RDKit
Open-source cheminformatics and machine learning.
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Public Member Functions | Public Attributes | List of all members
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 424 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 435 of file MarvinDefs.h.

◆ isExpanded

bool RDKit::MarvinMultipleSgroup::isExpanded = false

Definition at line 432 of file MarvinDefs.h.

◆ parentAtoms

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

Definition at line 433 of file MarvinDefs.h.

◆ title

std::string RDKit::MarvinMultipleSgroup::title

Definition at line 431 of file MarvinDefs.h.

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