RDKit
Open-source cheminformatics and machine learning.
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)
 
MarvinMolBasecopyMol (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
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 MarvinMolBasecopyMol (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
 
MarvinAtomfindAtomByRef (std::string atomId)
 
MarvinBondfindBondByRef (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)
 

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
 
std::vector< MarvinAtom * > atoms
 
std::vector< MarvinBond * > bonds
 
std::vector< std::unique_ptr< MarvinMolBase > > sgroups
 
MarvinMolBaseparent
 

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 437 of file MarvinDefs.h.

Constructor & Destructor Documentation

◆ MarvinMultipleSgroup() [1/2]

RDKit::MarvinMultipleSgroup::MarvinMultipleSgroup ( MarvinMolBase parent)

◆ MarvinMultipleSgroup() [2/2]

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

Member Function Documentation

◆ contractOneMultipleSgroup()

void RDKit::MarvinMultipleSgroup::contractOneMultipleSgroup ( )

◆ copyMol()

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

Implements RDKit::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 448 of file MarvinDefs.h.

◆ isExpanded

bool RDKit::MarvinMultipleSgroup::isExpanded = false

Definition at line 445 of file MarvinDefs.h.

◆ parentAtoms

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

Definition at line 446 of file MarvinDefs.h.

◆ title

std::string RDKit::MarvinMultipleSgroup::title

Definition at line 444 of file MarvinDefs.h.


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