OBBond Class Reference

Bond class. More...

#include <openbabel/bond.h>

Inheritance diagram for OBBond:
OBBase

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 OBBaseDoTransformations (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
OBAtomGetBeginAtom ()
const OBAtomGetBeginAtom () const
OBAtomGetEndAtom ()
const OBAtomGetEndAtom () const
OBAtomGetNbrAtom (OBAtom *ptr)
OBMolGetParent ()
double GetEquibLength () const
double GetLength () const
unsigned int GetNbrAtomIdx (OBAtom *ptr)
OBRingFindSmallestRing () 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
OBGenericDataGetData (const unsigned int type)
OBGenericDataGetData (const std::string &)
OBGenericDataGetData (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.
void SetFlag ( int  flag ) [inline, protected]

Sets the bitwise flag

void UnsetFlag ( int  flag ) [inline, protected]

Unsets the bitwise flag

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().

void SetId ( unsigned long  id ) [inline]
void SetBO ( int  order )
void SetBondOrder ( int  order )

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

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

void SetBegin ( OBAtom begin ) [inline]

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

Referenced by OBBuilder::Connect().

void SetEnd ( OBAtom end ) [inline]

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

Referenced by OBBuilder::Connect().

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().

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:
idxThe unique bond index for this bond (inside an OBMol)
beginThe 'beginning' atom for the bond
endThe 'end' atom for the bond
orderThe bond order (i.e., 1 = single, 2 = double... 5 = aromatic)
flagsAny initial property flags

Referenced by OBMol::AddBond().

void SetKTriple (  )
void SetAromatic (  ) [inline]

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

Referenced by OBMol::AddBond().

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().

void UnsetKekule (  ) [inline]

Clear all Kekule information for the bond.

unsigned long GetId (  ) const [inline]
unsigned int GetBondOrder (  ) const [inline]
Returns:
The bond order for the bond

Referenced by OBBuilder::Build(), OpenBabel::isFerroceneBond(), 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+=().

const OBAtom* GetBeginAtom (  ) const [inline]
const OBAtom* GetEndAtom (  ) const [inline]
OBMol* GetParent (  ) [inline]
Returns:
The enclosing OBMol for this bond, or NULL if none is defined.
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(), and OBBuilder::CorrectStereoAtoms().

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(), and OBQueryBond::Matches().

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 (  )
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 IsKTriple (  )
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().

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 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]
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 CloneData ( OBGenericData d ) [inherited]

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

Since:
version 2.2
size_t DataSize (  ) const [inline, inherited]
Returns:
the number of OBGenericData items attached to this molecule.
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::GetEnergies(), OBMol::GetEnergy(), and OBMol::SetEnergies().

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

OBDataIterator EndData (  ) [inline, inherited]
Returns:
An iterator pointing to the end of the data

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


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.

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 OBMol::OBMol().


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