RDKit::MarvinSuperatomSgroupExpanded Class Reference

#include <MarvinDefs.h>

Inheritance diagram for RDKit::MarvinSuperatomSgroupExpanded:

Public Member Functions
	MarvinSuperatomSgroupExpanded (MarvinMolBase *parent)
	MarvinSuperatomSgroupExpanded (MarvinMolBase *parent, ptree &molTree)
MarvinMolBase *	copyMol (const std::string &idAppend) const override
	~MarvinSuperatomSgroupExpanded () override
MarvinMolBase *	convertToOneSuperAtom ()
std::string	toString () const override
ptree	toPtree () const override
std::string	role () const override
bool	hasAtomBondBlocks () const override
bool	isPassiveRoleForContraction () const 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 ()
virtual bool	isPassiveRoleForExpansion () const
virtual void	processSpecialSgroups ()
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
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 398 of file MarvinDefs.h.

Constructor & Destructor Documentation

MarvinSuperatomSgroupExpanded() [1/2]

RDKit::MarvinSuperatomSgroupExpanded::MarvinSuperatomSgroupExpanded

(

MarvinMolBase *

parent

)

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

MarvinSuperatomSgroupExpanded() [2/2]

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

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

~MarvinSuperatomSgroupExpanded()

RDKit::MarvinSuperatomSgroupExpanded::~MarvinSuperatomSgroupExpanded ( )

override

Member Function Documentation

convertToOneSuperAtom()

MarvinMolBase * RDKit::MarvinSuperatomSgroupExpanded::convertToOneSuperAtom

(

)

References RDKit::MarvinMolBase::MarvinMolBase().

copyMol()

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

overridevirtual

Implements RDKit::MarvinMolBase.

References RDKit::MarvinMolBase::MarvinMolBase().

hasAtomBondBlocks()

bool RDKit::MarvinSuperatomSgroupExpanded::hasAtomBondBlocks ( ) const

overridevirtual

Implements RDKit::MarvinMolBase.

isPassiveRoleForContraction()

bool RDKit::MarvinSuperatomSgroupExpanded::isPassiveRoleForContraction ( ) const

overridevirtual

Reimplemented from RDKit::MarvinMolBase.

parseMoleculeSpecific()

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

overridevirtual

Reimplemented from RDKit::MarvinMolBase.

role()

std::string RDKit::MarvinSuperatomSgroupExpanded::role ( ) const

overridevirtual

Implements RDKit::MarvinMolBase.

toPtree()

ptree RDKit::MarvinSuperatomSgroupExpanded::toPtree ( ) const

overridevirtual

Reimplemented from RDKit::MarvinMolBase.

toString()

std::string RDKit::MarvinSuperatomSgroupExpanded::toString ( ) const

overridevirtual

Implements RDKit::MarvinMolBase.

Member Data Documentation

title

std::string RDKit::MarvinSuperatomSgroupExpanded::title

Definition at line 400 of file MarvinDefs.h.

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

• MarvinDefs.h