// // Copyright (c) 2007-2022, Novartis Institutes for BioMedical Research Inc. // and other RDKit contributors // // 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. // #include #ifndef RD_REACTIONPARSER_H_21Aug2006 #define RD_REACTIONPARSER_H_21Aug2006 #include #include #include #include #include #include #include #include namespace RDKit { class ChemicalReaction; //! used to indicate an error in parsing reaction data class RDKIT_CHEMREACTIONS_EXPORT ChemicalReactionParserException : public std::exception { public: //! construct with an error message explicit ChemicalReactionParserException(const char *msg) : _msg(msg) {} //! construct with an error message explicit ChemicalReactionParserException(std::string msg) : _msg(std::move(msg)) {} //! get the error message const char *what() const noexcept override { return _msg.c_str(); } ~ChemicalReactionParserException() noexcept override = default; private: std::string _msg; }; //--------------------------------------------------------------------------- //! \name Reaction SMARTS/SMILES Support //! @{ //! 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 \param allowCXSMILES if set, any CXSMILES extensions present will be parsed, otherwise it will be ignored */ RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction *RxnSmartsToChemicalReaction( const std::string &text, std::map *replacements = nullptr, bool useSmiles = false, bool allowCXSMILES = true); //! returns the reaction SMARTS for a reaction RDKIT_CHEMREACTIONS_EXPORT std::string ChemicalReactionToRxnSmarts( const ChemicalReaction &rxn); //! returns the reaction SMILES for a reaction RDKIT_CHEMREACTIONS_EXPORT std::string ChemicalReactionToRxnSmiles( const ChemicalReaction &rxn, bool canonical = true); //! @} //--------------------------------------------------------------------------- //! \name Reaction Mol Support //! @{ //! 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 */ RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction *RxnMolToChemicalReaction( const ROMol &mol); //! returns a ROMol with RXN roles used to describe the reaction RDKIT_CHEMREACTIONS_EXPORT ROMol *ChemicalReactionToRxnMol( const ChemicalReaction &rxn); //! @} //--------------------------------------------------------------------------- //! \name MDL rxn Support //! @{ //! Parse a text block in MDL rxn format into a ChemicalReaction RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction *RxnBlockToChemicalReaction( const std::string &rxnBlock, bool sanitize = false, bool removeHs = false, bool strictParsing = true); //! Parse a file in MDL rxn format into a ChemicalReaction RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction *RxnFileToChemicalReaction( const std::string &fileName, bool sanitize = false, bool removeHs = false, bool strictParsing = true); //! Parse a text stream in MDL rxn format into a ChemicalReaction RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction *RxnDataStreamToChemicalReaction( std::istream &rxnStream, unsigned int &line, bool sanitize = false, bool removeHs = false, bool strictParsing = true); //! returns an rxn block for a reaction /*! \param rxn chemical reaction \param separateAgents flag to decide if agents are put in a separate block, otherwise they are included in the reactants block (default) \param forceV3000 flag to cause the V3000 format to be used instead of V2000 */ RDKIT_CHEMREACTIONS_EXPORT std::string ChemicalReactionToRxnBlock( const ChemicalReaction &rxn, bool separateAgents = false, bool forceV3000 = false); //! returns an V3000 rxn block for a reaction /*! \param rxn chemical reaction \param separateAgents flag to decide if agents are put in a separate block, otherwise they are included in the reactants block (default) */ RDKIT_CHEMREACTIONS_EXPORT std::string ChemicalReactionToV3KRxnBlock( const ChemicalReaction &rxn, bool separateAgents = false); //! @} //--------------------------------------------------------------------------- //! \name PNG Support //! @{ //! Tags used for PNG metadata namespace PNGData { RDKIT_CHEMREACTIONS_EXPORT extern const std::string rxnSmilesTag; RDKIT_CHEMREACTIONS_EXPORT extern const std::string rxnSmartsTag; RDKIT_CHEMREACTIONS_EXPORT extern const std::string