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91212a4eb3
* Fixes #982 also changes bond-wedging algorithm to favor lighter non-ring bonds * prefer wedging bonds to lower-degree atoms * Fixes #983 * small fixes - Fix a problem where a chiral atom is selected to draw a wedge to instead of a ring atom - Fix a problem where two calls to PrepareMolForDrawing() led to two wedged bonds from an atom. * Fixes #985 This isn't the most satisfying solution (the wedged bonds are sometimes a bit too large), but it gives reasonable results on the test cases I've tried.
64 lines
1.9 KiB
C++
64 lines
1.9 KiB
C++
//
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// Copyright (C) 2016 Greg Landrum
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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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//
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#include <GraphMol/MolDraw2D/MolDraw2DUtils.h>
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#include <GraphMol/RWMol.h>
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#include <GraphMol/MolOps.h>
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#include <GraphMol/Depictor/RDDepictor.h>
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#include <GraphMol/FileParsers/MolFileStereochem.h>
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namespace RDKit {
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namespace MolDraw2DUtils {
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namespace {
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bool isAtomCandForChiralH(const RWMol &mol, const Atom *atom) {
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// conditions for needing a chiral H:
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// - stereochem specified
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// - in at least two rings
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if ((!mol.getRingInfo()->isInitialized() ||
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mol.getRingInfo()->numAtomRings(atom->getIdx()) > 1) &&
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(atom->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW ||
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atom->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW)) {
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return true;
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}
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return false;
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}
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} // end of anonymous namespace
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void prepareMolForDrawing(RWMol &mol, bool kekulize, bool addChiralHs,
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bool wedgeBonds, bool forceCoords) {
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if (kekulize) {
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MolOps::Kekulize(mol, false); // kekulize, but keep the aromatic flags!
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}
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if (addChiralHs) {
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std::vector<unsigned int> chiralAts;
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for (RWMol::AtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms();
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++atIt) {
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if (isAtomCandForChiralH(mol, *atIt)) {
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chiralAts.push_back((*atIt)->getIdx());
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}
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}
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if (chiralAts.size()) {
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bool addCoords = false;
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if (!forceCoords && mol.getNumConformers()) addCoords = true;
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MolOps::addHs(mol, false, addCoords, &chiralAts);
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}
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}
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if (forceCoords || !mol.getNumConformers()) {
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// compute 2D coordinates in a standard orientation:
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const bool canonOrient = true;
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RDDepict::compute2DCoords(mol, NULL, canonOrient);
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}
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if (wedgeBonds) {
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WedgeMolBonds(mol, &mol.getConformer());
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}
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}
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}
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}
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