RDKit
Open-source cheminformatics and machine learning.
Loading...
Searching...
No Matches
RDKit::FileParserUtils Namespace Reference

Functions

RDKIT_FILEPARSERS_EXPORT std::string_view strip (std::string_view orig, std::string stripChars=" \t\r\n")
 
template<typename T >
stripSpacesAndCast (std::string_view input, bool acceptSpaces=false)
 
template<typename T >
stripSpacesAndCast (const std::string &input, bool acceptSpaces=false)
 
RDKIT_FILEPARSERS_EXPORT int toInt (const std::string &input, bool acceptSpaces=true)
 
RDKIT_FILEPARSERS_EXPORT unsigned int toUnsigned (const std::string &input, bool acceptSpaces=true)
 
RDKIT_FILEPARSERS_EXPORT double toDouble (const std::string &input, bool acceptSpaces=true)
 
RDKIT_FILEPARSERS_EXPORT int toInt (const std::string_view input, bool acceptSpaces=true)
 
RDKIT_FILEPARSERS_EXPORT unsigned int toUnsigned (std::string_view input, bool acceptSpaces=true)
 
RDKIT_FILEPARSERS_EXPORT double toDouble (const std::string_view input, bool acceptSpaces=true)
 
RDKIT_FILEPARSERS_EXPORT std::string getV3000CTAB (const ROMol &tmol, const boost::dynamic_bitset<> &wasAromatic, int confId=-1, unsigned int precision=6)
 
std::string getV3000CTAB (const ROMol &tmol, int confId=-1, unsigned int precision=6)
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
 
RDKIT_FILEPARSERS_EXPORT std::string getV3000Line (std::istream *inStream, unsigned int &line)
 
RDKIT_FILEPARSERS_EXPORT bool ParseV3000CTAB (std::istream *inStream, unsigned int &line, RWMol *mol, Conformer *&conf, bool &chiralityPossible, unsigned int &nAtoms, unsigned int &nBonds, bool strictParsing=true, bool expectMEND=true)
 
RDKIT_FILEPARSERS_EXPORT bool ParseV2000CTAB (std::istream *inStream, unsigned int &line, RWMol *mol, Conformer *&conf, bool &chiralityPossible, unsigned int &nAtoms, unsigned int &nBonds, bool strictParsing=true)
 
RDKIT_FILEPARSERS_EXPORT void finishMolProcessing (RWMol *res, bool chiralityPossible, const v2::FileParsers::MolFileParserParams &ps)
 
void finishMolProcessing (RWMol *res, bool chiralityPossible, bool sanitize, bool removeHs)
 This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
 
RDKIT_FILEPARSERS_EXPORT AtomreplaceAtomWithQueryAtom (RWMol *mol, Atom *atom)
 Deprecated, please use QueryOps::replaceAtomWithQueryAtom instead.
 
template<typename T >
void applyMolListPropToAtoms (ROMol &mol, const std::string &pn, const std::string &prefix, const std::string &missingValueMarker="n/a")
 applies a particular property to the atoms as an atom property list
 
template<typename T >
void applyMolListPropsToAtoms (ROMol &mol, const std::string &prefix, const std::string missingValueMarker="n/a")
 
void processMolPropertyList (ROMol &mol, const std::string pn, const std::string &missingValueMarker="n/a")
 
void processMolPropertyLists (ROMol &mol, const std::string &missingValueMarker="n/a")
 
template<typename T >
std::string getAtomPropertyList (ROMol &mol, const std::string &atomPropName, std::string missingValueMarker="", unsigned int lineSize=190)
 
void createAtomIntPropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=190)
 
void createAtomDoublePropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=190)
 
void createAtomBoolPropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=190)
 
void createAtomStringPropertyList (ROMol &mol, const std::string &atomPropName, const std::string &missingValueMarker="", unsigned int lineSize=190)
 
RDKIT_FILEPARSERS_EXPORT void moveAdditionalPropertiesToSGroups (RWMol &mol)
 

Variables

static const std::string atomPropPrefix = "atom."
 

Function Documentation

◆ applyMolListPropsToAtoms()

template<typename T >
void RDKit::FileParserUtils::applyMolListPropsToAtoms ( ROMol & mol,
const std::string & prefix,
const std::string missingValueMarker = "n/a" )

applies all properties matching a particular prefix as an atom property list

Definition at line 156 of file FileParserUtils.h.

