rdkit/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h

//  Copyright (c) 2019, Novartis Institutes for BioMedical Research Inc.
//  All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
//     * Redistributions of source code must retain the above copyright
//       notice, this list of conditions and the following disclaimer.
//     * Redistributions in binary form must reproduce the above
//       copyright notice, this list of conditions and the following
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//       with the distribution.
//     * Neither the name of Novartis Institutes for BioMedical Research Inc.
//       nor the names of its contributors may be used to endorse or promote
//       products derived from this software without specific prior written
//       permission.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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//
// n.b. must be included at the END of SubstructLibrary.h
#ifndef RDK_SUBSTRUCT_LIBRARY_SERIALIZATION
#define RDK_SUBSTRUCT_LIBRARY_SERIALIZATION

#ifdef RDK_USE_BOOST_SERIALIZATION
#include <RDGeneral/BoostStartInclude.h>
#include <boost/archive/text_oarchive.hpp>
#include <boost/archive/text_iarchive.hpp>
#include <boost/serialization/vector.hpp>
#include <boost/serialization/shared_ptr.hpp>
#include <boost/archive/archive_exception.hpp>
#include <RDGeneral/BoostEndInclude.h>

BOOST_SERIALIZATION_ASSUME_ABSTRACT(RDKit::MolHolderBase)
BOOST_SERIALIZATION_ASSUME_ABSTRACT(RDKit::FPHolderBase)

namespace boost {
namespace serialization {

template <class Archive>
void serialize(Archive &, RDKit::MolHolderBase &, const unsigned int) {}

template <class Archive>
void save(Archive &ar, const RDKit::MolHolder &molholder,
          const unsigned int version) {
  ar &boost::serialization::base_object<RDKit::MolHolderBase>(molholder);

  if (version < 2) {
    std::int64_t pkl_count = molholder.getMols().size();
    ar &pkl_count;

    for (auto &mol : molholder.getMols()) {
      std::string pkl;
      RDKit::MolPickler::pickleMol(*mol.get(), pkl);
      ar << pkl;
    }
  } else {
    ar &molholder.getMols();
  }
}

template <class Archive>
void load(Archive &ar, RDKit::MolHolder &molholder,
          const unsigned int version) {
  ar &boost::serialization::base_object<RDKit::MolHolderBase>(molholder);

  std::vector<boost::shared_ptr<RDKit::ROMol>> &mols = molholder.getMols();
  mols.clear();

  if (version < 2) {
    std::int64_t pkl_count = -1;
    ar &pkl_count;

    for (std::int64_t i = 0; i < pkl_count; ++i) {
      std::string pkl;
      ar >> pkl;
      mols.push_back(boost::make_shared<RDKit::ROMol>(pkl));
    }
  } else {
    ar &mols;
  }
}

template <class Archive, class MolHolder>
void serialize_strings(Archive &ar, MolHolder &molholder,
                       const unsigned int version) {
  RDUNUSED_PARAM(version);
  ar &boost::serialization::base_object<RDKit::MolHolderBase>(molholder);
  ar &molholder.getMols();
}

template <class Archive>
void serialize(Archive &ar, RDKit::CachedMolHolder &molholder,
               const unsigned int version) {
  serialize_strings(ar, molholder, version);
}

template <class Archive>
void serialize(Archive &ar, RDKit::CachedSmilesMolHolder &molholder,
               const unsigned int version) {
  serialize_strings(ar, molholder, version);
}

template <class Archive>
void serialize(Archive &ar, RDKit::CachedTrustedSmilesMolHolder &molholder,
               const unsigned int version) {
  serialize_strings(ar, molholder, version);
}

template <class Archive>
void save(Archive &ar, const RDKit::FPHolderBase &fpholder,
          const unsigned int version) {
  RDUNUSED_PARAM(version);
  std::vector<std::string> pickles;
  for (auto &fp : fpholder.getFingerprints()) {
    pickles.push_back(fp->toString());
  }
  ar &pickles;
}

template <class Archive>
void load(Archive &ar, RDKit::FPHolderBase &fpholder,
          const unsigned int version) {
  RDUNUSED_PARAM(version);
  std::vector<std::string> pickles;
  std::vector<ExplicitBitVect *> &fps = fpholder.getFingerprints();

