
//  Copyright (C) 2003-2017 Greg Landrum and Rational Discovery LLC
//
//   @@ 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.
//
#define NO_IMPORT_ARRAY
#include <RDBoost/python.h>
#include <string>

#include "props.hpp"
#include "rdchem.h"
#include "seqs.hpp"
#include "substructmethods.h"

// ours
#include <GraphMol/MolBundle.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/QueryOps.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <RDBoost/Wrap.h>
#include <RDBoost/pyint_api.h>
#include <boost/python/copy_non_const_reference.hpp>
#include <boost/python/iterator.hpp>

namespace python = boost::python;

namespace RDKit {

void MolClearComputedPropsHelper(const ROMol &mol, bool includeRings) {
  mol.clearComputedProps(includeRings);
}

python::object MolToBinary(const ROMol &self) {
  std::string res;
  {
    NOGIL gil;
    MolPickler::pickleMol(self, res);
  }
  python::object retval = python::object(
      python::handle<>(PyBytes_FromStringAndSize(res.c_str(), res.length())));
  return retval;
}

python::object MolToBinaryWithProps(const ROMol &self, unsigned int props) {
  std::string res;
  {
    NOGIL gil;
    MolPickler::pickleMol(self, res, props);
  }
  python::object retval = python::object(
      python::handle<>(PyBytes_FromStringAndSize(res.c_str(), res.length())));
  return retval;
}

//
// allows molecules to be pickled.
//  since molecules have a constructor that takes a binary string
//  we only need to provide getinitargs()
//
struct mol_pickle_suite : rdkit_pickle_suite {
  static python::tuple getinitargs(const ROMol &self) {
    return python::make_tuple(MolToBinary(self));
  };
};

bool HasSubstructMatchStr(std::string pkl, const ROMol &query,
                          bool recursionPossible = true,
                          bool useChirality = false,
                          bool useQueryQueryMatches = false) {
  NOGIL gil;
  ROMol *mol;
  try {
    mol = new ROMol(pkl);
  } catch (...) {
    mol = nullptr;
  }
  if (!mol) {
    throw ValueErrorException("Null Molecule");
  }
  MatchVectType res;
  bool hasM = SubstructMatch(*mol, query, res, recursionPossible, useChirality,
                             useQueryQueryMatches);
  delete mol;
  return hasM;
}

unsigned int AddMolConformer(ROMol &mol, Conformer *conf,
                             bool assignId = false) {
  auto *nconf = new Conformer(*conf);
  return mol.addConformer(nconf, assignId);
}

Conformer *GetMolConformer(ROMol &mol, int id = -1) {
  return &(mol.getConformer(id));
}

void MolDebug(const ROMol &mol, bool useStdout) {
  if (useStdout) {
    mol.debugMol(std::cout);
  } else {
    std::ostream *dest = &std::cerr;
    if (rdInfoLog != nullptr) {
      if (rdInfoLog->teestream) {
        dest = rdInfoLog->teestream;
      } else if (rdInfoLog->dp_dest) {
        dest = rdInfoLog->dp_dest;
      }
      mol.debugMol(*dest);
    }
  }
}

// FIX: we should eventually figure out how to do iterators properly
QueryAtomIterSeq *MolGetAromaticAtoms(const ROMOL_SPTR &mol) {
  auto *qa = new QueryAtom();
  qa->setQuery(makeAtomAromaticQuery());
  QueryAtomIterSeq *res =
      new QueryAtomIterSeq(mol, mol->beginQueryAtoms(qa), mol->endQueryAtoms(),
                           AtomCountFunctor(mol));
  return res;
}
QueryAtomIterSeq *MolGetQueryAtoms(const ROMOL_SPTR &mol, QueryAtom *qa) {
  QueryAtomIterSeq *res =
      new QueryAtomIterSeq(mol, mol->beginQueryAtoms(qa), mol->endQueryAtoms(),
                           AtomCountFunctor(mol));
  return res;
}

ConformerIterSeq *GetMolConformers(const ROMOL_SPTR &mol) {
  ConformerIterSeq *res =
      new ConformerIterSeq(mol, mol->beginConformers(), mol->endConformers(),
                           ConformerCountFunctor(mol));
  return res;
}

int getMolNumAtoms(const ROMol &mol, int onlyHeavy, bool onlyExplicit) {
  if (onlyHeavy > -1) {
    BOOST_LOG(rdWarningLog)
        << "WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been "
           "deprecated. Please use the onlyExplicit argument instead or "
           "mol.GetNumHeavyAtoms() if you want the heavy atom count."
        << std::endl;
    return mol.getNumAtoms(onlyHeavy);
  }
  return mol.getNumAtoms(onlyExplicit);
}

namespace {
class pyobjFunctor {
 public:
  pyobjFunctor(python::object obj) : dp_obj(std::move(obj)) {}
  ~pyobjFunctor() = default;
  bool operator()(const ROMol &m, const std::vector<unsigned int> &match) {
    return python::extract<bool>(dp_obj(boost::ref(m), boost::ref(match)));
  }

 private:
  python::object dp_obj;
};
void setSubstructMatchFinalCheck(SubstructMatchParameters &ps,
                                 python::object func) {
  ps.extraFinalCheck = pyobjFunctor(func);
}

