rdkit/Code/GraphMol/ChemReactions/MDLParser.cpp

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#include <GraphMol/QueryOps.h>
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/FileParserUtils.h>
#include <sstream>
#include <RDGeneral/StreamOps.h>
#include <RDGeneral/FileParseException.h>

#include <fstream>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/lexical_cast.hpp>
#include <boost/algorithm/string/trim.hpp>
#include <boost/tokenizer.hpp>
#include <RDGeneral/BoostEndInclude.h>

#include "ReactionUtils.h"

namespace RDKit {

using namespace v2::FileParsers;

namespace {
void ParseV2000RxnBlock(std::istream &inStream, unsigned int &line,
                        const MolFileParserParams &params,
                        std::unique_ptr<ChemicalReaction> &rxn) {
  std::string tempStr;
  // FIX: parse name and comment fields
  line++;
  tempStr = getLine(inStream);
  line++;
  tempStr = getLine(inStream);
  line++;
  tempStr = getLine(inStream);
  line++;
  tempStr = getLine(inStream);
  if (inStream.eof()) {
    throw ChemicalReactionParserException("premature EOF hit.");
  }

  unsigned int nReacts = 0, nProds = 0, nAgents = 0;
  unsigned int spos = 0;
  if (tempStr.size() < 6) {
    throw ChemicalReactionParserException("rxn counts line is too short");
  }
  rxn.reset(new ChemicalReaction());
  try {
    nReacts =
        FileParserUtils::stripSpacesAndCast<unsigned int>(tempStr.substr(0, 3));
    spos = 3;
    nProds = FileParserUtils::stripSpacesAndCast<unsigned int>(
        tempStr.substr(spos, 3));
    spos = 6;
    ;
    if (tempStr.size() > 6) {
      std::string trimmed = boost::trim_copy(tempStr.substr(spos, 3));
      if (trimmed.size() > 0) {
        nAgents = FileParserUtils::stripSpacesAndCast<unsigned int>(
            tempStr.substr(spos, 3));
        spos = 9;
      }
    }
  } catch (boost::bad_lexical_cast &) {
    std::ostringstream errout;
    errout << "Cannot convert " << tempStr.substr(spos, 3) << " to int";
    throw ChemicalReactionParserException(errout.str());
  }

  for (unsigned int i = 0; i < nReacts; ++i) {
    line++;
    tempStr = getLine(inStream);
    if (inStream.eof()) {
      throw ChemicalReactionParserException("premature EOF hit.");
    }
    if (tempStr.substr(0, 4) != "$MOL") {
      throw ChemicalReactionParserException("$MOL header not found");
    }
    ROMol *react;
    try {
      react = MolFromMolDataStream(inStream, line, params).release();
    } catch (FileParseException &e) {
      std::ostringstream errout;
      errout << "Cannot parse reactant " << i << ". The error was:\n\t"
             << e.what();
      throw ChemicalReactionParserException(errout.str());
    }
    if (!react) {
      throw ChemicalReactionParserException("Null reactant in reaction file.");
    }
    rxn->addReactantTemplate(ROMOL_SPTR(react));
  }
  for (unsigned int i = 0; i < nProds; ++i) {
    line++;
    tempStr = getLine(inStream);
    if (inStream.eof()) {
      throw ChemicalReactionParserException("premature EOF hit.");
    }
    if (tempStr.substr(0, 4) != "$MOL") {
      throw ChemicalReactionParserException("$MOL header not found");
    }
    ROMol *prod;
    try {
      prod = MolFromMolDataStream(inStream, line, params).release();
    } catch (FileParseException &e) {
      std::ostringstream errout;
      errout << "Cannot parse product " << i << ". The error was:\n\t"
             << e.what();
      throw ChemicalReactionParserException(errout.str());
    }
    if (!prod) {
      throw ChemicalReactionParserException("Null product in reaction file.");
    }
    rxn->addProductTemplate(ROMOL_SPTR(prod));
  }

  for (unsigned int i = 0; i < nAgents; ++i) {
    line++;
    tempStr = getLine(inStream);
    if (inStream.eof()) {
      throw ChemicalReactionParserException("premature EOF hit.");
    }
    if (tempStr.substr(0, 4) != "$MOL") {
      throw ChemicalReactionParserException("$MOL header not found");
    }
    // we don't sanitize or remove Hs from agents
    MolFileParserParams agentParams;
    agentParams.sanitize = false;
    agentParams.removeHs = false;
    agentParams.strictParsing = params.strictParsing;
    ROMol *agent;
    try {
      agent = MolFromMolDataStream(inStream, line, agentParams).release();
    } catch (FileParseException &e) {
      std::ostringstream errout;
      errout << "Cannot parse agent " << i << ". The error was:\n\t"
             << e.what();
      throw ChemicalReactionParserException(errout.str());
    }
    rxn->addAgentTemplate(ROMOL_SPTR(agent));
  }
}

void ParseV3000RxnBlock(std::istream &inStream, unsigned int &line,
                        const MolFileParserParams &params,
                        std::unique_ptr<ChemicalReaction> &rxn) {
  std::string tempStr;

