RDKit
Open-source cheminformatics and machine learning.
|
Variables | |
static const std::string | atomPropPrefix = "atom." |
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 150 of file FileParserUtils.h.
References RDKit::RDProps::getPropList(), and RDKit::rdvalue_is().
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 107 of file FileParserUtils.h.
References BOOST_LOG, RDKit::ROMol::getAtomWithIdx(), RDKit::ROMol::getNumAtoms(), RDKit::RDProps::getProp(), RDKit::rdvalue_is(), rdWarningLog, and RDKit::RDProps::setProp().
|
inline |
Definition at line 245 of file FileParserUtils.h.
References RDKit::rdvalue_is(), and RDKit::RDProps::setProp().
|
inline |
Definition at line 237 of file FileParserUtils.h.
References RDKit::rdvalue_is(), and RDKit::RDProps::setProp().
|
inline |
Definition at line 229 of file FileParserUtils.h.
References RDKit::rdvalue_is(), and RDKit::RDProps::setProp().
|
inline |
Definition at line 253 of file FileParserUtils.h.
References RDKit::rdvalue_is(), and RDKit::RDProps::setProp().
|
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 94 of file FileParserUtils.h.
References finishMolProcessing(), RDKit::rdvalue_is(), and RDKit::v2::FileParsers::MolFileParserParams::sanitize.
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().
std::string RDKit::FileParserUtils::getAtomPropertyList | ( | ROMol & | mol, |
const std::string & | atomPropName, | ||
std::string | missingValueMarker = "", | ||
unsigned int | lineSize = 190 ) |
Definition at line 196 of file FileParserUtils.h.
References RDKit::ROMol::atoms(), and RDKit::rdvalue_is().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::FileParserUtils::getV3000CTAB | ( | const ROMol & | tmol, |
int | confId = -1, | ||
unsigned int | precision = 6 ) |
RDKIT_FILEPARSERS_EXPORT std::string RDKit::FileParserUtils::getV3000Line | ( | std::istream * | inStream, |
unsigned int & | line ) |
RDKIT_FILEPARSERS_EXPORT void RDKit::FileParserUtils::moveAdditionalPropertiesToSGroups | ( | RWMol & | mol | ) |
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 ) |
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 ) |
|
inline |
if the property name matches our rules for atom property lists, we'll apply it to the atoms
Definition at line 161 of file FileParserUtils.h.
References atomPropPrefix, and RDKit::rdvalue_is().
Referenced by processMolPropertyLists().
|
inline |
loops over all properties and applies the ones that match the rules for atom property lists to the atoms
Definition at line 189 of file FileParserUtils.h.
References RDKit::RDProps::getPropList(), processMolPropertyList(), and RDKit::rdvalue_is().
RDKIT_FILEPARSERS_EXPORT Atom * RDKit::FileParserUtils::replaceAtomWithQueryAtom | ( | RWMol * | mol, |
Atom * | atom ) |
Deprecated, please use QueryOps::replaceAtomWithQueryAtom instead.
|
inline |
Definition at line 29 of file FileParserUtils.h.
References RDKit::rdvalue_is().
Referenced by stripSpacesAndCast().
T RDKit::FileParserUtils::stripSpacesAndCast | ( | const std::string & | input, |
bool | acceptSpaces = false ) |
Definition at line 52 of file FileParserUtils.h.
References RDKit::rdvalue_is().
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().
RDKIT_FILEPARSERS_EXPORT double RDKit::FileParserUtils::toDouble | ( | const std::string & | input, |
bool | acceptSpaces = true ) |
RDKIT_FILEPARSERS_EXPORT double RDKit::FileParserUtils::toDouble | ( | const std::string_view | input, |
bool | acceptSpaces = true ) |
RDKIT_FILEPARSERS_EXPORT int RDKit::FileParserUtils::toInt | ( | const std::string & | input, |
bool | acceptSpaces = true ) |
RDKIT_FILEPARSERS_EXPORT int RDKit::FileParserUtils::toInt | ( | const std::string_view | input, |
bool | acceptSpaces = true ) |
RDKIT_FILEPARSERS_EXPORT unsigned int RDKit::FileParserUtils::toUnsigned | ( | const std::string & | input, |
bool | acceptSpaces = true ) |
RDKIT_FILEPARSERS_EXPORT unsigned int RDKit::FileParserUtils::toUnsigned | ( | std::string_view | input, |
bool | acceptSpaces = true ) |
|
static |
Definition at line 158 of file FileParserUtils.h.
Referenced by processMolPropertyList().