RDKit
Open-source cheminformatics and machine learning.
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Public Member Functions | Static Public Member Functions | Public Attributes | List of all members
RDKit::MarvinMolBase Class Referenceabstract

#include <MarvinDefs.h>

Inheritance diagram for RDKit::MarvinMolBase:
RDKit::MarvinDataSgroup RDKit::MarvinGenericSgroup RDKit::MarvinMol RDKit::MarvinMonomerSgroup RDKit::MarvinMulticenterSgroup RDKit::MarvinMultipleSgroup RDKit::MarvinSruCoModSgroup RDKit::MarvinSuperatomSgroup RDKit::MarvinSuperatomSgroupExpanded

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 238 of file MarvinDefs.h.

Constructor & Destructor Documentation

◆ MarvinMolBase()

RDKit::MarvinMolBase::MarvinMolBase ( )
inline

Definition at line 265 of file MarvinDefs.h.

Referenced by AnyOverLappingAtoms(), RDKit::MarvinSuperatomSgroupExpanded::convertToOneSuperAtom(), RDKit::MarvinDataSgroup::copyMol(), RDKit::MarvinGenericSgroup::copyMol(), RDKit::MarvinMol::copyMol(), copyMol(), RDKit::MarvinMonomerSgroup::copyMol(), RDKit::MarvinMulticenterSgroup::copyMol(), RDKit::MarvinMultipleSgroup::copyMol(), RDKit::MarvinSruCoModSgroup::copyMol(), RDKit::MarvinSuperatomSgroup::copyMol(), RDKit::MarvinSuperatomSgroupExpanded::copyMol(), RDKit::MarvinDataSgroup::MarvinDataSgroup(), RDKit::MarvinDataSgroup::MarvinDataSgroup(), RDKit::MarvinGenericSgroup::MarvinGenericSgroup(), RDKit::MarvinGenericSgroup::MarvinGenericSgroup(), RDKit::MarvinMonomerSgroup::MarvinMonomerSgroup(), RDKit::MarvinMonomerSgroup::MarvinMonomerSgroup(), RDKit::MarvinMulticenterSgroup::MarvinMulticenterSgroup(), RDKit::MarvinMulticenterSgroup::MarvinMulticenterSgroup(), RDKit::MarvinMultipleSgroup::MarvinMultipleSgroup(), RDKit::MarvinMultipleSgroup::MarvinMultipleSgroup(), RDKit::MarvinSruCoModSgroup::MarvinSruCoModSgroup(), RDKit::MarvinSruCoModSgroup::MarvinSruCoModSgroup(), RDKit::MarvinSuperatomSgroup::MarvinSuperatomSgroup(), RDKit::MarvinSuperatomSgroup::MarvinSuperatomSgroup(), RDKit::MarvinSuperatomSgroupExpanded::MarvinSuperatomSgroupExpanded(), and RDKit::MarvinSuperatomSgroupExpanded::MarvinSuperatomSgroupExpanded().

◆ ~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

References MarvinMolBase().

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

References MarvinMolBase().

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

◆ hasCoords()

bool RDKit::MarvinMolBase::hasCoords ( ) const

◆ isPassiveRoleForContraction()

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

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

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

◆ prepSgroupsForRDKit()

void RDKit::MarvinMolBase::prepSgroupsForRDKit ( )

◆ processSgroupsFromRDKit()

void RDKit::MarvinMolBase::processSgroupsFromRDKit ( )

◆ processSpecialSgroups()

virtual void RDKit::MarvinMolBase::processSpecialSgroups ( )
virtual

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

◆ setPrecision()

void RDKit::MarvinMolBase::setPrecision ( unsigned int precision)

◆ toPtree()

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

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

◆ toString()

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

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

Member Data Documentation

◆ atoms

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

Definition at line 243 of file MarvinDefs.h.

◆ bonds

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

Definition at line 244 of file MarvinDefs.h.

◆ coordinatePrecision

unsigned int RDKit::MarvinMolBase::coordinatePrecision = 6

Definition at line 242 of file MarvinDefs.h.

◆ id

std::string RDKit::MarvinMolBase::id

Definition at line 241 of file MarvinDefs.h.

◆ molID

std::string RDKit::MarvinMolBase::molID

Definition at line 240 of file MarvinDefs.h.

◆ parent

MarvinMolBase* RDKit::MarvinMolBase::parent

Definition at line 246 of file MarvinDefs.h.

Referenced by RDKit::MarvinDataSgroup::MarvinDataSgroup(), RDKit::MarvinDataSgroup::MarvinDataSgroup(), RDKit::MarvinGenericSgroup::MarvinGenericSgroup(), RDKit::MarvinGenericSgroup::MarvinGenericSgroup(), RDKit::MarvinMonomerSgroup::MarvinMonomerSgroup(), RDKit::MarvinMonomerSgroup::MarvinMonomerSgroup(), RDKit::MarvinMulticenterSgroup::MarvinMulticenterSgroup(), RDKit::MarvinMulticenterSgroup::MarvinMulticenterSgroup(), RDKit::MarvinMultipleSgroup::MarvinMultipleSgroup(), RDKit::MarvinMultipleSgroup::MarvinMultipleSgroup(), RDKit::MarvinSruCoModSgroup::MarvinSruCoModSgroup(), RDKit::MarvinSruCoModSgroup::MarvinSruCoModSgroup(), RDKit::MarvinSuperatomSgroup::MarvinSuperatomSgroup(), RDKit::MarvinSuperatomSgroup::MarvinSuperatomSgroup(), RDKit::MarvinSuperatomSgroupExpanded::MarvinSuperatomSgroupExpanded(), and RDKit::MarvinSuperatomSgroupExpanded::MarvinSuperatomSgroupExpanded().

◆ sgroups

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

Definition at line 245 of file MarvinDefs.h.

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