}  // namespace

class ReadWriteMol : public RWMol {
 public:
  ReadWriteMol() {};
  ReadWriteMol(const ROMol &m, bool quickCopy = false, int confId = -1)
      : RWMol(m, quickCopy, confId) {};

  void RemoveAtom(unsigned int idx) { removeAtom(idx); };
  void RemoveBond(unsigned int idx1, unsigned int idx2) {
    removeBond(idx1, idx2);
  };
  int AddBond(unsigned int begAtomIdx, unsigned int endAtomIdx,
              Bond::BondType order = Bond::UNSPECIFIED) {
    return addBond(begAtomIdx, endAtomIdx, order);
  };
  int AddAtom(Atom *atom) {
    PRECONDITION(atom, "bad atom");
    return addAtom(atom, true, false);
  };
  void ReplaceAtom(unsigned int idx, Atom *atom, bool updateLabel,
                   bool preserveProps) {
    PRECONDITION(atom, "bad atom");
    replaceAtom(idx, atom, updateLabel, preserveProps);
  };
  void ReplaceBond(unsigned int idx, Bond *bond, bool preserveProps,
                   bool keepSGroups) {
    PRECONDITION(bond, "bad bond");
    replaceBond(idx, bond, preserveProps, keepSGroups);
  };
  void SetStereoGroups(python::list &stereo_groups) {
    std::vector<StereoGroup> groups;
    pythonObjectToVect<StereoGroup>(stereo_groups, groups);
    for (const auto &group : groups) {
      for (const auto atom : group.getAtoms()) {
        if (!atom) {
          throw_value_error("NULL atom in StereoGroup");
        }
        if (&atom->getOwningMol() != this) {
          throw_value_error(
              "atom in StereoGroup does not belong to this molecule.");
        }
      }
    }
    setStereoGroups(std::move(groups));
  }
  ROMol *GetMol() const {
    auto *res = new ROMol(*this);
    return res;
  }

  ReadWriteMol *enter() {
    beginBatchEdit();
    return this;
  }
  bool exit(python::object exc_type, python::object exc_val,
            python::object traceback) {
    RDUNUSED_PARAM(exc_val);
    RDUNUSED_PARAM(traceback);
    if (exc_type != python::object()) {
      // exception thrown, abort the edits
      rollbackBatchEdit();
    } else {
      commitBatchEdit();
    }
    // we haven't handled any possible exceptions (and shouldn't do so),
    // so just return false;
    return false;
  }

 private:
  boost::shared_ptr<RWMol> dp_mol;
};

std::string molClassDoc =
    "The Molecule class.\n\n\
  In addition to the expected Atoms and Bonds, molecules contain:\n\
    - a collection of Atom and Bond bookmarks indexed with integers\n\
        that can be used to flag and retrieve particular Atoms or Bonds\n\
        using the {get|set}{Atom|Bond}Bookmark() methods.\n\n\
    - a set of string-valued properties. These can have arbitrary string\n\
        labels and can be set and retrieved using the {set|get}Prop() methods\n\
        Molecular properties can be tagged as being *computed*, in which case\n\
          they will be automatically cleared under certain circumstances (when the\n\
          molecule itself is modified, for example).\n\
        Molecules also have the concept of *private* properties, which are tagged\n\
          by beginning the property name with an underscore (_).\n";
std::string rwmolClassDoc =
    "The RW molecule class (read/write)\n\n\
  This class is a more-performant version of the EditableMolecule class in that\n\
  it is a 'live' molecule and shares the interface from the Mol class.\n\
  All changes are performed without the need to create a copy of the\n\
  molecule using GetMol() (this is still available, however).\n\
  \n\
  n.b. Eventually this class may become a direct replacement for EditableMol";

struct mol_wrapper {
  static void wrap() {
    python::register_exception_translator<ConformerException>(
        &rdExceptionTranslator);

    python::enum_<RDKit::PicklerOps::PropertyPickleOptions>(
        "PropertyPickleOptions")
        .value("NoProps", RDKit::PicklerOps::NoProps)
        .value("MolProps", RDKit::PicklerOps::MolProps)
        .value("AtomProps", RDKit::PicklerOps::AtomProps)
        .value("BondProps", RDKit::PicklerOps::BondProps)
        .value("QueryAtomData", RDKit::PicklerOps::QueryAtomData)
        .value("PrivateProps", RDKit::PicklerOps::PrivateProps)
        .value("ComputedProps", RDKit::PicklerOps::ComputedProps)
        .value("AllProps", RDKit::PicklerOps::AllProps)
        .value("CoordsAsDouble", RDKit::PicklerOps::CoordsAsDouble)
        .value("NoConformers", RDKit::PicklerOps::NoConformers)
        .export_values();
    ;

