OBAtom Class Reference

Atom class. More...

#include <openbabel/atom.h>

Inheritance diagram for OBAtom:

List of all members.

Public Types

enum  StereoFlag

Public Member Functions

 OBAtom ()
virtual ~OBAtom ()
OBAtomoperator= (OBAtom &)
bool operator== (const OBAtom *other) const
void Duplicate (OBAtom *)
bool Clear ()
double GetDistance (int index)
double GetDistance (OBAtom *)
double GetAngle (int b, int c)
double GetAngle (OBAtom *b, OBAtom *c)
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 *)
Methods to set atomic information
void SetIdx (int idx)
void SetId (unsigned long id)
void SetHyb (int hyb)
void SetAtomicNum (int atomicnum)
void SetIsotope (unsigned int iso)
void SetImplicitValence (int val)
void IncrementImplicitValence ()
void DecrementImplicitValence ()
void SetFormalCharge (int fcharge)
void SetSpinMultiplicity (short spin)
void SetType (const char *type)
void SetType (const std::string &type)
void SetPartialCharge (double pcharge)
void SetVector (const vector3 &v)
void SetVector (const double x, const double y, const double z)
void SetCoordPtr (double **c)
void SetVector ()
void SetResidue (OBResidue *res)
void SetParent (OBMol *ptr)
void SetAromatic ()
void UnsetAromatic ()
void SetClockwiseStereo ()
void SetAntiClockwiseStereo ()
void SetPositiveStereo ()
void SetNegativeStereo ()
void UnsetStereo ()
void SetInRing ()
void SetChiral ()
void ClearCoordPtr ()
Methods to retrieve atomic information
int GetFormalCharge () const
unsigned int GetAtomicNum () const
unsigned short int GetIsotope () const
int GetSpinMultiplicity () const
double GetAtomicMass () const
double GetExactMass () const
unsigned int GetIdx () const
unsigned int GetIndex () const
unsigned long GetId () const
unsigned int GetCoordinateIdx () const
unsigned int GetCIdx () const
unsigned int GetValence () const
unsigned int GetHyb () const
unsigned int GetImplicitValence () const
unsigned int GetHvyValence () const
unsigned int GetHeteroValence () const
char * GetType ()
double GetX () const
double GetY () const
double GetZ () const
double x () const
double y () const
double z () const
double * GetCoordinate ()
vector3GetVector ()
const vector3GetVector () const
double GetPartialCharge ()
OBResidueGetResidue ()
OBResidueGetResidue (bool perception)
OBMolGetParent ()
bool GetNewBondVector (vector3 &v, double length)
OBBondGetBond (OBAtom *)
OBAtomGetNextAtom ()
Iterator methods
OBBondIterator BeginBonds ()
OBBondIterator EndBonds ()
OBBondBeginBond (OBBondIterator &i)
OBBondNextBond (OBBondIterator &i)
OBAtomBeginNbrAtom (OBBondIterator &i)
OBAtomNextNbrAtom (OBBondIterator &i)
Addition of residue/bond info. for an atom
void NewResidue ()
void AddResidue (OBResidue *res)
void DeleteResidue ()
void AddBond (OBBond *bond)
void InsertBond (OBBondIterator &i, OBBond *bond)
bool DeleteBond (OBBond *bond)
void ClearBond ()
Builder utilities
bool HtoMethyl ()
bool SetHybAndGeom (int)
void ForceNoH ()
bool HasNoHForced ()
void ForceImplH ()
bool HasImplHForced ()
Property information
unsigned int CountFreeOxygens () const
unsigned int ImplicitHydrogenCount () const
unsigned int ExplicitHydrogenCount (bool ExcludeIsotopes=false) const
unsigned int MemberOfRingCount () const
unsigned int MemberOfRingSize () const
unsigned int CountRingBonds () const
double SmallestBondAngle ()
double AverageBondAngle ()
unsigned int BOSum () const
unsigned int KBOSum () const
bool HasResidue ()
bool IsHydrogen ()
bool IsHydrogen () const
bool IsCarbon ()
bool IsNitrogen ()
bool IsOxygen ()
bool IsSulfur ()
bool IsPhosphorus ()
bool IsAromatic () const
bool IsInRing () const
bool IsInRingSize (int) const
bool IsHeteroatom ()
bool IsNotCorH ()
bool IsConnected (OBAtom *)
bool IsOneThree (OBAtom *)
bool IsOneFour (OBAtom *)
bool IsCarboxylOxygen ()
bool IsPhosphateOxygen ()
bool IsSulfateOxygen ()
bool IsNitroOxygen ()
bool IsAmideNitrogen ()
bool IsPolarHydrogen ()
bool IsNonPolarHydrogen ()
bool IsAromaticNOxide ()
bool IsChiral ()
bool IsAxial ()
bool IsClockwise ()
bool IsAntiClockwise ()
bool IsPositiveStereo ()
bool IsNegativeStereo ()
bool HasChiralitySpecified ()
bool HasChiralVolume ()
bool IsHbondAcceptor ()
bool IsHbondDonor ()
bool IsHbondDonorH ()
bool HasAlphaBetaUnsat (bool includePandS=true)
bool HasBondOfOrder (unsigned int bo)
int CountBondsOfOrder (unsigned int bo)
bool HasNonSingleBond ()
bool HasSingleBond ()
bool HasDoubleBond ()
bool HasAromaticBond ()
bool MatchesSMARTS (const char *)
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

