addSgroupsToPtree(ptree &pt) const | RDKit::MarvinMolBase | |
AnyOverLappingAtoms(const MarvinMolBase *otherMol) const | RDKit::MarvinMolBase | |
atomRefInAtoms(MarvinAtom *a, std::string b) | RDKit::MarvinMolBase | static |
atoms | RDKit::MarvinMolBase | |
bondRefInBonds(MarvinBond *a, std::string b) | RDKit::MarvinMolBase | static |
bonds | RDKit::MarvinMolBase | |
cleanUpNumbering(int &molCount, int &atomCount, int &bondCount, int &sgCount, std::map< std::string, std::string > &sgMap, std::map< std::string, std::string > &atomMap, std::map< std::string, std::string > &bondMap) | RDKit::MarvinMolBase | |
cleanUpNumberingMolsAtomsBonds(int &molCount, int &atomCount, int &bondCount, std::map< std::string, std::string > &sgMap, std::map< std::string, std::string > &atomMap, std::map< std::string, std::string > &bondMap) | RDKit::MarvinMolBase | virtual |
cleanUpSgNumbering(int &sgCount, std::map< std::string, std::string > &sgMap) | RDKit::MarvinMolBase | |
context | RDKit::MarvinDataSgroup | |
coordinatePrecision | RDKit::MarvinMolBase | |
copyMol(const std::string &idAppend) const override | RDKit::MarvinDataSgroup | virtual |
fieldData | RDKit::MarvinDataSgroup | |
fieldName | RDKit::MarvinDataSgroup | |
findAtomByRef(std::string atomId) | RDKit::MarvinMolBase | |
findBondByRef(std::string atomId) | RDKit::MarvinMolBase | |
getAtomIndex(std::string id) const | RDKit::MarvinMolBase | |
getAtomList() const | RDKit::MarvinMolBase | |
getBondIndex(std::string id) const | RDKit::MarvinMolBase | |
getBondList() const | RDKit::MarvinMolBase | |
getExplicitValence(const MarvinAtom &marvinAtom) const | RDKit::MarvinMolBase | |
has2dCoords() const | RDKit::MarvinMolBase | |
has3dCoords() const | RDKit::MarvinMolBase | |
hasAny2dCoords() const | RDKit::MarvinMolBase | |
hasAny3dCoords() const | RDKit::MarvinMolBase | |
hasAtomBondBlocks() const override | RDKit::MarvinDataSgroup | virtual |
hasCoords() const | RDKit::MarvinMolBase | |
id | RDKit::MarvinMolBase | |
isPassiveRoleForContraction() const | RDKit::MarvinMolBase | virtual |
isPassiveRoleForExpansion() const | RDKit::MarvinMolBase | virtual |
isSgroupInSetOfAtoms(const std::vector< MarvinAtom * > &setOfAtoms) const | RDKit::MarvinMolBase | virtual |
MarvinDataSgroup(MarvinMolBase *parent) | RDKit::MarvinDataSgroup | |
MarvinDataSgroup(MarvinMolBase *parent, ptree &molTree) | RDKit::MarvinDataSgroup | |
MarvinMolBase() | RDKit::MarvinMolBase | inline |
molID | RDKit::MarvinMolBase | |
molIDInSgroups(std::string a, std::string b) | RDKit::MarvinMolBase | static |
parent | RDKit::MarvinMolBase | |
parseAtomsAndBonds(ptree &molTree) | RDKit::MarvinMolBase | |
parseMoleculeSpecific(RDKit::RWMol *mol, std::unique_ptr< SubstanceGroup > &sgroup, int sequenceId) override | RDKit::MarvinDataSgroup | virtual |
placement | RDKit::MarvinDataSgroup | |
prepSgroupsForRDKit() | RDKit::MarvinMolBase | |
processSgroupsFromRDKit() | RDKit::MarvinMolBase | |
processSpecialSgroups() | RDKit::MarvinMolBase | virtual |
pushOwnedAtom(MarvinAtom *atom) | RDKit::MarvinMolBase | virtual |
pushOwnedBond(MarvinBond *bond) | RDKit::MarvinMolBase | virtual |
queryOp | RDKit::MarvinDataSgroup | |
queryType | RDKit::MarvinDataSgroup | |
removeCoords() | RDKit::MarvinMolBase | |
removeOwnedAtom(MarvinAtom *atom) | RDKit::MarvinMolBase | virtual |
removeOwnedBond(MarvinBond *bond) | RDKit::MarvinMolBase | virtual |
role() const override | RDKit::MarvinDataSgroup | virtual |
setPrecision(unsigned int precision) | RDKit::MarvinMolBase | |
sgroups | RDKit::MarvinMolBase | |
toPtree() const override | RDKit::MarvinDataSgroup | virtual |
toString() const override | RDKit::MarvinDataSgroup | virtual |
units | RDKit::MarvinDataSgroup | |
unitsDisplayed | RDKit::MarvinDataSgroup | |
x | RDKit::MarvinDataSgroup | |
y | RDKit::MarvinDataSgroup | |
~MarvinMolBase() | RDKit::MarvinMolBase | virtual |