#include <openbabel/bond.h>

Inheritance diagram for OBBond:

Public Types
enum	Flag { Aromatic = (1<<1), Ring = (1<<4), Closure = (1<<10) }

enum	StereoFlag { Wedge = (1<<2), Hash = (1<<3), WedgeOrHash = (1<<11), CisOrTrans = (1<<12) }

Public Member Functions
	OBBond ()

virtual	~OBBond ()

virtual bool	Clear ()

virtual OBBase *	DoTransformations (const std::map< std::string, std::string > , OBConversion )

template<class T >
T *	CastAndClear (bool clear=true)

virtual const char *	GetTitle (bool replaceNewlines=true) const

virtual void	SetTitle (const char *)

Bond modification methods
void	SetIdx (int idx)

void	SetId (unsigned long id)

void	SetBondOrder (int order)

void	SetBegin (OBAtom *begin)

void	SetEnd (OBAtom *end)

void	SetParent (OBMol *ptr)

void	SetLength (OBAtom *fixed, double length)

void	SetLength (double length)

void	Set (int index, OBAtom begin, OBAtom end, int order, int flags)

void	SetAromatic (bool value=true)

void	SetWedge (bool value=true)

void	SetHash (bool value=true)

void	SetWedgeOrHash (bool value=true)

void	SetInRing (bool value=true)

void	SetClosure (bool value=true)

Bond data request methods
unsigned int	GetIdx () const

unsigned long	GetId () const

unsigned int	GetBondOrder () const

unsigned int	GetFlags () const

unsigned int	GetBeginAtomIdx () const

unsigned int	GetEndAtomIdx () const

OBAtom *	GetBeginAtom ()

const OBAtom *	GetBeginAtom () const

OBAtom *	GetEndAtom ()

const OBAtom *	GetEndAtom () const

OBAtom *	GetNbrAtom (OBAtom *ptr)

OBMol *	GetParent ()

double	GetEquibLength () const

double	GetLength () const

unsigned int	GetNbrAtomIdx (OBAtom *ptr)

OBRing *	FindSmallestRing () const

property request methods
bool	IsAromatic () const

bool	IsInRing () const

bool	IsRotor (bool includeRingBonds=false)

bool	IsAmide ()

bool	IsPrimaryAmide ()

bool	IsSecondaryAmide ()

bool	IsTertiaryAmide ()

bool	IsEster ()

bool	IsCarbonyl ()

bool	IsClosure ()

bool	IsWedge ()

bool	IsHash ()

bool	IsWedgeOrHash () const

bool	IsCisOrTrans () const

bool	IsDoubleBondGeometry ()

Generic data handling methods (via OBGenericData)
bool	HasData (const std::string &)

bool	HasData (const char *)

bool	HasData (const unsigned int type)

void	DeleteData (unsigned int type)

void	DeleteData (OBGenericData *)

void	DeleteData (std::vector< OBGenericData *> &)

bool	DeleteData (const std::string &s)

void	SetData (OBGenericData *d)

void	CloneData (OBGenericData *d)

size_t	DataSize () const

OBGenericData *	GetData (const unsigned int type)

OBGenericData *	GetData (const std::string &)

OBGenericData *	GetData (const char *)

std::vector< OBGenericData * > &	GetData ()

std::vector< OBGenericData * >	GetData (DataOrigin source)

std::vector< OBGenericData * >	GetAllData (const unsigned int type)

OBDataIterator	BeginData ()

OBDataIterator	EndData ()

Static Public Member Functions
static const char *	ClassDescription ()

Public Attributes
bool	Visit

Protected Member Functions
bool	HasFlag (int flag) const

void	SetFlag (int flag)

void	UnsetFlag (int flag)

Protected Attributes
unsigned int	_idx

OBMol *	_parent

OBAtom *	_bgn

OBAtom *	_end

char	_order

unsigned short int	_flags

unsigned long	_id

std::vector< OBGenericData * >	_vdata

Detailed Description

Bond class.

The OBBond class is straightforward in its data access and modification methods. OBBonds store pointers to the atoms on each end of the bond. In storing pointers to atoms instead of integer indices, the necessity of having to reorder bonds when atoms are shuffled, added, or delete is obviated.

