RDCode: ReactionParser.h Source File

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# ReactionParser.h

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    00001 //
    00002 //  Copyright (c) 2007, Novartis Institutes for BioMedical Research Inc.
    00003 //  All rights reserved.
    00004 //
    00005 // Redistribution and use in source and binary forms, with or without
    00006 // modification, are permitted provided that the following conditions are
    00007 // met:
    00008 //
    00009 //     * Redistributions of source code must retain the above copyright
    00010 //       notice, this list of conditions and the following disclaimer.
    00011 //     * Redistributions in binary form must reproduce the above
    00012 //       copyright notice, this list of conditions and the following
    00013 //       disclaimer in the documentation and/or other materials provided
    00014 //       with the distribution.
    00015 //     * Neither the name of Novartis Institutes for BioMedical Research Inc.
    00016 //       nor the names of its contributors may be used to endorse or promote
    00017 //       products derived from this software without specific prior written permission.
    00018 //
    00019 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
    00020 // "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
    00021 // LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
    00022 // A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
    00023 // OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
    00024 // SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
    00025 // LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
    00026 // DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
    00027 // THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
    00028 // (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
    00029 // OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
    00030 //
    00031
    00032 #ifndef __RD_REACTIONPARSER_H_21Aug2006__
    00033 #define __RD_REACTIONPARSER_H_21Aug2006__
    00034
    00035 #include <string>
    00036 #include <iostream>
    00037
    00038 namespace RDKit{
    00039   class ChemicalReaction;
    00040
    00041   //! used to indicate an error in parsing reaction data
    00042   class ChemicalReactionParserException : public std::exception {
    00043   public:
    00044     //! construct with an error message
    00045     explicit ChemicalReactionParserException(const char *msg) : _msg(msg) {};
    00046     //! construct with an error message
    00047     explicit ChemicalReactionParserException(const std::string msg) : _msg(msg) {};
    00048     //! get the error message
    00049     const char *message () const { return _msg.c_str(); };
    00050     ~ChemicalReactionParserException () throw () {};
    00051   private:
    00052     std::string _msg;
    00053   };
    00054
    00055
    00056
    00057   //! Parse a text block in MDL rxn format into a ChemicalReaction
    00058   ChemicalReaction * RxnBlockToChemicalReaction(const std::string &rxnBlock);
    00059   //! Parse a file in MDL rxn format into a ChemicalReaction
    00060   ChemicalReaction * RxnFileToChemicalReaction(const std::string &fileName);
    00061 //! Parse a text stream in MDL rxn format into a ChemicalReaction
    00062   ChemicalReaction * RxnDataStreamToChemicalReaction(std::istream &rxnStream,
    00063                                                      unsigned int &line);
    00064
    00065   //! Parse a string containing "Reaction SMARTS" into a ChemicalReaction
    00066   /*!
    00067    *  Our definition of Reaction SMARTS is something that looks a lot like
    00068    *  reaction SMILES, except that SMARTS queries are allowed on the reactant
    00069    *  side and that atom-map numbers are required (at least for now)
    00070    */
    00071   ChemicalReaction * RxnSmartsToChemicalReaction(const std::string &text);
    00072
    00073
    00074
    00075 }; // end of RDKit namespace
    00076
    00077 #endif