    RegisterVectorConverter<StereoGroup>("StereoGroup_vect");

    python::def("GetDefaultPickleProperties",
                MolPickler::getDefaultPickleProperties,
                "Get the current global mol pickler options.");
    python::def("SetDefaultPickleProperties",
                MolPickler::setDefaultPickleProperties, python::args("arg1"),
                "Set the current global mol pickler options.");

    // REVIEW: There's probably a better place for this definition
    python::class_<RDKit::SubstructMatchParameters, boost::noncopyable>(
        "SubstructMatchParameters",
        "Parameters controlling substructure matching")
        .def_readwrite(
            "useChirality", &RDKit::SubstructMatchParameters::useChirality,
            "Use chirality in determining whether or not atoms/bonds match")
        .def_readwrite(
            "useEnhancedStereo",
            &RDKit::SubstructMatchParameters::useEnhancedStereo,
            "take enhanced stereochemistry into account while doing the match. "
            "This only has an effect if useChirality is also True.")
        .def_readwrite(
            "aromaticMatchesConjugated",
            &RDKit::SubstructMatchParameters::aromaticMatchesConjugated,
            "aromatic and conjugated bonds match each other")
        .def_readwrite(
            "useGenericMatchers",
            &RDKit::SubstructMatchParameters::useGenericMatchers,
            "use generic groups (=homology groups) as a post-filtering step "
            "(if any are present in the molecule)")
        .def_readwrite("useQueryQueryMatches",
                       &RDKit::SubstructMatchParameters::useQueryQueryMatches,
                       "Consider query-query matches, not just simple matches")
        .def_readwrite("recursionPossible",
                       &RDKit::SubstructMatchParameters::recursionPossible,
                       "Allow recursive queries")
        .def_readwrite("uniquify", &RDKit::SubstructMatchParameters::uniquify,
                       "uniquify (by atom index) match results")
        .def_readwrite("maxMatches",
                       &RDKit::SubstructMatchParameters::maxMatches,
                       "maximum number of matches to return")
        .def_readwrite("maxRecursiveMatches",
                       &RDKit::SubstructMatchParameters::maxRecursiveMatches,
                       "maximum number of recursive matches to find")
        .def_readwrite(
            "numThreads", &RDKit::SubstructMatchParameters::numThreads,
            "number of threads to use when multi-threading is possible."
            "0 selects the number of concurrent threads supported by the"
            "hardware. negative values are added to the number of concurrent"
            "threads supported by the hardware.")
        .def_readwrite(
            "bondProperties", &RDKit::SubstructMatchParameters::bondProperties,
            "bond properties that must be equivalent in order to match.")
        .def_readwrite(
            "atomProperties", &RDKit::SubstructMatchParameters::atomProperties,
            "atom properties that must be equivalent in order to match.")
        .def_readwrite(
            "specifiedStereoQueryMatchesUnspecified",
            &RDKit::SubstructMatchParameters::
                specifiedStereoQueryMatchesUnspecified,
            "If set, query atoms and bonds with specified stereochemistry will match atoms and bonds with unspecified stereochemistry.")
        .def("setExtraFinalCheck", setSubstructMatchFinalCheck,
             python::with_custodian_and_ward<1, 2>(),
             python::args("self", "func"),
             R"DOC(allows you to provide a function that will be called
               with the molecule
           and a vector of atom IDs containing a potential match.
           The function should return true or false indicating whether or not
           that match should be accepted.)DOC");

    python::class_<ROMol, ROMOL_SPTR, boost::noncopyable>(
        "Mol", molClassDoc.c_str(),
        python::init<>(python::args("self"), "Constructor, takes no arguments"))
        .def(python::init<const std::string &>(
            python::args("self", "pklString")))
        .def(python::init<const std::string &, unsigned int>(
            (python::args("self", "pklString", "propertyFlags"))))
        .def(python::init<const ROMol &, bool, int>(
            (python::arg("self"), python::arg("mol"),
             python::arg("quickCopy") = false, python::arg("confId") = -1)))
        .def("__copy__", &generic__copy__<ROMol>, python::args("self"))
        .def("__deepcopy__", &generic__deepcopy__<ROMol>,
             python::args("self", "memo"))
        .def("GetNumAtoms", getMolNumAtoms,
             ((python::arg("self"), python::arg("onlyHeavy") = -1),
              python::arg("onlyExplicit") = true),
             "Returns the number of atoms in the molecule.\n\n"
             "  ARGUMENTS:\n"
             "    - onlyExplicit: (optional) include only explicit atoms "
             "(atoms in the molecular graph)\n"
             "                    defaults to 1.\n"
             "  NOTE: the onlyHeavy argument is deprecated\n"