int GetFlag () const
void SetFlag (int flag)
bool HasFlag (int flag)

Protected Attributes

unsigned char _ele
char _impval
char _type [6]
short _fcharge
unsigned short _isotope
short _spinmultiplicity
unsigned int _idx
std::vector< OBBond * > _vbond
unsigned int _cidx
unsigned short _hyb
unsigned short _flags
double _pcharge
double ** _c
vector3 _v
unsigned long _id
std::vector< OBGenericData * > _vdata

Detailed Description

Atom class.

To understand the OBAtom class it is important to state a key decision on which the design was based. The OBAtom class not only holds data, but facilitates extraction of data perceived from both the atom and the molecule. This prevents the OBMol class from becoming overly large and complicated.

A number of data extraction methods perform what is called `Lazy Evaluation,' which is essentially on-the-fly evaluation. For example, when an atom is queried as to whether it is cyclic or what it's hybridization state is the information is perceived automatically. The perception of a particular trait is actually performed on the entire molecule the first time it is requested of an atom or bond, and stored for subsequent requests for the same trait of additional atoms or bonds.The OBAtom class is similar to OBMol and the whole of Open Babel in that data access and modification is done through Get and Set methods.

The following code demonstrates how to print out the atom numbers, element numbers, and coordinates of a molecule:

      OBMol mol;

      FOR_ATOMS_OF_MOL(atom, mol)
         cout << atom->GetIdx() << ` `;
         cout << atom->GetAtomicNum() << ` `;
         cout << atom->GetVector() << endl;

A number of the property member functions indicate that atoms have some knowledge of their covalently attached neighbor atoms. Bonding information is partly redundant within a molecule in that an OBMol has a complete list of bonds in a molecule, and an OBAtom has a list bonds of which it is a member. The following code demonstrates how an OBAtom uses its bond information to loop over atoms attached to itself:

      OBMol mol;
      OBAtom *atom;

      atom = mol.GetAtom(1);
      FOR_NBORS_OF_ATOM(nbr, atom)
         cout << "atom #" << atom->GetIdx() << " is attached to atom #"
              << nbr->GetIdx() << endl;

should produce an output like

      atom #1 is attached to atom #2

Member Enumeration Documentation

enum StereoFlag

Constructor & Destructor Documentation

OBAtom (  )


~OBAtom (  ) [virtual]


