// $Id$
//
//  Copyright (C) 2001-2013 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.
//
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/MonomerInfo.h>
#include <RDGeneral/utils.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/StreamOps.h>
#include <RDGeneral/types.h>
#include <Query/QueryObjects.h>
#include <map>
#include <boost/cstdint.hpp>
using boost::int32_t;
using boost::uint32_t;
namespace RDKit {

const int32_t MolPickler::versionMajor = 7;
const int32_t MolPickler::versionMinor = 2;
const int32_t MolPickler::versionPatch = 0;
const int32_t MolPickler::endianId = 0xDEADBEEF;

void streamWrite(std::ostream &ss, const std::string &what) {
  unsigned int l = rdcast<unsigned int>(what.length());
  ss.write((const char *)&l, sizeof(l));
  ss.write(what.c_str(), sizeof(char) * l);
};

void streamWrite(std::ostream &ss, MolPickler::Tags tag) {
  unsigned char tmp = static_cast<unsigned char>(tag);
  streamWrite(ss, tmp);
}
template <typename T>
void streamWrite(std::ostream &ss, MolPickler::Tags tag, const T &what) {
  streamWrite(ss, tag);
  streamWrite(ss, what);
};

template <class T>
void streamRead(std::istream &ss, T &obj, int version) {
  RDUNUSED_PARAM(version);
  streamRead(ss, obj);
}

void streamRead(std::istream &ss, std::string &what, int version) {
  RDUNUSED_PARAM(version);
  unsigned int l;
  ss.read((char *)&l, sizeof(l));
  char *buff = new char[l + 1];
  ss.read(buff, sizeof(char) * l);
  buff[l] = 0;
  what = buff;
  delete[] buff;
};
void streamRead(std::istream &ss, MolPickler::Tags &tag, int version) {
  if (version < 7000) {
    int32_t tmp;
    streamRead(ss, tmp, version);
    tag = static_cast<MolPickler::Tags>(tmp);
  } else {
    unsigned char tmp;
    streamRead(ss, tmp, version);
    tag = static_cast<MolPickler::Tags>(tmp);
  }
}

namespace {
using namespace Queries;
template <class T>
void pickleQuery(std::ostream &ss, const Query<int, T const *, true> *query) {
  PRECONDITION(query, "no query");
  streamWrite(ss, query->getDescription());
  if (query->getNegation()) streamWrite(ss, MolPickler::QUERY_ISNEGATED);
  int32_t queryVal;
  // if (typeid(*query)==typeid(ATOM_BOOL_QUERY)){
  //  streamWrite(ss,QUERY_BOOL);
  if (typeid(*query) == typeid(AndQuery<int, T const *, true>)) {
    streamWrite(ss, MolPickler::QUERY_AND);
  } else if (typeid(*query) == typeid(OrQuery<int, T const *, true>)) {
    streamWrite(ss, MolPickler::QUERY_OR);
  } else if (typeid(*query) == typeid(XOrQuery<int, T const *, true>)) {
    streamWrite(ss, MolPickler::QUERY_XOR);
  } else if (typeid(*query) == typeid(EqualityQuery<int, T const *, true>)) {
    streamWrite(ss, MolPickler::QUERY_EQUALS);
    queryVal = static_cast<const EqualityQuery<int, T const *, true> *>(query)
                   ->getVal();
    streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
    queryVal = static_cast<const EqualityQuery<int, T const *, true> *>(query)
                   ->getTol();
    streamWrite(ss, queryVal);
  } else if (typeid(*query) == typeid(GreaterQuery<int, T const *, true>)) {
    streamWrite(ss, MolPickler::QUERY_GREATER);
    queryVal = static_cast<const GreaterQuery<int, T const *, true> *>(query)
                   ->getVal();
    streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
    queryVal = static_cast<const GreaterQuery<int, T const *, true> *>(query)
                   ->getTol();
    streamWrite(ss, queryVal);
  } else if (typeid(*query) ==
             typeid(GreaterEqualQuery<int, T const *, true>)) {
    streamWrite(ss, MolPickler::QUERY_GREATEREQUAL);
    queryVal =
        static_cast<const GreaterEqualQuery<int, T const *, true> *>(query)
            ->getVal();
    streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
    queryVal =
        static_cast<const GreaterEqualQuery<int, T const *, true> *>(query)
            ->getTol();
    streamWrite(ss, queryVal);
  } else if (typeid(*query) == typeid(LessQuery<int, T const *, true>)) {
    streamWrite(ss, MolPickler::QUERY_LESS);
    queryVal =
        static_cast<const LessQuery<int, T const *, true> *>(query)->getVal();
    streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
    queryVal =
        static_cast<const LessQuery<int, T const *, true> *>(query)->getTol();
    streamWrite(ss, queryVal);
  } else if (typeid(*query) == typeid(LessEqualQuery<int, T const *, true>)) {
    streamWrite(ss, MolPickler::QUERY_LESSEQUAL);
    queryVal = static_cast<const LessEqualQuery<int, T const *, true> *>(query)
                   ->getVal();
    streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
    queryVal = static_cast<const LessEqualQuery<int, T const *, true> *>(query)
                   ->getTol();
    streamWrite(ss, queryVal);
  } else if (typeid(*query) == typeid(RangeQuery<int, T const *, true>)) {
    streamWrite(ss, MolPickler::QUERY_RANGE);
    queryVal = static_cast<const RangeQuery<int, T const *, true> *>(query)
                   ->getLower();
    streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
    queryVal = static_cast<const RangeQuery<int, T const *, true> *>(query)
                   ->getUpper();
    streamWrite(ss, queryVal);
    queryVal =
        static_cast<const RangeQuery<int, T const *, true> *>(query)->getTol();
    streamWrite(ss, queryVal);
    char ends;
    bool lowerOpen, upperOpen;
    boost::tie(lowerOpen, upperOpen) =
        static_cast<const RangeQuery<int, T const *, true> *>(query)
            ->getEndsOpen();
    ends = 0 | (rdcast<int>(lowerOpen) << 1) | rdcast<int>(upperOpen);
    streamWrite(ss, ends);
  } else if (typeid(*query) == typeid(SetQuery<int, T const *, true>)) {
    streamWrite(ss, MolPickler::QUERY_SET);
    queryVal =
        static_cast<const SetQuery<int, T const *, true> *>(query)->size();
    streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
    typename SetQuery<int, T const *, true>::CONTAINER_TYPE::const_iterator cit;
    for (cit = static_cast<const SetQuery<int, T const *, true> *>(query)
                   ->beginSet();
         cit !=
         static_cast<const SetQuery<int, T const *, true> *>(query)->endSet();
         ++cit) {
      queryVal = *cit;
      streamWrite(ss, queryVal);
    }
  } else if (typeid(*query) == typeid(AtomRingQuery)) {
    streamWrite(ss, MolPickler::QUERY_ATOMRING);
    queryVal = static_cast<const EqualityQuery<int, T const *, true> *>(query)
                   ->getVal();
    streamWrite(ss, MolPickler::QUERY_VALUE, queryVal);
    queryVal = static_cast<const EqualityQuery<int, T const *, true> *>(query)
                   ->getTol();
    streamWrite(ss, queryVal);
  } else if (typeid(*query) == typeid(RecursiveStructureQuery)) {
    streamWrite(ss, MolPickler::QUERY_RECURSIVE);
    streamWrite(ss, MolPickler::QUERY_VALUE);
    MolPickler::pickleMol(
        ((const RecursiveStructureQuery *)query)->getQueryMol(), ss);
  } else if (typeid(*query) == typeid(Query<int, T const *, true>)) {
    streamWrite(ss, MolPickler::QUERY_NULL);
  } else {
    throw MolPicklerException("do not know how to pickle part of the query.");
  }