             )
        .def("GetNumHeavyAtoms", &ROMol::getNumHeavyAtoms, python::args("self"),
             "Returns the number of heavy atoms (atomic number >1) in the "
             "molecule.\n\n")
        .def("GetAtomWithIdx",
             (Atom * (ROMol::*)(unsigned int)) & ROMol::getAtomWithIdx,
             python::return_internal_reference<
                 1, python::with_custodian_and_ward_postcall<0, 1>>(),
             python::args("self", "idx"),
             "Returns a particular Atom.\n\n"
             "  ARGUMENTS:\n"
             "    - idx: which Atom to return\n\n"
             "  NOTE: atom indices start at 0\n")

        .def("GetNumBonds", &ROMol::getNumBonds,
             ((python::arg("self"), python::arg("onlyHeavy") = true)),
             "Returns the number of Bonds in the molecule.\n\n"
             "  ARGUMENTS:\n"
             "    - onlyHeavy: (optional) include only bonds to heavy atoms "
             "(not Hs)\n"
             "                  defaults to 1.\n")

        .def("GetBondWithIdx",
             (Bond * (ROMol::*)(unsigned int)) & ROMol::getBondWithIdx,
             python::return_internal_reference<
                 1, python::with_custodian_and_ward_postcall<0, 1>>(),
             python::args("self", "idx"),
             "Returns a particular Bond.\n\n"
             "  ARGUMENTS:\n"
             "    - idx: which Bond to return\n\n"
             "  NOTE: bond indices start at 0\n")

        .def("GetNumConformers", &ROMol::getNumConformers, python::args("self"),
             "Return the number of conformations on the molecule")

        .def("AddConformer", AddMolConformer,
             (python::arg("self"), python::arg("conf"),
              python::arg("assignId") = false),
             "Add a conformer to the molecule and return the conformer ID")

#if 0
        .def("AddConformersFromTrajectory", &ROMol::addConformersFromTrajectory,
             (python::arg("self"), python::arg("traj"),
              python::arg("nConf") = -1),
             "Add conformers from a Trajectory to the molecule and return\n"
             "the number of conformations that were added")
#endif

        .def("GetConformer", GetMolConformer,
             (python::arg("self"), python::arg("id") = -1),
             "Get the conformer with a specified ID",
             python::return_internal_reference<
                 1, python::with_custodian_and_ward_postcall<0, 1>>())

        .def("GetConformers", GetMolConformers,
             python::return_value_policy<
                 python::manage_new_object,
                 python::with_custodian_and_ward_postcall<0, 1>>(),
             python::args("self"),
             "Returns a read-only sequence containing all of the molecule's "
             "Conformers.")

        .def("RemoveAllConformers", &ROMol::clearConformers,
             python::args("self"),
             "Remove all the conformations on the molecule")

        .def("RemoveConformer", &ROMol::removeConformer,
             python::args("self", "id"),
             "Remove the conformer with the specified ID")
        .def("GetBondBetweenAtoms",
             (Bond * (ROMol::*)(unsigned int, unsigned int)) &
                 ROMol::getBondBetweenAtoms,
             python::return_internal_reference<
                 1, python::with_custodian_and_ward_postcall<0, 1>>(),
             python::args("self", "idx1", "idx2"),
             "Returns the bond between two atoms, if there is one.\n\n"
             "  ARGUMENTS:\n"
             "    - idx1,idx2: the Atom indices\n\n"
             "  Returns:\n"
             "    The Bond between the two atoms, if such a bond exists.\n"
             "    If there is no Bond between the atoms, None is returned "
             "instead.\n\n"
             "  NOTE: bond indices start at 0\n")

        .def("HasQuery", &ROMol::hasQuery, python::args("self"),
             "Returns if any atom or bond in molecule has a query")

