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//
// Copyright (C) 2015-2020 Greg Landrum
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <GraphMol/MolDraw2D/MolDraw2DDetails.h>
#include <cmath>
#ifndef M_PI
#define M_PI 3.14159265358979323846
#endif
// ****************************************************************************
namespace RDKit {
namespace MolDraw2D_detail {
// implementation from $RDBASE/rdkit/sping/pid.py
void arcPoints(const Point2D &cds1, const Point2D &cds2,
std::vector<Point2D> &res, float startAng, float extent) {
// Note: this implementation is simple and not particularly efficient.
float xScale = (cds2.x - cds1.x) / 2.0;
float yScale = (cds2.y - cds1.y) / 2.0;
if (xScale < 0) {
xScale *= -1;
}
if (yScale < 0) {
yScale *= -1;
}
float x = std::min(cds1.x, cds2.x) + xScale;
float y = std::min(cds1.y, cds2.y) + yScale;
int steps = std::max(static_cast<int>(extent * 2), 5);
float step = M_PI * extent / (180 * steps);
float angle = M_PI * startAng / 180;
for (int i = 0; i <= steps; ++i) {
Point2D point(x + xScale * cos(angle), y - yScale * sin(angle));
res.emplace_back(point);
angle += step;
}
}
void addStereoAnnotation(const ROMol &mol, bool includeRelativeCIP) {
const auto &sgs = mol.getStereoGroups();
std::vector<unsigned int> doneAts(mol.getNumAtoms(), 0);
unsigned int grpid = 1;
for (const auto &sg : sgs) {
for (const auto atom : sg.getAtoms()) {
if (doneAts[atom->getIdx()]) {
BOOST_LOG(rdWarningLog) << "Warning: atom " << atom->getIdx()
<< " is in more than one stereogroup. Only the "
"label from the first group will be used."
<< std::endl;
continue;
}
std::string lab;
std::string cip;
if (includeRelativeCIP ||
sg.getGroupType() == StereoGroupType::STEREO_ABSOLUTE) {
atom->getPropIfPresent(common_properties::_CIPCode, cip);
}
switch (sg.getGroupType()) {
case StereoGroupType::STEREO_ABSOLUTE:
lab = "abs";
break;
case StereoGroupType::STEREO_OR:
lab = (boost::format("or%d") % grpid).str();
break;
case StereoGroupType::STEREO_AND:
lab = (boost::format("and%d") % grpid).str();
break;
default:
break;
}
if (!lab.empty()) {
doneAts[atom->getIdx()] = 1;
if (!cip.empty()) {
lab += " (" + cip + ")";
}
atom->setProp(common_properties::atomNote, lab);
}
}
if (sg.getGroupType() != StereoGroupType::STEREO_ABSOLUTE) {
++grpid;
}
}
for (auto atom : mol.atoms()) {
std::string cip;
if (!doneAts[atom->getIdx()] &&
atom->getPropIfPresent(common_properties::_CIPCode, cip)) {
std::string lab = "(" + cip + ")";
atom->setProp(common_properties::atomNote, lab);
}
}
for (auto bond : mol.bonds()) {
std::string cip;
if (!bond->getPropIfPresent(common_properties::_CIPCode, cip)) {
if (bond->getStereo() == Bond::STEREOE) {
cip = "E";
} else if (bond->getStereo() == Bond::STEREOZ) {
cip = "Z";
}
}
if (!cip.empty()) {
std::string lab = "(" + cip + ")";
bond->setProp(common_properties::bondNote, lab);
}
}
}
} // namespace MolDraw2D_detail
} // namespace RDKit
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