While methods indicate "begin" and "end" atoms in the bond, all methods are designed to be independent of atom ordering, with the exception of stereochemically aware properties such as IsUp(), IsDown(), IsWedge, or IsHash().

Member Enumeration Documentation

◆ Flag

enum Flag

Enumerator
Aromatic	An aromatic bond (regardless of bond order)
Ring	A bond in a ring.
Closure	A bond which "closes" a ring when walking the molecular graph.

◆ StereoFlag

enum StereoFlag

Enumerator
Wedge	A solid black wedge in 2D representations – i.e., "up" from the 2D plane.
Hash	A dashed "hash" bond in 2D representations – i.e., "down" from the 2D plane.
WedgeOrHash	The bond is either wedge or hash, this is a seperate flag!
CisOrTrans	Indicates the 2D/3D coordinates are accidently cis/trans.

Constructor & Destructor Documentation

◆ OBBond()

OBBond ( )

Constructor.

◆ ~OBBond()

~OBBond ( )

virtual

Destructor.

Member Function Documentation

◆ HasFlag()

bool HasFlag ( int flag ) const

inlineprotected

Returns: True id the flag is set.

◆ SetFlag()

void SetFlag ( int flag )

inlineprotected

Sets the bitwise flag

◆ UnsetFlag()

void UnsetFlag ( int flag )

inlineprotected

Unsets the bitwise flag

◆ SetIdx()

void SetIdx ( int idx )

inline

Set the internal bond index.

Warning: This will not update the index in the parent OBMol. Intended mainly for internal use. Use with care.

Referenced by OBMol::DeleteBond(), and OBMol::NewBond().

◆ SetId()

void SetId ( unsigned long id )

inline

Referenced by OBMol::AddBond(), OBMol::NewBond(), and OBMol::operator+=().

◆ SetBondOrder()

void SetBondOrder ( int order )

Set the bond order to order (i.e., 1 = single, 2 = double, 5 = aromatic)

Referenced by OpenBabel::alternate(), OBChemTsfm::Apply(), OBBondTyper::AssignFunctionalGroupBonds(), OBBuilder::Connect(), OBMol::ConvertDativeBonds(), OBMol::ConvertZeroBonds(), and OBMol::MakeDativeBonds().

◆ SetBegin()

void SetBegin ( OBAtom * begin )

inline

Set the beginning atom of this bond to begin. Does not update begin.

Referenced by OBBuilder::Connect().

◆ SetEnd()

void SetEnd ( OBAtom * end )

inline

Set the ending atom of this bond to end. Does not update end.

Referenced by OBBuilder::Connect().

◆ SetParent()

void SetParent ( OBMol * ptr )

inline

Set the parent molecule to ptr. Does not update parent.

Referenced by OBMol::AddBond(), and OBMol::NewBond().

◆ SetLength() [1/2]

void SetLength	(	OBAtom *	fixed,
		double	length
	)

Change the bond length to length, while keeping fixed stationary.

Referenced by OBAtom::HtoMethyl().

◆ SetLength() [2/2]

void SetLength ( double length )

Change the bond length to length, moving both atoms halfway

Since: version 2.2

◆ Set()

void Set	(	int	idx,
		OBAtom *	begin,
		OBAtom *	end,
		int	order,
		int	flags
	)

Set the main bond information (i.e., when creating a bond)

Mark the main information for a bond

Parameters

idx	The unique bond index for this bond (inside an OBMol)
begin	The 'beginning' atom for the bond
end	The 'end' atom for the bond
order	The bond order (i.e., 1 = single, 2 = double... 5 = aromatic)
flags	Any initial property flags

Referenced by OBMol::AddBond().

◆ SetAromatic()

void SetAromatic ( bool value = true )

inline

Mark that this bond is aromatic. Does not update atoms or validate.

Referenced by OpenBabel::AssignOBAromaticityModel().

◆ SetWedge()

void SetWedge ( bool value = true )

inline

Mark that this bond has 2D "wedge" notation (i.e., goes in a positive Z direction from the beginning to end atoms)

Referenced by OBDepict::DrawMolecule().

