OBBond Class Reference

Bond class. More...

#include <openbabel/bond.h>

Inheritance diagram for OBBond:

List of all members.

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	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	SetLength (double length)
void	Set (int index, OBAtom *begin, OBAtom *end, int order, int flags)
void	SetKSingle ()
void	SetKDouble ()
void	SetKTriple ()
void	SetAromatic ()
void	SetWedge ()
void	SetHash ()
void	SetWedgeOrHash ()
void	SetUp ()
void	SetDown ()
void	SetInRing (bool set=true)
void	SetClosure ()
void	UnsetHash ()
void	UnsetWedge ()
void	UnsetUp ()
void	UnsetDown ()
void	UnsetAromatic ()
void	UnsetKekule ()
Bond data request methods
unsigned int	GetIdx () const
unsigned long	GetId () 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 () const
double	GetLength () const
unsigned int	GetNbrAtomIdx (OBAtom *ptr)
OBRing *	FindSmallestRing () const
property request methods
bool	IsAromatic () const
bool	IsInRing () const
bool	IsRotor ()
bool	IsAmide ()
bool	IsPrimaryAmide ()
bool	IsSecondaryAmide ()
bool	IsTertiaryAmide ()
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	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

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.

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

(

)

Constructor.

~OBBond

(

)

[virtual]

Destructor.

---

Member Function Documentation

bool HasFlag

(

int

flag

)

const [inline, protected]

Returns:

True id the flag is set.

Referenced by OBBond::IsAromatic(), OBBond::IsClosure(), OBBond::IsDouble(), OBBond::IsInRing(), OBBond::IsSingle(), and OBBond::IsTriple().

void SetFlag

(

int

flag

)

[inline, protected]

Sets the bitwise flag

Referenced by OBBond::Set().

void UnsetFlag

(

int

flag

)

[inline, protected]

Unsets the bitwise flag

Referenced by OBBond::SetBondOrder().

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(), OBMol::NewBond(), and OBBond::Set().

void SetId

(

unsigned long

id

)

[inline]

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

void SetBO

(

int

order

)

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

Deprecated:

Use SetBondOrder() instead.

Referenced by OBChemTsfm::Apply(), OBBondTyper::AssignFunctionalGroupBonds(), OBMol::ConvertDativeBonds(), OBMol::Kekulize(), OBMol::NewPerceiveKekuleBonds(), and OBMol::start_kekulize().

void SetBondOrder

(

int

order

)

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

Referenced by OpenBabel::alternate(), OBBuilder::Connect(), OBBond::Set(), and OBBond::SetBO().

void SetBegin

(

OBAtom *

begin

)

[inline]

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

Referenced by OBBuilder::Connect(), and OBBond::Set().

void SetEnd

(

OBAtom *

end

)

[inline]

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

Referenced by OBBuilder::Connect(), and OBBond::Set().

void SetParent

(

OBMol *

ptr

)

[inline]

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

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

void SetLength	(	OBAtom *	fixed,
		double	length
	)

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

Referenced by OBAtom::HtoMethyl(), and OBBond::SetLength().

void SetLength

(

double

length

)

Change the bond length to length, moving both atoms halfway

Since:

version 2.2

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().

void SetKSingle

(

)

Deprecated:

Use SetBondOrder() instead

Referenced by OpenBabel::CorrectBadResonanceForm(), OBMol::NewPerceiveKekuleBonds(), OBMol::PerceiveKekuleBonds(), and OBBond::SetBondOrder().

void SetKDouble

(

)

Deprecated:

Use SetBondOrder() instead

Referenced by OpenBabel::CorrectBadResonanceForm(), OBMol::PerceiveKekuleBonds(), OBBond::SetBondOrder(), and OBMol::start_kekulize().

void SetKTriple

(

)

Deprecated:

Use SetBondOrder() instead

Referenced by OBMol::PerceiveKekuleBonds(), and OBBond::SetBondOrder().

void SetAromatic

(

)

[inline]

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

Referenced by OBMol::AddBond(), and OBBond::SetBondOrder().

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 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 SetWedgeOrHash

(

)

[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

(

bool

set = true

)

[inline]

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

Referenced by OBMol::EndModify(), and OpenBabel::FindRings().

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()

Referenced by 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.

Referenced by OBAromaticTyper::AssignAromaticFlags(), and OBBond::SetBondOrder().

void UnsetKekule

(

)

[inline]

Clear all Kekule information for the bond.

unsigned int GetIdx

(

)

const [inline]

Returns:

The unique bond index in a molecule.

