charges were assigned
- See Also:
-
partialCharges
Assign the partial charges, all existing charges are cleared. Atom types must be assigned first.- Parameters:
mol
- molecule- Returns:
- charges were assigned
- See Also:
-
clearProps
Clear all transient properties assigned by this class. Assigned charges and atom type names remain set.- Parameters:
mol
- molecule
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