◆ SetHash()

void SetHash ( bool value = true )

inline

Mark that this bond has 2D "hash" notation (i.e., goes in a negative Z direction from the beginning to end atoms)

Referenced by OBDepict::DrawMolecule().

◆ SetWedgeOrHash()

void SetWedgeOrHash ( bool value = true )

inline

Set the WedgeOrHash flag on a bond (??)

◆ SetInRing()

void SetInRing ( bool value = true )

inline

Mark that this bond is in a ring. Primarily for internal use.

Referenced by OpenBabel::FindRings().

◆ SetClosure()

void SetClosure ( bool value = true )

inline

Mark that this bond indicates a ring closure when walking the molecule.

Warning: This is for internal use only. All closure bonds are marked automatically by lazy evaluation when requesting OBBond::IsClosure()

Referenced by OpenBabel::FindRings().

◆ GetIdx()

unsigned int GetIdx ( ) const

inline

Returns: The unique bond index in a molecule.

Referenced by OpenBabel::atomRingToBondRing(), OBMolBondBFSIter::CurrentDepth(), OBMol::DeleteBond(), OpenBabel::FindRings(), OBResidue::GetBonds(), OBRotorList::IsFixedBond(), OpenBabel::NeedsDoubleBond(), OBMolBondBFSIter::OBMolBondBFSIter(), OBMolBondBFSIter::operator++(), and OBChainsParser::PerceiveChains().

◆ GetId()

unsigned long GetId ( ) const

inline

Referenced by OBDepict::AddAtomLabels(), OBBuilder::CorrectStereoBonds(), OBMol::DeleteBond(), OBDepict::DrawMolecule(), and OpenBabel::intToStr().

◆ GetBondOrder()

unsigned int GetBondOrder ( ) const

inline

◆ GetFlags()

unsigned int GetFlags ( ) const

inline

Returns: The set of property flags defined for this bond.

Referenced by OBMol::AddBond(), AliasData::Expand(), and OBMol::operator+=().

◆ GetBeginAtomIdx()

unsigned int GetBeginAtomIdx ( ) const

inline

Returns: The atom index for the end atom in this bond (from OBAtom::GetIdx()

Referenced by OBMol::AddBond(), OBRingSearch::AddRingFromClosure(), OpenBabel::alternate(), OBAromaticTyper::AssignAromaticFlags(), OBBuilder::CorrectStereoAtoms(), OBRotorRules::GetRotorIncrements(), OpenBabel::intToStr(), OBRing::IsMember(), OBMol::operator+=(), OBChainsParser::PerceiveChains(), OBRotorList::SetEvalAtoms(), and OBConformerSearch::Setup().

◆ GetEndAtomIdx()

unsigned int GetEndAtomIdx ( ) const

inline

Returns: The atom index for the end atom in this bond (from OBAtom::GetIdx()

Referenced by OBMol::AddBond(), OBRingSearch::AddRingFromClosure(), OpenBabel::alternate(), OBBuilder::CorrectStereoAtoms(), OBRotorRules::GetRotorIncrements(), OpenBabel::intToStr(), OBRing::IsMember(), OBMol::operator+=(), OBChainsParser::PerceiveChains(), OBRotorList::SetEvalAtoms(), and OBConformerSearch::Setup().

◆ GetBeginAtom() [1/2]

OBAtom* GetBeginAtom ( )

inline

Returns: The "beginning" atom for this bond

Referenced by OBRingSearch::AddRingFromClosure(), OBChemTsfm::Apply(), OBGastChrg::AssignPartialCharges(), OBMol::ConvertZeroBonds(), OBMol::DeleteBond(), OpenBabel::findMetalloceneBonds(), OBMol::FindTorsions(), OBBuilder::GetNewBondVector(), OBRotorRules::GetRotorIncrements(), OBAtom::IsConnected(), OpenBabel::isFerroceneBond(), OBRotorList::IsFixedBond(), OpenBabel::OBBondGetSmallestRingSize(), OBMolBondBFSIter::OBMolBondBFSIter(), OBMolBondBFSIter::operator++(), and OBRotorList::RemoveSymVals().