Referenced by OpenBabel::atomRingToBondRing(), OBMolBondBFSIter::CurrentDepth(), OBMol::DeleteBond(), OpenBabel::expand_kekulize_lssr(), OpenBabel::FindRings(), OBResidue::GetBonds(), OBBond::IsClosure(), OBRotorList::IsFixedBond(), OpenBabel::KekulePropagate(), OBMolBondBFSIter::OBMolBondBFSIter(), OBMolBondBFSIter::operator++(), and OpenBabel::potentialAromaticBonds().

unsigned long GetId

(

)

const [inline]

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

unsigned int GetBO

(

)

const [inline]

Returns:

The bond order for the bond

Deprecated:

Use GetBondOrder() as this method may be removed.

Referenced by OBMol::AddBond(), OBResidueData::AssignBonds(), OBAtom::BOSum(), OBBuilder::Build(), OBMol::ConvertDativeBonds(), OBAtom::CountBondsOfOrder(), OBDepict::DrawMolecule(), OBSmartsMatcher::EvalBondExpr(), OpenBabel::ExpandKekule(), OBBond::GetEquibLength(), OBAtom::HasBondOfOrder(), OBAtom::HasNonSingleBond(), OBAtom::IsAmideNitrogen(), OBBond::IsCarbonyl(), OBBond::IsEster(), OBMol::operator+=(), OBMol::PerceiveKekuleBonds(), and OBMol::start_kekulize().

unsigned int GetBondOrder

(

)

const [inline]

Returns:

The bond order for the bond

Referenced by OBBuilder::Build(), OBBond::IsAmide(), OBBond::IsDouble(), OBBond::IsPrimaryAmide(), OBBond::IsSecondaryAmide(), OBBond::IsSingle(), OBBond::IsTertiaryAmide(), OBBond::IsTriple(), OBQueryBond::Matches(), and OBBuilder::Swap().

unsigned int GetFlags

(

)

const [inline]

Returns:

The set of property flags defined for this bond.

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

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(), OpenBabel::DetermineFRJ(), OpenBabel::FindRings(), OBRotorRules::GetRotorIncrements(), OBRing::IsMember(), OBMol::operator+=(), OBMol::PerceiveKekuleBonds(), OBRotorList::RemoveSymVals(), OBAromaticTyper::SelectRootAtoms(), OBRotorList::SetEvalAtoms(), and OBMol::start_kekulize().

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(), OpenBabel::DetermineFRJ(), OBRotorRules::GetRotorIncrements(), OBRing::IsMember(), OBMol::operator+=(), OBMol::PerceiveKekuleBonds(), OBRotorList::RemoveSymVals(), OBRotorList::SetEvalAtoms(), and OBMol::start_kekulize().

OBAtom* GetBeginAtom

(

)

[inline]

Returns:

The "beginning" atom for this bond

Referenced by OBRingSearch::AddRingFromClosure(), OBGastChrg::AssignPartialCharges(), OpenBabel::CalcSignedVolume(), OBMol::DeleteBond(), OpenBabel::expand_kekulize_lssr(), OpenBabel::expandKekulize(), OpenBabel::FindRings(), OBMol::FindTorsions(), OBBond::GetEquibLength(), OBBond::GetLength(), OBBuilder::GetNewBondVector(), OBRotorRules::GetRotorIncrements(), OBAtom::IsConnected(), OBRotorList::IsFixedBond(), OBMolBondBFSIter::OBMolBondBFSIter(), OBMolBondBFSIter::operator++(), OBBond::SetLength(), and OBMol::start_kekulize().

const OBAtom* GetBeginAtom

(

)

const [inline]

OBAtom* GetEndAtom

(

)

[inline]

Returns:

The "end" atom for this bond

Referenced by OBRingSearch::AddRingFromClosure(), OBGastChrg::AssignPartialCharges(), OpenBabel::CalcSignedVolume(), OBMol::DeleteBond(), OpenBabel::expand_kekulize_lssr(), OpenBabel::expandKekulize(), OpenBabel::FindRings(), OBMol::FindTorsions(), OBBond::GetEquibLength(), OBBond::GetLength(), OBRotorRules::GetRotorIncrements(), OBAtom::IsConnected(), OBRotorList::IsFixedBond(), OBMolBondBFSIter::OBMolBondBFSIter(), OBMolBondBFSIter::operator++(), OBBond::SetLength(), and OBMol::start_kekulize().

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

Referenced by OBMol::ConvertDativeBonds(), OBAtom::CountFreeOxygens(), OBAtom::GetBond(), OBResidue::GetBonds(), OpenBabel::GetDFFVector(), OBMol::GetGTDVector(), OBAtom::GetHeteroValence(), OBAtom::GetHvyValence(), OBBuilder::GetNewBondVector(), OBAtom::IsAmideNitrogen(), OBAtom::IsCarboxylOxygen(), OBAtom::IsHbondDonorH(), OBAtom::IsNitroOxygen(), OBAtom::IsNonPolarHydrogen(), OBAtom::IsOneFour(), OBAtom::IsOneThree(), OBAtom::IsPhosphateOxygen(), OBAtom::IsPolarHydrogen(), OBAtom::IsSulfateOxygen(), OBMol::NewPerceiveKekuleBonds(), and OBBond::SetLength().

