#include <MarvinDefs.h>

Inheritance diagram for RDKit::MarvinGenericSgroup:

Public Member Functions
	MarvinGenericSgroup (MarvinMolBase *parent)

	MarvinGenericSgroup (MarvinMolBase *parent, ptree &molTree)

MarvinMolBase *	copyMol (const std::string &idAppend) const override

std::string	toString () const override

ptree	toPtree () const override

std::string	role () const override

bool	hasAtomBondBlocks () 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 bool	isPassiveRoleForContraction () 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	charge

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)