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Added the missing atom type perception
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egonw committed Jul 10, 2012
1 parent 4aec25e commit 7020092
Showing 1 changed file with 4 additions and 3 deletions.
Expand Up @@ -2977,9 +2977,10 @@ public String getMDLMolfileString(IMolecule molecule_in) throws BioclipseExcepti
"fixing bond orders.");
FixBondOrdersTool fbt = new FixBondOrdersTool();
try {
IAtomContainer fixedAC = fbt.kekuliseAromaticRings(
(org.openscience.cdk.interfaces.IMolecule)
molecule.getAtomContainer());
org.openscience.cdk.interfaces.IMolecule cdkMol =
(org.openscience.cdk.interfaces.IMolecule)molecule.getAtomContainer();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(cdkMol);
IAtomContainer fixedAC = fbt.kekuliseAromaticRings(cdkMol);
molecule=new CDKMolecule(fixedAC);
} catch (CDKException e) {
logger.error(
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