OBMol* GetParent

(

)

[inline]

Returns:

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

Referenced by OBBond::FindSmallestRing(), OBBond::IsAromatic(), OBBond::IsClosure(), OBBond::IsDouble(), OBBond::IsInRing(), OBBond::IsKDouble(), OBBond::IsKSingle(), OBBond::IsKTriple(), OBBond::IsSingle(), and OBBond::IsTriple().

double GetEquibLength

(

)

const

Returns:

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

double GetLength

(

)

const

Returns:

The current length of this bond in Angstroms

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

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 OBMol::ContigFragList(), OBMol::FindLargestFragment(), OpenBabel::FindRings(), OpenBabel::GetDFFVector(), and OBMol::GetGTDVector().

OBRing * FindSmallestRing

(

)

const

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

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 OBBuilder::Build(), OBSmartsMatcher::EvalBondExpr(), OBBond::GetEquibLength(), and OBQueryBond::Matches().

bool IsInRing

(

)

const

Returns:

Is the bond part of a ring?

Referenced by OBAtom::CountRingBonds(), OBSmartsMatcher::EvalBondExpr(), OBBond::IsRotor(), OBMol::NewPerceiveKekuleBonds(), OBMol::PerceiveKekuleBonds(), OBBuilder::Swap(), and OBAromaticTyper::TraverseCycle().

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

Referenced by OBMol::NumRotors().

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.

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.

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.

bool IsTertiaryAmide

(

)

Returns:

Is the bond a teriary amide (i.e., between a carbonyl C and a NH0)? This function is new since release 2.3.

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?

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

bool IsSingle

(

)

Returns:

Is the bond a single bond?

bool IsDouble

(

)

Returns:

Is the bond is a double bond?

Referenced by OBMol::NewPerceiveKekuleBonds().

bool IsTriple

(

)

Returns:

Is the bond is a triple bond?

bool IsKSingle

(

)

Deprecated:

Use IsSingle() instead

Referenced by OBMol::Kekulize().

bool IsKDouble

(

)

Deprecated:

Use IsDouble() instead

Referenced by OpenBabel::GetCurrentValence(), OBAtom::KBOSum(), OBMol::Kekulize(), and OpenBabel::ValenceSum().

bool IsKTriple

(

)

Deprecated:

Use IsTriple() instead

Referenced by OpenBabel::GetCurrentValence(), OBAtom::KBOSum(), and OBMol::Kekulize().

bool IsClosure

(

)

Returns:

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

Referenced by OBMol::FindLSSR(), OBMol::FindSSSR(), and OBAromaticTyper::SelectRootAtoms().

bool IsUp

(

)

[inline]

Returns:

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

Referenced by OBSmartsMatcher::EvalBondExpr().

bool IsDown

(

)

[inline]

Returns:

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

Referenced by OBSmartsMatcher::EvalBondExpr().

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 OpenBabel::CalcSignedVolume(), and OBBuilder::GetNewBondVector().

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 OpenBabel::CalcSignedVolume(), and OBBuilder::GetNewBondVector().

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

bool IsCisOrTrans

(

)

const [inline]

Returns:

True if this bond is either a cis or trans.

Since:

version 2.3

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, OBReaction, and OBResidue.

Referenced by OBResidue::Clear(), OBMol::Clear(), and OBAtom::Clear().

virtual OBBase* DoTransformations	(	const std::map< std::string, std::string > *	,
		OBConversion *
	)			[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() Base type does nothing

Reimplemented in OBMol.

static const char* ClassDescription

(

)

[inline, static, inherited]

Returns:

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

Reimplemented in OBMol, and OBReaction.

T* CastAndClear

(

bool

clear = true

)

[inline, inherited]

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

virtual const char* GetTitle

(

bool

replaceNewlines = true

)

const [inline, virtual, inherited]

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

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

virtual void SetTitle

(

const char *

)

[inline, virtual, inherited]

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

bool HasData

(

const std::string &

s

)

[inherited]

Returns:

whether the generic attribute/value pair exists

Referenced by OBMol::AddAtom(), OBDepict::DrawMolecule(), OBMol::FindAngles(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetLSSR(), OBForceField::GetPartialCharges(), OBMol::GetSSSR(), OBBase::HasData(), OBDescriptor::MatchPairData(), OBMol::NewAtom(), OBMol::operator=(), OBMoleculeFormat::ReadChemObjectImpl(), and OBMol::SetEnergies().

bool HasData

(

const char *

s

)

[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.

