RDKit
Open-source cheminformatics and machine learning.
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Public Member Functions | Public Attributes | List of all members
RDKit::MarvinSuperatomSgroup Class Reference

#include <MarvinDefs.h>

Inheritance diagram for RDKit::MarvinSuperatomSgroup:
RDKit::MarvinMolBase

Public Member Functions

 MarvinSuperatomSgroup (MarvinMolBase *parent)
 
 MarvinSuperatomSgroup (MarvinMolBase *parent, ptree &molTree)
 
MarvinMolBase * copyMol (const std::string &idAppend) const override
 
 ~MarvinSuperatomSgroup () override
 
void convertFromOneSuperAtom ()
 
std::string role () const override
 
bool hasAtomBondBlocks () const override
 
bool isPassiveRoleForExpansion () const override
 
std::string toString () const override
 
ptree toPtree () const override
 
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) override
 
IsSgroupInAtomSetResult isSgroupInSetOfAtoms (const std::vector< MarvinAtom * > &setOfAtoms) const override
 
void processSpecialSgroups () override
 
- Public Member Functions inherited from RDKit::MarvinMolBase
void addSgroupsToPtree (ptree &pt) const
 
virtual void pushOwnedAtom (MarvinAtom *atom)
 
virtual void pushOwnedBond (MarvinBond *bond)
 
virtual void removeOwnedAtom (MarvinAtom *atom)
 
virtual void removeOwnedBond (MarvinBond *bond)
 
void setPrecision (unsigned int precision)
 
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)
 
void cleanUpSgNumbering (int &sgCount, std::map< std::string, std::string > &sgMap)
 
MarvinAtom * findAtomByRef (std::string atomId)
 
MarvinBond * findBondByRef (std::string atomId)
 
void prepSgroupsForRDKit ()
 
void processSgroupsFromRDKit ()
 
virtual bool isPassiveRoleForContraction () const
 
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)
 

Public Attributes

std::string title
 
std::vector< std::unique_ptr< MarvinAttachmentPoint > > attachmentPoints
 
- Public Attributes inherited from RDKit::MarvinMolBase
std::string molID
 
std::string id
 
unsigned int coordinatePrecision = 6
 
std::vector< MarvinAtom * > atoms
 
std::vector< MarvinBond * > bonds
 
std::vector< std::unique_ptr< MarvinMolBase > > sgroups
 
MarvinMolBase * parent
 

Additional Inherited Members

- Static Public Member Functions inherited from RDKit::MarvinMolBase
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)
 

Detailed Description

Definition at line 528 of file MarvinDefs.h.

Constructor & Destructor Documentation

◆ MarvinSuperatomSgroup() [1/2]

RDKit::MarvinSuperatomSgroup::MarvinSuperatomSgroup ( MarvinMolBase *  parent)

◆ MarvinSuperatomSgroup() [2/2]

RDKit::MarvinSuperatomSgroup::MarvinSuperatomSgroup ( MarvinMolBase *  parent,
ptree &  molTree 
)

◆ ~MarvinSuperatomSgroup()

RDKit::MarvinSuperatomSgroup::~MarvinSuperatomSgroup ( )
override

Member Function Documentation

◆ cleanUpNumberingMolsAtomsBonds()

void RDKit::MarvinSuperatomSgroup::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 
)
overridevirtual

Reimplemented from RDKit::MarvinMolBase.

◆ convertFromOneSuperAtom()

void RDKit::MarvinSuperatomSgroup::convertFromOneSuperAtom ( )

◆ copyMol()

MarvinMolBase * RDKit::MarvinSuperatomSgroup::copyMol ( const std::string &  idAppend) const
overridevirtual

Implements RDKit::MarvinMolBase.

◆ hasAtomBondBlocks()

bool RDKit::MarvinSuperatomSgroup::hasAtomBondBlocks ( ) const
overridevirtual

Implements RDKit::MarvinMolBase.

◆ isPassiveRoleForExpansion()

bool RDKit::MarvinSuperatomSgroup::isPassiveRoleForExpansion ( ) const
overridevirtual

Reimplemented from RDKit::MarvinMolBase.

◆ isSgroupInSetOfAtoms()

IsSgroupInAtomSetResult RDKit::MarvinSuperatomSgroup::isSgroupInSetOfAtoms ( const std::vector< MarvinAtom * > &  setOfAtoms) const
overridevirtual

Reimplemented from RDKit::MarvinMolBase.

◆ processSpecialSgroups()

void RDKit::MarvinSuperatomSgroup::processSpecialSgroups ( )
overridevirtual

Reimplemented from RDKit::MarvinMolBase.

◆ role()

std::string RDKit::MarvinSuperatomSgroup::role ( ) const
overridevirtual

Implements RDKit::MarvinMolBase.

◆ toPtree()

ptree RDKit::MarvinSuperatomSgroup::toPtree ( ) const
overridevirtual

Reimplemented from RDKit::MarvinMolBase.

◆ toString()

std::string RDKit::MarvinSuperatomSgroup::toString ( ) const
overridevirtual

Implements RDKit::MarvinMolBase.

Member Data Documentation

◆ attachmentPoints

std::vector<std::unique_ptr<MarvinAttachmentPoint> > RDKit::MarvinSuperatomSgroup::attachmentPoints

Definition at line 531 of file MarvinDefs.h.

◆ title

std::string RDKit::MarvinSuperatomSgroup::title

Definition at line 530 of file MarvinDefs.h.

The documentation for this class was generated from the following file: