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https://github.com/rdkit/rdkit.git
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f20b83bc64
* Conformer embedding timeout * Add README for patching * Don't raise Exception but set EmbedFailureCauses on timeout. * Fix * Remove wrongly added README * Debug segfault * Improve logging of failures * Fix pointer reference * Don't use optional
79 lines
2.4 KiB
C++
79 lines
2.4 KiB
C++
//
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// Copyright (C) 2021 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 "Embedder.h"
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#include <RDGeneral/BoostStartInclude.h>
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#include <boost/lexical_cast.hpp>
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#include <boost/property_tree/ptree.hpp>
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#include <boost/property_tree/json_parser.hpp>
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#include <RDGeneral/BoostEndInclude.h>
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namespace RDKit {
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namespace DGeomHelpers {
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#define PT_OPT_GET(opt) params.opt = pt.get(#opt, params.opt)
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void updateEmbedParametersFromJSON(EmbedParameters ¶ms,
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const std::string &json) {
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if (json.empty()) {
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return;
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}
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std::istringstream ss;
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ss.str(json);
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boost::property_tree::ptree pt;
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boost::property_tree::read_json(ss, pt);
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PT_OPT_GET(maxIterations);
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PT_OPT_GET(numThreads);
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PT_OPT_GET(randomSeed);
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PT_OPT_GET(clearConfs);
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PT_OPT_GET(useRandomCoords);
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PT_OPT_GET(ignoreSmoothingFailures);
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PT_OPT_GET(enforceChirality);
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PT_OPT_GET(useExpTorsionAnglePrefs);
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PT_OPT_GET(useBasicKnowledge);
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PT_OPT_GET(pruneRmsThresh);
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PT_OPT_GET(onlyHeavyAtomsForRMS);
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PT_OPT_GET(ETversion);
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PT_OPT_GET(embedFragmentsSeparately);
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PT_OPT_GET(useSmallRingTorsions);
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PT_OPT_GET(useMacrocycleTorsions);
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PT_OPT_GET(useMacrocycle14config);
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PT_OPT_GET(boundsMatForceScaling);
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PT_OPT_GET(forceTransAmides);
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PT_OPT_GET(useSymmetryForPruning);
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PT_OPT_GET(enableSequentialRandomSeeds);
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PT_OPT_GET(timeout);
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PT_OPT_GET(symmetrizeConjugatedTerminalGroupsForPruning);
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std::map<int, RDGeom::Point3D> *cmap = nullptr;
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const auto coordMap = pt.get_child_optional("coordMap");
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if (coordMap) {
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// NOTE: this leaks since EmbedParameters uses a naked pointer and we don't
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// have any way to tie the lifetime of the memory we allocate here to the
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// EmbedParameters object itself.
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cmap = new std::map<int, RDGeom::Point3D>();
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for (const auto &entry : *coordMap) {
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RDGeom::Point3D pt;
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auto itm = entry.second.begin();
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pt.x = itm->second.get_value<float>();
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++itm;
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pt.y = itm->second.get_value<float>();
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++itm;
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pt.z = itm->second.get_value<float>();
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(*cmap)[boost::lexical_cast<int>(entry.first)] = pt;
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}
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params.coordMap = cmap;
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}
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}
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} // namespace DGeomHelpers
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} // namespace RDKit
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