rdkit/Code/GraphMol/MolStandardize/MolStandardize.cpp

//
//  Copyright (C) 2018 Susan H. Leung
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include "MolStandardize.h"
#include "Metal.h"
#include "Normalize.h"
#include "Tautomer.h"
#include "Fragment.h"
#include <GraphMol/RDKitBase.h>
#include <iostream>
#include <GraphMol/ROMol.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h>
#include "Charge.h"
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmilesParse.h>

#include <RDGeneral/BoostStartInclude.h>
#include <boost/property_tree/ptree.hpp>
#include <boost/property_tree/json_parser.hpp>
#include <RDGeneral/BoostEndInclude.h>

using namespace std;
namespace RDKit {
namespace MolStandardize {
const CleanupParameters defaultCleanupParameters;

#define PT_OPT_GET(opt) params.opt = pt.get(#opt, params.opt)
void updateCleanupParamsFromJSON(CleanupParameters &params,
                                 const std::string &json) {
  if (json.empty()) {
    return;
  }
  std::istringstream ss;
  ss.str(json);
  boost::property_tree::ptree pt;
  boost::property_tree::read_json(ss, pt);
  PT_OPT_GET(rdbase);
  PT_OPT_GET(normalizations);
  PT_OPT_GET(acidbaseFile);
  PT_OPT_GET(fragmentFile);
  PT_OPT_GET(tautomerTransforms);
  PT_OPT_GET(maxRestarts);
  PT_OPT_GET(preferOrganic);
  PT_OPT_GET(doCanonical);
  PT_OPT_GET(maxTautomers);
  PT_OPT_GET(maxTransforms);
  PT_OPT_GET(tautomerRemoveSp3Stereo);
  PT_OPT_GET(tautomerRemoveBondStereo);
  PT_OPT_GET(tautomerRemoveIsotopicHs);
  PT_OPT_GET(tautomerReassignStereo);
  {
    const auto norm_tfs = pt.get_child_optional("normalizationData");
    if (norm_tfs) {
      for (const auto &entry : *norm_tfs) {
        std::string nm = entry.second.get<std::string>("name", "");
        std::string smarts = entry.second.get<std::string>("smarts", "");
        if (nm.empty() || smarts.empty()) {
          BOOST_LOG(rdWarningLog)
              << " empty transformation name or SMARTS" << std::endl;
          continue;
        }
        params.normalizationData.push_back(std::make_pair(nm, smarts));
      }
    }
  }
  {
    const auto frag_tfs = pt.get_child_optional("fragmentData");
    if (frag_tfs) {
      for (const auto &entry : *frag_tfs) {
        std::string nm = entry.second.get<std::string>("name", "");
        std::string smarts = entry.second.get<std::string>("smarts", "");
        if (nm.empty() || smarts.empty()) {
          BOOST_LOG(rdWarningLog)
              << " empty transformation name or SMARTS" << std::endl;
          continue;
        }
        params.fragmentData.push_back(std::make_pair(nm, smarts));
      }
    }
  }
  {
    const auto ab_data = pt.get_child_optional("acidbaseData");
    if (ab_data) {
      for (const auto &entry : *ab_data) {
        std::string nm = entry.second.get<std::string>("name", "");
        std::string acid = entry.second.get<std::string>("acid", "");
        std::string base = entry.second.get<std::string>("base", "");
        if (nm.empty() || acid.empty() || base.empty()) {
          BOOST_LOG(rdWarningLog)
              << " empty component in acidbaseData" << std::endl;
          continue;
        }
        params.acidbaseData.push_back(std::make_tuple(nm, acid, base));
      }
    }
  }
  {
    const auto taut_data = pt.get_child_optional("tautomerTransformData");
    if (taut_data) {
      for (const auto &entry : *taut_data) {
        std::string nm = entry.second.get<std::string>("name", "");
        std::string smarts = entry.second.get<std::string>("smarts", "");
        std::string bonds = entry.second.get<std::string>("bonds", "");
        std::string charges = entry.second.get<std::string>("charges", "");
        if (nm.empty() || smarts.empty()) {
          BOOST_LOG(rdWarningLog)
              << " empty component in tautomerTransformData" << std::endl;
          continue;
        }
        params.tautomerTransformData.push_back(
            std::make_tuple(nm, smarts, bonds, charges));
      }
    }
  }
}

RWMol *cleanup(const RWMol *mol, const CleanupParameters &params) {
  RWMol m(*mol);
  MolOps::removeHs(m);

  MolStandardize::MetalDisconnector md;
  md.disconnect(m);
  RWMOL_SPTR normalized(MolStandardize::normalize(&m, params));
  RWMol *reionized = MolStandardize::reionize(normalized.get(), params);
  bool cleanIt = true;
  bool force = true;
  MolOps::assignStereochemistry(*reionized, cleanIt, force);