  // now the children:
  streamWrite(ss, MolPickler::QUERY_NUMCHILDREN,
              static_cast<unsigned char>(query->endChildren() -
                                         query->beginChildren()));
  typename Query<int, T const *, true>::CHILD_VECT_CI cit;
  for (cit = query->beginChildren(); cit != query->endChildren(); ++cit) {
    pickleQuery(ss, cit->get());
  }
}

void finalizeQueryFromDescription(Query<int, Atom const *, true> *query,
                                  Atom const *owner) {
  RDUNUSED_PARAM(owner);
  std::string descr = query->getDescription();
  Query<int, Atom const *, true> *tmpQuery;
  if (descr == "AtomRingBondCount") {
    query->setDataFunc(queryAtomRingBondCount);
  } else if (descr == "AtomHasRingBond") {
    query->setDataFunc(queryAtomHasRingBond);
  } else if (descr == "AtomRingSize") {
    tmpQuery = makeAtomInRingOfSizeQuery(
        static_cast<ATOM_EQUALS_QUERY *>(query)->getVal());
    query->setDataFunc(tmpQuery->getDataFunc());
    delete tmpQuery;
  } else if (descr == "AtomMinRingSize") {
    query->setDataFunc(queryAtomMinRingSize);
  } else if (descr == "AtomRingBondCount") {
    query->setDataFunc(queryAtomRingBondCount);
  } else if (descr == "AtomImplicitValence") {
    query->setDataFunc(queryAtomImplicitValence);
  } else if (descr == "AtomTotalValence") {
    query->setDataFunc(queryAtomTotalValence);
  } else if (descr == "AtomAtomicNum") {
    query->setDataFunc(queryAtomNum);
  } else if (descr == "AtomExplicitDegree") {
    query->setDataFunc(queryAtomExplicitDegree);
  } else if (descr == "AtomTotalDegree") {
    query->setDataFunc(queryAtomTotalDegree);
  } else if (descr == "AtomHCount") {
    query->setDataFunc(queryAtomHCount);
  } else if (descr == "AtomImplicitHCount") {
    query->setDataFunc(queryAtomImplicitHCount);
  } else if (descr == "AtomHasImplicitH") {
    query->setDataFunc(queryAtomHasImplicitH);
  } else if (descr == "AtomIsAromatic") {
    query->setDataFunc(queryAtomAromatic);
  } else if (descr == "AtomIsAliphatic") {
    query->setDataFunc(queryAtomAliphatic);
  } else if (descr == "AtomUnsaturated") {
    query->setDataFunc(queryAtomUnsaturated);
  } else if (descr == "AtomMass") {
    query->setDataFunc(queryAtomMass);
  } else if (descr == "AtomIsotope") {
    query->setDataFunc(queryAtomIsotope);
  } else if (descr == "AtomFormalCharge") {
    query->setDataFunc(queryAtomFormalCharge);
  } else if (descr == "AtomHybridization") {
    query->setDataFunc(queryAtomHybridization);
  } else if (descr == "AtomInRing") {
    query->setDataFunc(queryIsAtomInRing);
  } else if (descr == "AtomInNRings") {
    query->setDataFunc(queryIsAtomInNRings);
  } else if (descr == "AtomNull") {
    query->setDataFunc(nullDataFun);
    query->setMatchFunc(nullQueryFun);
  } else if (descr == "AtomInNRings" || descr == "RecursiveStructure") {
    // don't need to do anything here because the classes
    // automatically have everything set
  } else if (descr == "AtomAnd" || descr == "AtomOr" || descr == "AtomXor") {
    // don't need to do anything here because the classes
    // automatically have everything set
  } else {
    throw MolPicklerException("Do not know how to finalize query: '" + descr +
                              "'");
  }
}

void finalizeQueryFromDescription(Query<int, Bond const *, true> *query,
                                  Bond const *owner) {
  RDUNUSED_PARAM(owner);
  std::string descr = query->getDescription();
  Query<int, Bond const *, true> *tmpQuery;
  if (descr == "BondRingSize") {
    tmpQuery = makeBondInRingOfSizeQuery(
        static_cast<BOND_EQUALS_QUERY *>(query)->getVal());
    query->setDataFunc(tmpQuery->getDataFunc());
    delete tmpQuery;
  } else if (descr == "BondMinRingSize") {
    query->setDataFunc(queryBondMinRingSize);
  } else if (descr == "BondOrder") {
    query->setDataFunc(queryBondOrder);
  } else if (descr == "BondDir") {
    query->setDataFunc(queryBondDir);
  } else if (descr == "BondInRing") {
    query->setDataFunc(queryIsBondInRing);
  } else if (descr == "BondInNRings") {
    query->setDataFunc(queryIsBondInNRings);
  } else if (descr == "BondNull") {
    query->setDataFunc(nullDataFun);
    query->setMatchFunc(nullQueryFun);
  } else if (descr == "BondAnd" || descr == "BondOr" || descr == "BondXor") {
    // don't need to do anything here because the classes
    // automatically have everything set
  } else {
    throw MolPicklerException("Do not know how to finalize query: '" + descr +
                              "'");
  }
}

template <class T>
Query<int, T const *, true> *buildBaseQuery(std::istream &ss, T const *owner,
                                            MolPickler::Tags tag, int version) {
  PRECONDITION(owner, "no query");
  std::string descr;
  Query<int, T const *, true> *res = 0;
  int32_t val;
  int32_t nMembers;
  switch (tag) {
    case MolPickler::QUERY_AND:
      res = new AndQuery<int, T const *, true>();
      break;
    case MolPickler::QUERY_OR:
      res = new OrQuery<int, T const *, true>();
      break;
    case MolPickler::QUERY_XOR:
      res = new XOrQuery<int, T const *, true>();
      break;
    case MolPickler::QUERY_EQUALS:
      res = new EqualityQuery<int, T const *, true>();
      streamRead(ss, tag, version);
      if (tag != MolPickler::QUERY_VALUE) {
        throw MolPicklerException(
            "Bad pickle format: QUERY_VALUE tag not found.");
      }
      streamRead(ss, val, version);
      static_cast<EqualityQuery<int, T const *, true> *>(res)->setVal(val);
      streamRead(ss, val, version);
      static_cast<EqualityQuery<int, T const *, true> *>(res)->setTol(val);
      break;
    case MolPickler::QUERY_GREATER:
      res = new GreaterQuery<int, T const *, true>();
      streamRead(ss, tag, version);
      if (tag != MolPickler::QUERY_VALUE) {
        throw MolPicklerException(
            "Bad pickle format: QUERY_VALUE tag not found.");
      }
      streamRead(ss, val, version);
      static_cast<GreaterQuery<int, T const *, true> *>(res)->setVal(val);
      streamRead(ss, val, version);
      static_cast<GreaterQuery<int, T const *, true> *>(res)->setTol(val);
      break;
    case MolPickler::QUERY_GREATEREQUAL:
      res = new GreaterEqualQuery<int, T const *, true>();
      streamRead(ss, tag, version);
      if (tag != MolPickler::QUERY_VALUE) {
        throw MolPicklerException(
            "Bad pickle format: QUERY_VALUE tag not found.");
      }
      streamRead(ss, val, version);
      static_cast<GreaterEqualQuery<int, T const *, true> *>(res)->setVal(val);
      streamRead(ss, val, version);
      static_cast<GreaterEqualQuery<int, T const *, true> *>(res)->setTol(val);
      break;
    case MolPickler::QUERY_LESS:
      res = new LessQuery<int, T const *, true>();
      streamRead(ss, tag, version);
      if (tag != MolPickler::QUERY_VALUE) {
        throw MolPicklerException(
            "Bad pickle format: QUERY_VALUE tag not found.");
      }
      streamRead(ss, val, version);
      static_cast<LessQuery<int, T const *, true> *>(res)->setVal(val);
      streamRead(ss, val, version);
      static_cast<LessQuery<int, T const *, true> *>(res)->setTol(val);
      break;
    case MolPickler::QUERY_LESSEQUAL:
      res = new LessEqualQuery<int, T const *, true>();
      streamRead(ss, tag, version);
      if (tag != MolPickler::QUERY_VALUE) {
        throw MolPicklerException(
            "Bad pickle format: QUERY_VALUE tag not found.");
      }
      streamRead(ss, val, version);
      static_cast<LessEqualQuery<int, T const *, true> *>(res)->setVal(val);
      streamRead(ss, val, version);
      static_cast<LessEqualQuery<int, T const *, true> *>(res)->setTol(val);
      break;
    case MolPickler::QUERY_RANGE:
      res = new RangeQuery<int, T const *, true>();
      streamRead(ss, tag, version);
      if (tag != MolPickler::QUERY_VALUE) {
        throw MolPicklerException(
            "Bad pickle format: QUERY_VALUE tag not found.");
      }
      streamRead(ss, val, version);
      static_cast<RangeQuery<int, T const *, true> *>(res)->setLower(val);
      streamRead(ss, val, version);
      static_cast<RangeQuery<int, T const *, true> *>(res)->setUpper(val);
      streamRead(ss, val, version);
      static_cast<RangeQuery<int, T const *, true> *>(res)->setTol(val);
      break;
    case MolPickler::QUERY_SET:
      res = new SetQuery<int, T const *, true>();
      streamRead(ss, tag, version);
      if (tag != MolPickler::QUERY_VALUE) {
        throw MolPicklerException(
            "Bad pickle format: QUERY_VALUE tag not found.");
      }
      streamRead(ss, nMembers);
      while (nMembers > 0) {
        streamRead(ss, val, version);
        static_cast<SetQuery<int, T const *, true> *>(res)->insert(val);
        --nMembers;
      }
      break;
    case MolPickler::QUERY_NULL:
      res = new Query<int, T const *, true>();
      break;
    default:
      throw MolPicklerException("unknown query-type tag encountered");
  }

