RDKit::MarvinMol Class Reference

#include <MarvinDefs.h>

Inheritance diagram for RDKit::MarvinMol:

Public Member Functions
	MarvinMol ()
	MarvinMol (ptree &molTree)
MarvinMolBase *	copyMol (const std::string &idAppend) const override
	~MarvinMol () override
void	pushOwnedAtom (MarvinAtom *atom) override
void	pushOwnedBond (MarvinBond *bond) override
void	removeOwnedAtom (MarvinAtom *atom) override
void	removeOwnedBond (MarvinBond *bond) override
std::string	role () const override
bool	hasAtomBondBlocks () const override
bool	isPassiveRoleForContraction () const override
std::string	toString () const override
ptree	toPtree () const override
std::string	generateMolString ()
ptree	toMolPtree () const
Public Member Functions inherited from RDKit::MarvinMolBase
void	addSgroupsToPtree (ptree &pt) const
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 ()
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::vector< std::unique_ptr< MarvinAtom > >	ownedAtoms
std::vector< std::unique_ptr< MarvinBond > >	ownedBonds
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 559 of file MarvinDefs.h.

Constructor & Destructor Documentation

MarvinMol() [1/2]

RDKit::MarvinMol::MarvinMol

(

)

MarvinMol() [2/2]

RDKit::MarvinMol::MarvinMol

(

ptree &

molTree

)

~MarvinMol()

RDKit::MarvinMol::~MarvinMol ( )

override

Member Function Documentation

copyMol()

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

overridevirtual

Implements RDKit::MarvinMolBase.

References RDKit::MarvinMolBase::MarvinMolBase().

generateMolString()

std::string RDKit::MarvinMol::generateMolString

(

)

hasAtomBondBlocks()

bool RDKit::MarvinMol::hasAtomBondBlocks ( ) const

overridevirtual

Implements RDKit::MarvinMolBase.

isPassiveRoleForContraction()

bool RDKit::MarvinMol::isPassiveRoleForContraction ( ) const

overridevirtual

Reimplemented from RDKit::MarvinMolBase.

pushOwnedAtom()

void RDKit::MarvinMol::pushOwnedAtom ( MarvinAtom * atom )

overridevirtual

Reimplemented from RDKit::MarvinMolBase.

pushOwnedBond()

void RDKit::MarvinMol::pushOwnedBond ( MarvinBond * bond )

overridevirtual

Reimplemented from RDKit::MarvinMolBase.

removeOwnedAtom()

void RDKit::MarvinMol::removeOwnedAtom ( MarvinAtom * atom )

overridevirtual

Reimplemented from RDKit::MarvinMolBase.

removeOwnedBond()

void RDKit::MarvinMol::removeOwnedBond ( MarvinBond * bond )

overridevirtual

Reimplemented from RDKit::MarvinMolBase.

role()

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

overridevirtual

Implements RDKit::MarvinMolBase.

toMolPtree()

ptree RDKit::MarvinMol::toMolPtree

(

)

const

toPtree()

ptree RDKit::MarvinMol::toPtree ( ) const

overridevirtual

Reimplemented from RDKit::MarvinMolBase.

toString()

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

overridevirtual

Implements RDKit::MarvinMolBase.

Member Data Documentation

ownedAtoms

std::vector<std::unique_ptr<MarvinAtom> > RDKit::MarvinMol::ownedAtoms

Definition at line 568 of file MarvinDefs.h.

ownedBonds

std::vector<std::unique_ptr<MarvinBond> > RDKit::MarvinMol::ownedBonds

Definition at line 569 of file MarvinDefs.h.

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

• MarvinDefs.h