rxnRxnTag; RDKIT_CHEMREACTIONS_EXPORT extern const std::string rxnPklTag; } // namespace PNGData //! \brief constructs a ChemicalReaction from the metadata in a PNG stream /*! Looks through the metadata in the PNG to find the first tag that matches one of the tags in \c RDKit::PNGData. A molecule is constructed from this chunk. Throws a \c FileParseException if no suitable tag is found. The caller is responsible for the returned pointer. */ RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction *PNGStreamToChemicalReaction( std::istream &pngStream); //! \brief constructs a ChemicalReaction from the metadata in a PNG string //! See \c PNGStreamToChemicalReaction() for more details inline ChemicalReaction *PNGStringToChemicalReaction(const std::string &data) { std::stringstream inStream(data); return PNGStreamToChemicalReaction(inStream); }; //! \brief constructs a ChemicalReaction from the metadata in a PNG file //! See \c PNGStreamToChemicalReaction() for more details inline ChemicalReaction *PNGFileToChemicalReaction(const std::string &fname) { std::ifstream inStream(fname.c_str(), std::ios::binary); if (!inStream || (inStream.bad())) { throw BadFileException((boost::format("Bad input file %s") % fname).str()); } return PNGStreamToChemicalReaction(inStream); }; //! \brief adds metadata for a ChemicalReaction to the data from a PNG stream. //! The modified PNG data is returned. /*! \param rxn the reaction to add \param iStream the stream to read from \param includePkl include a reaction pickle \param includeSmiles include reaction SMILES for the reaction \param includeSmarts include reaction SMARTS for the reaction \param includeRxn include an RXN block for the reaction */ RDKIT_CHEMREACTIONS_EXPORT std::string addChemicalReactionToPNGStream( const ChemicalReaction &rxn, std::istream &iStream, bool includePkl = true, bool includeSmiles = true, bool includeSmarts = false, bool includeRxn = false); //! \brief adds metadata for a ChemicalReaction to the data from a PNG string. //! See addChemicalReactionToPNGStream() for more details. inline std::string addChemicalReactionToPNGString(const ChemicalReaction &rxn, const std::string &pngString, bool includePkl = true, bool includeSmiles = true, bool includeSmarts = false, bool includeRxn = false) { std::stringstream inStream(pngString); return addChemicalReactionToPNGStream( rxn, inStream, includePkl, includeSmiles, includeSmarts, includeRxn); } //! \brief adds metadata for a ChemicalReaction to the data from a PNG string. //! See addChemicalReactionToPNGStream() for more details. inline std::string addChemicalReactionToPNGFile(const ChemicalReaction &rxn, const std::string &fname, bool includePkl = true, bool includeSmiles = true, bool includeSmarts = false, bool includeRxn = false) { std::ifstream inStream(fname.c_str(), std::ios::binary); return addChemicalReactionToPNGStream( rxn, inStream, includePkl, includeSmiles, includeSmarts, includeRxn); } //! @} inline std::unique_ptr operator"" _rxnsmarts(const char *text, size_t len) { std::string sma(text, len); ChemicalReaction *ptr = nullptr; try { ptr = RxnSmartsToChemicalReaction(sma); } catch (...) { ptr = nullptr; } return std::unique_ptr(ptr); } inline std::unique_ptr operator"" _rxnsmiles(const char *text, size_t len) { std::string sma(text, len); ChemicalReaction *ptr = nullptr; try { ptr = RxnSmartsToChemicalReaction(sma, nullptr, true); } catch (...) { ptr = nullptr; } return std::unique_ptr(ptr); } //--------------------------------------------------------------------------- //! \name CDXML rxn Support ///@{ //! Parse text in CDXML rxn format into a vector of ChemicalReactions RDKIT_CHEMREACTIONS_EXPORT std::vector> CDXMLToChemicalReactions(const std::string &rxnBlock, bool sanitize = false, bool removeHs = false); //! Parse a file in CDXML rxn format into a vector of ChemicalReactions RDKIT_CHEMREACTIONS_EXPORT std::vector> CDXMLFileToChemicalReactions(const std::string &fileName, bool sanitize = false, bool removeHs = false); //! Parse a text stream in CDXML rxn format into a vector of ChemicalReactions RDKIT_CHEMREACTIONS_EXPORT std::vector> CDXMLDataStreamToChemicalReactions(std::istream &rxnStream, bool sanitize = false, bool removeHs = false); } // namespace RDKit #endif