  POSTCONDITION(res, "no match found");
  return res;
}

Query<int, Atom const *, true> *unpickleQuery(std::istream &ss,
                                              Atom const *owner, int version) {
  PRECONDITION(owner, "no query");
  std::string descr;
  bool isNegated = false;
  Query<int, Atom const *, true> *res;
  streamRead(ss, descr, version);
  MolPickler::Tags tag;
  streamRead(ss, tag, version);
  if (tag == MolPickler::QUERY_ISNEGATED) {
    isNegated = true;
    streamRead(ss, tag, version);
  }
  int32_t val;
  ROMol *tmpMol;
  switch (tag) {
    case MolPickler::QUERY_ATOMRING:
      res = new AtomRingQuery();
      streamRead(ss, tag, version);
      if (tag != MolPickler::QUERY_VALUE) {
        throw MolPicklerException(
            "Bad pickle format: QUERY_VALUE tag not found.");
      }
      streamRead(ss, val, version);
      static_cast<EqualityQuery<int, Atom const *, true> *>(res)->setVal(val);
      streamRead(ss, val, version);
      static_cast<EqualityQuery<int, Atom const *, true> *>(res)->setTol(val);
      break;
    case MolPickler::QUERY_RECURSIVE:
      streamRead(ss, tag, version);
      if (tag != MolPickler::QUERY_VALUE) {
        throw MolPicklerException(
            "Bad pickle format: QUERY_VALUE tag not found.");
      }
      tmpMol = new ROMol();
      MolPickler::molFromPickle(ss, tmpMol);
      res = new RecursiveStructureQuery(tmpMol);
      break;
    default:
      res = buildBaseQuery(ss, owner, tag, version);
      break;
  }
  CHECK_INVARIANT(res, "no query!");

  res->setNegation(isNegated);
  res->setDescription(descr);

  finalizeQueryFromDescription(res, owner);

  // read in the children:
  streamRead(ss, tag, version);
  if (tag != MolPickler::QUERY_NUMCHILDREN) {
    throw MolPicklerException(
        "Bad pickle format: QUERY_NUMCHILDREN tag not found.");
  }
  unsigned char numChildren;
  streamRead(ss, numChildren, version);
  while (numChildren > 0) {
    Query<int, Atom const *, true> *child = unpickleQuery(ss, owner, version);
    res->addChild(Query<int, Atom const *, true>::CHILD_TYPE(child));
    --numChildren;
  }
  return res;
}
Query<int, Bond const *, true> *unpickleQuery(std::istream &ss,
                                              Bond const *owner, int version) {
  PRECONDITION(owner, "no query");
  std::string descr;
  bool isNegated = false;
  Query<int, Bond const *, true> *res;
  streamRead(ss, descr, version);
  MolPickler::Tags tag;
  streamRead(ss, tag, version);
  if (tag == MolPickler::QUERY_ISNEGATED) {
    isNegated = true;
    streamRead(ss, tag, version);
  }
  res = buildBaseQuery(ss, owner, tag, version);
  CHECK_INVARIANT(res, "no query!");

  res->setNegation(isNegated);
  res->setDescription(descr);

  finalizeQueryFromDescription(res, owner);

  // read in the children:
  streamRead(ss, tag, version);
  if (tag != MolPickler::QUERY_NUMCHILDREN) {
    throw MolPicklerException(
        "Bad pickle format: QUERY_NUMCHILDREN tag not found.");
  }
  unsigned char numChildren;
  streamRead(ss, numChildren, version);
  while (numChildren > 0) {
    Query<int, Bond const *, true> *child = unpickleQuery(ss, owner, version);
    res->addChild(Query<int, Bond const *, true>::CHILD_TYPE(child));
    --numChildren;
  }
  return res;
}

void pickleAtomPDBResidueInfo(std::ostream &ss,
                              const AtomPDBResidueInfo *info) {
  PRECONDITION(info, "no info");
  if (info->getSerialNumber())
    streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_SERIALNUMBER,
                info->getSerialNumber());
  if (info->getAltLoc() != "")
    streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_ALTLOC, info->getAltLoc());
  if (info->getResidueName() != "")
    streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_RESIDUENAME,
                info->getResidueName());
  if (info->getResidueNumber())
    streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_RESIDUENUMBER,
                info->getResidueNumber());
  if (info->getChainId() != "")
    streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_CHAINID, info->getChainId());
  if (info->getInsertionCode() != "")
    streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_INSERTIONCODE,
                info->getInsertionCode());
  if (info->getOccupancy())
    streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_OCCUPANCY,
                info->getOccupancy());
  if (info->getTempFactor())
    streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_TEMPFACTOR,
                info->getTempFactor());
  if (info->getIsHeteroAtom())
    streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_ISHETEROATOM,
                static_cast<char>(info->getIsHeteroAtom()));
  if (info->getSecondaryStructure())
    streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_SECONDARYSTRUCTURE,
                info->getSecondaryStructure());
  if (info->getSegmentNumber())
    streamWrite(ss, MolPickler::ATOM_PDB_RESIDUE_SEGMENTNUMBER,
                info->getSegmentNumber());
}

void unpickleAtomPDBResidueInfo(std::istream &ss, AtomPDBResidueInfo *info,
                                int version) {
  PRECONDITION(info, "no info");
  std::string sval;
  double dval;
  char cval;
  unsigned int uival;
  int ival;
  MolPickler::Tags tag = MolPickler::BEGIN_ATOM_MONOMER;
  while (tag != MolPickler::END_ATOM_MONOMER) {
    streamRead(ss, tag, version);
    switch (tag) {
      case MolPickler::ATOM_PDB_RESIDUE_SERIALNUMBER:
        streamRead(ss, ival, version);
        info->setSerialNumber(ival);
        break;
      case MolPickler::ATOM_PDB_RESIDUE_ALTLOC:
        streamRead(ss, sval, version);
        info->setAltLoc(sval);
        break;
      case MolPickler::ATOM_PDB_RESIDUE_RESIDUENAME:
        streamRead(ss, sval, version);
        info->setResidueName(sval);
        break;
      case MolPickler::ATOM_PDB_RESIDUE_RESIDUENUMBER:
        streamRead(ss, ival, version);
        info->setResidueNumber(ival);
        break;
      case MolPickler::ATOM_PDB_RESIDUE_CHAINID:
        streamRead(ss, sval, version);
        info->setChainId(sval);
        break;
      case MolPickler::ATOM_PDB_RESIDUE_INSERTIONCODE:
        streamRead(ss, sval, version);
        info->setInsertionCode(sval);
        break;
      case MolPickler::ATOM_PDB_RESIDUE_OCCUPANCY:
        streamRead(ss, dval, version);
        info->setOccupancy(dval);
        break;
      case MolPickler::ATOM_PDB_RESIDUE_TEMPFACTOR:
        streamRead(ss, dval, version);
        info->setTempFactor(dval);
        break;
      case MolPickler::ATOM_PDB_RESIDUE_ISHETEROATOM:
        streamRead(ss, cval, version);
        info->setIsHeteroAtom(cval);
        break;
      case MolPickler::ATOM_PDB_RESIDUE_SECONDARYSTRUCTURE:
        streamRead(ss, uival, version);
        info->setSecondaryStructure(uival);
        break;
      case MolPickler::ATOM_PDB_RESIDUE_SEGMENTNUMBER:
        streamRead(ss, uival, version);
        info->setSegmentNumber(uival);
        break;
      case MolPickler::END_ATOM_MONOMER:
        break;
      default:
        throw MolPicklerException(
            "unrecognized tag while parsing atom peptide residue info");
    }
  }
}