Member Function Documentation

int GetFlag (  ) const [inline, protected]
All flags

Referenced by OBAtom::Duplicate().

void SetFlag ( int  flag ) [inline, protected]

Sets the bitwise flag.

bool HasFlag ( int  flag ) [inline, protected]
True of the atom has the flag
OBAtom & operator= ( OBAtom src )


bool operator== ( const OBAtom other ) const [inline]


void Duplicate ( OBAtom src )

Duplicate another atom. Copies all information with the exception of index

version 2.2

Referenced by OBUnitCell::FillUnitCell().

bool Clear ( void   ) [virtual]

Clear all data. Calls OBBase::Clear() to handle any generic data.

True if successful.

Reimplemented from OBBase.

Referenced by OpenBabel::addFragment().

void SetIdx ( int  idx ) [inline]
void SetId ( unsigned long  id ) [inline]
void SetHyb ( int  hyb ) [inline]

Set atom hybridization (i.e., 1 = sp, 2 = sp2, 3 = sp3 ...)

Referenced by OBResidueData::AssignBonds(), OBAtomTyper::AssignHyb(), OBBuilder::GetNewBondVector(), and OBMol::PerceiveBondOrders().

void SetAtomicNum ( int  atomicnum ) [inline]
void SetIsotope ( unsigned int  iso )

Set isotope number (actual atomic weight is tabulated automatically, 0 = most abundant)

Referenced by AliasData::Expand().

void SetImplicitValence ( int  val ) [inline]

Set the implicit valence to val.

Referenced by OBAtomTyper::AssignImplicitValence().

void IncrementImplicitValence (  ) [inline]

Increase the implicit valence by one.

Referenced by OpenBabel::ExpandKekule().

void DecrementImplicitValence (  ) [inline]

Decrease the implicit valence by one.

Referenced by OpenBabel::ExpandKekule().

void SetFormalCharge ( int  fcharge ) [inline]
void SetSpinMultiplicity ( short  spin ) [inline]

Set the atomic spin to spin. See _spinmultiplicity.

Referenced by OpenBabel::addFragment(), and OBMol::AssignSpinMultiplicity().

void SetType ( const char *  type )
void SetType ( const std::string &  type )

Set the atomic type symbol (see OBTypeTable and OBAtomTyper for more)

void SetPartialCharge ( double  pcharge ) [inline]
void SetVector ( const double  x,
const double  y,
const double  z 

Set the coordinate vector for this atom based on x y & z.

void SetCoordPtr ( double **  c ) [inline]

Set the position of this atom from a pointer-driven array of coordinates.

Referenced by OBMol::AddHydrogens(), OBMol::ConnectTheDots(), OBMol::EndModify(), and OBMol::SetCoordinates().

void SetVector (  )

Set the position of this atom based on the internal pointer array (i.e. from SetCoordPtr() )

void SetResidue ( OBResidue res ) [inline]

Attach an OBResidue res as containing this atom.

Referenced by OBResidue::AddAtom(), OBMol::AddHydrogens(), and OBResidue::RemoveAtom().

void SetParent ( OBMol ptr ) [inline]

Attach an OBMol ptr as the parent container for this atom.

Referenced by OBMol::AddAtom(), and OBMol::NewAtom().

void SetAromatic (  ) [inline]
void UnsetAromatic (  ) [inline]

Clear aromatic information from the atom.

Referenced by OBAromaticTyper::AssignAromaticFlags().

void SetClockwiseStereo (  ) [inline]
void SetAntiClockwiseStereo (  ) [inline]
void SetPositiveStereo (  ) [inline]
void SetNegativeStereo (  ) [inline]
void UnsetStereo (  ) [inline]
void SetInRing (  ) [inline]

Mark an atom as belonging to at least one ring.

void SetChiral (  ) [inline]

Mark an atom as being chiral with unknown stereochemistry.

void ClearCoordPtr (  ) [inline]

Clear the internal coordinate pointer.

