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.
//
#include <RDGeneral/export.h>
#ifndef RD_RXNPICKLE_H_2JUNE2009
#define RD_RXNPICKLE_H_2JUNE2009
#include <GraphMol/MolPickler.h>
// 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 RDKIT_CHEMREACTIONS_EXPORT 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 RDKIT_CHEMREACTIONS_EXPORT ReactionPickler {
public:
static const std::int32_t versionMajor; //!< mark the pickle version
static const std::int32_t versionMinor; //!< mark the pickle version
static const std::int32_t versionPatch; //!< mark the pickle version
static const std::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,
BEGINPROPS,
ENDPROPS
} Tags;
//! pickles a reaction and sends the results to stream \c ss
static void pickleReaction(const ChemicalReaction *rxn, std::ostream &ss,
unsigned int propertyFlags);
static void pickleReaction(const ChemicalReaction *rxn, std::ostream &ss);
static void pickleReaction(const ChemicalReaction &rxn, std::ostream &ss) {
ReactionPickler::pickleReaction(&rxn, ss);
};
static void pickleReaction(const ChemicalReaction &rxn, std::ostream &ss,
unsigned int propertyFlags) {
ReactionPickler::pickleReaction(&rxn, ss, propertyFlags);
};
//! pickles a reaction and adds the results to string \c res
static void pickleReaction(const ChemicalReaction *rxn, std::string &res,
unsigned int propertyFlags);
static void pickleReaction(const ChemicalReaction *rxn, std::string &res);
static void pickleReaction(const ChemicalReaction &rxn, std::string &res) {
ReactionPickler::pickleReaction(&rxn, res);
};
static void pickleReaction(const ChemicalReaction &rxn, std::string &res,
unsigned int propertyFlags) {
ReactionPickler::pickleReaction(&rxn, res, propertyFlags);
};
//! 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,
unsigned int propertyFlags);
//! do the actual work of de-pickling a reaction
static void _depickle(std::istream &ss, ChemicalReaction *rxn, int version);
//! pickle standard properties
static void _pickleProperties(std::ostream &ss, const RDProps &props,
unsigned int pickleFlags);
//! unpickle standard properties
static void _unpickleProperties(std::istream &ss, RDProps &props);
};
}; // namespace RDKit
#endif
RDKit::ReactionPicklerException::message
const char * message() const
Definition: ReactionPickler.h:33
RDKit::ReactionPickler::pickleReaction
static void pickleReaction(const ChemicalReaction &rxn, std::string &res)
Definition: ReactionPickler.h:79
RDKit::EnumerationStrategyPickler::pickle
RDKIT_CHEMREACTIONS_EXPORT void pickle(const boost::shared_ptr< EnumerationStrategyBase > &enumerator, std::ostream &ss)
pickles a EnumerationStrategy and adds the results to a stream ss
RDKit::ReactionPickler::reactionFromPickle
static void reactionFromPickle(const std::string &pickle, ChemicalReaction &rxn)
Definition: ReactionPickler.h:91
RDKit::ReactionPickler::BEGINAGENTS
Definition: ReactionPickler.h:57
RDKit::ReactionPickler::pickleReaction
static void pickleReaction(const ChemicalReaction &rxn, std::ostream &ss, unsigned int propertyFlags)
Definition: ReactionPickler.h:71
RDKit::ReactionPicklerException::ReactionPicklerException
ReactionPicklerException(const std::string msg)
Definition: ReactionPickler.h:32
RDKit::ReactionPickler::reactionFromPickle
static void reactionFromPickle(std::istream &ss, ChemicalReaction &rxn)
Definition: ReactionPickler.h:99
RDKit::ReactionPickler::versionMajor
static const std::int32_t versionMajor
mark the pickle version
Definition: ReactionPickler.h:43
RDKit::ReactionPickler::BEGINPROPS
Definition: ReactionPickler.h:60
RDKit::ReactionPicklerException
used to indicate exceptions whilst pickling (serializing) reactions
Definition: ReactionPickler.h:28
RDKit::ReactionPickler::ENDREACTION
Definition: ReactionPickler.h:59
RDKit::ReactionPicklerException::ReactionPicklerException
ReactionPicklerException(const char *msg)
Definition: ReactionPickler.h:31
RDKit::ReactionPickler::ENDREACTANTS
Definition: ReactionPickler.h:54
RDKit::ReactionPickler::pickleReaction
static void pickleReaction(const ChemicalReaction &rxn, std::ostream &ss)
Definition: ReactionPickler.h:68
RDKit::ReactionPickler::ENDPRODUCTS
Definition: ReactionPickler.h:56
RDKit::ReactionPickler::reactionFromPickle
static void reactionFromPickle(const std::string &pickle, ChemicalReaction *rxn)
RDKit::ReactionPickler::pickleReaction
static void pickleReaction(const ChemicalReaction &rxn, std::string &res, unsigned int propertyFlags)
Definition: ReactionPickler.h:82
RDKit::ReactionPicklerException::~ReactionPicklerException
~ReactionPicklerException()
Definition: ReactionPickler.h:34
RDKit::ChemicalReaction
This is a class for storing and applying general chemical reactions.
Definition: Reaction.h:119
RDKit::RDProps
Definition: RDProps.h:10
RDKit::ReactionPickler::BEGINPRODUCTS
Definition: ReactionPickler.h:55
RDKit::ReactionPickler::BEGINREACTANTS
Definition: ReactionPickler.h:53
RDKit
Std stuff.
Definition: Atom.h:30
MolPickler.h
RDKit::ReactionPickler::versionMinor
static const std::int32_t versionMinor
mark the pickle version
Definition: ReactionPickler.h:44
RDKIT_CHEMREACTIONS_EXPORT
#define RDKIT_CHEMREACTIONS_EXPORT
Definition: export.h:60
RDKit::ReactionPickler
handles pickling (serializing) reactions
Definition: ReactionPickler.h:41
RDKit::ReactionPickler::pickleReaction
static void pickleReaction(const ChemicalReaction *rxn, std::ostream &ss, unsigned int propertyFlags)
pickles a reaction and sends the results to stream ss
RDKit::ReactionPickler::endianId
static const std::int32_t endianId
Definition: ReactionPickler.h:46
RDKit::ReactionPickler::versionPatch
static const std::int32_t versionPatch
mark the pickle version
Definition: ReactionPickler.h:45
RDKit::ReactionPickler::ENDAGENTS
Definition: ReactionPickler.h:58
export.h