  ar &pickles;
  for (size_t i = 0; i < fps.size(); ++i) {
    delete fps[i];
  }
  fps.clear();

  for (auto &pkl : pickles) {
    fps.push_back(new ExplicitBitVect(pkl));
  }
}

template <class Archive>
void serialize(Archive &ar, RDKit::PatternHolder &pattern_holder,
               const unsigned int version) {
  RDUNUSED_PARAM(version);
  ar &boost::serialization::base_object<RDKit::FPHolderBase>(pattern_holder);
  if (Archive::is_saving::value &&
      pattern_holder.getNumBits() != RDKit::PatternHolder::defaultNumBits()) {
    ar &pattern_holder.getNumBits();
  } else if (Archive::is_loading::value) {
    try {
      ar &pattern_holder.getNumBits();
    } catch (boost::archive::archive_exception &) {
      pattern_holder.getNumBits() = RDKit::PatternHolder::defaultNumBits();
    }
  }
}

template <class Archive>
void serialize(Archive &ar, RDKit::TautomerPatternHolder &pattern_holder,
               const unsigned int version) {
  RDUNUSED_PARAM(version);
  ar &boost::serialization::base_object<RDKit::FPHolderBase>(pattern_holder);
  ar &pattern_holder.getNumBits();
}

template <class Archive>
void serialize(Archive &, RDKit::KeyHolderBase &, const unsigned int) {}

template <class Archive>
void serialize(Archive &ar, RDKit::KeyFromPropHolder &key_holder,
               const unsigned int) {
  ar &boost::serialization::base_object<RDKit::KeyHolderBase>(key_holder);
  ar &key_holder.getPropName();
  ar &key_holder.getKeys();
}

template <class Archive>
void registerSubstructLibraryTypes(Archive &ar) {
  ar.register_type(static_cast<RDKit::MolHolder *>(nullptr));
  ar.register_type(static_cast<RDKit::CachedMolHolder *>(nullptr));
  ar.register_type(static_cast<RDKit::CachedSmilesMolHolder *>(nullptr));
  ar.register_type(static_cast<RDKit::CachedTrustedSmilesMolHolder *>(nullptr));
  ar.register_type(static_cast<RDKit::PatternHolder *>(nullptr));
  ar.register_type(static_cast<RDKit::TautomerPatternHolder *>(nullptr));
  ar.register_type(static_cast<RDKit::KeyFromPropHolder *>(nullptr));
}

template <class Archive>
void save(Archive &ar, const RDKit::SubstructLibrary &slib,
          const unsigned int version) {
  RDUNUSED_PARAM(version);
  registerSubstructLibraryTypes(ar);
  ar &slib.getSearchOrder();
  ar &slib.getKeyHolder();
  ar &slib.getMolHolder();
  ar &slib.getFpHolder();
}

template <class Archive>
void load(Archive &ar, RDKit::SubstructLibrary &slib,
          const unsigned int version) {
  RDUNUSED_PARAM(version);
  registerSubstructLibraryTypes(ar);
  if (version > 1) {
    ar &slib.getSearchOrder();
    ar &slib.getKeyHolder();
  }
  ar &slib.getMolHolder();
  ar &slib.getFpHolder();
  slib.resetHolders();
}

}  // end namespace serialization
}  // end namespace boost

BOOST_CLASS_VERSION(RDKit::MolHolder, 2);
BOOST_CLASS_VERSION(RDKit::CachedMolHolder, 1);
BOOST_CLASS_VERSION(RDKit::CachedSmilesMolHolder, 1);
BOOST_CLASS_VERSION(RDKit::CachedTrustedSmilesMolHolder, 1);
BOOST_CLASS_VERSION(RDKit::PatternHolder, 1);
BOOST_CLASS_VERSION(RDKit::TautomerPatternHolder, 1);
BOOST_CLASS_VERSION(RDKit::SubstructLibrary, 2);

BOOST_SERIALIZATION_SPLIT_FREE(RDKit::MolHolder);
BOOST_SERIALIZATION_SPLIT_FREE(RDKit::FPHolderBase);
BOOST_SERIALIZATION_SPLIT_FREE(RDKit::SubstructLibrary);

#endif
#endif