void pickleAtomMonomerInfo(std::ostream &ss, const AtomMonomerInfo *info) {
  PRECONDITION(info, "no info");
  streamWrite(ss, info->getName());
  streamWrite(ss, static_cast<unsigned int>(info->getMonomerType()));
  switch (info->getMonomerType()) {
    case AtomMonomerInfo::UNKNOWN:
    case AtomMonomerInfo::OTHER:
      break;
    case AtomMonomerInfo::PDBRESIDUE:
      pickleAtomPDBResidueInfo(ss,
                               static_cast<const AtomPDBResidueInfo *>(info));
      break;
    default:
      throw MolPicklerException("unrecognized MonomerType");
  }
}
AtomMonomerInfo *unpickleAtomMonomerInfo(std::istream &ss, int version) {
  MolPickler::Tags tag;
  std::string nm;
  streamRead(ss, nm, version);
  unsigned int typ;
  streamRead(ss, typ, version);

  AtomMonomerInfo *res;
  switch (typ) {
    case AtomMonomerInfo::UNKNOWN:
    case AtomMonomerInfo::OTHER:
      res =
          new AtomMonomerInfo(RDKit::AtomMonomerInfo::AtomMonomerType(typ), nm);
      streamRead(ss, tag, version);
      if (tag != MolPickler::END_ATOM_MONOMER)
        throw MolPicklerException(
            "did not find expected end of atom monomer info");
      break;
    case AtomMonomerInfo::PDBRESIDUE:
      res = static_cast<AtomMonomerInfo *>(new AtomPDBResidueInfo(nm));
      unpickleAtomPDBResidueInfo(ss, static_cast<AtomPDBResidueInfo *>(res),
                                 version);
      break;
    default:
      throw MolPicklerException("unrecognized MonomerType");
  }
  return res;
}

}  // end of anonymous namespace

void MolPickler::pickleMol(const ROMol *mol, std::ostream &ss) {
  PRECONDITION(mol, "empty molecule");
  streamWrite(ss, endianId);
  streamWrite(ss, static_cast<int>(VERSION));
  streamWrite(ss, versionMajor);
  streamWrite(ss, versionMinor);
  streamWrite(ss, versionPatch);
#ifndef OLD_PICKLE
  if (mol->getNumAtoms() > 255) {
    _pickle<int32_t>(mol, ss);
  } else {
    _pickle<unsigned char>(mol, ss);
  }
#else
  _pickleV1(mol, ss);
#endif
}
void MolPickler::pickleMol(const ROMol *mol, std::string &res) {
  PRECONDITION(mol, "empty molecule");
  std::stringstream ss(std::ios_base::binary | std::ios_base::out |
                       std::ios_base::in);
  MolPickler::pickleMol(mol, ss);
  res = ss.str();
}

// NOTE: if the mol passed in here already has atoms and bonds, they will
// be left intact.  The side effect is that ALL atom and bond bookmarks
// will be blown out by the end of this process.
void MolPickler::molFromPickle(std::istream &ss, ROMol *mol) {
  PRECONDITION(mol, "empty molecule");
  int32_t tmpInt;

  mol->clearAllAtomBookmarks();
  mol->clearAllBondBookmarks();

  streamRead(ss, tmpInt);
  if (tmpInt != endianId) {
    throw MolPicklerException(
        "Bad pickle format: bad endian ID or invalid file format");
  }

  streamRead(ss, tmpInt);
  if (static_cast<Tags>(tmpInt) != VERSION) {
    throw MolPicklerException("Bad pickle format: no version tag");
  }
  int32_t majorVersion, minorVersion, patchVersion;
  streamRead(ss, majorVersion);
  streamRead(ss, minorVersion);
  streamRead(ss, patchVersion);
  if (majorVersion > versionMajor ||
      (majorVersion == versionMajor && minorVersion > versionMinor)) {
    BOOST_LOG(rdWarningLog) << "Depickling from a version number ("
                            << majorVersion << "." << minorVersion << ")"
                            << "that is higher than our version ("
                            << versionMajor << "." << versionMinor
                            << ").\nThis probably won't work." << std::endl;
  }
  majorVersion = 1000 * majorVersion + minorVersion * 10 + patchVersion;
  if (majorVersion == 1) {
    _depickleV1(ss, mol);
  } else {
    int32_t numAtoms;
    streamRead(ss, numAtoms, majorVersion);
    if (numAtoms > 255) {
      _depickle<int32_t>(ss, mol, majorVersion, numAtoms);
    } else {
      _depickle<unsigned char>(ss, mol, majorVersion, numAtoms);
    }
  }
  mol->clearAllAtomBookmarks();
  mol->clearAllBondBookmarks();
  if (majorVersion < 4000) {
    // FIX for issue 220 - probably better to change the pickle format later
    MolOps::assignStereochemistry(*mol, true);
  }
}
void MolPickler::molFromPickle(const std::string &pickle, ROMol *mol) {
  PRECONDITION(mol, "empty molecule");
  std::stringstream ss(std::ios_base::binary | std::ios_base::out |
                       std::ios_base::in);
  ss.write(pickle.c_str(), pickle.length());
  MolPickler::molFromPickle(ss, mol);
}

//--------------------------------------
//
//            Molecules
//
//--------------------------------------
template <typename T>
void MolPickler::_pickle(const ROMol *mol, std::ostream &ss) {
  PRECONDITION(mol, "empty molecule");
  int32_t tmpInt;
  bool includeAtomCoords = true;
  std::map<int, int> atomIdxMap;

  tmpInt = static_cast<int32_t>(mol->getNumAtoms());
  streamWrite(ss, tmpInt);
  tmpInt = static_cast<int32_t>(mol->getNumBonds());
  streamWrite(ss, tmpInt);

  char flag = 0;
  if (includeAtomCoords) flag |= 0x1 << 7;
  streamWrite(ss, flag);

  // -------------------
  //
  // Write Atoms
  //
  // -------------------
  streamWrite(ss, BEGINATOM);
  ROMol::ConstAtomIterator atIt;
  int nWritten = 0;
  for (atIt = mol->beginAtoms(); atIt != mol->endAtoms(); ++atIt) {
    _pickleAtom<T>(ss, *atIt);
    atomIdxMap[(*atIt)->getIdx()] = nWritten;
    nWritten++;
  }

  // -------------------
  //
  // Write Bonds
  //
  // -------------------
  streamWrite(ss, BEGINBOND);
  for (unsigned int i = 0; i < mol->getNumBonds(); i++) {
    _pickleBond<T>(ss, mol->getBondWithIdx(i), atomIdxMap);
  }

  // -------------------
  //
  // Write Rings (if present)
  //
  // -------------------
  const RingInfo *ringInfo = mol->getRingInfo();
  if (ringInfo && ringInfo->isInitialized()) {
    streamWrite(ss, BEGINSSSR);
    _pickleSSSR<T>(ss, ringInfo, atomIdxMap);
  }

  // pickle the conformations if necessary

  if (includeAtomCoords) {
    streamWrite(ss, BEGINCONFS);
    tmpInt = static_cast<int32_t>(mol->getNumConformers());
    streamWrite(ss, tmpInt);

    ROMol::ConstConformerIterator ci;
    for (ci = mol->beginConformers(); ci != mol->endConformers(); ++ci) {
      const Conformer *conf = ci->get();
      _pickleConformer<T>(ss, conf);
    }
  }
  streamWrite(ss, ENDMOL);
}

template <typename T>
void MolPickler::_depickle(std::istream &ss, ROMol *mol, int version,
                           int numAtoms) {
  PRECONDITION(mol, "empty molecule");
  bool directMap = mol->getNumAtoms() == 0;
  Tags tag;
  int32_t tmpInt;
  // int numAtoms,numBonds;
  int numBonds;
  bool haveQuery = false;

  streamRead(ss, tmpInt, version);
  numBonds = tmpInt;