◆ GetBeginAtom() [2/2]

const OBAtom* GetBeginAtom ( ) const

inline

◆ GetEndAtom() [1/2]

OBAtom* GetEndAtom ( )

inline

Returns: The "end" atom for this bond

Referenced by OBRingSearch::AddRingFromClosure(), OBChemTsfm::Apply(), OBGastChrg::AssignPartialCharges(), OBMol::ConvertZeroBonds(), OBMol::DeleteBond(), OpenBabel::findMetalloceneBonds(), OBMol::FindTorsions(), OBRotorRules::GetRotorIncrements(), OBAtom::IsConnected(), OpenBabel::isFerroceneBond(), OBRotorList::IsFixedBond(), OpenBabel::OBBondGetSmallestRingSize(), OBMolBondBFSIter::OBMolBondBFSIter(), OBMolBondBFSIter::operator++(), and OBRotorList::RemoveSymVals().

◆ GetEndAtom() [2/2]

const OBAtom* GetEndAtom ( ) const

inline

◆ GetNbrAtom()

OBAtom* GetNbrAtom ( OBAtom * ptr )

inline

Returns: The neighboring atom to ptr (i.e., the end if ptr is the start)

Warning: If ptr is not part of the bond, the beginning atom will always be returned

Referenced by OpenBabel::ComparePairSecond(), OBMol::ConnectTheDots(), OBMol::ConvertDativeBonds(), OBAtom::CountFreeOxygens(), OBAtom::CountFreeSulfurs(), OpenBabel::FindRings(), OBAtom::GetBond(), OBResidue::GetBonds(), OpenBabel::GetDFFVector(), OBMol::GetGTDVector(), OBAtom::GetHeteroDegree(), OBAtom::GetHvyDegree(), OBBuilder::GetNewBondVector(), OBAtom::IsAmideNitrogen(), OBAtom::IsCarboxylOxygen(), OBAtom::IsHbondDonorH(), OBAtom::IsNitroOxygen(), OBAtom::IsNonPolarHydrogen(), OBAtom::IsOneFour(), OBAtom::IsOneThree(), OBAtom::IsPhosphateOxygen(), OBAtom::IsPolarHydrogen(), OBAtom::IsSulfateOxygen(), OpenBabel::IsSulfoneOxygen(), and OBMol::MakeDativeBonds().

◆ GetParent()

OBMol* GetParent ( )

inline

Returns: The enclosing OBMol for this bond, or NULL if none is defined.

Referenced by OpenBabel::OBBondGetSmallestRingSize().

◆ GetEquibLength()

double GetEquibLength ( ) const

Returns: The expected "equilibrium" length based on the covalent radii and bond order Length is given in Angstroms

◆ GetLength()

double GetLength ( ) const

Returns: The current length of this bond in Angstroms

Referenced by OBMol::ConnectTheDots(), and OBBuilder::CorrectStereoAtoms().

◆ GetNbrAtomIdx()

unsigned int GetNbrAtomIdx ( OBAtom * ptr )

inline

Returns: The index to the neighboring atom of ptr (i.e., the end if ptr is the start)

Warning: If ptr is not part of the bond, the beginning atom index will always be returned

Referenced by OpenBabel::ComparePairSecond(), OBMol::ContigFragList(), OBMol::FindLargestFragment(), OpenBabel::GetDFFVector(), and OBMol::GetGTDVector().

◆ FindSmallestRing()

OBRing * FindSmallestRing ( ) const

Find the smallest ring containing this bond (returns a NULL pointer if none exists)

◆ IsAromatic()

bool IsAromatic ( ) const

Returns: Is the bond aromatic? (Note that the two atoms of the bond may be aromatic, but not the bond)

Referenced by OpenBabel::ComparePairSecond(), OBSmartsMatcher::EvalBondExpr(), OpenBabel::findMetalloceneBonds(), and OBQueryBond::Matches().

◆ IsInRing()

bool IsInRing ( ) const

Returns: Is the bond part of a ring?

Referenced by OBAromaticTyper::AssignAromaticFlags(), OBBuilder::Connect(), OBBuilder::CorrectStereoAtoms(), OBAtom::CountRingBonds(), OBSmartsMatcher::EvalBondExpr(), OpenBabel::OBBondGetSmallestRingSize(), and OBBuilder::Swap().

