RDKit::MarvinSuperatomSgroup Class Reference

#include <MarvinDefs.h>

Inheritance diagram for RDKit::MarvinSuperatomSgroup:

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 521 of file MarvinDefs.h.

Constructor & Destructor Documentation

MarvinSuperatomSgroup() [1/2]

RDKit::MarvinSuperatomSgroup::MarvinSuperatomSgroup

(

MarvinMolBase *

parent

)

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

MarvinSuperatomSgroup() [2/2]

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

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

~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.

References RDKit::MarvinMolBase::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 524 of file MarvinDefs.h.

title

std::string RDKit::MarvinSuperatomSgroup::title

Definition at line 523 of file MarvinDefs.h.

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

• MarvinDefs.h