Referenced by OBMol::BeginModify(), and OBMol::ConnectTheDots().

unsigned short int GetIsotope (  ) const [inline]
the isotope for this atom, if specified, or 0 for unspecified

Referenced by OBDepict::DrawMolecule(), OBAtom::Duplicate(), OBSmartsMatcher::EvalAtomExpr(), and OBAtom::ExplicitHydrogenCount().

int GetSpinMultiplicity (  ) const [inline]
the atomic spin, e.g., 0 (default) for normal atoms - note that this value is a convention, 2 for radical 1 or 3 for carbene

Referenced by OBMol::AddHydrogens(), OpenBabel::alternate(), OBDepict::DrawMolecule(), OBAtom::Duplicate(), and OBMol::GetTotalSpinMultiplicity().

double GetAtomicMass (  ) const
the atomic mass of this atom given by standard IUPAC average molar mass

Referenced by OBMol::GetMolWt(), and OBMol::ToInertialFrame().

double GetExactMass (  ) const
the atomic mass of given by the isotope (default of 0 gives the most abundant isotope)

Referenced by OBMol::GetExactMass().

unsigned int GetIdx (  ) const [inline]
the internal atom index (e.g., inside an OBMol)

Referenced by OBMol::AddAtom(), OBMol::AddHydrogens(), OBMol::Align(), OpenBabel::ApplyRotMatToBond(), OBAromaticTyper::AssignAromaticFlags(), OBResidueData::AssignBonds(), OBGastChrg::AssignPartialCharges(), OBBuilder::Build(), OpenBabel::BuildOBRTreeVector(), OpenBabel::CalcSignedVolume(), OpenBabel::CartesianToInternal(), OBAromaticTyper::CheckAromaticity(), OBMol::ConnectTheDots(), OBMol::ContigFragList(), OBBuilder::CorrectStereoAtoms(), OpenBabel::CreateNewClassVector(), OBMolAtomBFSIter::CurrentDepth(), OBMol::DeleteAtom(), OBMol::DeleteHydrogen(), OBSmartsMatcher::EvalAtomExpr(), OBAromaticTyper::ExcludeSmallRing(), OpenBabel::expand_cycle(), OpenBabel::expand_kekulize_lssr(), OBMol::expandcycle(), OpenBabel::ExpandKekule(), OpenBabel::expandKekulize(), OBSmartsMatcher::FastSingleMatch(), OBMol::FindChildren(), OBMol::FindLargestFragment(), OBRTree::GetAtomIdx(), OpenBabel::GetDFFVector(), OpenBabel::getFragment(), OBBuilder::GetFragment(), OBForceField::GetGradient(), OBForceField::GetGrid(), OBMol::GetGTDVector(), OBRotorRules::GetRotorIncrements(), OpenBabel::has_leftover_electrons(), OBGrid::Init(), OpenBabel::InternalToCartesian(), OBBond::IsClosure(), OBRotorList::IsFixedBond(), OBForceField::IsInSameRing(), OBRing::IsMember(), OBBuilder::IsSpiroAtom(), OpenBabel::KekulePropagate(), OBSSMatch::Match(), OBAtom::MatchesSMARTS(), OBMol::NewAtom(), OBMol::NewPerceiveKekuleBonds(), OBMolAtomBFSIter::OBMolAtomBFSIter(), OBMolAtomDFSIter::OBMolAtomDFSIter(), OBMolPairIter::OBMolPairIter(), OBMolPairIter::operator++(), OBMolAtomBFSIter::operator++(), OBMolAtomDFSIter::operator++(), OBMol::operator=(), OBAtom::operator=(), OBAtom::operator==(), OBMol::PerceiveKekuleBonds(), OBAromaticTyper::PropagatePotentialAromatic(), OBMol::RenumberAtoms(), OBAromaticTyper::SelectRootAtoms(), OBRotorList::SetEvalAtoms(), OBAtom::SetHybAndGeom(), OBBond::SetLength(), OBMol::SetTorsion(), OBProxGrid::Setup(), OBSmartsMatcher::SetupAtomMatchTable(), OBMol::start_kekulize(), and OBAromaticTyper::TraverseCycle().

