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116 lines
3.5 KiB
C++
116 lines
3.5 KiB
C++
//
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// Copyright (C) 2015-2020 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/MolDraw2DDetails.h>
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#include <cmath>
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#ifndef M_PI
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#define M_PI 3.14159265358979323846
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#endif
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// ****************************************************************************
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namespace RDKit {
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namespace MolDraw2D_detail {
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// implementation from $RDBASE/rdkit/sping/pid.py
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void arcPoints(const Point2D &cds1, const Point2D &cds2,
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std::vector<Point2D> &res, float startAng, float extent) {
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// Note: this implementation is simple and not particularly efficient.
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float xScale = (cds2.x - cds1.x) / 2.0;
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float yScale = (cds2.y - cds1.y) / 2.0;
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if (xScale < 0) {
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xScale *= -1;
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}
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if (yScale < 0) {
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yScale *= -1;
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}
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float x = std::min(cds1.x, cds2.x) + xScale;
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float y = std::min(cds1.y, cds2.y) + yScale;
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int steps = std::max(static_cast<int>(extent * 2), 5);
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float step = M_PI * extent / (180 * steps);
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float angle = M_PI * startAng / 180;
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for (int i = 0; i <= steps; ++i) {
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Point2D point(x + xScale * cos(angle), y - yScale * sin(angle));
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res.emplace_back(point);
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angle += step;
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}
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}
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void addStereoAnnotation(const ROMol &mol, bool includeRelativeCIP) {
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const auto &sgs = mol.getStereoGroups();
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std::vector<unsigned int> doneAts(mol.getNumAtoms(), 0);
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unsigned int grpid = 1;
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for (const auto &sg : sgs) {
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for (const auto atom : sg.getAtoms()) {
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if (doneAts[atom->getIdx()]) {
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BOOST_LOG(rdWarningLog) << "Warning: atom " << atom->getIdx()
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<< " is in more than one stereogroup. Only the "
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"label from the first group will be used."
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<< std::endl;
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continue;
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}
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std::string lab;
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std::string cip;
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if (includeRelativeCIP ||
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sg.getGroupType() == StereoGroupType::STEREO_ABSOLUTE) {
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atom->getPropIfPresent(common_properties::_CIPCode, cip);
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}
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switch (sg.getGroupType()) {
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case StereoGroupType::STEREO_ABSOLUTE:
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lab = "abs";
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break;
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case StereoGroupType::STEREO_OR:
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lab = (boost::format("or%d") % grpid).str();
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break;
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case StereoGroupType::STEREO_AND:
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lab = (boost::format("and%d") % grpid).str();
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break;
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default:
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break;
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}
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if (!lab.empty()) {
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doneAts[atom->getIdx()] = 1;
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if (!cip.empty()) {
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lab += " (" + cip + ")";
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}
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atom->setProp(common_properties::atomNote, lab);
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}
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}
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if (sg.getGroupType() != StereoGroupType::STEREO_ABSOLUTE) {
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++grpid;
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}
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}
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for (auto atom : mol.atoms()) {
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std::string cip;
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if (!doneAts[atom->getIdx()] &&
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atom->getPropIfPresent(common_properties::_CIPCode, cip)) {
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std::string lab = "(" + cip + ")";
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atom->setProp(common_properties::atomNote, lab);
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}
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}
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for (auto bond : mol.bonds()) {
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std::string cip;
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if (!bond->getPropIfPresent(common_properties::_CIPCode, cip)) {
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if (bond->getStereo() == Bond::STEREOE) {
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cip = "E";
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} else if (bond->getStereo() == Bond::STEREOZ) {
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cip = "Z";
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}
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}
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if (!cip.empty()) {
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std::string lab = "(" + cip + ")";
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bond->setProp(common_properties::bondNote, lab);
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}
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}
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}
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} // namespace MolDraw2D_detail
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} // namespace RDKit
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