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//
// Copyright (C) 2016 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/MolDraw2DUtils.h>
#include <GraphMol/MolDraw2D/MolDraw2D.h>
#include <GraphMol/RWMol.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/Depictor/RDDepictor.h>
#include <GraphMol/FileParsers/MolFileStereochem.h>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/foreach.hpp>
#include <boost/lexical_cast.hpp>
#include <boost/property_tree/ptree.hpp>
#include <boost/property_tree/json_parser.hpp>
#include <RDGeneral/BoostEndInclude.h>
namespace RDKit {
namespace MolDraw2DUtils {
namespace {
bool isAtomCandForChiralH(const RWMol &mol, const Atom *atom) {
// conditions for needing a chiral H:
// - stereochem specified
// - in at least two rings
if ((!mol.getRingInfo()->isInitialized() ||
mol.getRingInfo()->numAtomRings(atom->getIdx()) > 1) &&
(atom->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW ||
atom->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW)) {
return true;
}
return false;
}
} // end of anonymous namespace
void prepareMolForDrawing(RWMol &mol, bool kekulize, bool addChiralHs,
bool wedgeBonds, bool forceCoords) {
if (kekulize) {
MolOps::Kekulize(mol, false); // kekulize, but keep the aromatic flags!
}
if (addChiralHs) {
std::vector<unsigned int> chiralAts;
for (RWMol::AtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms();
++atIt) {
if (isAtomCandForChiralH(mol, *atIt)) {
chiralAts.push_back((*atIt)->getIdx());
}
}
if (chiralAts.size()) {
bool addCoords = false;
if (!forceCoords && mol.getNumConformers()) addCoords = true;
MolOps::addHs(mol, false, addCoords, &chiralAts);
}
}
if (forceCoords || !mol.getNumConformers()) {
// compute 2D coordinates in a standard orientation:
const bool canonOrient = true;
RDDepict::compute2DCoords(mol, nullptr, canonOrient);
}
if (wedgeBonds) {
WedgeMolBonds(mol, &mol.getConformer());
}
}
void updateDrawerParamsFromJSON(MolDraw2D &drawer, const char *json) {
PRECONDITION(json, "no parameter string");
updateDrawerParamsFromJSON(drawer, std::string(json));
};
#define PT_OPT_GET(opt) opts.opt = pt.get(#opt, opts.opt)
void get_colour_option(boost::property_tree::ptree *pt, const char *pnm,
DrawColour &colour) {
PRECONDITION(pnm && strlen(pnm), "bad property name");
if (pt->find(pnm) == pt->not_found()) return;
boost::property_tree::ptree::const_iterator itm = pt->get_child(pnm).begin();
colour.get<0>() = itm->second.get_value<float>();
++itm;
colour.get<1>() = itm->second.get_value<float>();
++itm;
colour.get<2>() = itm->second.get_value<float>();
++itm;
}
void updateDrawerParamsFromJSON(MolDraw2D &drawer, const std::string &json) {
if (json == "") return;
std::istringstream ss;
ss.str(json);
MolDrawOptions &opts = drawer.drawOptions();
boost::property_tree::ptree pt;
boost::property_tree::read_json(ss, pt);
PT_OPT_GET(atomLabelDeuteriumTritium);
PT_OPT_GET(dummiesAreAttachments);
PT_OPT_GET(circleAtoms);
PT_OPT_GET(continuousHighlight);
PT_OPT_GET(flagCloseContactsDist);
PT_OPT_GET(includeAtomTags);
PT_OPT_GET(clearBackground);
PT_OPT_GET(legendFontSize);
PT_OPT_GET(multipleBondOffset);
PT_OPT_GET(padding);
PT_OPT_GET(additionalAtomLabelPadding);
get_colour_option(&pt, "highlightColour", opts.highlightColour);
get_colour_option(&pt, "backgroundColour", opts.backgroundColour);
get_colour_option(&pt, "legendColour", opts.legendColour);
if (pt.find("atomLabels") != pt.not_found()) {
BOOST_FOREACH (boost::property_tree::ptree::value_type const &item,
pt.get_child("atomLabels")) {
opts.atomLabels[boost::lexical_cast<int>(item.first)] =
item.second.get_value<std::string>();
}
}
}
} // end of MolDraw2DUtils namespace
} // end of RDKit namespace
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