◆ IsRotor()

bool IsRotor ( bool includeRingBonds = false )

Returns: Is the bond a rotatable bond? Currently, this function classifies any bond with at least one heavy atom, no sp-hybrid atoms (e.g., a triple bond somewhere) not in a ring as a potential rotor if includeRingsBonds is false. If true, rotors in rings with more than 3 atoms may be included. No other bond typing is attempted. For more detailed rotor detection, check the OBRotorList and OBRotorRules classes

◆ IsAmide()

bool IsAmide ( )

Returns: Is the bond an amide link (i.e., between a carbonyl C and a N)? No distinction is made between primary, secondary, and tertiary amides.

◆ IsPrimaryAmide()

bool IsPrimaryAmide ( )

Returns: Is the bond a primary amide (i.e., between carbonyl C and a NH2)? In versions prior to 2.3, this function incorrectly identified secondary amides.

◆ IsSecondaryAmide()

bool IsSecondaryAmide ( )

Returns: Is the bond a secondary amide (i.e., between a carbonyl C and a NH1)? In versions prior to 2.3, this function incorrectly identified tertiary amides.

◆ IsTertiaryAmide()

bool IsTertiaryAmide ( )

Returns: Is the bond a teriary amide (i.e., between a carbonyl C and a NH0)?

Since: version 2.3.

◆ IsEster()

bool IsEster ( )

Returns: Is the bond an ester link (i.e., between a carbonyl C and an O)?

Referenced by OBAtom::IsHbondAcceptor().

◆ IsCarbonyl()

bool IsCarbonyl ( )

Returns: Is the bond a carbonyl C=O?

Referenced by OBBond::IsAmide(), OBBond::IsEster(), OBBond::IsPrimaryAmide(), OBBond::IsSecondaryAmide(), and OBBond::IsTertiaryAmide().

◆ IsClosure()

bool IsClosure ( )

Returns: Does this bond "close" a ring when walking the molecular graph?

Referenced by OBAromaticTyper::AssignAromaticFlags(), OpenBabel::DetermineFRJ(), OBMol::FindLSSR(), and OBMol::FindSSSR().

◆ IsWedge()

bool IsWedge ( )

inline

Returns: Whether this bond is a "wedge" in 2D representations (i.e., goes in a positive Z direction from the beginning to end atoms)

Referenced by OBBuilder::GetNewBondVector(), and OpenBabel::intToStr().

◆ IsHash()

bool IsHash ( )

inline

Returns: Whether this bond is a "hash" in 2D representations (i.e., goes in a negative Z direction from the beginning to end atoms)

Referenced by OBBuilder::GetNewBondVector(), and OpenBabel::intToStr().

◆ IsWedgeOrHash()

bool IsWedgeOrHash ( ) const

inline

Returns: True if this bond is either a wedge or hash.

Note: : This is a seperate bond type

Since: version 2.3

◆ IsCisOrTrans()

bool IsCisOrTrans ( ) const

inline

Returns: True if this bond is either a cis or trans.

Since: version 2.3

◆ IsDoubleBondGeometry()

bool IsDoubleBondGeometry ( )

Returns: whether the geometry around this bond "looks" unsaturated

This method checks if the geometry around this bond looks unsaturated by measuring the torsion angles formed by all connected atoms X-start=end-Y and checking that they are close to 0 or 180 degrees

◆ Clear()

bool Clear ( void )

virtualinherited

Clear any and all data associated with this object.

This method can be called by OBConversion::Read() before reading data. Derived classes should be sure to call OBBase::Clear() to remove inherited generic data.

Returns: Whether the call was successful.

Since: version 2.1.

Reimplemented in OBMol, OBAtom, OBReaction, and OBResidue.

Referenced by OBResidue::Clear().

◆ DoTransformations()

virtual OBBase* DoTransformations	(	const std::map< std::string, std::string > *	,
		OBConversion *
	)

inlinevirtualinherited

Perform a set of transformations specified by the user

Typically these are program options to filter or modify an object For example, see OBMol::DoTransformations() and OBMol::ClassDescription() Base type does nothing

Reimplemented in OBMol.

