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4bbbc6611d
* Nonchiral atoms should be removed from StereoGroups This fixes a bug where atoms which have no chirality were left in StereoGroups In order to make this work, ROMol::setStereoGroups() needed to be made public. That shouldn't be a problem since it doesn't change connectivity. * support CXSmiles extensions in the hashes * initial tests for that * some cleanup * copyright header cleanup * minor refactoring * call out the changes in the release notes * extension and more testing * add python wrappers
61 lines
1.9 KiB
C++
61 lines
1.9 KiB
C++
//
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// Copyright (C) 2019-2022 NextMove Software and other RDKit contributors
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/RDKitQueries.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include "nmmolhash.h"
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namespace RDKit {
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namespace MolHash {
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void Strip(RWMol *mol, unsigned int striptype) {
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// The order of these operations is significant to some degree
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// - Hydrogens should be at the end as that is the common
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// use case
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if (striptype & static_cast<unsigned>(StripType::AtomStereo)) {
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for (auto aptr : mol->atoms()) {
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aptr->setChiralTag(RDKit::Atom::CHI_UNSPECIFIED);
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}
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if (!mol->getStereoGroups().empty()) {
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std::vector<StereoGroup> no_sgs;
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mol->setStereoGroups(std::move(no_sgs));
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}
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}
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if (striptype & static_cast<unsigned>(StripType::BondStereo)) {
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for (auto bptr : mol->bonds()) {
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if (bptr->getStereo() > RDKit::Bond::STEREOANY) {
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bptr->setStereo(RDKit::Bond::STEREOANY);
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}
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}
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}
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if (striptype & static_cast<unsigned>(StripType::Isotope)) {
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for (auto aptr : mol->atoms()) {
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aptr->setIsotope(0);
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}
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}
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if (striptype & static_cast<unsigned>(StripType::AtomMap)) {
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for (auto aptr : mol->atoms()) {
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aptr->setAtomMapNum(0);
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}
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}
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if (striptype & static_cast<unsigned>(StripType::Hydrogen)) {
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MolOps::removeHs(*mol);
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}
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}
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void SplitMolecule(RWMol *mol, std::vector<RWMol *> &molv) {
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auto mfrags = RDKit::MolOps::getMolFrags(*mol);
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for (const auto &frag : mfrags) {
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const auto *wrappedmol = frag.get(); // reach inside the shared pointer...
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molv.push_back(new RWMol(*wrappedmol)); // ...and make a copy
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}
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}
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} // namespace MolHash
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} // namespace RDKit
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