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// $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
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