ReactionParser.h
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#include <RDGeneral/export.h>
#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 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(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
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction *RxnBlockToChemicalReaction(
const std::string &rxnBlock);
//! Parse a file in MDL rxn format into a ChemicalReaction
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction *RxnFileToChemicalReaction(
const std::string &fileName);
//! Parse a text stream in MDL rxn format into a ChemicalReaction
RDKIT_CHEMREACTIONS_EXPORT 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
*/
RDKIT_CHEMREACTIONS_EXPORT 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
*/
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction *RxnMolToChemicalReaction(
const ROMol &mol);
//! 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);
//! returns an RXN block for a reaction
/*!
\param rxn chemical reaction
\param separateAgents flag to decide if agents were put in a separate block,
otherwise they were included in the reactants block
(default)
*/
RDKIT_CHEMREACTIONS_EXPORT std::string ChemicalReactionToRxnBlock(
const ChemicalReaction &rxn, bool separateAgents = false);
//! returns a ROMol with RXN roles used to describe the reaction
RDKIT_CHEMREACTIONS_EXPORT ROMol *ChemicalReactionToRxnMol(
const ChemicalReaction &rxn);
}; // namespace RDKit
#endif
RDKit::RxnMolToChemicalReaction
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RxnMolToChemicalReaction(const ROMol &mol)
Parse a ROMol into a ChemicalReaction, RXN role must be set before.
RDKit::ChemicalReactionParserException::ChemicalReactionParserException
ChemicalReactionParserException(const std::string &msg)
construct with an error message
Definition: ReactionParser.h:50
RDKit::RxnSmartsToChemicalReaction
RDKIT_CHEMREACTIONS_EXPORT 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.
RDKit::RxnFileToChemicalReaction
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RxnFileToChemicalReaction(const std::string &fileName)
Parse a file in MDL rxn format into a ChemicalReaction.
RDKit::ChemicalReactionToRxnMol
RDKIT_CHEMREACTIONS_EXPORT ROMol * ChemicalReactionToRxnMol(const ChemicalReaction &rxn)
returns a ROMol with RXN roles used to describe the reaction
RDKit::ChemicalReactionParserException::ChemicalReactionParserException
ChemicalReactionParserException(const char *msg)
construct with an error message
Definition: ReactionParser.h:48
RDKit::ChemicalReactionToRxnSmiles
RDKIT_CHEMREACTIONS_EXPORT std::string ChemicalReactionToRxnSmiles(const ChemicalReaction &rxn, bool canonical=true)
returns the reaction SMILES for a reaction
RDKit::ChemicalReactionParserException::~ChemicalReactionParserException
~ChemicalReactionParserException()
Definition: ReactionParser.h:54
RDKit::ChemicalReactionToRxnSmarts
RDKIT_CHEMREACTIONS_EXPORT std::string ChemicalReactionToRxnSmarts(const ChemicalReaction &rxn)
returns the reaction SMARTS for a reaction
RDKit::RxnBlockToChemicalReaction
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RxnBlockToChemicalReaction(const std::string &rxnBlock)
Parse a text block in MDL rxn format into a ChemicalReaction.
RDKit::ChemicalReactionParserException
used to indicate an error in parsing reaction data
Definition: ReactionParser.h:44
RDKit::RxnDataStreamToChemicalReaction
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RxnDataStreamToChemicalReaction(std::istream &rxnStream, unsigned int &line)
Parse a text stream in MDL rxn format into a ChemicalReaction.
RDKit
Std stuff.
Definition: Atom.h:30
RDKIT_CHEMREACTIONS_EXPORT
#define RDKIT_CHEMREACTIONS_EXPORT
Definition: export.h:60
RDKit::ChemicalReactionParserException::message
const char * message() const
get the error message
Definition: ReactionParser.h:53
RDKit::ChemicalReactionToRxnBlock
RDKIT_CHEMREACTIONS_EXPORT std::string ChemicalReactionToRxnBlock(const ChemicalReaction &rxn, bool separateAgents=false)
returns an RXN block for a reaction
export.h