unsigned int GetIndex (  ) const [inline]
unsigned int GetCoordinateIdx (  ) const [inline]
the index into a pointer-driven array as used by GetCoordPtr() or SetCoordPtr()
unsigned int GetCIdx (  ) const [inline]
unsigned int GetHeteroValence (  ) const
The number of heteroatoms connected to an atom
char * GetType (  )
the atomic type (e.g., for molecular mechanics)

Referenced by OBAtomTyper::AssignTypes(), and OBAtom::Duplicate().

double GetX (  ) const [inline]
the x coordinate

Referenced by OBDepict::DrawMolecule(), OBBond::GetLength(), and OBGrid::Init().

double GetY (  ) const [inline]
the y coordinate

Referenced by OBDepict::DrawMolecule(), OBBond::GetLength(), and OBGrid::Init().

double GetZ (  ) const [inline]
the z coordinate

Referenced by OBBond::GetLength(), and OBGrid::Init().

double z (  ) const [inline]
double* GetCoordinate (  ) [inline]
the coordinates as a double* or NULL if none.

See SetCoordPtr() for more. If no coordinate pointer is used (e.g., only vector3), NULL will be returned.

Referenced by OBForceField::GetGrid(), and OBForceField::UpdatePairsSimple().

const vector3 & GetVector (  ) const
the coordinates as a vector3 object
double GetPartialCharge (  )
the partial charge of this atom, calculating a Gasteiger charge if needed

Referenced by OBGastChrg::AssignPartialCharges(), OBAtom::Duplicate(), OBChargeModel::FillChargeVectors(), and OBForceField::GetPartialCharges().

OBResidue * GetResidue (  )
the residue which contains this atom, or NULL if none exists

Referenced by OBMol::AddHydrogens(), OBResidueData::AssignBonds(), and OBResidue::GetBonds().

OBResidue * GetResidue ( bool  perception )
perceptionimplies whether chain perception should occur
the residue which contains this atom, or NULL if none exists
OBMol* GetParent (  ) [inline]
bool GetNewBondVector ( vector3 v,
double  length 

Create a vector for a new bond from this atom, with length given by the supplied parameter

success or failure
OBBond * GetBond ( OBAtom nbr )
the OBBond object between this atom and that supplied, or NULL if the two atoms are not bonded

Referenced by OBBondTyper::AssignFunctionalGroupBonds(), OBBuilder::Build(), OpenBabel::CorrectBadResonanceForm(), OBBuilder::GetNewBondVector(), and OBMol::PerceiveBondOrders().

OBAtom * GetNextAtom (  )
a pointer to the "next" atom (by atom index) in the parent OBMol, or NULL if no such atom exists.
Use any of the other iterator methods. This method will be removed in the future.
OBBondIterator BeginBonds (  ) [inline]
An iterator to the beginning of the bonds to this atom

Referenced by OBResidueData::AssignBonds().

OBBondIterator EndBonds (  ) [inline]
An iterator to the end of the bonds to this atom
double GetDistance ( int  index )
the distance to the atom defined by OBMol::GetAtom()

Referenced by OBBondTyper::AssignFunctionalGroupBonds().

double GetDistance ( OBAtom b )
the distance to the supplied OBAtom
double GetAngle ( int  b,
int  c 
the angle defined by this atom -> b (vertex) -> c

Referenced by OBMol::GetAngle().

double GetAngle ( OBAtom b,
OBAtom c 
the angle defined by this atom -> b (vertex) -> c
void NewResidue (  ) [inline]

If no residue has been set for this atom, create a new one.

void AddResidue ( OBResidue res ) [inline]

Add (set) the residue for this atom.

void DeleteResidue (  ) [inline]

Delete any residue associated with this atom.

void AddBond ( OBBond bond ) [inline]

Add a bond to the internal list. Does not update the bond.