  // update properties of reionized using m.
  reionized->updateProps(m);

  return reionized;
}

RWMol *tautomerParent(const RWMol &mol, const CleanupParameters &params,
                      bool skip_standardize) {
  const RWMol *cleaned = nullptr;
  std::unique_ptr<RWMol> cleanedHolder;

  if (!skip_standardize) {
    cleanedHolder.reset(cleanup(mol, params));
    cleaned = cleanedHolder.get();
  } else {
    cleaned = &mol;
  }

  std::unique_ptr<RWMol> ct{canonicalTautomer(cleaned, params)};

  return cleanup(ct.get(), params);
}

// Return the fragment parent of a given molecule.
// The fragment parent is the largest organic covalent unit in the molecule.
//
RWMol *fragmentParent(const RWMol &mol, const CleanupParameters &params,
                      bool skip_standardize) {
  const RWMol *cleaned = nullptr;
  std::unique_ptr<RWMol> cleanedHolder;

  if (!skip_standardize) {
    cleanedHolder.reset(cleanup(mol, params));
    cleaned = cleanedHolder.get();
  } else {
    cleaned = &mol;
  }

  LargestFragmentChooser lfragchooser(params.preferOrganic);
  return static_cast<RWMol *>(lfragchooser.choose(*cleaned));
}

RWMol *stereoParent(const RWMol &mol, const CleanupParameters &params,
                    bool skip_standardize) {
  RWMol *res;
  if (!skip_standardize) {
    res = cleanup(mol, params);
  } else {
    res = new RWMol(mol);
  }

  MolOps::removeStereochemistry(*res);
  return res;
}

RWMol *isotopeParent(const RWMol &mol, const CleanupParameters &params,
                     bool skip_standardize) {
  RWMol *res;
  if (!skip_standardize) {
    res = cleanup(mol, params);
  } else {
    res = new RWMol(mol);
  }

  for (auto atom : res->atoms()) {
    atom->setIsotope(0);
  }
  return res;
}

RWMol *chargeParent(const RWMol &mol, const CleanupParameters &params,
                    bool skip_standardize) {
  // Return the charge parent of a given molecule.
  // The charge parent is the uncharged version of the fragment parent.

  RWMOL_SPTR fragparent(fragmentParent(mol, params, skip_standardize));

  // if fragment...
  ROMol nm(*fragparent);

  Uncharger uncharger(params.doCanonical);
  ROMOL_SPTR uncharged(uncharger.uncharge(nm));
  RWMol *omol = cleanup(static_cast<RWMol *>(uncharged.get()), params);
  return omol;
}

RWMol *superParent(const RWMol &mol, const CleanupParameters &params,
                   bool skip_standardize) {
  std::unique_ptr<RWMol> res;
  if (!skip_standardize) {
    res.reset(cleanup(mol, params));
  } else {
    res.reset(new RWMol(mol));
  }
  // we can skip fragmentParent since the chargeParent takes care of that
  res.reset(chargeParent(*res, params, true));
  res.reset(isotopeParent(*res, params, true));
  res.reset(stereoParent(*res, params, true));
  res.reset(tautomerParent(*res, params, true));
  return cleanup(*res, params);
}

RWMol *normalize(const RWMol *mol, const CleanupParameters &params) {
  PRECONDITION(mol, "bad molecule");
  std::unique_ptr<Normalizer> normalizer{normalizerFromParams(params)};
  return static_cast<RWMol *>(normalizer->normalize(*mol));
}

RWMol *reionize(const RWMol *mol, const CleanupParameters &params) {
  PRECONDITION(mol, "bad molecule");
  std::unique_ptr<Reionizer> reionizer{reionizerFromParams(params)};
  return static_cast<RWMol *>(reionizer->reionize(*mol));
}

RWMol *removeFragments(const RWMol *mol, const CleanupParameters &params) {
  PRECONDITION(mol, "bad molecule");
  std::unique_ptr<FragmentRemover> remover{fragmentRemoverFromParams(params)};
  return static_cast<RWMol *>(remover->remove(*mol));
}

RWMol *canonicalTautomer(const RWMol *mol, const CleanupParameters &params) {
  PRECONDITION(mol, "bad molecule");
  std::unique_ptr<TautomerEnumerator> te{tautomerEnumeratorFromParams(params)};
  return static_cast<RWMol *>(te->canonicalize(*mol));
}

std::string standardizeSmiles(const std::string &smiles) {
  RWMOL_SPTR mol(SmilesToMol(smiles, 0, false));
  if (!mol) {
    std::string message =
        "SMILES Parse Error: syntax error for input: " + smiles;
    throw ValueErrorException(message);
  }

  CleanupParameters params;
  RWMOL_SPTR cleaned(cleanup(*mol, params));
  return MolToSmiles(*cleaned);
}

std::vector<std::string> enumerateTautomerSmiles(
    const std::string &smiles, const CleanupParameters &params) {
  std::unique_ptr<RWMol> mol(SmilesToMol(smiles, 0, false));
  mol.reset(cleanup(mol.get(), params));
  MolOps::sanitizeMol(*mol);

  TautomerEnumerator te(params);

  auto res = te.enumerate(*mol);

  return res.smiles();
}

}  // end of namespace MolStandardize
}  // namespace RDKit