mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
d5d4d194ec
* atropisomer handling added * fixed non-used variables, linking directives * BOOST LIB start/stop fixes, linking fix * Fixes for RDKIT CI errors * minimalLib fix * changed vector<enum> for java builds * check for extra chars in CIP labeling * removed wrong deprecated message * fix ostrstream output error? * restored _ChiralAtomRank to lowercase first letter * changes for merged master * Fixed catch label for new Catch package * update expected psql results * get swig wrappers building * restore MolFileStereochem to FileParsers * fix java wrapper for reapplyMolBlockWedging * some suggestions * move a couple functions out of Bond * Merge branch 'master' into pr/atropisomers2 * merged master * Renamed setStereoanyFromSquiggleBond * atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol * fix for CI build * attempt to fix java build in CI * attempt to fix java build in CI #2 * New routine to remove non-explicit 3D-geneated chirality * changed to use pair for atrop atoms and related bonds * Changes as per PR reviews * PR review respnses * PR review reponse - more * Fix merge from master * fixing java ci after merge * Updated the help doc for atripisomers * update the atropisomer docs * improve the images * add the source CXSMILES --------- Co-authored-by: greg landrum <greg.landrum@gmail.com>
708 lines
25 KiB
C++
708 lines
25 KiB
C++
//
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// Copyright (C) 2018-2022 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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#ifdef _MSC_VER
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#pragma warning(disable : 4503)
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#endif
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#include <RDGeneral/Invariant.h>
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#include <RDGeneral/versions.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/MolPickler.h>
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#include <GraphMol/SubstanceGroup.h>
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#include <GraphMol/StereoGroup.h>
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#include <GraphMol/MolInterchange/MolInterchange.h>
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#include <GraphMol/MolInterchange/details.h>
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#include <RDGeneral/FileParseException.h>
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#include <sstream>
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#include <exception>
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#include <map>
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#include <rapidjson/document.h>
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#include <rapidjson/stringbuffer.h>
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#include <rapidjson/writer.h>
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#include "rapidjson/pointer.h"
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namespace rj = rapidjson;
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namespace RDKit {
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namespace MolInterchange {
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namespace {
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template <typename T>
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void addMol(const T &imol, rj::Value &rjMol, rj::Document &doc,
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const rj::Value &atomDefaults, const rj::Value &bondDefaults,
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const JSONWriteParameters ¶ms);
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void initAtomDefaults(rj::Value &rjDefaults, rj::Document &document) {
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// "atomDefaults": {"Z": 6, "impHs": 0, "chg": 0, "stereo": "unspecified",
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// "nrad": 0, "isotope": 0},
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rjDefaults.AddMember("z", 6, document.GetAllocator());
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rjDefaults.AddMember("impHs", 0, document.GetAllocator());
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rjDefaults.AddMember("chg", 0, document.GetAllocator());
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rjDefaults.AddMember("nRad", 0, document.GetAllocator());
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rjDefaults.AddMember("isotope", 0, document.GetAllocator());
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rjDefaults.AddMember("stereo", "unspecified", document.GetAllocator());
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}
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void initBondDefaults(rj::Value &rjDefaults, rj::Document &document) {
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// "bondDefaults": {"bo": 1, "stereo": "unspecified", "stereoAtoms": []},
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rjDefaults.AddMember("bo", 1, document.GetAllocator());
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rjDefaults.AddMember("stereo", "unspecified", document.GetAllocator());
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}
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void initHeader(rj::Value &rjHeader, rj::Document &document,
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const JSONWriteParameters ¶ms) {
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auto vers = currentRDKitJSONVersion;
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if (!params.useRDKitExtensions) {
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vers = currentMolJSONVersion;
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}
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rjHeader.AddMember("version", vers, document.GetAllocator());
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}
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void addIntVal(rj::Value &dest, const rj::Value &defaults, const char *tag,
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int val, rj::Document &doc) {
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const auto srt = rj::StringRef(tag);
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const auto &miter = defaults.FindMember(srt);
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if (miter != defaults.MemberEnd()) {
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int dval = miter->value.GetInt();
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if (dval != val) {
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dest.AddMember(srt, val, doc.GetAllocator());
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}
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} else {
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dest.AddMember(srt, val, doc.GetAllocator());
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}
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}
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void addIntVal(rj::Value &dest, const char *tag, int val, rj::Document &doc) {
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const auto srt = rj::StringRef(tag);
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dest.AddMember(srt, val, doc.GetAllocator());
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}
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void addStringVal(rj::Value &dest, const rj::Value &defaults, const char *tag,
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const std::string &val, rj::Document &doc) {
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rj::Value nmv;
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nmv.SetString(val.c_str(), val.size(), doc.GetAllocator());
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const auto srt = rj::StringRef(tag);
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const auto &miter = defaults.FindMember(srt);
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if (miter != defaults.MemberEnd()) {
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std::string dval = miter->value.GetString();
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if (val.size() && dval != val) {
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dest.AddMember(srt, nmv, doc.GetAllocator());
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}
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} else {
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dest.AddMember(srt, nmv, doc.GetAllocator());
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}
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}
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void addStringVal(rj::Value &dest, const char *tag, const std::string &val,
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rj::Document &doc) {
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rj::Value nmv;
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nmv.SetString(val.c_str(), val.size(), doc.GetAllocator());
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const auto srt = rj::StringRef(tag);
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dest.AddMember(srt, nmv, doc.GetAllocator());
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}
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void addAtom(const Atom &atom, rj::Value &rjAtom, rj::Document &doc,
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const rj::Value &rjDefaults) {
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addIntVal(rjAtom, rjDefaults, "z", atom.getAtomicNum(), doc);
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if (!atom.hasQuery()) {
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addIntVal(rjAtom, rjDefaults, "impHs", atom.getTotalNumHs(), doc);
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}
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addIntVal(rjAtom, rjDefaults, "chg", atom.getFormalCharge(), doc);
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addIntVal(rjAtom, rjDefaults, "isotope", atom.getIsotope(), doc);
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addIntVal(rjAtom, rjDefaults, "nRad", atom.getNumRadicalElectrons(), doc);
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std::string chi = "";
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if (inv_chilookup.find(atom.getChiralTag()) != inv_chilookup.end()) {
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chi = inv_chilookup.find(atom.getChiralTag())->second;
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} else {
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BOOST_LOG(rdWarningLog)
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<< " unrecognized atom chirality set to default while writing"
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<< std::endl;
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}
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addStringVal(rjAtom, rjDefaults, "stereo", chi, doc);
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}
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template <typename Q>
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void addQuery(const Q &query, rj::Value &rjQuery, rj::Document &doc,
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const JSONWriteParameters ¶ms) {
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rj::Value descr;
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descr.SetString(query.getDescription().c_str(), query.getDescription().size(),
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doc.GetAllocator());
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rjQuery.AddMember("descr", descr, doc.GetAllocator());
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if (!query.getTypeLabel().empty()) {
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rj::Value typ;
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typ.SetString(query.getTypeLabel().c_str(), query.getTypeLabel().size(),
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doc.GetAllocator());
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rjQuery.AddMember("type", typ, doc.GetAllocator());
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}
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if (query.getNegation()) {
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rjQuery.AddMember("negated", true, doc.GetAllocator());
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}
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if (typeid(query) == typeid(RecursiveStructureQuery)) {
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auto rq = (const RecursiveStructureQuery *)&query;
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auto submol = rq->getQueryMol();
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PRECONDITION(submol, "bad recursive query");
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rj::Value subquery(rj::kObjectType);
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addMol(*submol, subquery, doc,
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*rj::GetValueByPointer(doc, "/defaults/atom"),
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*rj::GetValueByPointer(doc, "/defaults/bond"), params);
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rjQuery.AddMember("tag", MolPickler::QUERY_RECURSIVE, doc.GetAllocator());
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rjQuery.AddMember("subquery", subquery, doc.GetAllocator());
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} else {
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auto qdetails = PicklerOps::getQueryDetails(&query);
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switch (qdetails.which()) {
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case 0:
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rjQuery.AddMember("tag", boost::get<MolPickler::Tags>(qdetails),
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doc.GetAllocator());
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break;
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case 1: {
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auto v = boost::get<std::tuple<MolPickler::Tags, int32_t>>(qdetails);
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rjQuery.AddMember("tag", std::get<0>(v), doc.GetAllocator());
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rjQuery.AddMember("val", std::get<1>(v), doc.GetAllocator());
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} break;
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case 2: {
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auto v = boost::get<std::tuple<MolPickler::Tags, int32_t, int32_t>>(
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qdetails);
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rjQuery.AddMember("tag", std::get<0>(v), doc.GetAllocator());
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rjQuery.AddMember("val", std::get<1>(v), doc.GetAllocator());
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if (std::get<2>(v)) {
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rjQuery.AddMember("tol", std::get<2>(v), doc.GetAllocator());
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}
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} break;
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case 3: {
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auto v = boost::get<
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std::tuple<MolPickler::Tags, int32_t, int32_t, int32_t, char>>(
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qdetails);
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rjQuery.AddMember("tag", std::get<0>(v), doc.GetAllocator());
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rjQuery.AddMember("lower", std::get<1>(v), doc.GetAllocator());
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rjQuery.AddMember("upper", std::get<2>(v), doc.GetAllocator());
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if (std::get<3>(v)) {
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rjQuery.AddMember("tol", std::get<3>(v), doc.GetAllocator());
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}
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rjQuery.AddMember("ends", std::get<4>(v), doc.GetAllocator());
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} break;
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case 4: {
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auto v = boost::get<std::tuple<MolPickler::Tags, std::set<int32_t>>>(
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qdetails);
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rjQuery.AddMember("tag", std::get<0>(v), doc.GetAllocator());
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const auto &tset = std::get<1>(v);
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rj::Value sval(rj::kArrayType);
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for (auto val : tset) {
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sval.PushBack(val, doc.GetAllocator());
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}
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rjQuery.AddMember("set", sval, doc.GetAllocator());
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} break;
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default:
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throw MolPicklerException(
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"do not know how to pickle part of the query.");
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}
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}
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if (query.endChildren() != query.beginChildren()) {
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rj::Value children(rj::kArrayType);
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for (auto cit = query.beginChildren(); cit != query.endChildren(); ++cit) {
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rj::Value child(rj::kObjectType);
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addQuery(**cit, child, doc, params);
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children.PushBack(child, doc.GetAllocator());
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}
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rjQuery.AddMember("children", children, doc.GetAllocator());
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}
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}
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void addBond(const Bond &bond, rj::Value &rjBond, rj::Document &doc,
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const rj::Value &rjDefaults, const JSONWriteParameters ¶ms) {
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int bo = -1;
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if (auto boIter = inv_bolookup.find(bond.getBondType());
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boIter != inv_bolookup.end()) {
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bo = boIter->second;
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}
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// commonchem only supports a few bond orders:
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if (!params.useRDKitExtensions && bo > 3) {
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bo = -1;
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}
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if (bo < 0) {
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bo = 0;
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BOOST_LOG(rdWarningLog) << " unrecognized bond type " << bond.getBondType()
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<< " set to zero while writing" << std::endl;
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}
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addIntVal(rjBond, rjDefaults, "bo", bo, doc);
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rj::Value rjAtoms(rj::kArrayType);
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rj::Value v1(static_cast<int>(bond.getBeginAtomIdx()));
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rj::Value v2(static_cast<int>(bond.getEndAtomIdx()));
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rjAtoms.PushBack(v1, doc.GetAllocator());
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rjAtoms.PushBack(v2, doc.GetAllocator());
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rjBond.AddMember("atoms", rjAtoms, doc.GetAllocator());
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std::string chi = "";
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if (auto sbIter = inv_stereoBondlookup.find(bond.getStereo());
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sbIter != inv_stereoBondlookup.end()) {
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chi = sbIter->second;
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} else {
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BOOST_LOG(rdWarningLog) << " unrecognized bond stereo " << bond.getStereo()
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<< " set to default while writing" << std::endl;
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}
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addStringVal(rjBond, rjDefaults, "stereo", chi, doc);
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if (chi != "unspecified" && bond.getStereoAtoms().size() == 2) {
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rj::Value rjStereoAtoms(rj::kArrayType);
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rj::Value v1(static_cast<int>(bond.getStereoAtoms()[0]));
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rj::Value v2(static_cast<int>(bond.getStereoAtoms()[1]));
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rjStereoAtoms.PushBack(v1, doc.GetAllocator());
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rjStereoAtoms.PushBack(v2, doc.GetAllocator());
