Class Mmff
- java.lang.Object
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- org.openscience.cdk.forcefield.mmff.Mmff
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public class Mmff extends Object
Facade to access Merck Molecular Force Field (MMFF) functions.- [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 withassignAtomTypes(IAtomContainer)
. The atom type name can be accessed withIAtomType.getAtomTypeName()
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Partial Charges Partial charges are assigned withpartialCharges(IAtomContainer)
. Atom types must be assigned before calling this function. Effective formal charges can also be obtained witheffectiveCharges(IAtomContainer)
both charge values are accessed withIAtom.getCharge()
. Atoms of unknown type are assigned a neutral charge - to avoid this check the return value ofassignAtomTypes(IAtomContainer)
.IAtomContainer mol = ...; Mmff mmff = new Mmff(); mmff.assignAtomTypes(mol); mmff.partialCharges(mol); mmff.clearProps(mol); // optional
- Author:
- John May
- Source code:
- main
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Constructor Summary
Constructors Constructor Description Mmff()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
assignAtomTypes(IAtomContainer mol)
Assign MMFF Symbolic atom types.void
clearProps(IAtomContainer mol)
Clear all transient properties assigned by this class.boolean
effectiveCharges(IAtomContainer mol)
Assign the effective formal charges used by MMFF in calculating the final partial charge values.boolean
partialCharges(IAtomContainer mol)
Assign the partial charges, all existing charges are cleared.
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Method Detail
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assignAtomTypes
public boolean assignAtomTypes(IAtomContainer mol)
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
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effectiveCharges
public boolean effectiveCharges(IAtomContainer mol)
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(IAtomContainer)
,assignAtomTypes(IAtomContainer)
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partialCharges
public boolean partialCharges(IAtomContainer mol)
Assign the partial charges, all existing charges are cleared. Atom types must be assigned first.- Parameters:
mol
- molecule- Returns:
- charges were assigned
- See Also:
effectiveCharges(IAtomContainer)
,assignAtomTypes(IAtomContainer)
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clearProps
public void clearProps(IAtomContainer mol)
Clear all transient properties assigned by this class. Assigned charges and atom type names remain set.- Parameters:
mol
- molecule
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