ReactionParser.h
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#include <RDGeneral/export.h>
#ifndef RD_REACTIONPARSER_H_21Aug2006
#define RD_REACTIONPARSER_H_21Aug2006
#include <string>
#include <iostream>
#include <fstream>
#include <sstream>
#include <utility>
#include <boost/format.hpp>
#include <RDGeneral/BadFileException.h>
#include <RDGeneral/FileParseException.h>
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
*/
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction *RxnSmartsToChemicalReaction(
const std::string &text,
std::map<std::string, std::string> *replacements = nullptr,
bool useSmiles = false);
//! 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 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);
//@}
//---------------------------------------------------------------------------
//! \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<ChemicalReaction> 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<ChemicalReaction>(ptr);
}
inline std::unique_ptr<ChemicalReaction> 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<ChemicalReaction>(ptr);
}
}; // namespace RDKit
#endif
BadFileException.h
FileParseException.h
RDKit::BadFileException
used by various file parsing classes to indicate a bad file
Definition: BadFileException.h:22
RDKit::ChemicalReactionParserException
used to indicate an error in parsing reaction data
Definition: ReactionParser.h:51
RDKit::ChemicalReactionParserException::what
const char * what() const noexcept override
get the error message
Definition: ReactionParser.h:59
RDKit::ChemicalReactionParserException::ChemicalReactionParserException
ChemicalReactionParserException(std::string msg)
construct with an error message
Definition: ReactionParser.h:56
RDKit::ChemicalReactionParserException::~ChemicalReactionParserException
~ChemicalReactionParserException() noexcept override=default
RDKit::ChemicalReactionParserException::ChemicalReactionParserException
ChemicalReactionParserException(const char *msg)
construct with an error message
Definition: ReactionParser.h:54
RDKit::ChemicalReaction
This is a class for storing and applying general chemical reactions.
Definition: Reaction.h:121
RDKit::ROMol
Definition: ROMol.h:178
export.h
RDKIT_CHEMREACTIONS_EXPORT
#define RDKIT_CHEMREACTIONS_EXPORT
Definition: export.h:49
RDKit::MolOps::removeHs
RDKIT_GRAPHMOL_EXPORT ROMol * removeHs(const ROMol &mol, bool implicitOnly=false, bool updateExplicitCount=false, bool sanitize=true)
returns a copy of a molecule with hydrogens removed
RDKit::PNGData::rxnRxnTag
RDKIT_CHEMREACTIONS_EXPORT const std::string rxnRxnTag
RDKit::PNGData::rxnSmilesTag
RDKIT_CHEMREACTIONS_EXPORT const std::string rxnSmilesTag
RDKit::PNGData::rxnSmartsTag
RDKIT_CHEMREACTIONS_EXPORT const std::string rxnSmartsTag
RDKit::PNGData::rxnPklTag
RDKIT_CHEMREACTIONS_EXPORT const std::string rxnPklTag
RDKit
Std stuff.
Definition: Abbreviations.h:18
RDKit::ChemicalReactionToRxnSmiles
RDKIT_CHEMREACTIONS_EXPORT std::string ChemicalReactionToRxnSmiles(const ChemicalReaction &rxn, bool canonical=true)
returns the reaction SMILES for a reaction
RDKit::PNGFileToChemicalReaction
ChemicalReaction * PNGFileToChemicalReaction(const std::string &fname)
constructs a ChemicalReaction from the metadata in a PNG file See PNGStreamToChemicalReaction() for m...
Definition: ReactionParser.h:179
RDKit::PNGStreamToChemicalReaction
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * PNGStreamToChemicalReaction(std::istream &pngStream)
constructs a ChemicalReaction from the metadata in a PNG stream
RDKit::RxnBlockToChemicalReaction
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RxnBlockToChemicalReaction(const std::string &rxnBlock, bool sanitize=false, bool removeHs=false, bool strictParsing=true)
Parse a text block in MDL rxn format into a ChemicalReaction.
RDKit::addChemicalReactionToPNGStream
RDKIT_CHEMREACTIONS_EXPORT std::string addChemicalReactionToPNGStream(const ChemicalReaction &rxn, std::istream &iStream, bool includePkl=true, bool includeSmiles=true, bool includeSmarts=false, bool includeRxn=false)
adds metadata for a ChemicalReaction to the data from a PNG stream. The modified PNG data is returned...
RDKit::ChemicalReactionToRxnMol
RDKIT_CHEMREACTIONS_EXPORT ROMol * ChemicalReactionToRxnMol(const ChemicalReaction &rxn)
returns a ROMol with RXN roles used to describe the reaction
RDKit::PNGStringToChemicalReaction
ChemicalReaction * PNGStringToChemicalReaction(const std::string &data)
constructs a ChemicalReaction from the metadata in a PNG string See PNGStreamToChemicalReaction() for...
Definition: ReactionParser.h:173
RDKit::RxnDataStreamToChemicalReaction
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RxnDataStreamToChemicalReaction(std::istream &rxnStream, unsigned int &line, bool sanitize=false, bool removeHs=false, bool strictParsing=true)
Parse a text stream in MDL rxn format into a ChemicalReaction.
RDKit::ChemicalReactionToRxnSmarts
RDKIT_CHEMREACTIONS_EXPORT std::string ChemicalReactionToRxnSmarts(const ChemicalReaction &rxn)
returns the reaction SMARTS for a reaction
RDKit::addChemicalReactionToPNGFile
std::string addChemicalReactionToPNGFile(const ChemicalReaction &rxn, const std::string &fname, bool includePkl=true, bool includeSmiles=true, bool includeSmarts=false, bool includeRxn=false)
adds metadata for a ChemicalReaction to the data from a PNG string. See addChemicalReactionToPNGStrea...
Definition: ReactionParser.h:217
RDKit::RxnFileToChemicalReaction
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RxnFileToChemicalReaction(const std::string &fileName, bool sanitize=false, bool removeHs=false, bool strictParsing=true)
Parse a file in MDL rxn format into a ChemicalReaction.
RDKit::ChemicalReactionToRxnBlock
RDKIT_CHEMREACTIONS_EXPORT std::string ChemicalReactionToRxnBlock(const ChemicalReaction &rxn, bool separateAgents=false)
returns an rxn block for a reaction
RDKit::RxnMolToChemicalReaction
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RxnMolToChemicalReaction(const ROMol &mol)
Parse a ROMol into a ChemicalReaction, RXN role must be set before.
RDKit::RxnSmartsToChemicalReaction
RDKIT_CHEMREACTIONS_EXPORT ChemicalReaction * RxnSmartsToChemicalReaction(const std::string &text, std::map< std::string, std::string > *replacements=nullptr, bool useSmiles=false)
Parse a string containing "Reaction SMARTS" into a ChemicalReaction.
RDKit::addChemicalReactionToPNGString
std::string addChemicalReactionToPNGString(const ChemicalReaction &rxn, const std::string &pngString, bool includePkl=true, bool includeSmiles=true, bool includeSmarts=false, bool includeRxn=false)
adds metadata for a ChemicalReaction to the data from a PNG string. See addChemicalReactionToPNGStrea...
Definition: ReactionParser.h:205