RDKit
Open-source cheminformatics and machine learning.
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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, int confId=-1)
 
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, bool sanitize, bool removeHs)
 
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 141 of file FileParserUtils.h.

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

◆ 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 98 of file FileParserUtils.h.

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

◆ createAtomBoolPropertyList()

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

Definition at line 236 of file FileParserUtils.h.

References RDKit::rdvalue_is(), 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 228 of file FileParserUtils.h.

References RDKit::rdvalue_is(), 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 220 of file FileParserUtils.h.

References RDKit::rdvalue_is(), 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 244 of file FileParserUtils.h.

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

◆ finishMolProcessing()

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

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

◆ getAtomPropertyList()

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

Definition at line 187 of file FileParserUtils.h.

References RDKit::ROMol::atoms(), and RDKit::rdvalue_is().

◆ getV3000CTAB()

RDKIT_FILEPARSERS_EXPORT std::string RDKit::FileParserUtils::getV3000CTAB ( const ROMol tmol,
int  confId = -1 
)

◆ 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 152 of file FileParserUtils.h.

References atomPropPrefix, and RDKit::rdvalue_is().

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 180 of file FileParserUtils.h.

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

◆ 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.

References RDKit::rdvalue_is().

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 RDKit::rdvalue_is().

◆ 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 RDKit::rdvalue_is(), and strip().

◆ 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 149 of file FileParserUtils.h.

Referenced by processMolPropertyList().