Package org.openscience.cdk.forcefield.mmff

Class Mmff

java.lang.Object

org.openscience.cdk.forcefield.mmff.Mmff

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 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

Constructor	Description
Mmff()

Method Summary

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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Mmff

public Mmff()

Method Detail

assignAtomTypes

public boolean assignAtomTypes(IAtomContainer mol)

Assign MMFF Symbolic atom types. The symbolic type can be accessed with IAtomType.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

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)

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)

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