thsa
commented
4 years ago copyMoleculeByAtoms() expects that hydrogen atoms, if they exist, are at the end of the atom list. Otherwise, it will move hydrogens to the end, because it calls ensureHelperArrays() for the ring detection, if recognizeDelocalizedBonds is true. Thus, if some hydrogens are not at the end of the atom table and if you pass an includeAtom list, then the atomMap is not correct because of the resorting of the atoms.
Von: Luc Patiny notifications@github.com Gesendet: Sonntag, 26. Januar 2020 16:49 An: Actelion/openchemlib openchemlib@noreply.github.com Cc: Thomas Sander thomas.sander@idorsia.com; Mention mention@noreply.github.com Betreff: [Actelion/openchemlib] Wrong mapping with copyMoleculeByAtoms (#58)
If a molecule contains hydrogen and we replace one of the hydrogens by a 'X' (not the first one, the second one), after copyMoleculeByAtoms the new position of the 'X' is not the one that is specified in the atomMap.
import OCL from 'openchemlib';
import { initOCL } from '../src';
initOCL(OCL);
const molecule = OCL.Molecule.fromSmiles('C'); molecule.addImplicitHydrogens(); molecule.setAtomicNo(2, 153); // we set a 'X' as atom
const copy = new OCL.Molecule(0, 0); copy.setFragment(false); const atomMap = []; molecule.copyMoleculeByAtoms( copy, [true, true, true, false, false], true, atomMap, );
console.log(copy.getAllAtoms()); // returns 1
console.log(atomMap); // returns [ 0, 1, 2, -1, -1 ]
console.log(copy.getAtomicNo(1)); // returns 153, should be 1 console.log(copy.getAtomicNo(2)); // returns -1, should be 153 based on atomMap
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lpatiny
@thsa
Related to #57
If a molecule contains hydrogen and we replace one of the hydrogens by a 'X' (not the first one, the second one), after copyMoleculeByAtoms the new position of the 'X' is not the one that is specified in the
atomMap.