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RDKit
Open-source cheminformatics and machine learning.
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static const std::string | atomPropPrefix = "atom." |
void RDKit::FileParserUtils::applyMolListPropsToAtoms | ( | ROMol & | mol, |
const std::string & | prefix, | ||
const std::string | missingValueMarker = "n/a" |
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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().
void RDKit::FileParserUtils::applyMolListPropToAtoms | ( | ROMol & | mol, |
const std::string & | pn, | ||
const std::string & | prefix, | ||
const std::string & | missingValueMarker = "n/a" |
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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().
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Definition at line 236 of file FileParserUtils.h.
References RDKit::rdvalue_is(), and RDKit::RDProps::setProp().
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Definition at line 228 of file FileParserUtils.h.
References RDKit::rdvalue_is(), and RDKit::RDProps::setProp().
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Definition at line 220 of file FileParserUtils.h.
References RDKit::rdvalue_is(), and RDKit::RDProps::setProp().
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Definition at line 244 of file FileParserUtils.h.
References RDKit::rdvalue_is(), and RDKit::RDProps::setProp().
RDKIT_FILEPARSERS_EXPORT void RDKit::FileParserUtils::finishMolProcessing | ( | RWMol * | res, |
bool | chiralityPossible, | ||
bool | sanitize, | ||
bool | removeHs | ||
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finishes up the processing (sanitization, etc.) of a molecule read from CTAB
std::string RDKit::FileParserUtils::getAtomPropertyList | ( | ROMol & | mol, |
const std::string & | atomPropName, | ||
std::string | missingValueMarker = "" , |
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unsigned int | lineSize = 190 |
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Definition at line 187 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 |
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RDKIT_FILEPARSERS_EXPORT std::string RDKit::FileParserUtils::getV3000Line | ( | std::istream * | inStream, |
unsigned int & | line | ||
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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 |
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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 , |
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bool | expectMEND = true |
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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().
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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().
RDKIT_FILEPARSERS_EXPORT Atom * RDKit::FileParserUtils::replaceAtomWithQueryAtom | ( | RWMol * | mol, |
Atom * | atom | ||
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Deprecated, please use QueryOps::replaceAtomWithQueryAtom instead.
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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 |
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Definition at line 52 of file FileParserUtils.h.
References RDKit::rdvalue_is().
T RDKit::FileParserUtils::stripSpacesAndCast | ( | std::string_view | input, |
bool | acceptSpaces = false |
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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 |
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RDKIT_FILEPARSERS_EXPORT double RDKit::FileParserUtils::toDouble | ( | const std::string_view | input, |
bool | acceptSpaces = true |
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RDKIT_FILEPARSERS_EXPORT int RDKit::FileParserUtils::toInt | ( | const std::string & | input, |
bool | acceptSpaces = true |
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RDKIT_FILEPARSERS_EXPORT int RDKit::FileParserUtils::toInt | ( | const std::string_view | input, |
bool | acceptSpaces = true |
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RDKIT_FILEPARSERS_EXPORT unsigned int RDKit::FileParserUtils::toUnsigned | ( | const std::string & | input, |
bool | acceptSpaces = true |
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RDKIT_FILEPARSERS_EXPORT unsigned int RDKit::FileParserUtils::toUnsigned | ( | std::string_view | input, |
bool | acceptSpaces = true |
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Definition at line 149 of file FileParserUtils.h.
Referenced by processMolPropertyList().