References applyMolListPropToAtoms(), and RDKit::RDProps::getPropList().

◆ applyMolListPropToAtoms()

template<typename T >
void RDKit::FileParserUtils::applyMolListPropToAtoms ( ROMol & mol,
const std::string & pn,
const std::string & prefix,
const std::string & missingValueMarker = "n/a" )

applies a particular property to the atoms as an atom property list

Definition at line 113 of file FileParserUtils.h.

References BOOST_LOG, RDKit::ROMol::getAtomWithIdx(), RDKit::ROMol::getNumAtoms(), RDKit::RDProps::getProp(), rdWarningLog, and RDKit::RDProps::setProp().

Referenced by applyMolListPropsToAtoms(), and processMolPropertyList().

◆ createAtomBoolPropertyList()

void RDKit::FileParserUtils::createAtomBoolPropertyList ( ROMol & mol,
const std::string & atomPropName,
const std::string & missingValueMarker = "",
unsigned int lineSize = 190 )
inline

Definition at line 251 of file FileParserUtils.h.

References getAtomPropertyList(), and RDKit::RDProps::setProp().

◆ createAtomDoublePropertyList()

void RDKit::FileParserUtils::createAtomDoublePropertyList ( ROMol & mol,
const std::string & atomPropName,
const std::string & missingValueMarker = "",
unsigned int lineSize = 190 )
inline

Definition at line 243 of file FileParserUtils.h.

References getAtomPropertyList(), and RDKit::RDProps::setProp().

◆ createAtomIntPropertyList()

void RDKit::FileParserUtils::createAtomIntPropertyList ( ROMol & mol,
const std::string & atomPropName,
const std::string & missingValueMarker = "",
unsigned int lineSize = 190 )
inline

Definition at line 235 of file FileParserUtils.h.

References getAtomPropertyList(), and RDKit::RDProps::setProp().

◆ createAtomStringPropertyList()

void RDKit::FileParserUtils::createAtomStringPropertyList ( ROMol & mol,
const std::string & atomPropName,
const std::string & missingValueMarker = "",
unsigned int lineSize = 190 )
inline

Definition at line 259 of file FileParserUtils.h.

References getAtomPropertyList(), and RDKit::RDProps::setProp().

◆ finishMolProcessing() [1/2]

void RDKit::FileParserUtils::finishMolProcessing ( RWMol * res,
bool chiralityPossible,
bool sanitize,
bool removeHs )
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 100 of file FileParserUtils.h.

References finishMolProcessing(), RDKit::v2::FileParsers::MolFileParserParams::removeHs, and RDKit::v2::FileParsers::MolFileParserParams::sanitize.

◆ finishMolProcessing() [2/2]

RDKIT_FILEPARSERS_EXPORT void RDKit::FileParserUtils::finishMolProcessing ( RWMol * res,
bool chiralityPossible,
const v2::FileParsers::MolFileParserParams & ps )

finishes up the processing (sanitization, etc.) of a molecule read from CTAB

Referenced by finishMolProcessing().

◆ getAtomPropertyList()

template<typename T >
std::string RDKit::FileParserUtils::getAtomPropertyList ( ROMol & mol,
const std::string & atomPropName,
std::string missingValueMarker = "",
unsigned int lineSize = 190 )

◆ getV3000CTAB() [1/2]

RDKIT_FILEPARSERS_EXPORT std::string RDKit::FileParserUtils::getV3000CTAB ( const ROMol & tmol,
const boost::dynamic_bitset<> & wasAromatic,
int confId = -1,
unsigned int precision = 6 )

Referenced by getV3000CTAB().

◆ getV3000CTAB() [2/2]

std::string RDKit::FileParserUtils::getV3000CTAB ( const ROMol & tmol,
int confId = -1,
unsigned int precision = 6 )
inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 73 of file FileParserUtils.h.

References RDKit::ROMol::getNumBonds(), and getV3000CTAB().