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rjBond.AddMember("stereoAtoms", rjStereoAtoms, doc.GetAllocator());
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}
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}
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template <typename T>
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void addProperties(const T &obj, const std::vector<std::string> &propNames,
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rj::Value &properties, rj::Document &doc) {
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for (const auto &pN : propNames) {
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rj::Value rjv;
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try {
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auto val = obj.template getProp<int>(pN);
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rjv = val;
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} catch (const std::bad_any_cast &) {
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try {
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auto val = obj.template getProp<double>(pN);
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rjv = val;
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} catch (const std::bad_any_cast &) {
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try {
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auto val = obj.template getProp<std::string>(pN);
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rjv.SetString(val.c_str(), val.size(), doc.GetAllocator());
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} catch (const std::bad_any_cast &) {
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BOOST_LOG(rdWarningLog)
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<< "Warning: Could not convert property " << pN
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<< " to a recognized type. Skipping it." << std::endl;
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continue;
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}
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}
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}
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rj::Value rjpN;
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rjpN.SetString(pN.c_str(), pN.size(), doc.GetAllocator());
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properties.AddMember(rjpN, rjv, doc.GetAllocator());
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}
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}
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void addStereoGroup(const StereoGroup &sg, rj::Value &rjSG, rj::Document &doc) {
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if (inv_stereoGrouplookup.find(sg.getGroupType()) ==
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inv_stereoGrouplookup.end()) {
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throw ValueErrorException("unrecognized StereoGroup type");
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}
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addStringVal(rjSG, "type", inv_stereoGrouplookup.at(sg.getGroupType()), doc);
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if (sg.getGroupType() != StereoGroupType::STEREO_ABSOLUTE) {
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addIntVal(rjSG, "id", sg.getWriteId(), doc);
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}
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rj::Value rjAtoms(rj::kArrayType);
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for (const auto atm : sg.getAtoms()) {
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rj::Value v1(static_cast<int>(atm->getIdx()));
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rjAtoms.PushBack(v1, doc.GetAllocator());
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}
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rjSG.AddMember("atoms", rjAtoms, doc.GetAllocator());
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}
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void addSubstanceGroup(const SubstanceGroup &sg, rj::Value &rjSG,
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rj::Document &doc) {
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bool includePrivate = false, includeComputed = false;
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auto propNames = sg.getPropList(includePrivate, includeComputed);
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if (propNames.size()) {
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rj::Value properties(rj::kObjectType);
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addProperties(sg, propNames, properties, doc);
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rjSG.AddMember("properties", properties, doc.GetAllocator());
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}
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if (!sg.getAtoms().empty()) {
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rj::Value rjArr(rj::kArrayType);
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for (const auto idx : sg.getAtoms()) {
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rj::Value v1(static_cast<int>(idx));
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rjArr.PushBack(v1, doc.GetAllocator());
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}
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rjSG.AddMember("atoms", rjArr, doc.GetAllocator());
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}
