32 #ifndef __RD_REACTIONPARSER_H_21Aug2006__ 33 #define __RD_REACTIONPARSER_H_21Aug2006__ 39 class ChemicalReaction;
49 const char *
message ()
const {
return _msg.c_str(); };
78 std::map<std::string,std::string> *replacements=0,
79 bool useSmiles=
false);
ChemicalReactionParserException(const char *msg)
construct with an error message
used to indicate an error in parsing reaction data
~ChemicalReactionParserException()
ChemicalReactionParserException(const std::string msg)
construct with an error message
ChemicalReaction * RxnMolToChemicalReaction(const ROMol &mol)
Parse a ROMol into a ChemicalReaction, RXN role must be set before.
const char * message() const
get the error message
This is a class for storing and applying general chemical reactions.
ROMol is a molecule class that is intended to have a fixed topology.
ROMol * ChemicalReactionToRxnMol(const ChemicalReaction &rxn)
returns a ROMol with RXN roles used to describe the reaction
ChemicalReaction * RxnBlockToChemicalReaction(const std::string &rxnBlock)
Parse a text block in MDL rxn format into a ChemicalReaction.
ChemicalReaction * RxnFileToChemicalReaction(const std::string &fileName)
Parse a file in MDL rxn format into a ChemicalReaction.
Includes a bunch of functionality for handling Atom and Bond queries.
std::string ChemicalReactionToRxnSmarts(const ChemicalReaction &rxn)
returns the reaction SMARTS for a reaction
ChemicalReaction * RxnDataStreamToChemicalReaction(std::istream &rxnStream, unsigned int &line)
Parse a text stream in MDL rxn format into a ChemicalReaction.
ChemicalReaction * RxnSmartsToChemicalReaction(const std::string &text, std::map< std::string, std::string > *replacements=0, bool useSmiles=false)
Parse a string containing "Reaction SMARTS" into a ChemicalReaction.
std::string ChemicalReactionToRxnSmiles(const ChemicalReaction &rxn, bool canonical=true)
returns the reaction SMILES for a reaction
std::string ChemicalReactionToRxnBlock(const ChemicalReaction &rxn, bool separateAgents=false)
returns an RXN block for a reaction