@@ -137,7 +137,7 @@ void ReactionPickler::_pickle(const ChemicalReaction *rxn, std::ostream &ss) {
   streamWrite(ss, BEGINPRODUCTS);
   for (MOL_SPTR_VECT::const_iterator tmpl = rxn->beginProductTemplates();
        tmpl != rxn->endProductTemplates(); ++tmpl) {
-    MolPickler::pickleMol(tmpl->get(), ss);
+    MolPickler::pickleMol(tmpl->get(), ss, PropertyPickleOptions::AllProps);
   }
   streamWrite(ss, ENDPRODUCTS);
 
// $Id: MolPickler.cpp 1123 2009-06-01 13:04:33Z glandrum $
//
//  Copyright (C) 2009 Greg Landrum
//  Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
//
//   @@ 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 <sstream>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionPickler.h>
#include <RDGeneral/utils.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/StreamOps.h>
#include <RDGeneral/types.h>
#include <boost/cstdint.hpp>
using boost::int32_t;
using boost::uint32_t;

namespace RDKit {
const int32_t ReactionPickler::versionMajor = 1;
const int32_t ReactionPickler::versionMinor = 1;
const int32_t ReactionPickler::versionPatch = 0;
const int32_t ReactionPickler::endianId = 0xDEADBEEF;

void streamWrite(std::ostream &ss, ReactionPickler::Tags tag) {
  int32_t tmp = tag;
  streamWrite(ss, tmp);
}
template <typename T>
void streamWrite(std::ostream &ss, ReactionPickler::Tags tag, const T &what) {
  streamWrite(ss, tag);
  streamWrite(ss, what);
};

void streamRead(std::istream &ss, ReactionPickler::Tags &tag) {
  int32_t tmp;
  streamRead(ss, tmp);
  tag = static_cast<ReactionPickler::Tags>(tmp);
}

void ReactionPickler::pickleReaction(const ChemicalReaction *rxn,
                                     std::ostream &ss) {
  PRECONDITION(rxn, "empty reaction");
  streamWrite(ss, endianId);
  streamWrite(ss, VERSION);
  streamWrite(ss, versionMajor);
  streamWrite(ss, versionMinor);
  streamWrite(ss, versionPatch);
  _pickle(rxn, ss);
}
void ReactionPickler::pickleReaction(const ChemicalReaction *rxn,
                                     std::string &res) {
  PRECONDITION(rxn, "empty reaction");
  std::stringstream ss(std::ios_base::binary | std::ios_base::out |
                       std::ios_base::in);
  ReactionPickler::pickleReaction(rxn, ss);
  res = ss.str();
}

// NOTE: if the reaction passed in here already has reactants and products
// be left intact.
void ReactionPickler::reactionFromPickle(std::istream &ss,
                                         ChemicalReaction *rxn) {
  PRECONDITION(rxn, "empty reaction");
  Tags tag;
  int32_t tmpInt;

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

  streamRead(ss, tag);
  if (tag != VERSION) {
    throw ReactionPicklerException("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;

  _depickle(ss, rxn, majorVersion);
}
void ReactionPickler::reactionFromPickle(const std::string &pickle,
                                         ChemicalReaction *rxn) {
  PRECONDITION(rxn, "empty reaction");
  std::stringstream ss(std::ios_base::binary | std::ios_base::out |
                       std::ios_base::in);
  ss.write(pickle.c_str(), pickle.length());
  ReactionPickler::reactionFromPickle(ss, rxn);
}

void ReactionPickler::_pickle(const ChemicalReaction *rxn, std::ostream &ss) {
  PRECONDITION(rxn, "empty reaction");
  uint32_t tmpInt;

  tmpInt = static_cast<int32_t>(rxn->getNumReactantTemplates());
  streamWrite(ss, tmpInt);
  tmpInt = static_cast<int32_t>(rxn->getNumProductTemplates());
  streamWrite(ss, tmpInt);
  tmpInt = static_cast<int32_t>(rxn->getNumAgentTemplates());
  streamWrite(ss, tmpInt);

  uint32_t flag = 0;
  if (rxn->getImplicitPropertiesFlag()) flag |= 0x1;
  if (rxn->df_needsInit) flag |= 0x2;
  streamWrite(ss, flag);

