Bug in copyMoleculeByAtoms when H are mapped

Sorry for the javascript example ...

It seems there is a bug in copyMoleculeByAtoms when we have recognizeDelocalizedBonds:true and one of the mapped atom in an hydrogen. The atomMap is correct but the hydrogen is not copied.


import OCL from 'openchemlib'
const { Molecule } = OCL

const molecule = Molecule.fromSmiles('C')
molecule.addImplicitHydrogens()
const atomMap = []
const atomMask = [true, true, false, false, false]

let fragment = new Molecule(0, 0)
molecule.copyMoleculeByAtoms(fragment, atomMask, false, atomMap);
console.log(fragment.getAllAtoms(), atomMap) // 2 [ 0, 1, -1, -1, -1 ]

fragment = new Molecule(0, 0)
molecule.copyMoleculeByAtoms(fragment, atomMask, true, atomMap);
// if recognizeDelocalizedBonds is true we have the atomMap but the fragment do not contain the H it points to incorrect atom. We have a mapping to 0 and 1 but only atom 0 exists.
console.log(fragment.getAllAtoms(), atomMap) // 1 [ 0, 1, -1, -1, -1 ]

This is the expected behaviour:

If only a subset of atoms is copied as a new molecule, this new molecule is automatically considered a fragment (a substructure)
when calculating neighbours on a fragment, simple hydrogen atoms are automatically removed and converted into a hydrogen query feature

Von: Luc Patiny @.> Gesendet: Montag, 31. Juli 2023 13:34 An: Actelion/openchemlib @.> Cc: Subscribed @.***> Betreff: [Actelion/openchemlib] Bug in copyMoleculeByAtoms when H are mapped (Issue #97)

Sorry for the javascript example ...

It seems there is a bug in copyMoleculeByAtoms when we have recognizeDelocalizedBonds:true and one of the mapped atom in an hydrogen. The atomMap is correct but the hydrogen is not copied.

import OCL from 'openchemlib' const { Molecule } = OCL

const molecule = Molecule.fromSmiles('C') molecule.addImplicitHydrogens() const atomMap = [] const atomMask = [true, true, false, false, false]

let fragment = new Molecule(0, 0) molecule.copyMoleculeByAtoms(fragment, atomMask, false, atomMap); console.log(fragment.getAllAtoms(), atomMap) // 2 [ 0, 1, -1, -1, -1 ]

fragment = new Molecule(0, 0) molecule.copyMoleculeByAtoms(fragment, atomMask, true, atomMap); // if recognizeDelocalizedBonds is true the atomMap is correct but the fragment do not contain the H as is wrong console.log(fragment.getAllAtoms(), atomMap) // 1 [ 0, 1, -1, -1, -1 ]

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Actelion / openchemlib

Bug in copyMoleculeByAtoms when H are mapped #97