rdkit/External/ChemDraw/reaction.cpp

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#include "chemdraw.h"
#include "chemdrawreaction.h"
#include "reaction.h"
#include "utils.h"

#include <GraphMol/QueryOps.h>
#include <GraphMol/ChemReactions/SanitizeRxn.h>
#include <GraphMol/ChemReactions/ReactionUtils.h>
#include <GraphMol/ChemTransforms/ChemTransforms.h>

namespace RDKit {
namespace ChemDraw {
void ReactionStepInfo::set_reaction_data(
    std::string type, std::string prop, const std::vector<int> &frag_ids,
    const std::map<unsigned int, size_t> &fragments,
    std::map<unsigned int, std::vector<int>> &grouped_fragments,
    const std::vector<std::unique_ptr<RWMol>> &mols) const {
  unsigned int reagent_idx = 0;
  for (auto idx : frag_ids) {
    auto iter = grouped_fragments.find(idx);
    if (iter == grouped_fragments.end()) {
      BOOST_LOG(rdWarningLog) << "CDXMLParser: Schema " << scheme_id << " step "
                              << step_id << " " << type << " reaction fragment "
                              << idx << " not found in document." << std::endl;
      continue;
    }
    for (auto reaction_fragment_id : iter->second) {
      auto fragment = fragments.find(reaction_fragment_id);
      if (fragment == fragments.end()) {
        BOOST_LOG(rdWarningLog)
            << "CDXMLParser: Schema " << scheme_id << " step " << step_id << " "
            << type << " fragment " << idx << " not found in document."
            << std::endl;
        continue;
      }
      auto &mol = mols[fragment->second];
      mol->setProp(CDX_SCHEME_ID, scheme_id);
      mol->setProp(CDX_STEP_ID, step_id);
      mol->setProp(prop, reagent_idx);
    }
    reagent_idx += 1;
  }
}

void ReactionStepInfo::set_reaction_step(
    size_t scheme_id, std::map<unsigned int, Atom *> &atoms,
    const std::map<unsigned int, size_t> &fragments,
    std::map<unsigned int, std::vector<int>> &grouped_fragments,
    const std::vector<std::unique_ptr<RWMol>> &mols) const {
  // Set the molecule properties
  set_reaction_data("ReactionStepReactants", CDX_REAGENT_ID,
                    ReactionStepReactants, fragments, grouped_fragments, mols);
  set_reaction_data("ReactionStepProducts", CDX_PRODUCT_ID,
                    ReactionStepProducts, fragments, grouped_fragments, mols);

  auto agents = ReactionStepObjectsAboveArrow;
  agents.insert(agents.end(), ReactionStepObjectsBelowArrow.begin(),
                ReactionStepObjectsBelowArrow.end());
  set_reaction_data("ReactionStepAgents", CDX_AGENT_ID, agents, fragments,
                    grouped_fragments, mols);

  // Set the Atom Maps
  int atommap = 0;
  for (auto mapping : ReactionStepAtomMap) {
    ++atommap;
    unsigned int idx1 = mapping.first;
    unsigned int idx2 = mapping.second;
    if (atoms.find(idx1) != atoms.end()) {
      atoms[idx1]->setAtomMapNum(atommap);
    } else {
      BOOST_LOG(rdWarningLog)
          << "CDXMLParser: Schema " << scheme_id << " step " << step_id
          << " ReactionStepAtomMap cannot find atom with node id " << idx1
          << "skipping schema..." << std::endl;
    }
    if (atoms.find(idx2) != atoms.end()) {
      atoms[idx2]->setAtomMapNum(atommap);
    } else {
      // XXX log error
      BOOST_LOG(rdWarningLog)
          << "CDXMLParser: Schema " << scheme_id << " step " << step_id
          << " ReactionStepAtomMap cannot find atom with node id " << idx2
          << " skipping schema..." << std::endl;
    }
  }
}

ReactionInfo::ReactionInfo(CDXReactionScheme &scheme)
    : scheme_id(static_cast<unsigned int>(scheme.GetObjectID())) {
  for (auto &rxnNode : scheme.ContainedObjects()) {
    auto type_id = (CDXDatumID)rxnNode.second->GetTag();
    if (type_id == kCDXObj_ReactionStep) {
      auto &step = (CDXReactionStep &)(*rxnNode.second);
      auto step_id = step.GetObjectID();
      steps.emplace_back(ReactionStepInfo());
      ReactionStepInfo &scheme = steps.back();
      scheme.scheme_id = scheme_id;
      scheme.step_id = step_id;
      scheme.ReactionStepProducts = step.m_products;
      scheme.ReactionStepReactants = step.m_reactants;
      scheme.ReactionStepObjectsBelowArrow = step.m_objectsBelowArrow;
      scheme.ReactionStepAtomMap = step.m_aamap;
      steps.push_back(scheme);
    }
  }
}

void ReactionInfo::set_reaction_steps(
    std::map<unsigned int, std::vector<int>> &grouped_fragments,
    const std::vector<std::unique_ptr<RWMol>> &mols) const {
  if (steps.size()) {
    std::map<unsigned int, size_t> fragments;
    std::map<unsigned int, size_t> agents;
    std::map<unsigned int, size_t> products;
    std::map<unsigned int, Atom *> atoms;
    size_t mol_idx = 0;
    for (auto &mol : mols) {
      auto idx = mol->getProp<unsigned int>(CDX_FRAG_ID);
      fragments[idx] = mol_idx++;
      for (auto &atom : mol->atoms()) {
        auto idx = atom->getProp<unsigned int>(CDX_ATOM_ID);
        atoms[idx] = atom;
      }
    }

    for (auto &step : steps) {
      step.set_reaction_step(scheme_id, atoms, fragments, grouped_fragments,
                             mols);
    }
  }
}
}  // namespace ChemDraw
}  // namespace RDKit