RDKit::MarvinMolBase Class Reference

#include <MarvinDefs.h>

Inheritance diagram for RDKit::MarvinMolBase:

Public Member Functions
virtual std::string	role () const =0
virtual bool	hasAtomBondBlocks () const =0
virtual std::string	toString () const =0
virtual ptree	toPtree () const
void	addSgroupsToPtree (ptree &pt) const
virtual MarvinMolBase *	copyMol (const std::string &idAppend) const =0
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 ()
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)

Static Public Member Functions
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)

Public Attributes
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

Detailed Description

Definition at line 245 of file MarvinDefs.h.

Constructor & Destructor Documentation

MarvinMolBase()

RDKit::MarvinMolBase::MarvinMolBase ( )

inline

Definition at line 272 of file MarvinDefs.h.

~MarvinMolBase()

virtual RDKit::MarvinMolBase::~MarvinMolBase ( )

virtual

Member Function Documentation

addSgroupsToPtree()

void RDKit::MarvinMolBase::addSgroupsToPtree

(

ptree &

pt

)

const

AnyOverLappingAtoms()

bool RDKit::MarvinMolBase::AnyOverLappingAtoms

(

const MarvinMolBase *

otherMol

)

const

atomRefInAtoms()

static bool RDKit::MarvinMolBase::atomRefInAtoms ( MarvinAtom * a, std::string b )

static

bondRefInBonds()

static bool RDKit::MarvinMolBase::bondRefInBonds ( MarvinBond * a, std::string b )

static

cleanUpNumbering()

void RDKit::MarvinMolBase::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 )

cleanUpNumberingMolsAtomsBonds()

virtual void RDKit::MarvinMolBase::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 )

virtual

Reimplemented in RDKit::MarvinSuperatomSgroup.

cleanUpSgNumbering()

void RDKit::MarvinMolBase::cleanUpSgNumbering	(	int &	sgCount,
		std::map< std::string, std::string > &	sgMap )

copyMol()

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

pure virtual

Implemented in RDKit::MarvinSruCoModSgroup, RDKit::MarvinDataSgroup, RDKit::MarvinSuperatomSgroupExpanded, RDKit::MarvinMultipleSgroup, RDKit::MarvinMulticenterSgroup, RDKit::MarvinGenericSgroup, RDKit::MarvinMonomerSgroup, RDKit::MarvinSuperatomSgroup, and RDKit::MarvinMol.

findAtomByRef()

MarvinAtom * RDKit::MarvinMolBase::findAtomByRef

(

std::string

atomId

)

findBondByRef()

MarvinBond * RDKit::MarvinMolBase::findBondByRef

(

std::string

atomId

)

getAtomIndex()

int RDKit::MarvinMolBase::getAtomIndex

(

std::string

id

)

const

getAtomList()

const std::vector< std::string > RDKit::MarvinMolBase::getAtomList

(

)

const

getBondIndex()

int RDKit::MarvinMolBase::getBondIndex

(

std::string

id

)

const

getBondList()

const std::vector< std::string > RDKit::MarvinMolBase::getBondList

(

)

const

getExplicitValence()

int RDKit::MarvinMolBase::getExplicitValence

(

const MarvinAtom &

marvinAtom

)

const

has2dCoords()

bool RDKit::MarvinMolBase::has2dCoords

(

)

const

has3dCoords()

bool RDKit::MarvinMolBase::has3dCoords

(

)

const

hasAny2dCoords()

bool RDKit::MarvinMolBase::hasAny2dCoords

(

)

const

hasAny3dCoords()

bool RDKit::MarvinMolBase::hasAny3dCoords

(

)

const

hasAtomBondBlocks()

virtual bool RDKit::MarvinMolBase::hasAtomBondBlocks ( ) const

pure virtual

Implemented in RDKit::MarvinSruCoModSgroup, RDKit::MarvinDataSgroup, RDKit::MarvinSuperatomSgroupExpanded, RDKit::MarvinMultipleSgroup, RDKit::MarvinMulticenterSgroup, RDKit::MarvinGenericSgroup, RDKit::MarvinMonomerSgroup, RDKit::MarvinSuperatomSgroup, and RDKit::MarvinMol.

hasCoords()

bool RDKit::MarvinMolBase::hasCoords

(

)

const

isPassiveRoleForContraction()

virtual bool RDKit::MarvinMolBase::isPassiveRoleForContraction ( ) const

virtual

Reimplemented in RDKit::MarvinSuperatomSgroupExpanded, RDKit::MarvinMultipleSgroup, and RDKit::MarvinMol.

isPassiveRoleForExpansion()

virtual bool RDKit::MarvinMolBase::isPassiveRoleForExpansion ( ) const

virtual

Reimplemented in RDKit::MarvinMultipleSgroup, and RDKit::MarvinSuperatomSgroup.

