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

#include <MarvinDefs.h>

Inheritance diagram for RDKit::MarvinMol:
RDKit::MarvinMolBase

Public Member Functions

 MarvinMol ()
 
 MarvinMol (ptree &molTree)
 
MarvinMolBase * copyMol (const std::string &idAppend) const override
 
 ~MarvinMol () override
 
void pushOwnedAtom (MarvinAtom *atom) override
 
void pushOwnedBond (MarvinBond *bond) override
 
void removeOwnedAtom (MarvinAtom *atom) override
 
void removeOwnedBond (MarvinBond *bond) override
 
std::string role () const override
 
bool hasAtomBondBlocks () const override
 
bool isPassiveRoleForContraction () const override
 
std::string toString () const override
 
ptree toPtree () const override
 
std::string generateMolString ()
 
ptree toMolPtree () const
 
- Public Member Functions inherited from RDKit::MarvinMolBase
void addSgroupsToPtree (ptree &pt) const
 
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)
 
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 prepSgroupsForRDKit ()
 
void processSgroupsFromRDKit ()
 
virtual bool isPassiveRoleForExpansion () 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)
 

Public Attributes

std::vector< std::unique_ptr< MarvinAtom > > ownedAtoms
 
std::vector< std::unique_ptr< MarvinBond > > ownedBonds
 
- 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 567 of file MarvinDefs.h.

Constructor & Destructor Documentation

◆ MarvinMol() [1/2]

RDKit::MarvinMol::MarvinMol ( )

◆ MarvinMol() [2/2]

RDKit::MarvinMol::MarvinMol ( ptree & molTree)

◆ ~MarvinMol()

RDKit::MarvinMol::~MarvinMol ( )
override

Member Function Documentation

◆ copyMol()

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

Implements RDKit::MarvinMolBase.

◆ generateMolString()

std::string RDKit::MarvinMol::generateMolString ( )

◆ hasAtomBondBlocks()

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

Implements RDKit::MarvinMolBase.

◆ isPassiveRoleForContraction()

bool RDKit::MarvinMol::isPassiveRoleForContraction ( ) const
overridevirtual

Reimplemented from RDKit::MarvinMolBase.

◆ pushOwnedAtom()

void RDKit::MarvinMol::pushOwnedAtom ( MarvinAtom * atom)
overridevirtual

Reimplemented from RDKit::MarvinMolBase.

◆ pushOwnedBond()

void RDKit::MarvinMol::pushOwnedBond ( MarvinBond * bond)
overridevirtual

Reimplemented from RDKit::MarvinMolBase.

◆ removeOwnedAtom()

void RDKit::MarvinMol::removeOwnedAtom ( MarvinAtom * atom)
overridevirtual

Reimplemented from RDKit::MarvinMolBase.

◆ removeOwnedBond()

void RDKit::MarvinMol::removeOwnedBond ( MarvinBond * bond)
overridevirtual

Reimplemented from RDKit::MarvinMolBase.

◆ role()

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

Implements RDKit::MarvinMolBase.

◆ toMolPtree()

ptree RDKit::MarvinMol::toMolPtree ( ) const

◆ toPtree()

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

Reimplemented from RDKit::MarvinMolBase.

◆ toString()

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

Implements RDKit::MarvinMolBase.

Member Data Documentation

◆ ownedAtoms

std::vector<std::unique_ptr<MarvinAtom> > RDKit::MarvinMol::ownedAtoms

Definition at line 576 of file MarvinDefs.h.

◆ ownedBonds

std::vector<std::unique_ptr<MarvinBond> > RDKit::MarvinMol::ownedBonds

Definition at line 577 of file MarvinDefs.h.

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