◆ getV3000Line()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::FileParserUtils::getV3000Line ( std::istream * inStream,
unsigned int & line )

◆ moveAdditionalPropertiesToSGroups()

RDKIT_FILEPARSERS_EXPORT void RDKit::FileParserUtils::moveAdditionalPropertiesToSGroups ( RWMol & mol)

◆ ParseV2000CTAB()

RDKIT_FILEPARSERS_EXPORT bool RDKit::FileParserUtils::ParseV2000CTAB ( std::istream * inStream,
unsigned int & line,
RWMol * mol,
Conformer *& conf,
bool & chiralityPossible,
unsigned int & nAtoms,
unsigned int & nBonds,
bool strictParsing = true )

◆ ParseV3000CTAB()

RDKIT_FILEPARSERS_EXPORT bool RDKit::FileParserUtils::ParseV3000CTAB ( std::istream * inStream,
unsigned int & line,
RWMol * mol,
Conformer *& conf,
bool & chiralityPossible,
unsigned int & nAtoms,
unsigned int & nBonds,
bool strictParsing = true,
bool expectMEND = true )

◆ processMolPropertyList()

void RDKit::FileParserUtils::processMolPropertyList ( ROMol & mol,
const std::string pn,
const std::string & missingValueMarker = "n/a" )
inline

if the property name matches our rules for atom property lists, we'll apply it to the atoms

Definition at line 167 of file FileParserUtils.h.

References applyMolListPropToAtoms(), and atomPropPrefix.

Referenced by processMolPropertyLists().

◆ processMolPropertyLists()

void RDKit::FileParserUtils::processMolPropertyLists ( ROMol & mol,
const std::string & missingValueMarker = "n/a" )
inline

loops over all properties and applies the ones that match the rules for atom property lists to the atoms

Definition at line 195 of file FileParserUtils.h.

References RDKit::RDProps::getPropList(), and processMolPropertyList().

◆ replaceAtomWithQueryAtom()

RDKIT_FILEPARSERS_EXPORT Atom * RDKit::FileParserUtils::replaceAtomWithQueryAtom ( RWMol * mol,
Atom * atom )

Deprecated, please use QueryOps::replaceAtomWithQueryAtom instead.

◆ strip()

RDKIT_FILEPARSERS_EXPORT std::string_view RDKit::FileParserUtils::strip ( std::string_view orig,
std::string stripChars = " \t\r\n" )
inline

Definition at line 29 of file FileParserUtils.h.

Referenced by stripSpacesAndCast().

◆ stripSpacesAndCast() [1/2]

template<typename T >
T RDKit::FileParserUtils::stripSpacesAndCast ( const std::string & input,
bool acceptSpaces = false )

Definition at line 52 of file FileParserUtils.h.

References stripSpacesAndCast().

◆ stripSpacesAndCast() [2/2]

template<typename T >
T RDKit::FileParserUtils::stripSpacesAndCast ( std::string_view input,
bool acceptSpaces = false )

Definition at line 43 of file FileParserUtils.h.

References strip().

Referenced by stripSpacesAndCast().

◆ toDouble() [1/2]

RDKIT_FILEPARSERS_EXPORT double RDKit::FileParserUtils::toDouble ( const std::string & input,
bool acceptSpaces = true )

◆ toDouble() [2/2]

RDKIT_FILEPARSERS_EXPORT double RDKit::FileParserUtils::toDouble ( const std::string_view input,
bool acceptSpaces = true )

◆ toInt() [1/2]

RDKIT_FILEPARSERS_EXPORT int RDKit::FileParserUtils::toInt ( const std::string & input,
bool acceptSpaces = true )

◆ toInt() [2/2]

RDKIT_FILEPARSERS_EXPORT int RDKit::FileParserUtils::toInt ( const std::string_view input,
bool acceptSpaces = true )

◆ toUnsigned() [1/2]

RDKIT_FILEPARSERS_EXPORT unsigned int RDKit::FileParserUtils::toUnsigned ( const std::string & input,
bool acceptSpaces = true )

◆ toUnsigned() [2/2]

RDKIT_FILEPARSERS_EXPORT unsigned int RDKit::FileParserUtils::toUnsigned ( std::string_view input,
bool acceptSpaces = true )

Variable Documentation

◆ atomPropPrefix

const std::string RDKit::FileParserUtils::atomPropPrefix = "atom."
static

Definition at line 164 of file FileParserUtils.h.

Referenced by processMolPropertyList().