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RDKit
Open-source cheminformatics and machine learning.
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Functions | |
template<typename T > | |
T | stripSpacesAndCast (const std::string &input, bool acceptSpaces=false) |
RDKIT_FILEPARSERS_EXPORT int | toInt (const std::string &input, bool acceptSpaces=false) |
RDKIT_FILEPARSERS_EXPORT double | toDouble (const std::string &input, bool acceptSpaces=true) |
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) |
finishes up the processing (sanitization, etc.) of a molecule read from CTAB More... | |
RDKIT_FILEPARSERS_EXPORT Atom * | replaceAtomWithQueryAtom (RWMol *mol, Atom *atom) |
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 More... | |
template<typename T > | |
void | 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 More... | |
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) |
Variables | |
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 107 of file FileParserUtils.h.
References RDKit::RDProps::getPropList().
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 65 of file FileParserUtils.h.
References BOOST_LOG, RDKit::ROMol::getAtomWithIdx(), RDKit::ROMol::getNumAtoms(), RDKit::RDProps::getProp(), rdWarningLog, and RDKit::RDProps::setProp().
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Definition at line 202 of file FileParserUtils.h.
References RDKit::RDProps::setProp().
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inline |
Definition at line 194 of file FileParserUtils.h.
References RDKit::RDProps::setProp().
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inline |
Definition at line 186 of file FileParserUtils.h.
References RDKit::RDProps::setProp().
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inline |
Definition at line 210 of file FileParserUtils.h.
References 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 153 of file FileParserUtils.h.
References RDKit::ROMol::atoms().
RDKIT_FILEPARSERS_EXPORT std::string RDKit::FileParserUtils::getV3000Line | ( | std::istream * | inStream, |
unsigned int & | line | ||
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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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inline |
if the property name matches our rules for atom property lists, we'll apply it to the atoms
Definition at line 118 of file FileParserUtils.h.
References atomPropPrefix.
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 146 of file FileParserUtils.h.
References RDKit::RDProps::getPropList(), and processMolPropertyList().
RDKIT_FILEPARSERS_EXPORT Atom* RDKit::FileParserUtils::replaceAtomWithQueryAtom | ( | RWMol * | mol, |
Atom * | atom | ||
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T RDKit::FileParserUtils::stripSpacesAndCast | ( | const std::string & | input, |
bool | acceptSpaces = false |
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Definition at line 28 of file FileParserUtils.h.
RDKIT_FILEPARSERS_EXPORT double RDKit::FileParserUtils::toDouble | ( | const std::string & | input, |
bool | acceptSpaces = true |
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RDKIT_FILEPARSERS_EXPORT int RDKit::FileParserUtils::toInt | ( | const std::string & | input, |
bool | acceptSpaces = false |
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static |
Definition at line 115 of file FileParserUtils.h.
Referenced by processMolPropertyList().