RDKit
Open-source cheminformatics and machine learning.
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RDKit::MarvinMultipleSgroup Class Reference

#include <MarvinDefs.h>

Inheritance diagram for RDKit::MarvinMultipleSgroup:
RDKit::MarvinMolBase

Public Member Functions

 MarvinMultipleSgroup (MarvinMolBase *parent)
 MarvinMultipleSgroup (MarvinMolBase *parent, ptree &molTree)
MarvinMolBase * copyMol (const std::string &idAppend) const override
void expandOneMultipleSgroup ()
void contractOneMultipleSgroup ()
int getMatchedOrphanBondIndex (std::string atomIdToCheck, std::vector< MarvinBond * > &bondsToTry, std::vector< MarvinBond * > &orphanedBonds) const
std::string toString () const override
ptree toPtree () const override
std::string role () const override
bool hasAtomBondBlocks () const override
bool isPassiveRoleForExpansion () const override
bool isPassiveRoleForContraction () const override
void processSpecialSgroups () override
void parseMoleculeSpecific (RDKit::RWMol *mol, std::unique_ptr< SubstanceGroup > &sgroup, int sequenceId) 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)
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 ()
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
bool isExpanded = false
std::vector< MarvinAtom * > parentAtoms
std::vector< MarvinBond * > bondsToAtomsNotInExpandedGroup
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 423 of file MarvinDefs.h.

Constructor & Destructor Documentation

◆ MarvinMultipleSgroup() [1/2]

RDKit::MarvinMultipleSgroup::MarvinMultipleSgroup ( MarvinMolBase * parent)

References RDKit::MarvinMolBase::MarvinMolBase(), and RDKit::MarvinMolBase::parent.

◆ MarvinMultipleSgroup() [2/2]

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

References RDKit::MarvinMolBase::MarvinMolBase(), and RDKit::MarvinMolBase::parent.

Member Function Documentation

◆ contractOneMultipleSgroup()

void RDKit::MarvinMultipleSgroup::contractOneMultipleSgroup ( )

◆ copyMol()

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

Implements RDKit::MarvinMolBase.

References RDKit::MarvinMolBase::MarvinMolBase().

◆ expandOneMultipleSgroup()

void RDKit::MarvinMultipleSgroup::expandOneMultipleSgroup ( )

◆ getMatchedOrphanBondIndex()

int RDKit::MarvinMultipleSgroup::getMatchedOrphanBondIndex ( std::string atomIdToCheck,
std::vector< MarvinBond * > & bondsToTry,
std::vector< MarvinBond * > & orphanedBonds ) const

◆ hasAtomBondBlocks()

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

Implements RDKit::MarvinMolBase.

◆ isPassiveRoleForContraction()

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

Reimplemented from RDKit::MarvinMolBase.

◆ isPassiveRoleForExpansion()

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

Reimplemented from RDKit::MarvinMolBase.

◆ parseMoleculeSpecific()

void RDKit::MarvinMultipleSgroup::parseMoleculeSpecific ( RDKit::RWMol * mol,
std::unique_ptr< SubstanceGroup > & sgroup,
int sequenceId )
overridevirtual

Reimplemented from RDKit::MarvinMolBase.

◆ processSpecialSgroups()

void RDKit::MarvinMultipleSgroup::processSpecialSgroups ( )
overridevirtual

Reimplemented from RDKit::MarvinMolBase.

◆ role()

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

Implements RDKit::MarvinMolBase.

◆ toPtree()

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

Reimplemented from RDKit::MarvinMolBase.

◆ toString()

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

Implements RDKit::MarvinMolBase.

Member Data Documentation

◆ bondsToAtomsNotInExpandedGroup

std::vector<MarvinBond *> RDKit::MarvinMultipleSgroup::bondsToAtomsNotInExpandedGroup

Definition at line 434 of file MarvinDefs.h.

◆ isExpanded

bool RDKit::MarvinMultipleSgroup::isExpanded = false

Definition at line 431 of file MarvinDefs.h.

◆ parentAtoms

std::vector<MarvinAtom *> RDKit::MarvinMultipleSgroup::parentAtoms

Definition at line 432 of file MarvinDefs.h.

◆ title

std::string RDKit::MarvinMultipleSgroup::title

Definition at line 430 of file MarvinDefs.h.

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