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//
// Copyright (c) 2007-2014, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#ifndef __RD_REACTIONPARSER_H_21Aug2006__
#define __RD_REACTIONPARSER_H_21Aug2006__
#include <string>
#include <iostream>
namespace RDKit {
class ChemicalReaction;
//! used to indicate an error in parsing reaction data
class ChemicalReactionParserException : public std::exception {
public:
//! construct with an error message
explicit ChemicalReactionParserException(const char *msg) : _msg(msg){};
//! construct with an error message
explicit ChemicalReactionParserException(const std::string &msg)
: _msg(msg){};
//! get the error message
const char *message() const { return _msg.c_str(); };
~ChemicalReactionParserException() throw(){};
private:
std::string _msg;
};
//! Parse a text block in MDL rxn format into a ChemicalReaction
ChemicalReaction *RxnBlockToChemicalReaction(const std::string &rxnBlock);
//! Parse a file in MDL rxn format into a ChemicalReaction
ChemicalReaction *RxnFileToChemicalReaction(const std::string &fileName);
//! Parse a text stream in MDL rxn format into a ChemicalReaction
ChemicalReaction *RxnDataStreamToChemicalReaction(std::istream &rxnStream,
unsigned int &line);
//! Parse a string containing "Reaction SMARTS" into a ChemicalReaction
/*!
Our definition of Reaction SMARTS is something that looks a lot like
reaction SMILES, except that SMARTS queries are allowed on the reactant
side and that atom-map numbers are required (at least for now)
\param text the SMARTS to convert
\param replacements a string->string map of replacement strings.
\see SmilesToMol for more information about replacements
\param useSmiles if set, the SMILES parser will be used instead of the
SMARTS
parserfor the individual components
*/
ChemicalReaction *RxnSmartsToChemicalReaction(
const std::string &text,
std::map<std::string, std::string> *replacements = 0,
bool useSmiles = false);
//! Parse a ROMol into a ChemicalReaction, RXN role must be set before
/*!
Alternative to build a reaction from a molecule (fragments) which have RXN
roles
set as atom properties: common_properties::molRxnRole (1=reactant, 2=product,
3=agent)
\param mol ROMol with RXN roles set
*/
ChemicalReaction *RxnMolToChemicalReaction(const ROMol &mol);
//! returns the reaction SMARTS for a reaction
std::string ChemicalReactionToRxnSmarts(const ChemicalReaction &rxn);
//! returns the reaction SMILES for a reaction
std::string ChemicalReactionToRxnSmiles(const ChemicalReaction &rxn,
bool canonical = true);
//! returns an RXN block for a reaction
/*!
\param rxn chemical reaction
\param separateAgents flag to decide if agents were put in a seperate block,
otherwise they were included in the reactants block
(default)
*/
std::string ChemicalReactionToRxnBlock(const ChemicalReaction &rxn,
bool separateAgents = false);
//! returns a ROMol with RXN roles used to describe the reaction
ROMol *ChemicalReactionToRxnMol(const ChemicalReaction &rxn);
}; // end of RDKit namespace
#endif
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