  // -------------------
  //
  // Write Reactants
  //
  // -------------------
  streamWrite(ss, BEGINREACTANTS);
  for (MOL_SPTR_VECT::const_iterator tmpl = rxn->beginReactantTemplates();
       tmpl != rxn->endReactantTemplates(); ++tmpl) {
    MolPickler::pickleMol(tmpl->get(), ss);
  }
  streamWrite(ss, ENDREACTANTS);

  streamWrite(ss, BEGINPRODUCTS);
  for (MOL_SPTR_VECT::const_iterator tmpl = rxn->beginProductTemplates();
       tmpl != rxn->endProductTemplates(); ++tmpl) {
    MolPickler::pickleMol(tmpl->get(), ss);
  }
  streamWrite(ss, ENDPRODUCTS);

  if (rxn->getNumAgentTemplates()) {
    streamWrite(ss, BEGINAGENTS);
    for (MOL_SPTR_VECT::const_iterator tmpl = rxn->beginAgentTemplates();
         tmpl != rxn->endAgentTemplates(); ++tmpl) {
      MolPickler::pickleMol(tmpl->get(), ss);
    }
    streamWrite(ss, ENDAGENTS);
  }
  streamWrite(ss, ENDREACTION);
}  // end of _pickle

void ReactionPickler::_depickle(std::istream &ss, ChemicalReaction *rxn,
                                int version) {
  PRECONDITION(rxn, "empty reaction");

  Tags tag;
  uint32_t numReactants, numProducts, numAgents = 0;

  streamRead(ss, numReactants);
  streamRead(ss, numProducts);
  if (version > 1000) {
    streamRead(ss, numAgents);
  }
  // we use this here and below to set df_needsInit, so don't re-use the
  // variable
  uint32_t flag = 0;
  streamRead(ss, flag);
  rxn->setImplicitPropertiesFlag(flag & 0x1);

  // -------------------
  //
  // Read Reactants
  //
  // -------------------
  streamRead(ss, tag);
  if (tag != BEGINREACTANTS) {
    throw ReactionPicklerException(
        "Bad pickle format: BEGINREACTANTS tag not found.");
  }
  for (unsigned int i = 0; i < numReactants; ++i) {
    ROMol *mol = new ROMol();
    MolPickler::molFromPickle(ss, mol);
    rxn->addReactantTemplate(ROMOL_SPTR(mol));
  }
  streamRead(ss, tag);
  if (tag != ENDREACTANTS) {
    throw ReactionPicklerException(
        "Bad pickle format: ENDREACTANTS tag not found.");
  }
  streamRead(ss, tag);
  if (tag != BEGINPRODUCTS) {
    throw ReactionPicklerException(
        "Bad pickle format: BEGINPRODUCTS tag not found.");
  }
  for (unsigned int i = 0; i < numProducts; ++i) {
    ROMol *mol = new ROMol();
    MolPickler::molFromPickle(ss, mol);
    rxn->addProductTemplate(ROMOL_SPTR(mol));
  }
  streamRead(ss, tag);
  if (tag != ENDPRODUCTS) {
    throw ReactionPicklerException(
        "Bad pickle format: ENDPRODUCTS tag not found.");
  }
  if (numAgents != 0) {
    streamRead(ss, tag);
    if (tag != BEGINAGENTS) {
      throw ReactionPicklerException(
          "Bad pickle format: BEGINAGENTS tag not found.");
    }
    for (unsigned int i = 0; i < numAgents; ++i) {
      ROMol *mol = new ROMol();
      MolPickler::molFromPickle(ss, mol);
      rxn->addAgentTemplate(ROMOL_SPTR(mol));
    }
    streamRead(ss, tag);
    if (tag != ENDAGENTS) {
      throw ReactionPicklerException(
          "Bad pickle format: ENDAGENTS tag not found.");
    }
  }

  // need to do this after we add reactants and products
  rxn->df_needsInit = flag & 0x2;

}  // end of _depickle
};  // end of RDKit namespace

Just confirming that it's intentional (I believe it is) that reactions always pickle all molecular properties.