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if (!sg.getBonds().empty()) {
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rj::Value rjArr(rj::kArrayType);
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for (const auto idx : sg.getBonds()) {
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rj::Value v1(static_cast<int>(idx));
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rjArr.PushBack(v1, doc.GetAllocator());
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}
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rjSG.AddMember("bonds", rjArr, doc.GetAllocator());
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}
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if (!sg.getParentAtoms().empty()) {
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rj::Value rjArr(rj::kArrayType);
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for (const auto idx : sg.getParentAtoms()) {
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rj::Value v1(static_cast<int>(idx));
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rjArr.PushBack(v1, doc.GetAllocator());
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}
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rjSG.AddMember("parentAtoms", rjArr, doc.GetAllocator());
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}
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if (!sg.getBrackets().empty()) {
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rj::Value rjArr(rj::kArrayType);
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for (const auto &brk : sg.getBrackets()) {
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rj::Value rjBrk(rj::kArrayType);
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for (const auto &pt : brk) {
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rj::Value rjPos(rj::kArrayType);
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rjPos.PushBack(pt.x, doc.GetAllocator());
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rjPos.PushBack(pt.y, doc.GetAllocator());
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rjPos.PushBack(pt.z, doc.GetAllocator());
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rjBrk.PushBack(rjPos, doc.GetAllocator());
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}
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rjArr.PushBack(rjBrk, doc.GetAllocator());
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}
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rjSG.AddMember("brackets", rjArr, doc.GetAllocator());
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}
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if (!sg.getCStates().empty()) {
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rj::Value rjArr(rj::kArrayType);
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for (const auto &cs : sg.getCStates()) {
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rj::Value rjCS(rj::kObjectType);
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rjCS.AddMember("bond", cs.bondIdx, doc.GetAllocator());
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if ("SUP" == sg.getProp<std::string>("TYPE")) {
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rj::Value rjLoc(rj::kArrayType);
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rjLoc.PushBack(cs.vector.x, doc.GetAllocator());
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rjLoc.PushBack(cs.vector.y, doc.GetAllocator());
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rjLoc.PushBack(cs.vector.z, doc.GetAllocator());
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rjCS.AddMember("vector", rjLoc, doc.GetAllocator());
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}
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rjArr.PushBack(rjCS, doc.GetAllocator());
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}
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rjSG.AddMember("cstates", rjArr, doc.GetAllocator());
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}
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if (!sg.getAttachPoints().empty()) {
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rj::Value rjArr(rj::kArrayType);
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for (const auto &ap : sg.getAttachPoints()) {
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rj::Value rjAP(rj::kObjectType);
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rjAP.AddMember("aIdx", ap.aIdx, doc.GetAllocator());
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if (ap.lvIdx != -1) {
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rjAP.AddMember("lvIdx", ap.lvIdx, doc.GetAllocator());
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}
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if (!ap.id.empty()) {
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addStringVal(rjAP, "id", ap.id, doc);
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}
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rjArr.PushBack(rjAP, doc.GetAllocator());
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}
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rjSG.AddMember("attachPoints", rjArr, doc.GetAllocator());
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}
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}
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void addConformer(const Conformer &conf, rj::Value &rjConf, rj::Document &doc) {
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int dim = 2;
