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09aa009f19
* basic approach to v2api * does not work, backup commit * well, that now compiles * cleaner * more cleanup and testing * get the SWIG wrappers to build * swig wrappers now build * switch back to using references to default values * adjust to new catch version * move the implementation to v2 and call it from v1 * update the parameter object too * move debugParse down * a couple of review changes * make v2 naming consistent with Python * first pass at v2 for the ctab parsers * move a the writing functionality to a different header this is just an organizational thing at the moment; we still import the writers header in the parsers header so as to not break code * do v2 of the tpl parser * fix missing dependency * Mol2 parser * move over the XYZ parser * switch over the PDB parsers too * get mac and java builds working (hopefully) * add v2 API for the reaction parsers Fixes #7075 * v2 of the fileparser API about done This cannot be completed until the CDXML changes are merged
87 lines
2.9 KiB
C++
87 lines
2.9 KiB
C++
//
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// Copyright (c) 2020 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 <GraphMol/ChemReactions/Reaction.h>
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#include <GraphMol/ChemReactions/ReactionPickler.h>
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#include <GraphMol/ChemReactions/ReactionParser.h>
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#include <GraphMol/FileParsers/PNGParser.h>
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#include <boost/algorithm/string.hpp>
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namespace RDKit {
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namespace PNGData {
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const std::string rxnSmilesTag = "ReactionSmiles";
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const std::string rxnSmartsTag = "ReactionSmarts";
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const std::string rxnRxnTag = "ReactionRxn";
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const std::string rxnPklTag = "rdkitReactionPKL";
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} // namespace PNGData
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std::string addChemicalReactionToPNGStream(const ChemicalReaction &rxn,
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std::istream &iStream,
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bool includePkl, bool includeSmiles,
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bool includeSmarts,
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bool includeRxn) {
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std::vector<std::pair<std::string, std::string>> metadata;
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if (includePkl) {
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std::string pkl;
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ReactionPickler::pickleReaction(rxn, pkl);
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metadata.push_back(std::make_pair(augmentTagName(PNGData::rxnPklTag), pkl));
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}
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if (includeSmiles) {
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std::string smi = ChemicalReactionToRxnSmiles(rxn);
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metadata.push_back(
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std::make_pair(augmentTagName(PNGData::rxnSmilesTag), smi));
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}
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if (includeSmarts) {
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std::string smi = ChemicalReactionToRxnSmarts(rxn);
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metadata.push_back(
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std::make_pair(augmentTagName(PNGData::rxnSmartsTag), smi));
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}
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if (includeRxn) {
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std::string mb = ChemicalReactionToRxnBlock(rxn);
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metadata.push_back(std::make_pair(augmentTagName(PNGData::rxnRxnTag), mb));
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}
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return addMetadataToPNGStream(iStream, metadata);
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};
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namespace v2 {
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namespace ReactionParser {
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std::unique_ptr<ChemicalReaction> ReactionFromPNGStream(
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std::istream &inStream) {
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std::unique_ptr<ChemicalReaction> res;
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auto metadata = PNGStreamToMetadata(inStream);
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bool formatFound = false;
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for (const auto &pr : metadata) {
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if (boost::starts_with(pr.first, PNGData::rxnPklTag)) {
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res.reset(new ChemicalReaction(pr.second));
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formatFound = true;
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} else if (boost::starts_with(pr.first, PNGData::rxnSmilesTag)) {
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ReactionFromSmiles(pr.second).swap(res);
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formatFound = true;
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} else if (boost::starts_with(pr.first, PNGData::rxnSmartsTag)) {
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ReactionFromSmarts(pr.second).swap(res);
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formatFound = true;
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} else if (boost::starts_with(pr.first, PNGData::rxnRxnTag)) {
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ReactionFromRxnBlock(pr.second).swap(res);
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formatFound = true;
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}
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if (formatFound) {
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break;
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}
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}
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if (!formatFound) {
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throw FileParseException("No suitable metadata found.");
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}
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return res;
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}
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} // namespace ReactionParser
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} // namespace v2
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} // namespace RDKit
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