  // skip the header block:
  line++;
  tempStr = getLine(inStream);
  line++;
  tempStr = getLine(inStream);
  line++;
  tempStr = getLine(inStream);
  line++;

  tempStr = FileParserUtils::getV3000Line(&inStream, line);
  boost::to_upper(tempStr);
  tempStr = boost::trim_copy(tempStr);
  std::vector<std::string> tokens;
  boost::split(tokens, tempStr, boost::is_any_of(" \t"),
               boost::token_compress_on);
  if (tokens.size() < 3 || tokens[0] != "COUNTS") {
    throw ChemicalReactionParserException("bad counts line");
  }
  auto nReacts = FileParserUtils::stripSpacesAndCast<unsigned int>(tokens[1]);
  auto nProds = FileParserUtils::stripSpacesAndCast<unsigned int>(tokens[2]);
  unsigned int nAgents = 0;
  if (tokens.size() > 3) {
    nAgents = FileParserUtils::stripSpacesAndCast<unsigned int>(tokens[3]);
  }

  tempStr = FileParserUtils::getV3000Line(&inStream, line);
  boost::to_upper(tempStr);
  if (tempStr.length() < 14 || tempStr.substr(0, 14) != "BEGIN REACTANT") {
    throw FileParseException("BEGIN REACTANT line not found");
  }
  rxn.reset(new ChemicalReaction());
  const bool expectMEND = false;
  for (unsigned int i = 0; i < nReacts; ++i) {
    RWMol *react;
    unsigned int natoms, nbonds;
    bool chiralityPossible = false;
    Conformer *conf = nullptr;
    react = new RWMol();
    try {
      FileParserUtils::ParseV3000CTAB(&inStream, line, react, conf,
                                      chiralityPossible, natoms, nbonds,
                                      params.strictParsing, expectMEND);
      FileParserUtils::finishMolProcessing(react, chiralityPossible, params);
    } catch (FileParseException &e) {
      std::ostringstream errout;
      errout << "Cannot parse reactant " << i << ". The error was:\n\t"
             << e.what();
      delete react;
      throw ChemicalReactionParserException(errout.str());
    }
    if (!react) {
      throw ChemicalReactionParserException("Null reactant in reaction file.");
    }
    rxn->addReactantTemplate(ROMOL_SPTR(dynamic_cast<ROMol *>(react)));
  }
  tempStr = FileParserUtils::getV3000Line(&inStream, line);
  boost::to_upper(tempStr);
  if (tempStr.length() < 12 || tempStr.substr(0, 12) != "END REACTANT") {
    throw FileParseException("END REACTANT line not found");
  }
  tempStr = FileParserUtils::getV3000Line(&inStream, line);
  boost::to_upper(tempStr);
  if (tempStr.length() < 13 || tempStr.substr(0, 13) != "BEGIN PRODUCT") {
    throw FileParseException("BEGIN PRODUCT line not found");
  }
  for (unsigned int i = 0; i < nProds; ++i) {
    RWMol *prod;
    unsigned int natoms, nbonds;
    bool chiralityPossible = false;
    Conformer *conf = nullptr;
    prod = new RWMol();
    try {
      FileParserUtils::ParseV3000CTAB(&inStream, line, prod, conf,
                                      chiralityPossible, natoms, nbonds,
                                      params.strictParsing, expectMEND);
      FileParserUtils::finishMolProcessing(prod, chiralityPossible, params);
    } catch (FileParseException &e) {
      std::ostringstream errout;
      errout << "Cannot parse product " << i << ". The error was:\n\t"
             << e.what();
      delete prod;
      throw ChemicalReactionParserException(errout.str());
    }
    if (!prod) {
      throw ChemicalReactionParserException("Null product in reaction file.");
    }
    rxn->addProductTemplate(ROMOL_SPTR(dynamic_cast<ROMol *>(prod)));
  }
  tempStr = FileParserUtils::getV3000Line(&inStream, line);
  boost::to_upper(tempStr);
  if (tempStr.length() < 11 || tempStr.substr(0, 11) != "END PRODUCT") {
    throw FileParseException("END PRODUCT line not found");
  }