Referenced by OBMol::AddBond(), and OBBuilder::Connect().

void InsertBond ( OBBondIterator i,
OBBond bond 
) [inline]

Insert bond into the internal list at the position from i Does not modify the bond.

Referenced by OBMol::AddBond().

bool DeleteBond ( OBBond bond )

Find bond and remove it from the internal list. Does not update the bond.

void ClearBond (  ) [inline]

Clear all bonding information in this atom (does not delete them)

bool HtoMethyl (  )

If this is a hydrogen atom, transform into a methyl group.

success or failure
bool SetHybAndGeom ( int  hyb )

Change the hybridization of this atom and modify the geometry accordingly

success or failure
This will be removed in future versions of Open Babel
void ForceNoH (  ) [inline]

Mark that atom has no hydrogens attached.

bool HasNoHForced (  ) [inline]
if atom has been marked as having no hydrogens attached

Referenced by OBMol::AssignSpinMultiplicity().

void ForceImplH (  ) [inline]

Mark that atom is not hydrogen deficient (For SMILES input)

version 2.2
bool HasImplHForced (  ) [inline]
if atom has been marked as having no hydrogens attached
version 2.2

Referenced by OBMol::AssignSpinMultiplicity().

unsigned int CountFreeOxygens (  ) const
The number of oxygen atoms connected that only have one heavy valence

Referenced by OBAtom::IsCarboxylOxygen(), OBAtom::IsNitroOxygen(), OBAtom::IsPhosphateOxygen(), and OBAtom::IsSulfateOxygen().

unsigned int ImplicitHydrogenCount (  ) const
The number of hydrogens needed to fill the implicit valence of this atom

Referenced by OBDepict::DrawMolecule(), OBSmartsMatcher::EvalAtomExpr(), OBMol::GetExactMass(), and OBMol::GetMolWt().

unsigned int ExplicitHydrogenCount ( bool  ExcludeIsotopes = false ) const
The number of hydrogens explicitly bound to this atom, optionally excluding D,T and isotope explicitly set to 1

Referenced by OBMol::AssignSpinMultiplicity(), and OBSmartsMatcher::EvalAtomExpr().

unsigned int MemberOfRingCount (  ) const
The number of rings that contain this atom

Referenced by OBSmartsMatcher::EvalAtomExpr().

unsigned int MemberOfRingSize (  ) const
The size of the smallest ring that contains this atom (0 if not in a ring)
unsigned int CountRingBonds (  ) const
The number of explicit ring connections to this atom

Referenced by OBSmartsMatcher::EvalAtomExpr().

double SmallestBondAngle (  )
The smallest angle of bonds to this atom

Referenced by OBMol::ConnectTheDots().

double AverageBondAngle (  )
The average angle of bonds to this atom

Referenced by OBBondTyper::AssignFunctionalGroupBonds(), and OBMol::PerceiveBondOrders().

unsigned int BOSum (  ) const
The sum of the bond orders of the bonds to the atom (i.e. double bond = 2...)

Referenced by OBMol::ConnectTheDots(), OBRing::GetRootAtom(), and OBMol::PerceiveBondOrders().

unsigned int KBOSum (  ) const
The sum of the bond orders of bonds to the atom, considering only KDouble, KTriple bonds
Use BOSum() instead

Referenced by OBSmartsMatcher::EvalAtomExpr().

bool HasResidue (  ) [inline]
Is there any residue information?

Referenced by OBMol::AddHydrogens().

bool IsHydrogen (  ) const [inline]
bool IsCarbon (  ) [inline]
bool IsPhosphorus (  ) [inline]
Is the atom phosphorus?

