rdkit/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp

//
//  Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
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#include <GraphMol/RDKitBase.h>
#include <DataStructs/ExplicitBitVect.h>
#include <DataStructs/BitOps.h>
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/Fingerprints/Fingerprints.h>
#include <GraphMol/Fingerprints/AtomPairs.h>
#include "GraphMol/ChemReactions/ReactionFingerprints.h"
#include <GraphMol/Fingerprints/MACCS.h>
#include <GraphMol/Fingerprints/MorganFingerprints.h>
#include <DataStructs/SparseIntVect.h>
#include <GraphMol/ChemReactions/ReactionUtils.h>

namespace {

RDKit::SparseIntVect<std::uint32_t> *generateFingerprint(
    RDKit::ROMol &mol, unsigned int fpSize, RDKit::FingerprintType t) {
  mol.updatePropertyCache(false);
  RDKit::SparseIntVect<std::uint32_t> *res;
  switch (t) {
    case RDKit::AtomPairFP: {
      RDKit::SparseIntVect<std::int32_t> *tmp1 =
          RDKit::AtomPairs::getHashedAtomPairFingerprint(mol, fpSize);
      res = new RDKit::SparseIntVect<std::uint32_t>(fpSize);
      BOOST_FOREACH (
          RDKit::SparseIntVect<std::int32_t>::StorageType::value_type val,
          tmp1->getNonzeroElements()) {
        res->setVal(static_cast<std::uint32_t>(val.first), val.second);
      }
      delete tmp1;
    } break;
    case RDKit::TopologicalTorsion: {
      RDKit::SparseIntVect<boost::int64_t> *tmp2 =
          RDKit::AtomPairs::getHashedTopologicalTorsionFingerprint(mol, fpSize);
      res = new RDKit::SparseIntVect<std::uint32_t>(fpSize);
      BOOST_FOREACH (
          RDKit::SparseIntVect<boost::int64_t>::StorageType::value_type val,
          tmp2->getNonzeroElements()) {
        res->setVal(static_cast<std::uint32_t>(val.first), val.second);
      }
      delete tmp2;
    } break;
    case RDKit::MorganFP: {
      if (!mol.getRingInfo()->isInitialized()) {
        mol.updatePropertyCache();
        RDKit::MolOps::findSSSR(mol);
      }
      res = RDKit::MorganFingerprints::getHashedFingerprint(mol, 2, fpSize);
    } break;
    default:
      std::stringstream err;
      err << ">> unsupported fingerprint type" << std::endl;
      throw RDKit::ChemicalReactionException(err.str());
  }
  return res;
}

ExplicitBitVect *generateFingerprintAsBitVect(RDKit::ROMol &mol,
                                              unsigned int fpSize,
                                              RDKit::FingerprintType t) {
  mol.updatePropertyCache(false);
  ExplicitBitVect *res;
  switch (t) {
    case RDKit::AtomPairFP:
      res =
          RDKit::AtomPairs::getHashedAtomPairFingerprintAsBitVect(mol, fpSize);
      break;
    case RDKit::RDKitFP:
      res = RDKit::RDKFingerprintMol(mol, 1, 7, fpSize);
      break;
    case RDKit::TopologicalTorsion:
      res = RDKit::AtomPairs::getHashedTopologicalTorsionFingerprintAsBitVect(
          mol);
      break;
    case RDKit::MorganFP: {
      if (!mol.getRingInfo()->isInitialized()) {
        mol.updatePropertyCache();
        RDKit::MolOps::findSSSR(mol);
      }
      res = RDKit::MorganFingerprints::getFingerprintAsBitVect(mol, 2, fpSize);
    } break;
    case RDKit::PatternFP:
      res = RDKit::PatternFingerprintMol(mol, fpSize);
      break;
    default:
      std::stringstream err;
      err << ">> unsupported fingerprint type" << std::endl;
      throw RDKit::ChemicalReactionException(err.str());
  }
  return res;
}
}

namespace RDKit {

const ReactionFingerprintParams DefaultStructuralFPParams(true, 0.2, 1, 1, 4096,
                                                            PatternFP);
const ReactionFingerprintParams DefaultDifferenceFPParams(true, 0.0, 10, 1,
                                                            2048, AtomPairFP);