  // did we include coordinates
  bool includeCoords = false;
  if (version >= 3000) {
    char flag;
    streamRead(ss, flag, version);
    if (flag & 0x1 << 7) includeCoords = true;
  }
  // -------------------
  //
  // Read Atoms
  //
  // -------------------
  streamRead(ss, tag, version);
  if (tag != BEGINATOM) {
    throw MolPicklerException("Bad pickle format: BEGINATOM tag not found.");
  }
  Conformer *conf = 0;
  if ((version >= 2000 && version < 3000) && includeCoords) {
    // there can only one conformation - since the poositions were stored on
    // the atoms themselves in this version
    conf = new Conformer(numAtoms);
    mol->addConformer(conf, true);
  }
  for (int i = 0; i < numAtoms; i++) {
    RDGeom::Point3D pos;
    Atom *atom = _addAtomFromPickle<T>(ss, mol, pos, version, directMap);
    if ((version >= 2000 && version < 3000) && includeCoords) {
      // this is a older pickle so we go the pos
      conf->setAtomPos(i, pos);
    }
    if (!directMap) {
      mol->setAtomBookmark(atom, i);
    }
    if (atom->hasQuery()) {
      haveQuery = true;
    }
  }

  // -------------------
  //
  // Read Bonds
  //
  // -------------------
  streamRead(ss, tag, version);
  if (tag != BEGINBOND) {
    throw MolPicklerException("Bad pickle format: BEGINBOND tag not found.");
  }
  for (int i = 0; i < numBonds; i++) {
    Bond *bond = _addBondFromPickle<T>(ss, mol, version, directMap);
    if (!directMap) {
      mol->setBondBookmark(bond, i);
    }
  }

  // -------------------
  //
  // Read Rings (if needed)
  //
  // -------------------
  streamRead(ss, tag, version);
  if (tag == BEGINSSSR) {
    _addRingInfoFromPickle<T>(ss, mol, version, directMap);
    streamRead(ss, tag, version);
  }

  if (tag == BEGINCONFS) {
    // read in the conformation
    streamRead(ss, tmpInt, version);
    int i;
    for (i = 0; i < tmpInt; i++) {
      Conformer *conf = _conformerFromPickle<T>(ss, version);
      mol->addConformer(conf);
    }
    streamRead(ss, tag, version);
  }

  if (tag != ENDMOL) {
    throw MolPicklerException("Bad pickle format: ENDMOL tag not found.");
  }

  if (haveQuery) {
    // we didn't read any property info for atoms with associated
    // queries. update their property caches
    // (was sf.net Issue 3316407)
    for (ROMol::AtomIterator atIt = mol->beginAtoms(); atIt != mol->endAtoms();
         atIt++) {
      Atom *atom = *atIt;
      if (atom->hasQuery()) {
        atom->updatePropertyCache(false);
      }
    }
  }
}

//--------------------------------------
//
//            Atoms
//
//--------------------------------------

namespace {
bool getAtomMapNumber(const Atom *atom, int &mapNum) {
  PRECONDITION(atom, "bad atom");
  if (!atom->hasProp(common_properties::molAtomMapNumber)) return false;
  bool res = true;
  int tmpInt;
  try {
    atom->getProp(common_properties::molAtomMapNumber, tmpInt);
  } catch (boost::bad_any_cast &) {
    const std::string &tmpSVal =
        atom->getProp<std::string>(common_properties::molAtomMapNumber);
    try {
      tmpInt = boost::lexical_cast<int>(tmpSVal);
    } catch (boost::bad_lexical_cast &) {
      res = false;
    }
  }
  if (res) mapNum = tmpInt;
  return res;
}
}

// T refers to the type of the atom indices written
template <typename T>
void MolPickler::_pickleAtom(std::ostream &ss, const Atom *atom) {
  PRECONDITION(atom, "empty atom");
  char tmpChar;
  unsigned char tmpUchar;
  signed char tmpSchar;
  int tmpInt;
  char flags;

  tmpUchar = atom->getAtomicNum() % 256;
  streamWrite(ss, tmpUchar);

  flags = 0;
  if (atom->getIsAromatic()) flags |= 0x1 << 6;
  if (atom->getNoImplicit()) flags |= 0x1 << 5;
  if (atom->hasQuery()) flags |= 0x1 << 4;
  if (getAtomMapNumber(atom, tmpInt)) flags |= 0x1 << 3;
  if (atom->hasProp(common_properties::dummyLabel)) flags |= 0x1 << 2;
  if (atom->getMonomerInfo()) flags |= 0x1 << 1;

  streamWrite(ss, flags);

  if (!atom->hasQuery()) {
    std::stringstream tss(std::ios_base::binary | std::ios_base::out |
                          std::ios_base::in);
    int32_t propFlags = 0;
    // tmpFloat=atom->getMass()-PeriodicTable::getTable()->getAtomicWeight(atom->getAtomicNum());
    // if(fabs(tmpFloat)>.0001){
    //   propFlags |= 1;
    //   streamWrite(tss,tmpFloat);
    // }
    tmpSchar = static_cast<signed char>(atom->getFormalCharge());
    if (tmpSchar != 0) {
      propFlags |= 1 << 1;
      streamWrite(tss, tmpSchar);
    }
    tmpChar = static_cast<char>(atom->getChiralTag());
    if (tmpChar != 0) {
      propFlags |= 1 << 2;
      streamWrite(tss, tmpChar);
    }
    tmpChar = static_cast<char>(atom->getHybridization());
    if (tmpChar != static_cast<char>(Atom::SP3)) {
      propFlags |= 1 << 3;
      streamWrite(tss, tmpChar);
    }

    tmpChar = static_cast<char>(atom->getNumExplicitHs());
    if (tmpChar != 0) {
      propFlags |= 1 << 4;
      streamWrite(tss, tmpChar);
    }
    if (atom->d_explicitValence > 0) {
      tmpChar = static_cast<char>(atom->d_explicitValence);
      propFlags |= 1 << 5;
      streamWrite(tss, tmpChar);
    }
    if (atom->d_implicitValence > 0) {
      tmpChar = static_cast<char>(atom->d_implicitValence);
      propFlags |= 1 << 6;
      streamWrite(tss, tmpChar);
    }
    tmpChar = static_cast<char>(atom->getNumRadicalElectrons());
    if (tmpChar != 0) {
      propFlags |= 1 << 7;
      streamWrite(tss, tmpChar);
    }

    unsigned int tmpuint = atom->getIsotope();
    if (tmpuint > 0) {
      propFlags |= 1 << 8;
      streamWrite(tss, tmpuint);
    }

    streamWrite(ss, propFlags);
    ss.write(tss.str().c_str(), tss.str().size());
  } else {
    streamWrite(ss, BEGINQUERY);
    pickleQuery(ss, static_cast<const QueryAtom *>(atom)->getQuery());
    streamWrite(ss, ENDQUERY);
  }
  if (getAtomMapNumber(atom, tmpInt)) {
    tmpChar = static_cast<char>(tmpInt % 256);
    streamWrite(ss, ATOM_MAPNUMBER, tmpChar);
  }
  if (atom->hasProp(common_properties::dummyLabel)) {
    streamWrite(ss, ATOM_DUMMYLABEL,
                atom->getProp<std::string>(common_properties::dummyLabel));
  }
  if (atom->getMonomerInfo()) {
    streamWrite(ss, BEGIN_ATOM_MONOMER);
    pickleAtomMonomerInfo(ss, atom->getMonomerInfo());
    streamWrite(ss, END_ATOM_MONOMER);
  }
}

template <typename T>
void MolPickler::_pickleConformer(std::ostream &ss, const Conformer *conf) {
  PRECONDITION(conf, "empty conformer");
  char tmpChr = static_cast<int>(conf->is3D());
  streamWrite(ss, tmpChr);
  int32_t tmpInt = static_cast<int32_t>(conf->getId());
  streamWrite(ss, tmpInt);
  T tmpT = static_cast<T>(conf->getNumAtoms());
  streamWrite(ss, tmpT);
  const RDGeom::POINT3D_VECT &pts = conf->getPositions();
  for (RDGeom::POINT3D_VECT_CI pti = pts.begin(); pti != pts.end(); pti++) {
    float tmpFloat;
    tmpFloat = static_cast<float>(pti->x);
    streamWrite(ss, tmpFloat);
    tmpFloat = static_cast<float>(pti->y);
    streamWrite(ss, tmpFloat);
    tmpFloat = static_cast<float>(pti->z);
    streamWrite(ss, tmpFloat);
  }
}

