Open Babel: OBBond Class Reference

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().

Constructor & Destructor Documentation

OBBond ( )

Constructor.

~OBBond ( ) [virtual]

Destructor.

Member Function Documentation

bool HasFlag ( int flag ) [inline, protected]

void SetFlag ( int flag ) [inline, protected]

void UnsetFlag ( int flag ) [inline, protected]

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.

void SetBO ( int order )

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

Deprecated:: Use SetBondOrder() instead.

void SetBondOrder ( int order )

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

void SetBegin ( OBAtom * begin ) [inline]

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

void SetEnd ( OBAtom * end ) [inline]

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

void SetParent ( OBMol * ptr ) [inline]

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

void SetLength	(	OBAtom *	fixed,
		double	length
	)

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

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

void SetKSingle ( )

Deprecated:: Use SetBondOrder() instead

void SetKDouble ( )

Deprecated:: Use SetBondOrder() instead

void SetKTriple ( )

Deprecated:: Use SetBondOrder() instead

void SetAromatic ( ) [inline]

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

void SetHash ( ) [inline]

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

void SetWedge ( ) [inline]

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

void SetUp ( ) [inline]

Mark that this bond has an "up" torsion for double-bond stereochem (i.e., "/" in SMILES notation.

void SetDown ( ) [inline]

Mark that this bond has an "down" torsion for double-bond stereochem (i.e., "\" in SMILES notation.

void SetInRing ( ) [inline]

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

void SetClosure ( ) [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()

void UnsetHash ( ) [inline]

Clear any indication of 2D "hash" notation from SetHash().

void UnsetWedge ( ) [inline]

Clear any indication of 2D "wedge" notation from SetWedge().

void UnsetUp ( ) [inline]

Clear any indication of "/" double bond stereochemistry from SetUp().

void UnsetDown ( ) [inline]

Clear any indication of "\" double bond stereochemistry from SetDown().

void UnsetAromatic ( ) [inline]

Clear all aromaticity information for the bond.

void UnsetKekule ( ) [inline]

Clear all Kekule information for the bond.

unsigned int GetIdx ( ) const [inline]

Returns:: The unique bond index in a molecule.

unsigned int GetBO ( ) const [inline]

Returns:: The bond order for the bond

Deprecated:: Use GetBondOrder() as this method may be removed.

unsigned int GetBondOrder ( ) const [inline]

Returns:: The bond order for the bond

unsigned int GetFlags ( ) const [inline]

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

unsigned int GetBeginAtomIdx ( ) const [inline]

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

unsigned int GetEndAtomIdx ( ) const [inline]

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

OBAtom* GetBeginAtom ( ) [inline]

Returns:: The "beginning" atom for this bond

const OBAtom* GetBeginAtom ( ) const [inline]

OBAtom* GetEndAtom ( ) [inline]

Returns:: The "end" atom for this bond

const OBAtom* GetEndAtom ( ) const [inline]

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

OBMol* GetParent ( ) [inline]

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

double GetEquibLength ( )

Returns:: The expected "equilibrium" length based on the covalent radii and bond order

Length is given in Angstroms

double GetLength ( )

Returns:: The current length of this bond in Angstroms

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

bool IsAromatic ( ) const

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

bool IsInRing ( ) const

Returns:: Is the bond part of a ring?

bool IsRotor ( )

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. No other bond typing is attempted. For more detailed rotor detection, check the OBRotorList and OBRotorRules classes

bool IsAmide ( )

Returns:: Is the bond an amide link (i.e., between a carbonyl C and a N)

bool IsPrimaryAmide ( )

Returns:: Is the bond an amide (i.e., between carbonyl C and a NH group)

bool IsSecondaryAmide ( )

Returns:: Is the bond an amide between a carbonyl C and a N with no hydrogens

bool IsEster ( )

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

bool IsCarbonyl ( )

Returns:: Is the bond a carbonyl C=O?

bool IsSingle ( )

Returns:: Is the bond a single bond?

bool IsDouble ( )

Returns:: Is the bond is a double bond?

bool IsTriple ( )

Returns:: Is the bond is a triple bond?

bool IsKSingle ( )

Deprecated:: Use IsSingle() instead

bool IsKDouble ( )

Deprecated:: Use IsDouble() instead

bool IsKTriple ( )

Deprecated:: Use IsTriple() instead

bool IsClosure ( )

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

bool IsUp ( ) [inline]

Returns:: Whether this is the "upper" bond in a double bond cis/trans isomer (i.e., "/" in SMILES)

bool IsDown ( ) [inline]

Returns:: Whether this is the "lower" bond in a double bond cis/trans isomer (i.e., "\" in SMILES)

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)

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)

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

bool Clear ( void ) [virtual, inherited]

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 OBAtom, OBMol, and OBResidue.

virtual OBBase* DoTransformations ( const std::map< std::string, std::string > * ) [inline, virtual, inherited]

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()

Reimplemented in OBMol.

static const char* ClassDescription ( ) [inline, static, inherited]

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

Reimplemented in OBMol.

