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// $Id: MolPickler.cpp 1123 2009-06-01 13:04:33Z glandrum $
//
// Copyright (C) 2009 Greg Landrum
//
// @@ 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=0;
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);
uint32_t flag = 0;
if(rxn->getImplicitPropertiesFlag()) flag |= 0x1;
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);
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;
streamRead(ss,numReactants);
streamRead(ss,numProducts);
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.");
}
} // end of _depickle
}; // end of RDKit namespace
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