template <typename T>
Conformer *MolPickler::_conformerFromPickle(std::istream &ss, int version) {
  float tmpFloat;
  bool is3D = true;
  if (version > 4000) {
    char tmpChr;
    streamRead(ss, tmpChr, version);
    is3D = static_cast<bool>(tmpChr);
  }
  int tmpInt;
  streamRead(ss, tmpInt, version);
  unsigned int cid = static_cast<unsigned int>(tmpInt);
  T tmpT;
  streamRead(ss, tmpT, version);
  unsigned int numAtoms = static_cast<unsigned int>(tmpT);
  Conformer *conf = new Conformer(numAtoms);
  conf->setId(cid);
  conf->set3D(is3D);
  for (unsigned int i = 0; i < numAtoms; i++) {
    streamRead(ss, tmpFloat, version);
    conf->getAtomPos(i).x = static_cast<double>(tmpFloat);
    streamRead(ss, tmpFloat, version);
    conf->getAtomPos(i).y = static_cast<double>(tmpFloat);
    streamRead(ss, tmpFloat, version);
    conf->getAtomPos(i).z = static_cast<double>(tmpFloat);
  }
  return conf;
}

template <typename T>
Atom *MolPickler::_addAtomFromPickle(std::istream &ss, ROMol *mol,
                                     RDGeom::Point3D &pos, int version,
                                     bool directMap) {
  RDUNUSED_PARAM(directMap);
  PRECONDITION(mol, "empty molecule");
  float x, y, z;
  char tmpChar;
  unsigned char tmpUchar;
  signed char tmpSchar;
  char flags;
  Tags tag;
  Atom *atom = 0;
  int atomicNum = 0;

  streamRead(ss, tmpUchar, version);
  atomicNum = tmpUchar;

  bool hasQuery = false;
  streamRead(ss, flags, version);
  if (version > 5000) {
    hasQuery = flags & 0x1 << 4;
  }
  if (!hasQuery) {
    atom = new Atom(atomicNum);
  } else {
    atom = new QueryAtom();
    if (atomicNum) {
      // can't set this in the constructor because that builds a
      // query and we're going to take care of that later:
      atom->setAtomicNum(atomicNum);
    }
  }
  atom->setIsAromatic(flags & 0x1 << 6);
  atom->setNoImplicit(flags & 0x1 << 5);

  bool hasAtomMap = 0, hasDummyLabel = 0;
  if (version >= 6020) {
    hasAtomMap = flags & 0x1 << 3;
    hasDummyLabel = flags & 0x1 << 2;
  }
  bool hasMonomerInfo = 0;
  if (version >= 7020) {
    hasMonomerInfo = flags & 0x1 << 1;
  }

  // are coordinates present?
  if (flags & 0x1 << 7) {
    streamRead(ss, x, version);
    pos.x = static_cast<double>(x);
    streamRead(ss, y, version);
    pos.y = static_cast<double>(y);
    streamRead(ss, z, version);
    pos.z = static_cast<double>(z);
  }

  if (version <= 5000 || !hasQuery) {
    if (version < 7000) {
      if (version < 6030) {
        streamRead(ss, tmpSchar, version);
        // FIX: technically should be handling this in order to maintain true
        // backwards compatibility
        // atom->setMass(PeriodicTable::getTable()->getAtomicWeight(atom->getAtomicNum())+
        //              static_cast<int>(tmpSchar));
      } else {
        float tmpFloat;
        streamRead(ss, tmpFloat, version);
        // FIX: technically should be handling this in order to maintain true
        // backwards compatibility
        // atom->setMass(tmpFloat);
      }

      streamRead(ss, tmpSchar, version);
      atom->setFormalCharge(static_cast<int>(tmpSchar));

      streamRead(ss, tmpChar, version);
      atom->setChiralTag(static_cast<Atom::ChiralType>(tmpChar));
      streamRead(ss, tmpChar, version);
      atom->setHybridization(static_cast<Atom::HybridizationType>(tmpChar));
      streamRead(ss, tmpChar, version);
      atom->setNumExplicitHs(static_cast<int>(tmpChar));
      streamRead(ss, tmpChar, version);
      atom->d_explicitValence = tmpChar;
      streamRead(ss, tmpChar, version);
      atom->d_implicitValence = tmpChar;
      if (version > 6000) {
        streamRead(ss, tmpChar, version);
        atom->d_numRadicalElectrons = static_cast<unsigned int>(tmpChar);
      }
    } else {
      int propFlags;
      streamRead(ss, propFlags, version);
      if (propFlags & 1) {
        float tmpFloat;
        streamRead(ss, tmpFloat, version);
        int iso = static_cast<int>(floor(tmpFloat + atom->getMass() + .0001));
        atom->setIsotope(iso);
      }

      if (propFlags & (1 << 1)) {
        streamRead(ss, tmpSchar, version);
      } else {
        tmpSchar = 0;
      }
      atom->setFormalCharge(static_cast<int>(tmpSchar));

      if (propFlags & (1 << 2)) {
        streamRead(ss, tmpChar, version);
      } else {
        tmpChar = 0;
      }
      atom->setChiralTag(static_cast<Atom::ChiralType>(tmpChar));

      if (propFlags & (1 << 3)) {
        streamRead(ss, tmpChar, version);
      } else {
        tmpChar = Atom::SP3;
      }
      atom->setHybridization(static_cast<Atom::HybridizationType>(tmpChar));

      if (propFlags & (1 << 4)) {
        streamRead(ss, tmpChar, version);
      } else {
        tmpChar = 0;
      }
      atom->setNumExplicitHs(tmpChar);

      if (propFlags & (1 << 5)) {
        streamRead(ss, tmpChar, version);
      } else {
        tmpChar = 0;
      }
      atom->d_explicitValence = tmpChar;

      if (propFlags & (1 << 6)) {
        streamRead(ss, tmpChar, version);
      } else {
        tmpChar = 0;
      }
      atom->d_implicitValence = tmpChar;
      if (propFlags & (1 << 7)) {
        streamRead(ss, tmpChar, version);
      } else {
        tmpChar = 0;
      }
      atom->d_numRadicalElectrons = static_cast<unsigned int>(tmpChar);

      atom->d_isotope = 0;
      if (propFlags & (1 << 8)) {
        unsigned int tmpuint;
        streamRead(ss, tmpuint, version);
        atom->setIsotope(tmpuint);
      }
    }

  } else if (version > 5000) {
    // we have a query:
    streamRead(ss, tag, version);
    if (tag != BEGINQUERY) {
      throw MolPicklerException("Bad pickle format: BEGINQUERY tag not found.");
    }
    static_cast<QueryAtom *>(atom)->setQuery(unpickleQuery(ss, atom, version));
    streamRead(ss, tag, version);
    if (tag != ENDQUERY) {
      throw MolPicklerException("Bad pickle format: ENDQUERY tag not found.");
    }
    atom->setNumExplicitHs(0);
  }

  if (version > 5000) {
    if (version < 6020) {
      unsigned int sPos = rdcast<unsigned int>(ss.tellg());
      Tags tag;
      streamRead(ss, tag, version);
      if (tag == ATOM_MAPNUMBER) {
        int tmpInt;
        streamRead(ss, tmpChar, version);
        tmpInt = tmpChar;
        atom->setProp(common_properties::molAtomMapNumber, tmpInt);
      } else {
        ss.seekg(sPos);
      }
    } else {
      if (hasAtomMap) {
        Tags tag;
        streamRead(ss, tag, version);
        if (tag != ATOM_MAPNUMBER) {
          throw MolPicklerException(
              "Bad pickle format: ATOM_MAPNUMBER tag not found.");
        }
        int tmpInt;
        streamRead(ss, tmpChar, version);
        tmpInt = tmpChar;
        atom->setProp(common_properties::molAtomMapNumber, tmpInt);
      }
      if (hasDummyLabel) {
        streamRead(ss, tag, version);
        if (tag != ATOM_DUMMYLABEL) {
          throw MolPicklerException(
              "Bad pickle format: ATOM_DUMMYLABEL tag not found.");
        }
        std::string tmpStr;
        streamRead(ss, tmpStr, version);
        atom->setProp(common_properties::dummyLabel, tmpStr);
      }
    }
  }
  if (version >= 7020) {
    if (hasMonomerInfo) {
      streamRead(ss, tag, version);
      if (tag != BEGIN_ATOM_MONOMER) {
        throw MolPicklerException(
            "Bad pickle format: BEGIN_ATOM_MONOMER tag not found.");
      }
      atom->setMonomerInfo(unpickleAtomMonomerInfo(ss, version));
    }
  }
  mol->addAtom(atom, false, true);
  return atom;
}

