void MolDraw2DSVG::tagAtoms(const ROMol &mol, double radius,
const std::map<std::string, std::string> &events) {
PRECONDITION(d_os, "no output stream");
for (const auto &at : mol.atoms()) {
auto this_idx = at->getIdx();
auto pos = getDrawCoords(atomCoords()[this_idx]);
d_os << "<circle "
<< " cx='" << pos.x << "'"
<< " cy='" << pos.y << "'"
<< " r='" << (scale() * radius) << "'";
d_os << " class='atom-selector atom-" << this_idx;
if (d_activeClass != "") {
d_os << " " << d_activeClass;
}
d_os << "'";
d_os << " style='fill:#fff;stroke:#fff;stroke-width:1px;fill-opacity:0;"
"stroke-opacity:0' ";
for (const auto &event : events) {
d_os << " " << event.first << "='" << event.second << "(" << this_idx
<< ");"
<< "'";
}
d_os << "/>\n";
}
}
bool isOrganic(const ROMol &frag) {
// Returns true if fragment contains at least one carbon atom.
for (const auto at : frag.atoms()) {
if (at->getAtomicNum() == 6) {
return true;
}
}
return false;
}
void MolDraw2DSVG::addMoleculeMetadata(const ROMol &mol, int confId) const {
PRECONDITION(d_os, "no output stream");
d_os << "<metadata>" << std::endl;
d_os << "<rdkit:mol"
<< " xmlns:rdkit = \"http://www.rdkit.org/xml\""
<< " version=\"" << RDKIT_SVG_VERSION << "\""
<< ">" << std::endl;
for (const auto atom : mol.atoms()) {
d_os << "<rdkit:atom idx=\"" << atom->getIdx() + 1 << "\"";
bool doKekule = false, allHsExplicit = true, isomericSmiles = true;
d_os << " atom-smiles=\""
<< SmilesWrite::GetAtomSmiles(atom, doKekule, nullptr, allHsExplicit,
isomericSmiles)
<< "\"";
auto tag = boost::str(boost::format("_atomdrawpos_%d") % confId);
const Conformer &conf = mol.getConformer(confId);
RDGeom::Point3D pos = conf.getAtomPos(atom->getIdx());
Point2D dpos(pos.x, pos.y);
if (atom->hasProp(tag))
dpos = atom->getProp<Point2D>(tag);
else
dpos = getDrawCoords(dpos);
d_os << " drawing-x=\"" << dpos.x << "\""
<< " drawing-y=\"" << dpos.y << "\"";
d_os << " x=\"" << pos.x << "\""
<< " y=\"" << pos.y << "\""
<< " z=\"" << pos.z << "\"";
d_os << " />" << std::endl;
}
for (const auto bond : mol.bonds()) {
d_os << "<rdkit:bond idx=\"" << bond->getIdx() + 1 << "\"";
d_os << " begin-atom-idx=\"" << bond->getBeginAtomIdx() + 1 << "\"";
d_os << " end-atom-idx=\"" << bond->getEndAtomIdx() + 1 << "\"";
bool doKekule = false, allBondsExplicit = true;
d_os << " bond-smiles=\""
<< SmilesWrite::GetBondSmiles(bond, -1, doKekule, allBondsExplicit)
<< "\"";
d_os << " />" << std::endl;
}
d_os << "</rdkit:mol></metadata>" << std::endl;
}
