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

#include <MarvinDefs.h>

Inheritance diagram for RDKit::MarvinDataSgroup:
RDKit::MarvinMolBase

Public Member Functions

 MarvinDataSgroup (MarvinMolBase *parent)
 
 MarvinDataSgroup (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 context
 
std::string fieldName
 
std::string placement
 
std::string unitsDisplayed
 
std::string queryType
 
std::string queryOp
 
std::string fieldData
 
std::string units
 
double x
 
double y
 
- 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 371 of file MarvinDefs.h.

Constructor & Destructor Documentation

◆ MarvinDataSgroup() [1/2]

RDKit::MarvinDataSgroup::MarvinDataSgroup ( MarvinMolBase * parent)

References RDKit::MarvinMolBase::MarvinMolBase(), and RDKit::MarvinMolBase::parent.

◆ MarvinDataSgroup() [2/2]

RDKit::MarvinDataSgroup::MarvinDataSgroup ( MarvinMolBase * parent,
ptree & molTree )

References RDKit::MarvinMolBase::MarvinMolBase(), and RDKit::MarvinMolBase::parent.

Member Function Documentation

◆ copyMol()

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

Implements RDKit::MarvinMolBase.

References RDKit::MarvinMolBase::MarvinMolBase().

◆ hasAtomBondBlocks()

bool RDKit::MarvinDataSgroup::hasAtomBondBlocks ( ) const
overridevirtual

Implements RDKit::MarvinMolBase.

◆ parseMoleculeSpecific()

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

Reimplemented from RDKit::MarvinMolBase.

◆ role()

std::string RDKit::MarvinDataSgroup::role ( ) const
overridevirtual

Implements RDKit::MarvinMolBase.

◆ toPtree()

ptree RDKit::MarvinDataSgroup::toPtree ( ) const
overridevirtual

Reimplemented from RDKit::MarvinMolBase.

◆ toString()

std::string RDKit::MarvinDataSgroup::toString ( ) const
overridevirtual

Implements RDKit::MarvinMolBase.

Member Data Documentation

◆ context

std::string RDKit::MarvinDataSgroup::context

Definition at line 378 of file MarvinDefs.h.

◆ fieldData

std::string RDKit::MarvinDataSgroup::fieldData

Definition at line 384 of file MarvinDefs.h.

◆ fieldName

std::string RDKit::MarvinDataSgroup::fieldName

Definition at line 379 of file MarvinDefs.h.

◆ placement

std::string RDKit::MarvinDataSgroup::placement

Definition at line 380 of file MarvinDefs.h.

◆ queryOp

std::string RDKit::MarvinDataSgroup::queryOp

Definition at line 383 of file MarvinDefs.h.

◆ queryType

std::string RDKit::MarvinDataSgroup::queryType

Definition at line 382 of file MarvinDefs.h.

◆ units

std::string RDKit::MarvinDataSgroup::units

Definition at line 385 of file MarvinDefs.h.

◆ unitsDisplayed

std::string RDKit::MarvinDataSgroup::unitsDisplayed

Definition at line 381 of file MarvinDefs.h.

◆ x

double RDKit::MarvinDataSgroup::x

Definition at line 386 of file MarvinDefs.h.

◆ y

double RDKit::MarvinDataSgroup::y

Definition at line 387 of file MarvinDefs.h.

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