RDKit::MarvinMultipleSgroup Class Reference

#include <MarvinDefs.h>

Inheritance diagram for RDKit::MarvinMultipleSgroup:

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

)

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 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.

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

• MarvinDefs.h