        // substructures
        .def("HasSubstructMatch",
             (bool (*)(const ROMol &m, const ROMol &query, bool, bool,
                       bool))HasSubstructMatch,
             (python::arg("self"), python::arg("query"),
              python::arg("recursionPossible") = true,
              python::arg("useChirality") = false,
              python::arg("useQueryQueryMatches") = false),
             "Queries whether or not the molecule contains a particular "
             "substructure.\n\n"
             "  ARGUMENTS:\n"
             "    - query: a Molecule\n\n"
             "    - recursionPossible: (optional)\n\n"
             "    - useChirality: enables the use of stereochemistry in the "
             "matching\n\n"
             "    - useQueryQueryMatches: use query-query matching logic\n\n"
             "  RETURNS: True or False\n")
        .def("GetSubstructMatch",
             (PyObject * (*)(const ROMol &m, const ROMol &query, bool, bool))
                 GetSubstructMatch,
             (python::arg("self"), python::arg("query"),
              python::arg("useChirality") = false,
              python::arg("useQueryQueryMatches") = false),
             "Returns the indices of the molecule's atoms that match a "
             "substructure query.\n\n"
             "  ARGUMENTS:\n"
             "    - query: a Molecule\n\n"
             "    - useChirality: enables the use of stereochemistry in the "
             "matching\n\n"
             "    - useQueryQueryMatches: use query-query matching logic\n\n"
             "  RETURNS: a tuple of integers\n\n"
             "  NOTES:\n"
             "     - only a single match is returned\n"
             "     - the ordering of the indices corresponds to the atom "
             "ordering\n"
             "         in the query. For example, the first index is for the "
             "atom in\n"
             "         this molecule that matches the first atom in the "
             "query.\n")

        .def("GetSubstructMatches",
             (PyObject * (*)(const ROMol &m, const ROMol &query, bool, bool,
                             bool, unsigned int)) GetSubstructMatches,
             (python::arg("self"), python::arg("query"),
              python::arg("uniquify") = true,
              python::arg("useChirality") = false,
              python::arg("useQueryQueryMatches") = false,
              python::arg("maxMatches") = 1000),
             "Returns tuples of the indices of the molecule's atoms that "
             "match "
             "a substructure query.\n\n"
             "  ARGUMENTS:\n"
             "    - query: a Molecule.\n"
             "    - uniquify: (optional) determines whether or not the "
             "matches "
             "are uniquified.\n"
             "                Defaults to 1.\n\n"
             "    - useChirality: enables the use of stereochemistry in the "
             "matching\n\n"
             "    - useQueryQueryMatches: use query-query matching logic\n\n"
             "    - maxMatches: The maximum number of matches that will be "
             "returned.\n"
             "                  In high-symmetry cases with medium-sized "
             "molecules, it is\n"
             "                  very easy to end up with a combinatorial "
             "explosion in the\n"
             "                  number of possible matches. This argument "
             "prevents that from\n"
             "                  having unintended consequences\n\n"
             "  RETURNS: a tuple of tuples of integers\n\n"
             "  NOTE:\n"
             "     - the ordering of the indices corresponds to the atom "
             "ordering\n"
             "         in the query. For example, the first index is for the "
             "atom in\n"
             "         this molecule that matches the first atom in the "
             "query.\n")

        .def("HasSubstructMatch",
             (bool (*)(const ROMol &m, const MolBundle &query, bool, bool,
                       bool))HasSubstructMatch,
             (python::arg("self"), python::arg("query"),
              python::arg("recursionPossible") = true,
              python::arg("useChirality") = false,
              python::arg("useQueryQueryMatches") = false))
        .def("GetSubstructMatch",
             (PyObject * (*)(const ROMol &m, const MolBundle &query, bool,
                             bool)) GetSubstructMatch,
             (python::arg("self"), python::arg("query"),
              python::arg("useChirality") = false,
              python::arg("useQueryQueryMatches") = false))

        .def("GetSubstructMatches",
             (PyObject * (*)(const ROMol &m, const MolBundle &query, bool, bool,
                             bool, unsigned int)) GetSubstructMatches,
             (python::arg("self"), python::arg("query"),
              python::arg("uniquify") = true,
              python::arg("useChirality") = false,
              python::arg("useQueryQueryMatches") = false,
              python::arg("maxMatches") = 1000))

        //--------------------------------------------
        .def("HasSubstructMatch",
             (bool (*)(const ROMol &m, const ROMol &query,
                       const SubstructMatchParameters &))helpHasSubstructMatch,
             (python::arg("self"), python::arg("query"), python::arg("params")),
             "Queries whether or not the molecule contains a particular "
             "substructure.\n\n"
             "  ARGUMENTS:\n"
             "    - query: a Molecule\n\n"
             "    - params: parameters controlling the substructure match\n\n"
             "  RETURNS: True or False\n")
        .def("GetSubstructMatch",
             (PyObject * (*)(const ROMol &m, const ROMol &query,
                             const SubstructMatchParameters &params))
                 helpGetSubstructMatch,
             (python::arg("self"), python::arg("query"), python::arg("params")),
             "Returns the indices of the molecule's atoms that match a "
             "substructure query.\n\n"
             "  ARGUMENTS:\n"
             "    - query: a Molecule\n\n"
             "    - params: parameters controlling the substructure match\n\n"
             "  RETURNS: a tuple of integers\n\n"
             "  NOTES:\n"
             "     - only a single match is returned\n"
             "     - the ordering of the indices corresponds to the atom "
             "ordering\n"
             "         in the query. For example, the first index is for the "
             "atom in\n"
             "         this molecule that matches the first atom in the "
             "query.\n")