T* CastAndClear ( bool clear = true ) [inline, inherited]

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

bool HasData ( const std::string & ) [inherited]

Returns:: whether the generic attribute/value pair exists

bool HasData ( const char * ) [inherited]

Returns:: whether the generic attribute/value pair exists

bool HasData ( const unsigned int type ) [inherited]

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

void DeleteData ( unsigned int type ) [inherited]

Delete any data matching the given OBGenericDataType.

void DeleteData ( OBGenericData * ) [inherited]

Delete the given generic data from this object.

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

Delete all of the given generic data from this object.

void SetData ( OBGenericData * d ) [inline, inherited]

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

unsigned int DataSize ( ) const [inline, inherited]

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

OBGenericData * GetData ( const unsigned int type ) [inherited]

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

OBGenericData * GetData ( const std::string & ) [inherited]

Returns:: the value given an attribute name

OBGenericData * GetData ( const char * ) [inherited]

Returns:: the value given an attribute name

std::vector<OBGenericData*>& GetData ( ) [inline, inherited]

Returns:: all data, suitable for iterating

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

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

OBDataIterator BeginData ( ) [inline, inherited]

Returns:: An iterator pointing to the beginning of the data

OBDataIterator EndData ( ) [inline, inherited]

Returns:: An iterator pointing to the end of the data

Member Data Documentation

unsigned int _idx [protected]

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

OBMol* _parent [protected]

The molecule which contains me (if any).

OBAtom* _bgn [protected]

I connect one node.

OBAtom* _end [protected]

to another node

char _order [protected]

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

unsigned short int _flags [protected]

Any flags for this bond.

bool Visit

Whether this bond has been visited by a graph algorithm.

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

std::vector<OBGenericData*> _vdata [protected, inherited]

Custom data.


Public Member Functions
	OBBond ()
virtual	~OBBond ()
virtual bool	Clear ()
virtual OBBase *	DoTransformations (const std::map< std::string, std::string > *)
template<class T>
T *	CastAndClear (bool clear=true)
Bond modification methods
void	SetIdx (int idx)
void	SetBO (int order)
void	SetBondOrder (int order)
void	SetBegin (OBAtom *begin)
void	SetEnd (OBAtom *end)
void	SetParent (OBMol *ptr)
void	SetLength (OBAtom *fixed, double length)
void	Set (int index, OBAtom begin, OBAtom end, int order, int flags)
void	SetKSingle ()
void	SetKDouble ()
void	SetKTriple ()
void	SetAromatic ()
void	SetHash ()
void	SetWedge ()
void	SetUp ()
void	SetDown ()
void	SetInRing ()
void	SetClosure ()
void	UnsetHash ()
void	UnsetWedge ()
void	UnsetUp ()
void	UnsetDown ()
void	UnsetAromatic ()
void	UnsetKekule ()
Bond data request methods
unsigned int	GetIdx () const
unsigned int	GetBO () 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 ()
double	GetLength ()
unsigned int	GetNbrAtomIdx (OBAtom *ptr)
property request methods
bool	IsAromatic () const
bool	IsInRing () const
bool	IsRotor ()
bool	IsAmide ()
bool	IsPrimaryAmide ()
bool	IsSecondaryAmide ()
bool	IsEster ()
bool	IsCarbonyl ()
bool	IsSingle ()
bool	IsDouble ()
bool	IsTriple ()
bool	IsKSingle ()
bool	IsKDouble ()
bool	IsKTriple ()
bool	IsClosure ()
bool	IsUp ()
bool	IsDown ()
bool	IsWedge ()
bool	IsHash ()
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 * > &)
void	SetData (OBGenericData *d)
unsigned int	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)
OBDataIterator	BeginData ()
OBDataIterator	EndData ()
Static Public Member Functions
static const char *	ClassDescription ()
Public Attributes
bool	Visit
Protected Member Functions
bool	HasFlag (int flag)
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
std::vector< OBGenericData * >	_vdata

OBBond Class Reference

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation