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RDKit
Open-source cheminformatics and machine learning.
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#include <MarvinDefs.h>
Public Member Functions | |
virtual std::string | role () const =0 |
virtual bool | hasAtomBondBlocks () const =0 |
virtual std::string | toString () const =0 |
virtual ptree | toPtree () const |
void | addSgroupsToPtree (ptree &pt) const |
virtual MarvinMolBase * | copyMol (const std::string &idAppend) const =0 |
virtual void | pushOwnedAtom (MarvinAtom *atom) |
virtual void | pushOwnedBond (MarvinBond *bond) |
virtual void | removeOwnedAtom (MarvinAtom *atom) |
virtual void | removeOwnedBond (MarvinBond *bond) |
int | getExplicitValence (const MarvinAtom &marvinAtom) const |
MarvinMolBase () | |
virtual | ~MarvinMolBase () |
int | getAtomIndex (std::string id) const |
int | getBondIndex (std::string id) const |
const std::vector< std::string > | getBondList () const |
const std::vector< std::string > | getAtomList () const |
bool | AnyOverLappingAtoms (const MarvinMolBase *otherMol) const |
void | 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) |
virtual void | 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) |
void | cleanUpSgNumbering (int &sgCount, std::map< std::string, std::string > &sgMap) |
virtual IsSgroupInAtomSetResult | isSgroupInSetOfAtoms (const std::vector< MarvinAtom * > &setOfAtoms) const |
MarvinAtom * | findAtomByRef (std::string atomId) |
MarvinBond * | findBondByRef (std::string atomId) |
void | clearMaps () |
void | prepSgroupsForRDKit () |
void | processSgroupsFromRDKit () |
virtual bool | isPassiveRoleForExpansion () const |
virtual bool | isPassiveRoleForContraction () const |
virtual void | processSpecialSgroups () |
virtual void | parseMoleculeSpecific (RDKit::RWMol *mol, std::unique_ptr< SubstanceGroup > &sgroup, int sequenceId) |
bool | has2dCoords () const |
bool | has3dCoords () const |
bool | hasAny3dCoords () const |
bool | hasAny2dCoords () const |
bool | hasCoords () const |
void | removeCoords () |
void | parseAtomsAndBonds (ptree &molTree) |
Static Public Member Functions | |
static bool | atomRefInAtoms (MarvinAtom *a, std::string b) |
static bool | bondRefInBonds (MarvinBond *a, std::string b) |
static bool | molIDInSgroups (std::string a, std::string b) |
Public Attributes | |
std::string | molID |
std::string | id |
std::vector< MarvinAtom * > | atoms |
std::vector< MarvinBond * > | bonds |
std::vector< std::unique_ptr< MarvinMolBase > > | sgroups |
MarvinMolBase * | parent |
Definition at line 246 of file MarvinDefs.h.
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inline |
Definition at line 275 of file MarvinDefs.h.
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virtual |
void RDKit::MarvinMolBase::addSgroupsToPtree | ( | ptree & | pt | ) | const |
bool RDKit::MarvinMolBase::AnyOverLappingAtoms | ( | const MarvinMolBase * | otherMol | ) | const |
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static |
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static |
void 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 | ||
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virtual |
Reimplemented in RDKit::MarvinSuperatomSgroup.
void RDKit::MarvinMolBase::cleanUpSgNumbering | ( | int & | sgCount, |
std::map< std::string, std::string > & | sgMap | ||
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void RDKit::MarvinMolBase::clearMaps | ( | ) |
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pure virtual |
MarvinAtom * RDKit::MarvinMolBase::findAtomByRef | ( | std::string | atomId | ) |
MarvinBond * RDKit::MarvinMolBase::findBondByRef | ( | std::string | atomId | ) |
int RDKit::MarvinMolBase::getAtomIndex | ( | std::string | id | ) | const |
const std::vector< std::string > RDKit::MarvinMolBase::getAtomList | ( | ) | const |
int RDKit::MarvinMolBase::getBondIndex | ( | std::string | id | ) | const |
const std::vector< std::string > RDKit::MarvinMolBase::getBondList | ( | ) | const |
int RDKit::MarvinMolBase::getExplicitValence | ( | const MarvinAtom & | marvinAtom | ) | const |
bool RDKit::MarvinMolBase::has2dCoords | ( | ) | const |
bool RDKit::MarvinMolBase::has3dCoords | ( | ) | const |
bool RDKit::MarvinMolBase::hasAny2dCoords | ( | ) | const |
bool RDKit::MarvinMolBase::hasAny3dCoords | ( | ) | const |
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pure virtual |
bool RDKit::MarvinMolBase::hasCoords | ( | ) | const |
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virtual |
Reimplemented in RDKit::MarvinSuperatomSgroupExpanded, RDKit::MarvinMultipleSgroup, and RDKit::MarvinMol.
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virtual |
Reimplemented in RDKit::MarvinMultipleSgroup, and RDKit::MarvinSuperatomSgroup.
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virtual |
Reimplemented in RDKit::MarvinSuperatomSgroup.
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static |
void RDKit::MarvinMolBase::parseAtomsAndBonds | ( | ptree & | molTree | ) |
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virtual |
void RDKit::MarvinMolBase::prepSgroupsForRDKit | ( | ) |
void RDKit::MarvinMolBase::processSgroupsFromRDKit | ( | ) |
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virtual |
Reimplemented in RDKit::MarvinMultipleSgroup, RDKit::MarvinMulticenterSgroup, and RDKit::MarvinSuperatomSgroup.
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virtual |
Reimplemented in RDKit::MarvinMol.
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virtual |
Reimplemented in RDKit::MarvinMol.
void RDKit::MarvinMolBase::removeCoords | ( | ) |
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virtual |
Reimplemented in RDKit::MarvinMol.
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virtual |
Reimplemented in RDKit::MarvinMol.
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pure virtual |
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virtual |
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pure virtual |
std::vector<MarvinAtom *> RDKit::MarvinMolBase::atoms |
Definition at line 254 of file MarvinDefs.h.
std::vector<MarvinBond *> RDKit::MarvinMolBase::bonds |
Definition at line 255 of file MarvinDefs.h.
std::string RDKit::MarvinMolBase::id |
Definition at line 249 of file MarvinDefs.h.
std::string RDKit::MarvinMolBase::molID |
Definition at line 248 of file MarvinDefs.h.
MarvinMolBase* RDKit::MarvinMolBase::parent |
Definition at line 258 of file MarvinDefs.h.
std::vector<std::unique_ptr<MarvinMolBase> > RDKit::MarvinMolBase::sgroups |
Definition at line 257 of file MarvinDefs.h.