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if (conf.is3D()) {
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dim = 3;
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}
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rjConf.AddMember("dim", dim, doc.GetAllocator());
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rj::Value rjCoords(rj::kArrayType);
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for (const auto &pos : conf.getPositions()) {
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rj::Value rjPos(rj::kArrayType);
|
|
rjPos.PushBack(pos.x, doc.GetAllocator());
|
|
rjPos.PushBack(pos.y, doc.GetAllocator());
|
|
if (dim == 3) {
|
|
rjPos.PushBack(pos.z, doc.GetAllocator());
|
|
}
|
|
rjCoords.PushBack(rjPos, doc.GetAllocator());
|
|
}
|
|
rjConf.AddMember("coords", rjCoords, doc.GetAllocator());
|
|
}
|
|
|
|
template <typename T>
|
|
void addMol(const T &imol, rj::Value &rjMol, rj::Document &doc,
|
|
const rj::Value &atomDefaults, const rj::Value &bondDefaults,
|
|
const JSONWriteParameters ¶ms) {
|
|
RWMol mol(imol);
|
|
if (!mol.getRingInfo()->isSymmSssr()) {
|
|
MolOps::symmetrizeSSSR(mol);
|
|
}
|
|
if (mol.needsUpdatePropertyCache()) {
|
|
mol.updatePropertyCache(false);
|
|
}
|
|
try {
|
|
MolOps::Kekulize(mol, false);
|
|
} catch (const KekulizeException &) {
|
|
mol = imol;
|
|
if (mol.needsUpdatePropertyCache()) {
|
|
mol.updatePropertyCache(false);
|
|
}
|
|
}
|
|
if (mol.hasProp(common_properties::_Name)) {
|
|
rj::Value nmv;
|
|
const std::string &nm =
|
|
mol.getProp<std::string>(common_properties::_Name).c_str();
|
|
nmv.SetString(nm.c_str(), nm.size(), doc.GetAllocator());
|
|
rjMol.AddMember("name", nmv, doc.GetAllocator());
|
|
}
|
|
rj::Value rjAtoms(rj::kArrayType);
|
|
bool hasQueryAtoms = false;
|
|
for (const auto &at : mol.atoms()) {
|
|
rj::Value rjAtom(rj::kObjectType);
|
|
addAtom(*at, rjAtom, doc, atomDefaults);
|
|
rjAtoms.PushBack(rjAtom, doc.GetAllocator());
|
|
if (at->hasQuery()) {
|
|
hasQueryAtoms = true;
|
|
}
|
|
}
|
|
rjMol.AddMember("atoms", rjAtoms, doc.GetAllocator());
|
|
|
|
rj::Value rjBonds(rj::kArrayType);
|
|
bool hasQueryBonds = false;
|
|
for (const auto &bnd : mol.bonds()) {
|
|
rj::Value rjBond(rj::kObjectType);
|
|
addBond(*bnd, rjBond, doc, bondDefaults, params);
|
|
rjBonds.PushBack(rjBond, doc.GetAllocator());
|
|
if (bnd->hasQuery()) {
|
|
hasQueryBonds = true;
|
|
}
|
|
}
|
|
rjMol.AddMember("bonds", rjBonds, doc.GetAllocator());
|
|
|
|
if (params.useRDKitExtensions && !mol.getStereoGroups().empty()) {
|
|
rj::Value rjStereoGroups(rj::kArrayType);
|
|
for (const auto &sg : mol.getStereoGroups()) {
|
|
rj::Value rjSG(rj::kObjectType);
|
|
addStereoGroup(sg, rjSG, doc);
|
|
rjStereoGroups.PushBack(rjSG, doc.GetAllocator());
|
|
}
|
|
rjMol.AddMember("stereoGroups", rjStereoGroups, doc.GetAllocator());
|
|
}
|
|
|
|
if (params.useRDKitExtensions && !getSubstanceGroups(mol).empty()) {
|
|
rj::Value rjSubstanceGroups(rj::kArrayType);
|
|
for (const auto &sg : getSubstanceGroups(mol)) {
|
|
rj::Value rjSG(rj::kObjectType);
|
|
addSubstanceGroup(sg, rjSG, doc);
|
|
rjSubstanceGroups.PushBack(rjSG, doc.GetAllocator());
|
|
}
|
|
rjMol.AddMember("substanceGroups", rjSubstanceGroups, doc.GetAllocator());
|
|
}
|
|
|
|
if (mol.getNumConformers()) {
|
|
rj::Value rjConfs(rj::kArrayType);
|
|
for (auto conf = mol.beginConformers(); conf != mol.endConformers();
|
|
++conf) {
|
|
rj::Value rjConf(rj::kObjectType);
|
|
addConformer(*(conf->get()), rjConf, doc);
|
|
rjConfs.PushBack(rjConf, doc.GetAllocator());
|
|
}
|
|
|
|
rjMol.AddMember("conformers", rjConfs, doc.GetAllocator());
|
|
}
|
|
|
|
bool includePrivate = false, includeComputed = false;
|
|
auto propNames = mol.getPropList(includePrivate, includeComputed);
|
|
if (propNames.size()) {
|
|
rj::Value properties(rj::kObjectType);
|
|
addProperties(mol, propNames, properties, doc);
|
|
rjMol.AddMember("properties", properties, doc.GetAllocator());
|
|
}
|
|
|
|
rj::Value representation(rj::kObjectType);
|
|
representation.AddMember("name", "rdkitRepresentation", doc.GetAllocator());
|
|
representation.AddMember("formatVersion", currentRDKitRepresentationVersion,
|
|
doc.GetAllocator());
|
|
rj::Value toolkitVersion;
|
|
toolkitVersion.SetString(rj::StringRef(rdkitVersion));
|
|
representation.AddMember("toolkitVersion", toolkitVersion,
|
|
doc.GetAllocator());
|
|
|
|
bool hasArom = false;
|
|
for (const auto &atom : mol.atoms()) {
|
|
if (atom->getIsAromatic()) {
|
|
hasArom = true;
|
|
break;
|
|
}
|
|
}
|
|
if (hasArom) {
|
|
{
|
|
rj::Value rjArr(rj::kArrayType);
|
|
for (const auto &atom : mol.atoms()) {
|
|
if (atom->getIsAromatic()) {
|
|
rjArr.PushBack(atom->getIdx(), doc.GetAllocator());
|
|
}
|
|
}
|
|
representation.AddMember("aromaticAtoms", rjArr, doc.GetAllocator());
|
|
}
|
|
{
|
|
rj::Value rjArr(rj::kArrayType);
|
|
for (const auto &bond : mol.bonds()) {
|
|
if (bond->getIsAromatic()) {
|
|
rjArr.PushBack(bond->getIdx(), doc.GetAllocator());
|
|
}
|
|
}
|
|
representation.AddMember("aromaticBonds", rjArr, doc.GetAllocator());
|
|
}
|
|
}
|
|
{
|
|
rj::Value rjArr(rj::kArrayType);
|
|
if (mol.getAtomWithIdx(0)->hasProp(common_properties::_CIPRank)) {
|
|
for (const auto &atom : mol.atoms()) {
|
|
rjArr.PushBack(atom->getProp<unsigned int>(common_properties::_CIPRank),
|
|
doc.GetAllocator());
|
|
}
|
|
}
|
|
if (rjArr.Size()) {
|
|
representation.AddMember("cipRanks", rjArr, doc.GetAllocator());
|
|
}
|
|
}
|
|
{
|
|
rj::Value rjArr(rj::kArrayType);
|
|
for (const auto &atom : mol.atoms()) {
|
|
