The calculation of the MMFF94 partial charges. Charges are stored as atom
properties ("MMFF94charge") for an AtomContainer ac, values are calculated with:
HydrogenAdder hAdder = new HydrogenAdder();
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer ac = sp.parseSmiles("CC");
hAdder.addExplicitHydrogensToSatisfyValency((Molecule)ac);
MMFF94PartialCharges mmff = new MMFF94PartialCharges();
mmff.assignMMFF94PartialCharges(ac);
and for each atom, the value is given by:
( (Double)atom.getProperty("MMFF94charge") ).doubleValue().
Note: This class delegates to
Mmff and charges are also assigned
directly to the atom attribute
IAtom#getCharge().