SparseIntVect<std::uint32_t> *generateFingerprintChemReactionAsCountVect(
    const ChemicalReaction &rxn, unsigned int fpSize, FingerprintType t,
    ReactionMoleculeType mt) {
  PRECONDITION(fpSize != 0, "fpSize==0");

  auto *result = new SparseIntVect<std::uint32_t>(fpSize);
  auto begin = getStartIterator(rxn, mt);
  auto end = getEndIterator(rxn, mt);
  for (; begin != end; ++begin) {
    SparseIntVect<std::uint32_t> *tmp =
        generateFingerprint(**begin, fpSize, t);
    (*result) += *tmp;
    delete tmp;
  }
  return result;
}

ExplicitBitVect *generateFingerprintChemReactionAsBitVect(
    const ChemicalReaction &rxn, unsigned int fpSize, FingerprintType t,
    ReactionMoleculeType mt) {
  PRECONDITION(fpSize != 0, "fpSize==0");

  auto *result = new ExplicitBitVect(fpSize);
  auto begin = getStartIterator(rxn, mt);
  auto end = getEndIterator(rxn, mt);
  for (; begin != end; ++begin) {
    ExplicitBitVect *tmp = generateFingerprintAsBitVect(**begin, fpSize, t);
    (*result) |= *tmp;
    delete tmp;
  }
  return result;
}

// caller owns the result, it must be deleted
ExplicitBitVect *StructuralFingerprintChemReaction(
    const ChemicalReaction &rxn, const ReactionFingerprintParams &params) {
  PRECONDITION(params.fpSize != 0, "fpSize==0");

  unsigned int fpSize_final = params.fpSize / 2;
  if (params.includeAgents) {
    unsigned agent_fp_size = params.fpSize / 3;
    if (params.bitRatioAgents < 1.0) {
      agent_fp_size =
          int(ceil(static_cast<double>(params.fpSize) * params.bitRatioAgents));
    }
    unsigned scaling = !(agent_fp_size % 2) ? agent_fp_size : agent_fp_size - 1;
    fpSize_final = (params.fpSize - scaling) / 2;
  }
  unsigned int fpSize_agent = params.fpSize - 2 * fpSize_final;

  ExplicitBitVect *reactantFP = generateFingerprintChemReactionAsBitVect(
      rxn, fpSize_final, params.fpType, Reactant);
  ExplicitBitVect *productFP = generateFingerprintChemReactionAsBitVect(
      rxn, fpSize_final, params.fpType, Product);
  auto *res = new ExplicitBitVect;
  /* concatenate the two bitvectors */
  (*res) = *reactantFP + *productFP;
  if (fpSize_agent > 0) {
    ExplicitBitVect *agentFP = generateFingerprintChemReactionAsBitVect(
        rxn, fpSize_agent, params.fpType, Agent);
    (*res) += *agentFP;
    delete agentFP;
  }

  delete reactantFP;
  delete productFP;
  return res;
}

SparseIntVect<std::uint32_t> *DifferenceFingerprintChemReaction(
    const ChemicalReaction &rxn, const ReactionFingerprintParams &params) {
  PRECONDITION(params.fpSize != 0, "fpSize==0");
  PRECONDITION(params.fpType > 0 && params.fpType < 4,
               "Fingerprinttype not supported");

  SparseIntVect<std::uint32_t> *reactantFP =
      generateFingerprintChemReactionAsCountVect(rxn, params.fpSize,
                                                 params.fpType, Reactant);
  SparseIntVect<std::uint32_t> *productFP =
      generateFingerprintChemReactionAsCountVect(rxn, params.fpSize,
                                                 params.fpType, Product);
  auto *res = new SparseIntVect<std::uint32_t>;
  if (params.includeAgents) {
    SparseIntVect<std::uint32_t> *agentFP =
        generateFingerprintChemReactionAsCountVect(rxn, params.fpSize,
                                                   params.fpType, Agent);
    (*productFP) *= params.nonAgentWeight;
    (*reactantFP) *= params.nonAgentWeight;
    (*agentFP) *= params.agentWeight;
    (*res) = *productFP - *reactantFP + *agentFP;
    delete agentFP;
  }
  /* subtract product FP from reactant FP */
  else {
    (*res) = *productFP - *reactantFP;
  }

  delete reactantFP;
  delete productFP;
  return res;
}
}