ReactionPickler.h
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//
// 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.
//
#ifndef _RD_RXNPICKLE_H_2JUNE2009_
#define _RD_RXNPICKLE_H_2JUNE2009_
// Std stuff
#include <iostream>
#include <string>
#include <exception>
#ifdef WIN32
#include <ios>
#endif
namespace RDKit {
class ChemicalReaction;
//! used to indicate exceptions whilst pickling (serializing) reactions
class ReactionPicklerException : public std::exception {
public:
ReactionPicklerException(const char *msg) : _msg(msg){};
ReactionPicklerException(const std::string msg) : _msg(msg){};
const char *message() const { return _msg.c_str(); };
~ReactionPicklerException() throw(){};
private:
std::string _msg;
};
//! handles pickling (serializing) reactions
class ReactionPickler {
public:
static const boost::int32_t versionMajor, versionMinor,
versionPatch; //!< mark the pickle version
static const boost::int32_t endianId; //! mark the endian-ness of the pickle
//! the pickle format is tagged using these tags:
//! NOTE: if you add to this list, be sure to put new entries AT THE BOTTOM,
// otherwise
//! you will break old pickles.
typedef enum {
VERSION = 10000,
BEGINREACTANTS,
ENDREACTANTS,
BEGINPRODUCTS,
ENDPRODUCTS,
BEGINAGENTS,
ENDAGENTS,
ENDREACTION,
} Tags;
//! pickles a reaction and sends the results to stream \c ss
static void pickleReaction(const ChemicalReaction *rxn, std::ostream &ss);
static void pickleReaction(const ChemicalReaction &rxn, std::ostream &ss) {
ReactionPickler::pickleReaction(&rxn, ss);
};
//! pickles a reaction and adds the results to string \c res
static void pickleReaction(const ChemicalReaction *rxn, std::string &res);
static void pickleReaction(const ChemicalReaction &rxn, std::string &res) {
ReactionPickler::pickleReaction(&rxn, res);
};
//! constructs a reaction from a pickle stored in a string
static void reactionFromPickle(const std::string &pickle,
ChemicalReaction *rxn);
static void reactionFromPickle(const std::string &pickle,
ChemicalReaction &rxn) {
ReactionPickler::reactionFromPickle(pickle, &rxn);
};
//! constructs a reaction from a pickle stored in a stream
static void reactionFromPickle(std::istream &ss, ChemicalReaction *rxn);
static void reactionFromPickle(std::istream &ss, ChemicalReaction &rxn) {
ReactionPickler::reactionFromPickle(ss, &rxn);
};
private:
//! do the actual work of pickling a reaction
static void _pickle(const ChemicalReaction *rxn, std::ostream &ss);
//! do the actual work of de-pickling a reaction
static void _depickle(std::istream &ss, ChemicalReaction *rxn, int version);
};
};
#endif
RDCatalog::versionMinor
const int versionMinor
Definition: Catalog.h:32
RDKit::ReactionPickler::ENDREACTANTS
Definition: ReactionPickler.h:51
RDKit::ReactionPickler::versionPatch
static const boost::int32_t versionPatch
mark the pickle version
Definition: ReactionPickler.h:40
RDKit::ReactionPickler::pickleReaction
static void pickleReaction(const ChemicalReaction &rxn, std::ostream &ss)
Definition: ReactionPickler.h:61
RDKit::ReactionPicklerException::message
const char * message() const
Definition: ReactionPickler.h:30
RDKit::ChemicalReaction
This is a class for storing and applying general chemical reactions.
Definition: Reaction.h:116
RDKit::ReactionPicklerException::ReactionPicklerException
ReactionPicklerException(const std::string msg)
Definition: ReactionPickler.h:29
RDKit::ReactionPicklerException
used to indicate exceptions whilst pickling (serializing) reactions
Definition: ReactionPickler.h:26
RDKit::ReactionPickler::reactionFromPickle
static void reactionFromPickle(const std::string &pickle, ChemicalReaction *rxn)
constructs a reaction from a pickle stored in a string
RDKit::ReactionPickler::ENDREACTION
Definition: ReactionPickler.h:56
RDKit::ReactionPickler::reactionFromPickle
static void reactionFromPickle(const std::string &pickle, ChemicalReaction &rxn)
Definition: ReactionPickler.h:73
RDKit::ReactionPickler::BEGINREACTANTS
Definition: ReactionPickler.h:50
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
RDKit::ReactionPickler::BEGINAGENTS
Definition: ReactionPickler.h:54
RDKit::ReactionPickler::Tags
Tags
mark the endian-ness of the pickle
Definition: ReactionPickler.h:48
RDKit::ReactionPickler::pickleReaction
static void pickleReaction(const ChemicalReaction &rxn, std::string &res)
Definition: ReactionPickler.h:66
RDKit::ReactionPickler::endianId
static const boost::int32_t endianId
Definition: ReactionPickler.h:42
RDKit::ReactionPickler::reactionFromPickle
static void reactionFromPickle(std::istream &ss, ChemicalReaction &rxn)
Definition: ReactionPickler.h:80
RDKit::ReactionPickler::ENDPRODUCTS
Definition: ReactionPickler.h:53
RDCatalog::versionMajor
const int versionMajor
Definition: Catalog.h:31
RDKit::ReactionPicklerException::~ReactionPicklerException
~ReactionPicklerException()
Definition: ReactionPickler.h:31
RDKit::ReactionPickler::ENDAGENTS
Definition: ReactionPickler.h:55
RDKit::ReactionPickler
handles pickling (serializing) reactions
Definition: ReactionPickler.h:38
RDKit::ReactionPicklerException::ReactionPicklerException
ReactionPicklerException(const char *msg)
Definition: ReactionPickler.h:28
RDKit::ReactionPickler::pickleReaction
static void pickleReaction(const ChemicalReaction *rxn, std::ostream &ss)
pickles a reaction and sends the results to stream ss
RDKit::ReactionPickler::BEGINPRODUCTS
Definition: ReactionPickler.h:52