        .def("GetSubstructMatches",
             (PyObject * (*)(const ROMol &m, const ROMol &query,
                             const SubstructMatchParameters &))
                 helpGetSubstructMatches,
             (python::arg("self"), python::arg("query"), python::arg("params")),
             "Returns tuples of the indices of the molecule's atoms that "
             "match "
             "a substructure query.\n\n"
             "  ARGUMENTS:\n"
             "    - query: a Molecule.\n"
             "    - params: parameters controlling the substructure match\n\n"
             "  RETURNS: a tuple of tuples of integers\n\n"
             "  NOTE:\n"
             "     - the ordering of the indices corresponds to the atom "
             "ordering\n"
             "         in the query. For example, the first index is for the "
             "atom in\n"
             "         this molecule that matches the first atom in the "
             "query.\n")

        .def("HasSubstructMatch",
             (bool (*)(const ROMol &m, const MolBundle &query,
                       const SubstructMatchParameters &))helpHasSubstructMatch,
             (python::arg("self"), python::arg("query"),
              python::arg("params") = true))
        .def("GetSubstructMatch",
             (PyObject * (*)(const ROMol &m, const MolBundle &query,
                             const SubstructMatchParameters &))
                 helpGetSubstructMatch,
             (python::arg("self"), python::arg("query"), python::arg("params")))
        .def("GetSubstructMatches",
             (PyObject * (*)(const ROMol &m, const MolBundle &query,
                             const SubstructMatchParameters &))
                 helpGetSubstructMatches,
             (python::arg("self"), python::arg("query"), python::arg("params")))

        // properties
        .def("SetProp", MolSetProp<ROMol, std::string>,
             (python::arg("self"), python::arg("key"), python::arg("val"),
              python::arg("computed") = false),
             "Sets a molecular property\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to be set (a string).\n"
             "    - value: the property value (a string).\n"
             "    - computed: (optional) marks the property as being "
             "computed.\n"
             "                Defaults to False.\n\n")
        .def("SetDoubleProp", MolSetProp<ROMol, double>,
             (python::arg("self"), python::arg("key"), python::arg("val"),
              python::arg("computed") = false),
             "Sets a double valued molecular property\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to be set (a string).\n"
             "    - value: the property value as a double.\n"
             "    - computed: (optional) marks the property as being "
             "computed.\n"
             "                Defaults to 0.\n\n")
        .def("SetIntProp", MolSetProp<ROMol, int>,
             (python::arg("self"), python::arg("key"), python::arg("val"),
              python::arg("computed") = false),
             "Sets an integer valued molecular property\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to be set (an unsigned "
             "number).\n"
             "    - value: the property value as an integer.\n"
             "    - computed: (optional) marks the property as being "
             "computed.\n"
             "                Defaults to False.\n\n")
        .def("SetUnsignedProp", MolSetProp<ROMol, unsigned int>,
             (python::arg("self"), python::arg("key"), python::arg("val"),
              python::arg("computed") = false),
             "Sets an unsigned integer valued molecular property\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to be set (a string).\n"
             "    - value: the property value as an unsigned integer.\n"
             "    - computed: (optional) marks the property as being "
             "computed.\n"
             "                Defaults to False.\n\n")
        .def("SetBoolProp", MolSetProp<ROMol, bool>,
             (python::arg("self"), python::arg("key"), python::arg("val"),
              python::arg("computed") = false),
             "Sets a boolean valued molecular property\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to be set (a string).\n"
             "    - value: the property value as a bool.\n"
             "    - computed: (optional) marks the property as being "
             "computed.\n"
             "                Defaults to False.\n\n")
        .def("HasProp", MolHasProp<ROMol>, python::args("self", "key"),
             "Queries a molecule to see if a particular property has been "
             "assigned.\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to check for (a string).\n")
        .def(
            "GetProp", GetPyProp<ROMol>,
            (python::arg("self"), python::arg("key"),
             python::arg("autoConvert") = false),
            "Returns the value of the property.\n\n"
            "  ARGUMENTS:\n"
            "    - key: the name of the property to return (a string).\n\n"
            "    - autoConvert: if True attempt to convert the property into a python object\n\n"
            "  RETURNS: a string\n\n"
            "  NOTE:\n"
            "    - If the property has not been set, a KeyError exception "
            "will be raised.\n")
        .def("GetDoubleProp", GetProp<ROMol, double>,
             python::args("self", "key"),
             "Returns the double value of the property if possible.\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to return (a string).\n\n"
             "  RETURNS: a double\n\n"
             "  NOTE:\n"
             "    - If the property has not been set, a KeyError exception "
             "will be raised.\n")
        .def("GetIntProp", GetProp<ROMol, int>, python::args("self", "key"),
             "Returns the integer value of the property if possible.\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to return (a string).\n\n"
             "  RETURNS: an integer\n\n"
             "  NOTE:\n"
             "    - If the property has not been set, a KeyError exception "
             "will be raised.\n")
        .def("GetUnsignedProp", GetProp<ROMol, unsigned int>,
             python::args("self", "key"),
             "Returns the unsigned int value of the property if possible.\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to return (a string).\n\n"
             "  RETURNS: an unsigned integer\n\n"
             "  NOTE:\n"
             "    - If the property has not been set, a KeyError exception "
             "will be raised.\n")
        .def("GetBoolProp", GetProp<ROMol, bool>, python::args("self", "key"),
             "Returns the Bool value of the property if possible.\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to return (a string).\n\n"
             "  RETURNS: a bool\n\n"
             "  NOTE:\n"
             "    - If the property has not been set, a KeyError exception "
             "will be raised.\n")
        .def("ClearProp", MolClearProp<ROMol>, python::args("self", "key"),
             "Removes a property from the molecule.\n\n"
             "  ARGUMENTS:\n"
             "    - key: the name of the property to clear (a string).\n")