◆ ClassDescription()

static const char* ClassDescription ( )

inlinestaticinherited

Returns: A list of descriptions of command-line options for DoTransformations()

◆ CastAndClear()

T* CastAndClear ( bool clear = true )

inlineinherited

By default clears the object. Called from ReadMolecule of most format classes.

◆ GetTitle()

virtual const char* GetTitle ( bool replaceNewlines = true ) const

inlinevirtualinherited

Base type does nothing Made virtual around r3535 to simplify code which passes around OBBase*.

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

◆ SetTitle()

virtual void SetTitle ( const char * )

inlinevirtualinherited

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

◆ HasData() [1/3]

bool HasData ( const std::string & s )

inherited

Returns: whether the generic attribute/value pair exists

Referenced by OBDepict::AddAtomLabels(), OBDepict::DrawMolecule(), AliasData::Expand(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBForceField::GetPartialCharges(), OBDescriptor::MatchPairData(), OBMoleculeFormat::ReadChemObjectImpl(), and OBMol::SetEnergies().

◆ HasData() [2/3]

bool HasData ( const char * s )

inherited

Returns: whether the generic attribute/value pair exists

◆ HasData() [3/3]

bool HasData ( const unsigned int type )

inherited

Returns: whether the generic attribute/value pair exists, for a given OBGenericDataType

◆ DeleteData() [1/4]

void DeleteData ( unsigned int type )

inherited

Delete any data matching the given OBGenericDataType.

Referenced by OpenBabel::CanonicalLabels(), OBDescriptor::DeleteProperties(), OpenBabel::DeleteStereoOnAtom(), and OBMol::RenumberAtoms().

◆ DeleteData() [2/4]

void DeleteData ( OBGenericData * gd )

inherited

Delete the given generic data from this object.

◆ DeleteData() [3/4]

void DeleteData ( std::vector< OBGenericData *> & vg )

inherited

Delete all of the given generic data from this object.

◆ DeleteData() [4/4]

bool DeleteData ( const std::string & s )

inherited

Deletes the generic data with the specified attribute, returning false if not found.

◆ SetData()

void SetData ( OBGenericData * d )

inlineinherited

Adds a data object; does nothing if d==NULL.

Referenced by OBGastChrg::AssignPartialCharges(), OBMol::CopySubstructure(), AliasData::Expand(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBForceField::GetPartialCharges(), OBMoleculeFormat::MakeCombinedMolecule(), OBDescriptor::PredictAndSave(), AliasData::RevertToAliasForm(), and OBMol::SetEnergies().

◆ CloneData()

void CloneData ( OBGenericData * d )

inherited

Adds a copy of a data object; does nothing if d == NULL

Since: version 2.2

Referenced by AliasData::Expand().

◆ DataSize()

size_t DataSize ( ) const

inlineinherited

Returns: the number of OBGenericData items attached to this molecule.

◆ GetData() [1/5]

OBGenericData * GetData ( const unsigned int type )

inherited

Returns: the first matching data for a given type from OBGenericDataType or NULL if nothing matches

Referenced by OBDepict::AddAtomLabels(), OBDepict::DrawMolecule(), OpenBabel::extract_thermochemistry(), OBDescriptor::FilterCompare(), OpenBabel::GetAtomSymClass(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBForceField::GetPartialCharges(), OBDescriptor::GetValues(), OpenBabel::IsSuppressibleHydrogen(), OBMoleculeFormat::MakeCombinedMolecule(), OBMolAngleIter::OBMolAngleIter(), OBMolRingIter::OBMolRingIter(), OBMolTorsionIter::OBMolTorsionIter(), and OBDescriptor::PredictAndSave().

◆ GetData() [2/5]

OBGenericData * GetData ( const std::string & s )

inherited

Returns: any data matching the given attribute name or NULL if nothing matches; the value given an attribute name

◆ GetData() [3/5]

OBGenericData * GetData ( const char * s )

inherited

Returns: any data matching the given attribute name or NULL if nothing matches; the value given an attribute name

◆ GetData() [4/5]

std::vector<OBGenericData*>& GetData ( )

inlineinherited

Returns: all data, suitable for iterating

Referenced by OBMol::GetEnergies(), OBMol::GetEnergy(), and OBMol::SetEnergies().