Referenced by OBMol::AddAtom(), OBMol::BeginModify(), OpenBabel::CanonicalLabels(), OBDescriptor::DeleteProperties(), OBMol::EndModify(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::NewAtom(), OBMol::RenumberAtoms(), and OBForceField::Setup().

void DeleteData

(

OBGenericData *

gd

)

[inherited]

Delete the given generic data from this object.

void DeleteData

(

std::vector< OBGenericData * > &

vg

)

[inherited]

Delete all of the given generic data from this object.

bool DeleteData

(

const std::string &

s

)

[inherited]

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

void SetData

(

OBGenericData *

d

)

[inline, inherited]

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

Referenced by OBMol::AddBond(), OBGastChrg::AssignPartialCharges(), OpenBabel::CalcSignedVolume(), OBMol::DoTransformations(), OBAtom::Duplicate(), AliasData::Expand(), OBMol::FindAngles(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetFormula(), OBMol::GetLSSR(), OBMol::GetNextFragment(), OBForceField::GetPartialCharges(), OBMol::GetSSSR(), OBMoleculeFormat::MakeCombinedMolecule(), OBMol::operator=(), OBDescriptor::PredictAndSave(), OBMol::SetEnergies(), and OBMol::SetFormula().

void CloneData

(

OBGenericData *

d

)

[inherited]

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

Since:

version 2.2

Referenced by OBMol::AddBond().

size_t 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

Referenced by OpenBabel::CalcSignedVolume(), OpenBabel::CorrectChirality(), OBDepict::DrawMolecule(), AliasData::Expand(), OBDescriptor::FilterCompare(), OpenBabel::GetAtomSymClass(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetNextFragment(), OBForceField::GetPartialCharges(), OBDescriptor::GetValues(), OBMoleculeFormat::MakeCombinedMolecule(), OBMolAngleIter::OBMolAngleIter(), OBMolRingIter::OBMolRingIter(), OBMolTorsionIter::OBMolTorsionIter(), OBMol::operator=(), and OBDescriptor::PredictAndSave().

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

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

std::vector<OBGenericData*>& GetData

(

)

[inline, inherited]

Returns:

all data, suitable for iterating

Referenced by OBMol::BeginModify(), OBMol::DoTransformations(), OBBase::GetData(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetFormula(), OBMol::GetLSSR(), OBMol::GetSSSR(), OBMol::SetEnergies(), and OBMol::SetFormula().

std::vector< OBGenericData * > GetData

(

DataOrigin

source

)

[inherited]

Returns:

all data with a specific origin, suitable for iterating

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(), OBBuilder::CorrectStereoAtoms(), and OBBuilder::CorrectStereoBonds().

OBDataIterator BeginData

(

)

[inline, inherited]

Returns:

An iterator pointing to the beginning of the data

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

OBDataIterator EndData

(

)

[inline, inherited]

Returns:

An iterator pointing to the end of the data

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

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Member Data Documentation

unsigned int _idx [protected]

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

Referenced by OBBond::OBBond().

OBMol* _parent [protected]

The molecule which contains me (if any).

OBAtom* _bgn [protected]

I connect one node.

Referenced by OBBond::IsAmide(), OBBond::IsCarbonyl(), OBBond::IsDoubleBondGeometry(), OBBond::IsEster(), OBBond::IsPrimaryAmide(), OBBond::IsRotor(), OBBond::IsSecondaryAmide(), OBBond::IsTertiaryAmide(), OBBond::OBBond(), and OBBond::SetBondOrder().

OBAtom* _end [protected]

to another node

Referenced by OBBond::IsAmide(), OBBond::IsCarbonyl(), OBBond::IsDoubleBondGeometry(), OBBond::IsEster(), OBBond::IsPrimaryAmide(), OBBond::IsRotor(), OBBond::IsSecondaryAmide(), OBBond::IsTertiaryAmide(), OBBond::OBBond(), and OBBond::SetBondOrder().

char _order [protected]

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

Referenced by OBBond::IsRotor(), OBBond::OBBond(), and OBBond::SetBondOrder().

unsigned short int _flags [protected]

Any flags for this bond.

Referenced by OBBond::IsKDouble(), OBBond::IsKSingle(), OBBond::IsKTriple(), OBBond::OBBond(), OBBond::SetKDouble(), OBBond::SetKSingle(), and OBBond::SetKTriple().

unsigned long _id [protected]

unique id

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.

Referenced by OBBase::Clear(), OBBase::CloneData(), OBBase::DeleteData(), OBAtom::Duplicate(), OBBase::GetAllData(), OBBase::GetData(), OBBase::HasData(), OBBond::OBBond(), OBMol::OBMol(), and OBResidue::OBResidue().

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

• bond.h
• bond.cpp