        .def("ClearComputedProps", MolClearComputedPropsHelper,
             (python::arg("self"), python::arg("includeRings") = true),
             "Removes all computed properties from the molecule.\n\n")

        .def("UpdatePropertyCache", &ROMol::updatePropertyCache,
             (python::arg("self"), python::arg("strict") = true),
             "Regenerates computed properties like implicit valence and ring "
             "information.\n\n")

        .def("NeedsUpdatePropertyCache", &ROMol::needsUpdatePropertyCache,
             (python::arg("self")),
             "Returns true or false depending on whether implicit and "
             "explicit "
             "valence of the molecule have already been calculated.\n\n")

        .def("GetStereoGroups", &ROMol::getStereoGroups,
             "Returns a list of StereoGroups defining the relative "
             "stereochemistry "
             "of the atoms.\n",
             python::return_internal_reference<
                 1, python::with_custodian_and_ward_postcall<0, 1>>(),
             python::args("self"))

        .def("GetPropNames", &ROMol::getPropList,
             (python::arg("self"), python::arg("includePrivate") = false,
              python::arg("includeComputed") = false),
             "Returns a tuple with all property names for this molecule.\n\n"
             "  ARGUMENTS:\n"
             "    - includePrivate: (optional) toggles inclusion of private "
             "properties in the result set.\n"
             "                      Defaults to 0.\n"
             "    - includeComputed: (optional) toggles inclusion of computed "
             "properties in the result set.\n"
             "                      Defaults to 0.\n\n"
             "  RETURNS: a tuple of strings\n")

        .def("GetPropsAsDict", GetPropsAsDict<ROMol>,
             (python::arg("self"), python::arg("includePrivate") = false,
              python::arg("includeComputed") = false,
              python::arg("autoConvertStrings") = true),
             "Returns a dictionary populated with the molecules properties.\n"
             " n.b. Some properties are not able to be converted to python "
             "types.\n\n"
             "  ARGUMENTS:\n"
             "    - includePrivate: (optional) toggles inclusion of private "
             "properties in the result set.\n"
             "                      Defaults to False.\n"
             "    - includeComputed: (optional) toggles inclusion of computed "
             "properties in the result set.\n"
             "                      Defaults to False.\n\n"
             "  RETURNS: a dictionary\n")

        .def("GetAromaticAtoms", MolGetAromaticAtoms,
             python::return_value_policy<
                 python::manage_new_object,
                 python::with_custodian_and_ward_postcall<0, 1>>(),
             python::args("self"),
             "Returns a read-only sequence containing all of the molecule's "
             "aromatic Atoms.\n")
        .def("GetAtomsMatchingQuery", MolGetQueryAtoms,
             python::return_value_policy<
                 python::manage_new_object,
                 python::with_custodian_and_ward_postcall<0, 1>>(),
             python::args("self", "qa"),
             "Returns a read-only sequence containing all of the atoms in a "
             "molecule that match the query atom. "
             "Atom query options are defined in the rdkit.Chem.rdqueries module.\n")

        // enable pickle support
        .def_pickle(mol_pickle_suite())

        .def("Debug", MolDebug,
             (python::arg("self"), python::arg("useStdout") = true),
             "Prints debugging information about the molecule.\n")

        .def("ToBinary", MolToBinary, python::args("self"),
             "Returns a binary string representation of the molecule.\n")
        .def("ToBinary", MolToBinaryWithProps,
             (python::arg("self"), python::arg("propertyFlags")),
             "Returns a binary string representation of the molecule pickling "
             "the "
             "specified properties.\n")