isSgroupInSetOfAtoms()

virtual IsSgroupInAtomSetResult RDKit::MarvinMolBase::isSgroupInSetOfAtoms ( const std::vector< MarvinAtom * > & setOfAtoms ) const

virtual

Reimplemented in RDKit::MarvinSuperatomSgroup.

molIDInSgroups()

static bool RDKit::MarvinMolBase::molIDInSgroups ( std::string a, std::string b )

static

parseAtomsAndBonds()

void RDKit::MarvinMolBase::parseAtomsAndBonds

(

ptree &

molTree

)

parseMoleculeSpecific()

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

virtual

Reimplemented in RDKit::MarvinSruCoModSgroup, RDKit::MarvinDataSgroup, RDKit::MarvinSuperatomSgroupExpanded, RDKit::MarvinMultipleSgroup, RDKit::MarvinMulticenterSgroup, RDKit::MarvinGenericSgroup, and RDKit::MarvinMonomerSgroup.

prepSgroupsForRDKit()

void RDKit::MarvinMolBase::prepSgroupsForRDKit

(

)

processSgroupsFromRDKit()

void RDKit::MarvinMolBase::processSgroupsFromRDKit

(

)

processSpecialSgroups()

virtual void RDKit::MarvinMolBase::processSpecialSgroups ( )

virtual

Reimplemented in RDKit::MarvinMultipleSgroup, RDKit::MarvinMulticenterSgroup, and RDKit::MarvinSuperatomSgroup.

pushOwnedAtom()

virtual void RDKit::MarvinMolBase::pushOwnedAtom ( MarvinAtom * atom )

virtual

Reimplemented in RDKit::MarvinMol.

pushOwnedBond()

virtual void RDKit::MarvinMolBase::pushOwnedBond ( MarvinBond * bond )

virtual

Reimplemented in RDKit::MarvinMol.

removeCoords()

void RDKit::MarvinMolBase::removeCoords

(

)

removeOwnedAtom()

virtual void RDKit::MarvinMolBase::removeOwnedAtom ( MarvinAtom * atom )

virtual

Reimplemented in RDKit::MarvinMol.

removeOwnedBond()

virtual void RDKit::MarvinMolBase::removeOwnedBond ( MarvinBond * bond )

virtual

Reimplemented in RDKit::MarvinMol.

role()

virtual std::string RDKit::MarvinMolBase::role ( ) const

pure virtual

Implemented in RDKit::MarvinSruCoModSgroup, RDKit::MarvinDataSgroup, RDKit::MarvinSuperatomSgroupExpanded, RDKit::MarvinMultipleSgroup, RDKit::MarvinMulticenterSgroup, RDKit::MarvinGenericSgroup, RDKit::MarvinMonomerSgroup, RDKit::MarvinSuperatomSgroup, and RDKit::MarvinMol.

setPrecision()

void RDKit::MarvinMolBase::setPrecision

(

unsigned int

precision

)

toPtree()

virtual ptree RDKit::MarvinMolBase::toPtree ( ) const

virtual

Reimplemented in RDKit::MarvinSruCoModSgroup, RDKit::MarvinDataSgroup, RDKit::MarvinSuperatomSgroupExpanded, RDKit::MarvinMultipleSgroup, RDKit::MarvinMulticenterSgroup, RDKit::MarvinGenericSgroup, RDKit::MarvinMonomerSgroup, RDKit::MarvinSuperatomSgroup, and RDKit::MarvinMol.

toString()

virtual std::string RDKit::MarvinMolBase::toString ( ) const

pure virtual

Implemented in RDKit::MarvinSruCoModSgroup, RDKit::MarvinDataSgroup, RDKit::MarvinSuperatomSgroupExpanded, RDKit::MarvinMultipleSgroup, RDKit::MarvinMulticenterSgroup, RDKit::MarvinGenericSgroup, RDKit::MarvinMonomerSgroup, RDKit::MarvinSuperatomSgroup, and RDKit::MarvinMol.

Member Data Documentation

atoms

std::vector<MarvinAtom *> RDKit::MarvinMolBase::atoms

Definition at line 250 of file MarvinDefs.h.

bonds

std::vector<MarvinBond *> RDKit::MarvinMolBase::bonds

Definition at line 251 of file MarvinDefs.h.

coordinatePrecision

unsigned int RDKit::MarvinMolBase::coordinatePrecision = 6

Definition at line 249 of file MarvinDefs.h.

id

std::string RDKit::MarvinMolBase::id

Definition at line 248 of file MarvinDefs.h.

molID

std::string RDKit::MarvinMolBase::molID

Definition at line 247 of file MarvinDefs.h.

parent

MarvinMolBase* RDKit::MarvinMolBase::parent

Definition at line 253 of file MarvinDefs.h.

sgroups

std::vector<std::unique_ptr<MarvinMolBase> > RDKit::MarvinMolBase::sgroups

Definition at line 252 of file MarvinDefs.h.

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

• MarvinDefs.h