◆ GetData() [5/5]

std::vector< OBGenericData * > GetData ( DataOrigin source )

inherited

Returns: all data with a specific origin, suitable for iterating

◆ GetAllData()

std::vector< OBGenericData * > GetAllData ( const unsigned int type )

inherited

Returns: the all matching data for a given type from OBGenericDataType or an empty vector if nothing matches

Since: version 2.2

Referenced by OpenBabel::CanonicalLabels(), OBMol::CopySubstructure(), OBBuilder::CorrectStereoAtoms(), OBBuilder::CorrectStereoBonds(), OpenBabel::DeleteStereoOnAtom(), and OBMol::operator+=().

◆ BeginData()

OBDataIterator BeginData ( )

inlineinherited

Returns: An iterator pointing to the beginning of the data

Referenced by OBMol::AddBond(), OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), and OBMol::operator=().

◆ EndData()

OBDataIterator EndData ( )

inlineinherited

Returns: An iterator pointing to the end of the data

Referenced by OBMol::AddBond(), OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), and OBMol::operator=().

Member Data Documentation

◆ _idx

unsigned int _idx

protected

Unique edge index used by GetIdx() and SetIdx()

◆ _parent

OBMol* _parent

protected

The molecule which contains me (if any)

◆ _bgn

OBAtom* _bgn

protected

I connect one node.

◆ _end

OBAtom* _end

protected

to another node

◆ _order

char _order

protected

Bond order (1, 2, 3, 5=aromatic)

◆ _flags

unsigned short int _flags

protected

Any flags for this bond.

◆ _id

unsigned long _id

protected

unique id

◆ Visit

bool Visit

Whether this bond has been visited by a graph algorithm.

Deprecated:: Use OBBitVec objects instead to be fully thread-safe.

◆ _vdata

std::vector<OBGenericData*> _vdata

protectedinherited

Custom data.

Referenced by OBMol::OBMol().

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

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

◆ Flag

◆ StereoFlag

Constructor & Destructor Documentation

◆ OBBond()

◆ ~OBBond()

Member Function Documentation

◆ HasFlag()

◆ SetFlag()

◆ UnsetFlag()

◆ SetIdx()

◆ SetId()

◆ SetBondOrder()

◆ SetBegin()

◆ SetEnd()

◆ SetParent()

◆ SetLength() [1/2]

◆ SetLength() [2/2]

◆ Set()

◆ SetAromatic()

◆ SetWedge()

◆ SetHash()

◆ SetWedgeOrHash()

◆ SetInRing()

◆ SetClosure()

◆ GetIdx()

◆ GetId()

◆ GetBondOrder()

◆ GetFlags()

◆ GetBeginAtomIdx()

◆ GetEndAtomIdx()

◆ GetBeginAtom() [1/2]

◆ GetBeginAtom() [2/2]

◆ GetEndAtom() [1/2]

◆ GetEndAtom() [2/2]

◆ GetNbrAtom()

◆ GetParent()

◆ GetEquibLength()

◆ GetLength()

◆ GetNbrAtomIdx()

◆ FindSmallestRing()

◆ IsAromatic()

◆ IsInRing()

◆ IsRotor()

◆ IsAmide()

◆ IsPrimaryAmide()

◆ IsSecondaryAmide()

◆ IsTertiaryAmide()

◆ IsEster()

◆ IsCarbonyl()

◆ IsClosure()

◆ IsWedge()

◆ IsHash()

◆ IsWedgeOrHash()

◆ IsCisOrTrans()

◆ IsDoubleBondGeometry()

◆ Clear()

◆ DoTransformations()

◆ ClassDescription()

◆ CastAndClear()

◆ GetTitle()

◆ SetTitle()

◆ HasData() [1/3]

◆ HasData() [2/3]

◆ HasData() [3/3]

◆ DeleteData() [1/4]

◆ DeleteData() [2/4]

◆ DeleteData() [3/4]

◆ DeleteData() [4/4]

◆ SetData()

◆ CloneData()

◆ DataSize()

◆ GetData() [1/5]