//--------------------------------------
//
//            Bonds
//
//--------------------------------------

template <typename T>
void MolPickler::_pickleBond(std::ostream &ss, const Bond *bond,
                             std::map<int, int> &atomIdxMap) {
  PRECONDITION(bond, "empty bond");
  T tmpT;
  char tmpChar;
  char flags;

  tmpT = static_cast<T>(atomIdxMap[bond->getBeginAtomIdx()]);
  streamWrite(ss, tmpT);
  tmpT = static_cast<T>(atomIdxMap[bond->getEndAtomIdx()]);
  streamWrite(ss, tmpT);

  flags = 0;
  if (bond->getIsAromatic()) flags |= 0x1 << 6;
  if (bond->getIsConjugated()) flags |= 0x1 << 5;
  if (bond->hasQuery()) flags |= 0x1 << 4;
  if (bond->getBondType() != Bond::SINGLE) flags |= 0x1 << 3;
  if (bond->getBondDir() != Bond::NONE) flags |= 0x1 << 2;
  if (bond->getStereo() != Bond::STEREONONE) flags |= 0x1 << 1;
  streamWrite(ss, flags);

  if (bond->getBondType() != Bond::SINGLE) {
    tmpChar = static_cast<char>(bond->getBondType());
    streamWrite(ss, tmpChar);
  }
  if (bond->getBondDir() != Bond::NONE) {
    tmpChar = static_cast<char>(bond->getBondDir());
    streamWrite(ss, tmpChar);
  }

  // write info about the stereochemistry:
  if (bond->getStereo() != Bond::STEREONONE) {
    tmpChar = static_cast<char>(bond->getStereo());
    streamWrite(ss, tmpChar);
    const INT_VECT &stereoAts = bond->getStereoAtoms();
    tmpChar = rdcast<unsigned int>(stereoAts.size());
    streamWrite(ss, tmpChar);
    for (INT_VECT_CI idxIt = stereoAts.begin(); idxIt != stereoAts.end();
         ++idxIt) {
      tmpT = static_cast<T>(*idxIt);
      streamWrite(ss, tmpT);
    }
  }
  if (bond->hasQuery()) {
    streamWrite(ss, BEGINQUERY);
    pickleQuery(ss, static_cast<const QueryBond *>(bond)->getQuery());
    streamWrite(ss, ENDQUERY);
  }
}

template <typename T>
Bond *MolPickler::_addBondFromPickle(std::istream &ss, ROMol *mol, int version,
                                     bool directMap) {
  PRECONDITION(mol, "empty molecule");
  char tmpChar;
  char flags;
  int begIdx, endIdx;
  T tmpT;

  Bond *bond = NULL;
  streamRead(ss, tmpT, version);
  if (directMap) {
    begIdx = tmpT;
  } else {
    begIdx = mol->getAtomWithBookmark(static_cast<int>(tmpT))->getIdx();
  }
  streamRead(ss, tmpT, version);
  if (directMap) {
    endIdx = tmpT;

  } else {
    endIdx = mol->getAtomWithBookmark(static_cast<int>(tmpT))->getIdx();
  }
  streamRead(ss, flags, version);
  bool hasQuery = flags & 0x1 << 4;

  if (version <= 5000 || (version <= 7000 && !hasQuery) || version > 7000) {
    bond = new Bond();
    bond->setIsAromatic(flags & 0x1 << 6);
    bond->setIsConjugated(flags & 0x1 << 5);

    if (version < 7000) {
      streamRead(ss, tmpChar, version);
      bond->setBondType(static_cast<Bond::BondType>(tmpChar));
      streamRead(ss, tmpChar, version);
      bond->setBondDir(static_cast<Bond::BondDir>(tmpChar));

      if (version > 3000) {
        streamRead(ss, tmpChar, version);
        Bond::BondStereo stereo = static_cast<Bond::BondStereo>(tmpChar);
        bond->setStereo(stereo);
        if (stereo != Bond::STEREONONE) {
          streamRead(ss, tmpChar, version);
          for (char i = 0; i < tmpChar; ++i) {
            streamRead(ss, tmpT, version);
            bond->getStereoAtoms().push_back(static_cast<int>(tmpT));
          }
        }
      }
    } else {
      if (flags & (0x1 << 3)) {
        streamRead(ss, tmpChar, version);
        bond->setBondType(static_cast<Bond::BondType>(tmpChar));
      } else {
        bond->setBondType(Bond::SINGLE);
      }

      if (flags & (0x1 << 2)) {
        streamRead(ss, tmpChar, version);
        bond->setBondDir(static_cast<Bond::BondDir>(tmpChar));
      } else {
        bond->setBondDir(Bond::NONE);
      }

      if (flags & (0x1 << 1)) {
        streamRead(ss, tmpChar, version);
        Bond::BondStereo stereo = static_cast<Bond::BondStereo>(tmpChar);
        bond->setStereo(stereo);
        streamRead(ss, tmpChar, version);
        for (char i = 0; i < tmpChar; ++i) {
          streamRead(ss, tmpT, version);
          bond->getStereoAtoms().push_back(static_cast<int>(tmpT));
        }
      } else {
        bond->setStereo(Bond::STEREONONE);
      }
    }
  }
  if (version > 5000 && hasQuery) {
    Tags tag;
    if (bond) {
      Bond *tbond = bond;
      bond = new QueryBond(*bond);
      delete tbond;
    } else {
      bond = new QueryBond();
    }

    // we have a query:
    streamRead(ss, tag, version);
    if (tag != BEGINQUERY) {
      throw MolPicklerException("Bad pickle format: BEGINQUERY tag not found.");
    }
    static_cast<QueryBond *>(bond)->setQuery(unpickleQuery(ss, bond, version));
    streamRead(ss, tag, version);
    if (tag != ENDQUERY) {
      throw MolPicklerException("Bad pickle format: ENDQUERY tag not found.");
    }
  }
  if (bond) {
    bond->setBeginAtomIdx(begIdx);
    bond->setEndAtomIdx(endIdx);
    mol->addBond(bond, true);
  }
  return bond;
}

//--------------------------------------
//
//            Rings
//
//--------------------------------------
template <typename T>
void MolPickler::_pickleSSSR(std::ostream &ss, const RingInfo *ringInfo,
                             std::map<int, int> &atomIdxMap) {
  PRECONDITION(ringInfo, "missing ring info");
  T tmpT;
  tmpT = ringInfo->numRings();
  streamWrite(ss, tmpT);
  for (unsigned int i = 0; i < ringInfo->numRings(); i++) {
    INT_VECT ring;
    ring = ringInfo->atomRings()[i];
    tmpT = static_cast<T>(ring.size());
    streamWrite(ss, tmpT);
    for (unsigned int j = 0; j < ring.size(); j++) {
      tmpT = static_cast<T>(atomIdxMap[ring[j]]);
      streamWrite(ss, tmpT);
    }
#if 0
      ring = ringInfo->bondRings()[i];
      tmpT = static_cast<T>(ring.size());
      streamWrite(ss,tmpT);
      for(unsigned int j=0;j<ring.size();j++){
	tmpT = static_cast<T>(ring[j]);
	streamWrite(ss,tmpT);
      }
#endif
  }
}

template <typename T>
void MolPickler::_addRingInfoFromPickle(std::istream &ss, ROMol *mol,
                                        int version, bool directMap) {
  PRECONDITION(mol, "empty molecule");
  RingInfo *ringInfo = mol->getRingInfo();
  if (!ringInfo->isInitialized()) ringInfo->initialize();

