[Cdk-user] AtomContainerManipulator and percieveAtomTypesAndConfigureAtoms

[Syed A. R. <as...@eb...>]

Hello,

Please update the code in AtomContainerManipulator as 
percieveAtomTypesAndConfigureAtoms tries to configure PseudoAtoms (i.e. 
"R" etc) leading to modifications in the original molecule.

This update will skip PseudoAtom configuration.

public static void percieveAtomTypesAndConfigureAtoms(IAtomContainer 
container) throws CDKException {
        CDKAtomTypeMatcher matcher = 
CDKAtomTypeMatcher.getInstance(container.getBuilder());
        for (IAtom atom : container.atoms()) {
            if(atom instanceof PseudoAtom){
            }else{
            IAtomType matched = matcher.findMatchingAtomType(container, 
atom);
            if (matched != null) {
                AtomTypeManipulator.configure(atom, matched);
            }

            }
        }
    }


Best wishes,

Asad


-- 

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Syed Asad Rahman (BEngg, PhD)
Research Scientist

EMBL-EBI                                 Phone:+44-(0)1223-492537
Wellcome Trust Genome Campus             Fax:+44-(0)1223 494486
Hinxton CB10 1SD                         E-mail: as...@eb...
Cambridge, UK                            Home Page: www.ebi.ac.uk/~asad

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