        .def("GetRingInfo", &ROMol::getRingInfo,
             python::return_value_policy<python::reference_existing_object>(),
             python::args("self"),
             "Returns the number of molecule's RingInfo object.\n\n");
    python::register_ptr_to_python<std::shared_ptr<ROMol>>();

    // ---------------------------------------------------------------------------------------------
    python::def("_HasSubstructMatchStr", HasSubstructMatchStr,
                (python::arg("pkl"), python::arg("query"),
                 python::arg("recursionPossible") = true,
                 python::arg("useChirality") = false,
                 python::arg("useQueryQueryMatches") = false),
                "This function is included to speed substructure queries from "
                "databases, \n"
                "it's probably not of\n"
                "general interest.\n\n"
                "  ARGUMENTS:\n"
                "    - pkl: a Molecule pickle\n\n"
                "    - query: a Molecule\n\n"
                "    - recursionPossible: (optional)\n\n"
                "    - useChirality: (optional)\n\n"
                "    - useQueryQueryMatches: use query-query matching logic\n\n"
                "  RETURNS: True or False\n");

    python::class_<ReadWriteMol, python::bases<ROMol>>(
        "RWMol", rwmolClassDoc.c_str(),
        python::init<const ROMol &>(python::args("self", "m"),
                                    "Construct from a Mol"))
        .def(python::init<>(python::args("self")))
        .def(python::init<const std::string &>(
            python::args("self", "pklString")))
        .def(python::init<const std::string &, unsigned int>(
            (python::args("self", "pklString", "propertyFlags"))))
        .def(python::init<const ROMol &, bool, int>(
            (python::arg("self"), python::arg("mol"),
             python::arg("quickCopy") = false, python::arg("confId") = -1)))
        .def("__copy__", &generic__copy__<ReadWriteMol>, python::args("self"))
        .def("__deepcopy__", &generic__deepcopy__<ReadWriteMol>,
             python::args("self", "memo"))
        .def("__enter__", &ReadWriteMol::enter,
             python::return_internal_reference<>())
        .def("__exit__", &ReadWriteMol::exit)

        .def("RemoveAtom", &ReadWriteMol::RemoveAtom,
             python::args("self", "idx"),
             "Remove the specified atom from the molecule")
        .def("RemoveBond", &ReadWriteMol::RemoveBond,
             python::args("self", "idx1", "idx2"),
             "Remove the specified bond from the molecule")

        .def("AddBond", &ReadWriteMol::AddBond,
             ((python::arg("self"), python::arg("beginAtomIdx")),
              python::arg("endAtomIdx"),
              python::arg("order") = Bond::UNSPECIFIED),
             "add a bond, returns the new number of bonds")

        .def("AddAtom", &ReadWriteMol::AddAtom,
             ((python::arg("self"), python::arg("atom"))),
             "add an atom, returns the index of the newly added atom")
        .def("ReplaceAtom", &ReadWriteMol::ReplaceAtom,
             ((python::arg("self"), python::arg("index")),
              python::arg("newAtom"), python::arg("updateLabel") = false,
              python::arg("preserveProps") = false),
             "replaces the specified atom with the provided one\n"
             "If updateLabel is True, the new atom becomes the active atom\n"
             "If preserveProps is True preserve keep the existing props unless "
             "explicit set on the new atom")
        .def("ReplaceBond", &ReadWriteMol::ReplaceBond,
             ((python::arg("self"), python::arg("index")),
              python::arg("newBond"), python::arg("preserveProps") = false,
              python::arg("keepSGroups") = true),
             "replaces the specified bond with the provided one.\n"
             "If preserveProps is True preserve keep the existing props unless "
             "explicit set on the new bond. If keepSGroups is False, all"
             "Substance Groups referencing the bond will be dropped.")
        .def("GetMol", &ReadWriteMol::GetMol,
             "Returns a Mol (a normal molecule)",
             python::return_value_policy<python::manage_new_object>(),
             python::args("self"))

        .def("SetStereoGroups", &ReadWriteMol::SetStereoGroups,
             ((python::arg("self"), python::arg("stereo_groups"))),
             "Set the stereo groups")

        .def("InsertMol", &ReadWriteMol::insertMol,
             ((python::arg("self"), python::arg("mol"))),
             "Insert (add) the given molecule into this one")

        .def("BeginBatchEdit", &RWMol::beginBatchEdit, python::args("self"),
             "starts batch editing")
        .def("RollbackBatchEdit", &RWMol::rollbackBatchEdit,
             python::args("self"), "cancels batch editing")
        .def("CommitBatchEdit", &RWMol::commitBatchEdit, python::args("self"),
             "finishes batch editing and makes the actual changes")

        // enable pickle support
        .def_pickle(mol_pickle_suite());
  };
};

}  // namespace RDKit
void wrap_mol() { RDKit::mol_wrapper::wrap(); }