std::string cip;
|
|
if (atom->getPropIfPresent(common_properties::_CIPCode, cip)) {
|
|
rj::Value cipv;
|
|
cipv.SetString(cip.c_str(), cip.size(), doc.GetAllocator());
|
|
rj::Value rjElement(rj::kArrayType);
|
|
rjElement.PushBack(rj::Value(atom->getIdx()), doc.GetAllocator());
|
|
rjElement.PushBack(cipv, doc.GetAllocator());
|
|
rjArr.PushBack(rjElement, doc.GetAllocator());
|
|
}
|
|
}
|
|
if (rjArr.Size()) {
|
|
representation.AddMember("cipCodes", rjArr, doc.GetAllocator());
|
|
}
|
|
}
|
|
if (mol.getRingInfo()->numRings()) {
|
|
{
|
|
rj::Value rjArr(rj::kArrayType);
|
|
for (const auto &ring : mol.getRingInfo()->atomRings()) {
|
|
rj::Value rjRing(rj::kArrayType);
|
|
for (const auto &ai : ring) {
|
|
rjRing.PushBack(ai, doc.GetAllocator());
|
|
}
|
|
rjArr.PushBack(rjRing, doc.GetAllocator());
|
|
}
|
|
representation.AddMember("atomRings", rjArr, doc.GetAllocator());
|
|
}
|
|
}
|
|
|
|
rj::Value rjReprs(rj::kArrayType);
|
|
rjReprs.PushBack(representation, doc.GetAllocator());
|
|
|
|
if (mol.getAtomWithIdx(0)->hasProp(common_properties::_GasteigerCharge)) {
|
|
rj::Value representation(rj::kObjectType);
|
|
representation.AddMember("name", "partialCharges", doc.GetAllocator());
|
|
representation.AddMember("generator", "RDKit", doc.GetAllocator());
|
|
representation.AddMember("formatVersion",
|
|
currentChargeRepresentationVersion,
|
|
doc.GetAllocator());
|
|
rj::Value toolkitVersion;
|
|
toolkitVersion.SetString(rj::StringRef(rdkitVersion));
|
|
representation.AddMember("generatorVersion", toolkitVersion,
|
|
doc.GetAllocator());
|
|
|
|
rj::Value rjArr(rj::kArrayType);
|
|
for (const auto &at : mol.atoms()) {
|
|
rj::Value rjval;
|
|
if (at->hasProp(common_properties::_GasteigerCharge)) {
|
|
rjval = at->getProp<double>(common_properties::_GasteigerCharge);
|
|
} else {
|
|
rjval = 0.0;
|
|
}
|
|
rjArr.PushBack(rjval, doc.GetAllocator());
|
|
}
|
|
representation.AddMember("values", rjArr, doc.GetAllocator());
|
|
rjReprs.PushBack(representation, doc.GetAllocator());
|
|
}
|
|
|
|
if (hasQueryAtoms || hasQueryBonds) {
|
|
rj::Value representation(rj::kObjectType);
|
|
representation.AddMember("name", "rdkitQueries", doc.GetAllocator());
|
|
representation.AddMember("formatVersion", currentQueryRepresentationVersion,
|
|
doc.GetAllocator());
|
|
rj::Value toolkitVersion;
|
|
toolkitVersion.SetString(rj::StringRef(rdkitVersion));
|
|
representation.AddMember("toolkitVersion", toolkitVersion,
|
|
doc.GetAllocator());
|
|
|
|
if (hasQueryAtoms) {
|
|
rj::Value rjArr(rj::kArrayType);
|
|
for (const auto &atom : mol.atoms()) {
|
|
rj::Value rjQ(rj::kObjectType);
|
|
if (atom->hasQuery()) {
|
|
addQuery(*atom->getQuery(), rjQ, doc, params);
|
|
}
|
|
rjArr.PushBack(rjQ, doc.GetAllocator());
|
|
}
|
|
representation.AddMember("atomQueries", rjArr, doc.GetAllocator());
|
|
}
|
|
if (hasQueryBonds) {
|
|
rj::Value rjArr(rj::kArrayType);
|
|
for (const auto &bond : mol.bonds()) {
|
|
rj::Value rjQ(rj::kObjectType);
|
|
if (bond->hasQuery()) {
|
|
addQuery(*bond->getQuery(), rjQ, doc, params);
|
|
}
|
|
rjArr.PushBack(rjQ, doc.GetAllocator());
|
|
}
|
|
representation.AddMember("bondQueries", rjArr, doc.GetAllocator());
|
|
}
|
|
rjReprs.PushBack(representation, doc.GetAllocator());
|
|
}
|
|
rjMol.AddMember("extensions", rjReprs, doc.GetAllocator());
|
|
}
|
|
} // end of anonymous namespace
|
|
|
|
template <typename T>
|
|
std::string MolsToJSONData(const std::vector<T> &mols,
|
|
const JSONWriteParameters ¶ms) {
|
|
std::string res = "";
|
|
rj::Document doc;
|
|
doc.SetObject();
|
|
|
|
rj::Value header(rj::kObjectType);
|
|
initHeader(header, doc, params);
|
|
if (!params.useRDKitExtensions) {
|
|
doc.AddMember("commonchem", header, doc.GetAllocator());
|
|
} else {
|
|
doc.AddMember("rdkitjson", header, doc.GetAllocator());
|
|
}
|
|
|
|
rj::Value defaults(rj::kObjectType);
|
|
|
|
rj::Value atomDefaults(rj::kObjectType);
|
|
initAtomDefaults(atomDefaults, doc);
|
|
defaults.AddMember("atom", atomDefaults, doc.GetAllocator());
|
|
|
|
rj::Value bondDefaults(rj::kObjectType);
|
|
initBondDefaults(bondDefaults, doc);
|
|
defaults.AddMember("bond", bondDefaults, doc.GetAllocator());
|
|
doc.AddMember("defaults", defaults, doc.GetAllocator());
|
|
|
|
rj::Value rjMols(rj::kArrayType);
|
|
for (const auto &mol : mols) {
|
|
if (!mol) {
|
|
throw ValueErrorException("null molecule passed to MolsToJSONData");
|
|
}
|
|
rj::Value rjMol(rj::kObjectType);
|
|
// write mol;
|
|
addMol(*mol, rjMol, doc, *rj::GetValueByPointer(doc, "/defaults/atom"),
|
|
*rj::GetValueByPointer(doc, "/defaults/bond"), params);
|
|
rjMols.PushBack(rjMol, doc.GetAllocator());
|
|
}
|
|
doc.AddMember("molecules", rjMols, doc.GetAllocator());
|
|
|
|
rj::StringBuffer buffer;
|
|
rj::Writer<rj::StringBuffer> writer(buffer);
|
|
writer.SetMaxDecimalPlaces(4);
|
|
doc.Accept(writer);
|
|
return buffer.GetString();
|
|
};
|
|
|
|
template RDKIT_MOLINTERCHANGE_EXPORT std::string MolsToJSONData<ROMol *>(
|
|
const std::vector<ROMol *> &, const JSONWriteParameters &);
|
|
template RDKIT_MOLINTERCHANGE_EXPORT std::string MolsToJSONData<RWMol *>(
|
|
const std::vector<RWMol *> &, const JSONWriteParameters &);
|
|
template RDKIT_MOLINTERCHANGE_EXPORT std::string MolsToJSONData<const ROMol *>(
|
|
const std::vector<const ROMol *> &, const JSONWriteParameters &);
|
|
template RDKIT_MOLINTERCHANGE_EXPORT std::string MolsToJSONData<const RWMol *>(
|
|
const std::vector<const RWMol *> &, const JSONWriteParameters &);
|
|
|
|
} // end of namespace MolInterchange
|
|
} // end of namespace RDKit
|