  if (nAgents) {
    tempStr = FileParserUtils::getV3000Line(&inStream, line);
    boost::to_upper(tempStr);
    if (tempStr.length() < 11 || tempStr.substr(0, 11) != "BEGIN AGENT") {
      throw FileParseException("BEGIN AGENT line not found");
    }
  }
  for (unsigned int i = 0; i < nAgents; ++i) {
    RWMol *agent;
    unsigned int natoms, nbonds;
    bool chiralityPossible = false;
    Conformer *conf = nullptr;
    agent = new RWMol();
    try {
      FileParserUtils::ParseV3000CTAB(&inStream, line, agent, conf,
                                      chiralityPossible, natoms, nbonds, true,
                                      false);
      FileParserUtils::finishMolProcessing(agent, chiralityPossible, params);

    } catch (FileParseException &e) {
      std::ostringstream errout;
      errout << "Cannot parse agent " << i << ". The error was:\n\t"
             << e.what();
      delete agent;
      throw ChemicalReactionParserException(errout.str());
    }
    rxn->addAgentTemplate(ROMOL_SPTR(dynamic_cast<ROMol *>(agent)));
  }
  if (nAgents) {
    tempStr = FileParserUtils::getV3000Line(&inStream, line);
    boost::to_upper(tempStr);
    if (tempStr.length() < 9 || tempStr.substr(0, 9) != "END AGENT") {
      throw FileParseException("END AGENT line not found");
    }
  }
}
}  // namespace

namespace v2 {
namespace ReactionParser {

//! Parse a text stream in MDL rxn format into a ChemicalReaction
std::unique_ptr<ChemicalReaction> ReactionFromRxnDataStream(
    std::istream &inStream, unsigned int &line,
    const MolFileParserParams &params) {
  std::string tempStr;

  // header line
  line++;
  tempStr = getLine(inStream);
  if (inStream.eof()) {
    throw ChemicalReactionParserException("premature EOF hit.");
  }
  if (tempStr.substr(0, 4) != "$RXN") {
    throw ChemicalReactionParserException("$RXN header not found");
  }
  int version = 2000;
  if (tempStr.size() >= 10 && tempStr.substr(5, 5) == "V3000") {
    version = 3000;
  }

  std::unique_ptr<ChemicalReaction> res;
  try {
    if (version == 2000) {
      ParseV2000RxnBlock(inStream, line, params, res);
    } else {
      ParseV3000RxnBlock(inStream, line, params, res);
    }
  } catch (ChemicalReactionParserException &e) {
    // catch our exceptions and throw them back after cleanup
    res.reset();
    throw e;
  }
  // convert atoms to queries:
  for (MOL_SPTR_VECT::const_iterator iter = res->beginReactantTemplates();
       iter != res->endReactantTemplates(); ++iter) {
    // to write the mol block, we need ring information:
    for (ROMol::AtomIterator atomIt = (*iter)->beginAtoms();
         atomIt != (*iter)->endAtoms(); ++atomIt) {
      QueryOps::replaceAtomWithQueryAtom((RWMol *)iter->get(), (*atomIt));
    }
  }
  for (MOL_SPTR_VECT::const_iterator iter = res->beginProductTemplates();
       iter != res->endProductTemplates(); ++iter) {
    // to write the mol block, we need ring information:
    for (ROMol::AtomIterator atomIt = (*iter)->beginAtoms();
         atomIt != (*iter)->endAtoms(); ++atomIt) {
      QueryOps::replaceAtomWithQueryAtom((RWMol *)iter->get(), (*atomIt));
    }
  }
  updateProductsStereochem(res.get());

  // RXN-based reactions do not have implicit properties
  res->setImplicitPropertiesFlag(false);
  return res;
};

std::unique_ptr<ChemicalReaction> ReactionFromRxnBlock(
    const std::string &rxnBlock, const MolFileParserParams &params) {
  std::istringstream inStream(rxnBlock);
  unsigned int line = 0;
  return ReactionFromRxnDataStream(inStream, line, params);
};

std::unique_ptr<ChemicalReaction> ReactionFromRxnFile(
    const std::string &fName, const MolFileParserParams &params) {
  std::ifstream inStream(fName.c_str());
  if (!inStream || inStream.eof()) {
    return nullptr;
  }
  unsigned int line = 0;
  return ReactionFromRxnDataStream(inStream, line, params);
};
}  // namespace ReactionParser
}  // namespace v2
}  // namespace RDKit