  T numRings;
  streamRead(ss, numRings, version);

  if (numRings > 0) {
    ringInfo->preallocate(mol->getNumAtoms(), mol->getNumBonds());
    for (unsigned int i = 0; i < static_cast<unsigned int>(numRings); i++) {
      T tmpT;
      T ringSize;
      streamRead(ss, ringSize, version);

      INT_VECT atoms(static_cast<int>(ringSize));
      INT_VECT bonds(static_cast<int>(ringSize));
      for (unsigned int j = 0; j < static_cast<unsigned int>(ringSize); j++) {
        streamRead(ss, tmpT, version);
        if (directMap) {
          atoms[j] = static_cast<int>(tmpT);
        } else {
          atoms[j] = mol->getAtomWithBookmark(static_cast<int>(tmpT))->getIdx();
        }
      }
      if (version < 7000) {
        for (unsigned int j = 0; j < static_cast<unsigned int>(ringSize); j++) {
          streamRead(ss, tmpT, version);
          if (directMap) {
            bonds[j] = static_cast<int>(tmpT);
          } else {
            bonds[j] =
                mol->getBondWithBookmark(static_cast<int>(tmpT))->getIdx();
          }
        }
      } else {
        for (unsigned int j = 1; j < static_cast<unsigned int>(ringSize); ++j) {
          bonds[j - 1] =
              mol->getBondBetweenAtoms(atoms[j - 1], atoms[j])->getIdx();
        }
        bonds[ringSize - 1] =
            mol->getBondBetweenAtoms(atoms[0], atoms[ringSize - 1])->getIdx();
      }
      ringInfo->addRing(atoms, bonds);
    }
  }
}

//--------------------------------------
//
//            Version 1 Pickler:
//
//  NOTE: this is not 64bit clean, but it shouldn't be used anymore anyway
//
//--------------------------------------

void MolPickler::_pickleV1(const ROMol *mol, std::ostream &ss) {
  PRECONDITION(mol, "empty molecule");
  ROMol::ConstAtomIterator atIt;
  const Conformer *conf = 0;
  if (mol->getNumConformers() > 0) {
    conf = &(mol->getConformer());
  }
  for (atIt = mol->beginAtoms(); atIt != mol->endAtoms(); atIt++) {
    const Atom *atom = *atIt;

    streamWrite(ss, BEGINATOM);
    streamWrite(ss, ATOM_NUMBER, atom->getAtomicNum());

    streamWrite(ss, ATOM_INDEX, atom->getIdx());

    streamWrite(ss, ATOM_POS);
    RDGeom::Point3D p;
    if (conf) {
      p = conf->getAtomPos(atom->getIdx());
    }
    streamWrite(ss, p.x);
    streamWrite(ss, p.y);
    streamWrite(ss, p.z);

    if (atom->getFormalCharge() != 0) {
      streamWrite(ss, ATOM_CHARGE, atom->getFormalCharge());
    }
    if (atom->getNumExplicitHs() != 0) {
      streamWrite(ss, ATOM_NEXPLICIT, atom->getNumExplicitHs());
    }
    if (atom->getChiralTag() != 0) {
      streamWrite(ss, ATOM_CHIRALTAG, atom->getChiralTag());
    }
    if (atom->getIsAromatic()) {
      streamWrite(ss, ATOM_ISAROMATIC,
                  static_cast<char>(atom->getIsAromatic()));
    }
    streamWrite(ss, ENDATOM);
  }

  ROMol::ConstBondIterator bondIt;
  for (bondIt = mol->beginBonds(); bondIt != mol->endBonds(); bondIt++) {
    const Bond *bond = *bondIt;
    streamWrite(ss, BEGINBOND);
    streamWrite(ss, BOND_INDEX, bond->getIdx());
    streamWrite(ss, BOND_BEGATOMIDX, bond->getBeginAtomIdx());
    streamWrite(ss, BOND_ENDATOMIDX, bond->getEndAtomIdx());
    streamWrite(ss, BOND_TYPE, bond->getBondType());
    if (bond->getBondDir()) {
      streamWrite(ss, BOND_DIR, bond->getBondDir());
    }
    streamWrite(ss, ENDBOND);
  }
  streamWrite(ss, ENDMOL);
}

void MolPickler::_depickleV1(std::istream &ss, ROMol *mol) {
  PRECONDITION(mol, "empty molecule");
  Tags tag;

  Conformer *conf = new Conformer();
  mol->addConformer(conf);
  streamRead(ss, tag, 1);
  while (tag != ENDMOL) {
    switch (tag) {
      case BEGINATOM:
        _addAtomFromPickleV1(ss, mol);
        break;
      case BEGINBOND:
        _addBondFromPickleV1(ss, mol);
        break;
      default:
        UNDER_CONSTRUCTION("bad tag in pickle");
    }
    streamRead(ss, tag, 1);
  }
  mol->clearAllAtomBookmarks();
  mol->clearAllBondBookmarks();
}

void MolPickler::_addAtomFromPickleV1(std::istream &ss, ROMol *mol) {
  PRECONDITION(mol, "empty molecule");
  Tags tag;
  int intVar;
  double dblVar;
  char charVar;
  int version = 1;
  streamRead(ss, tag, version);
  Atom *atom = new Atom();
  Conformer &conf = mol->getConformer();
  RDGeom::Point3D pos;
  while (tag != ENDATOM) {
    switch (tag) {
      case ATOM_INDEX:
        streamRead(ss, intVar, version);
        mol->setAtomBookmark(atom, intVar);
        break;
      case ATOM_NUMBER:
        streamRead(ss, intVar, version);
        atom->setAtomicNum(intVar);
        break;
      case ATOM_POS:
        streamRead(ss, pos.x, version);
        streamRead(ss, pos.y, version);
        streamRead(ss, pos.z, version);
        break;
      case ATOM_CHARGE:
        streamRead(ss, intVar, version);
        atom->setFormalCharge(intVar);
        break;
      case ATOM_NEXPLICIT:
        streamRead(ss, intVar, version);
        atom->setNumExplicitHs(intVar);
        break;
      case ATOM_CHIRALTAG:
        streamRead(ss, intVar, version);
        atom->setChiralTag(static_cast<Atom::ChiralType>(intVar));
        break;
      case ATOM_MASS:
        streamRead(ss, dblVar, version);
        // we don't need to set this anymore, but we do need to read it in order
        // to
        // maintain backwards compatibility
        break;
      case ATOM_ISAROMATIC:
        streamRead(ss, charVar, version);
        atom->setIsAromatic(charVar);
        break;
      default:
        ASSERT_INVARIANT(0, "bad tag in atom block of pickle");
    }
    streamRead(ss, tag, version);
  }
  unsigned int id = mol->addAtom(atom, false, true);
  conf.setAtomPos(id, pos);
}
void MolPickler::_addBondFromPickleV1(std::istream &ss, ROMol *mol) {
  PRECONDITION(mol, "empty molecule");
  Tags tag;
  int intVar, idx = -1;
  int version = 1;
  Bond::BondType bt;
  Bond::BondDir bd;
  streamRead(ss, tag, version);
  Bond *bond = new Bond();
  while (tag != ENDBOND) {
    switch (tag) {
      case BOND_INDEX:
        streamRead(ss, idx, version);
        break;
      case BOND_BEGATOMIDX:
        streamRead(ss, intVar, version);
        bond->setBeginAtomIdx(mol->getAtomWithBookmark(intVar)->getIdx());
        break;
      case BOND_ENDATOMIDX:
        streamRead(ss, intVar, version);
        bond->setEndAtomIdx(mol->getAtomWithBookmark(intVar)->getIdx());
        break;
      case BOND_TYPE:
        streamRead(ss, bt, version);
        bond->setBondType(bt);
        break;
      case BOND_DIR:
        streamRead(ss, bd, version);
        bond->setBondDir(bd);
        break;
      default:
        ASSERT_INVARIANT(0, "bad tag in bond block of pickle");
    }
    streamRead(ss, tag, version);
  }
  mol->addBond(bond, true);
}
};