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//
// Copyright (C) 2021 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 "Embedder.h"
#include <RDGeneral/BoostStartInclude.h>
#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 DGeomHelpers {
#define PT_OPT_GET(opt) params.opt = pt.get(#opt, params.opt)
void updateEmbedParametersFromJSON(EmbedParameters ¶ms,
const std::string &json) {
if (json.empty()) {
return;
}
std::istringstream ss;
ss.str(json);
boost::property_tree::ptree pt;
boost::property_tree::read_json(ss, pt);
PT_OPT_GET(maxIterations);
PT_OPT_GET(numThreads);
PT_OPT_GET(randomSeed);
PT_OPT_GET(clearConfs);
PT_OPT_GET(useRandomCoords);
PT_OPT_GET(ignoreSmoothingFailures);
PT_OPT_GET(enforceChirality);
PT_OPT_GET(useExpTorsionAnglePrefs);
PT_OPT_GET(useBasicKnowledge);
PT_OPT_GET(pruneRmsThresh);
PT_OPT_GET(onlyHeavyAtomsForRMS);
PT_OPT_GET(ETversion);
PT_OPT_GET(embedFragmentsSeparately);
PT_OPT_GET(useSmallRingTorsions);
PT_OPT_GET(useMacrocycleTorsions);
PT_OPT_GET(useMacrocycle14config);
PT_OPT_GET(boundsMatForceScaling);
PT_OPT_GET(forceTransAmides);
PT_OPT_GET(useSymmetryForPruning);
PT_OPT_GET(enableSequentialRandomSeeds);
PT_OPT_GET(timeout);
PT_OPT_GET(symmetrizeConjugatedTerminalGroupsForPruning);
std::map<int, RDGeom::Point3D> *cmap = nullptr;
const auto coordMap = pt.get_child_optional("coordMap");
if (coordMap) {
// NOTE: this leaks since EmbedParameters uses a naked pointer and we don't
// have any way to tie the lifetime of the memory we allocate here to the
// EmbedParameters object itself.
cmap = new std::map<int, RDGeom::Point3D>();
for (const auto &entry : *coordMap) {
RDGeom::Point3D pt;
auto itm = entry.second.begin();
pt.x = itm->second.get_value<float>();
++itm;
pt.y = itm->second.get_value<float>();
++itm;
pt.z = itm->second.get_value<float>();
(*cmap)[boost::lexical_cast<int>(entry.first)] = pt;
}
params.coordMap = cmap;
}
}
} // namespace DGeomHelpers
} // namespace RDKit
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