Referenced by OBMol::AddHydrogens(), and OBAtom::HasAlphaBetaUnsat().

bool IsAromatic (  ) const
bool IsInRingSize ( int  size ) const
Is the atom in a ring of a given size?

Referenced by OBSmartsMatcher::EvalAtomExpr(), OpenBabel::findMetalloceneBonds(), and OBMol::getorden().

bool IsHeteroatom (  )
Is this atom an element in the 15th or 16th main groups (i.e., N, O, P, S ...) ?

Referenced by OpenBabel::alternate(), and OBAtom::GetHeteroValence().

bool IsNotCorH (  )
Is this atom any element except carbon or hydrogen?
bool IsOneThree ( OBAtom a1 )
Is this atom related to the supplied OBAtom in a 1,3 bonding pattern?

Referenced by OBMolPairIter::OBMolPairIter(), and OBMolPairIter::operator++().

bool IsOneFour ( OBAtom a1 )
Is this atom related to the supplied OBAtom in a 1,4 bonding pattern?
bool IsCarboxylOxygen (  )
Is this atom an oxygen in a carboxyl (-CO2 or CO2H) group?

Referenced by OBBuilder::GetNewBondVector().

bool IsPhosphateOxygen (  )
Is this atom an oxygen in a phosphate (R-PO3) group?
bool IsSulfateOxygen (  )
Is this atom an oxygen in a sulfate (-SO3) group?
bool IsNitroOxygen (  )
Is this atom an oxygen in a nitro (-NO2) group?
bool IsAmideNitrogen (  )

Returns true if nitrogen is part of an amide.

Is this atom a nitrogen in an amide (-C(=O)NR2) group?

Referenced by OBMol::getorden().

bool IsPolarHydrogen (  )
Is this atom a hydrogen connected to a polar atom (i.e., N, O, P, S)
bool IsNonPolarHydrogen (  )
Is this atom a hydrogen connected to a non-polar atom (i.e., C)

Referenced by OBMol::DeleteNonPolarHydrogens().

bool IsAromaticNOxide (  )
Is this atom an aromatic nitrogen with at least one double bond to an oxygen atom
bool IsChiral (  )
Is this atom chiral?

Referenced by OBMol::IsChiral().

bool IsAxial (  )
Is this atom an axial atom in a ring
bool IsClockwise (  ) [inline]
bool IsAntiClockwise (  ) [inline]
bool IsPositiveStereo (  ) [inline]
bool IsNegativeStereo (  ) [inline]
bool HasChiralitySpecified (  ) [inline]
bool HasChiralVolume (  ) [inline]
bool IsHbondAcceptor (  )
Is this atom a hydrogen-bond acceptor (receptor)?
bool IsHbondDonor (  )
Is this atom a hydrogen-bond donor?

Referenced by OBAtom::IsHbondDonorH().

bool IsHbondDonorH (  )
Is this a hydrogen atom attached to a hydrogen-bond donor?
bool HasAlphaBetaUnsat ( bool  includePandS = true )
Whether a neighboring atom (alpha) has an unsaturated bond to a third atom (beta).
includePandSWhether to include phosphorus and sulfur neighbors in this determination (or to exclude them)

This can be sketched as follows


where a and b are the 'apha' and 'beta' atoms, respectively and '*' indicates the current atom.

bool HasBondOfOrder ( unsigned int  bo )
Whether this atom is connected to any bond with order == bo

Referenced by OBMol::PerceiveBondOrders().

int CountBondsOfOrder ( unsigned int  bo )
The count of bonds connected to this atom with order == bo
bool HasNonSingleBond (  )
Whether this atom is connected to any bond with order >1

Referenced by OBMol::PerceiveBondOrders().

bool HasSingleBond (  ) [inline]
Does this atom have a single bond
bool HasDoubleBond (  ) [inline]
Does this atom have a double bond

Referenced by OBBondTyper::AssignFunctionalGroupBonds().

bool HasAromaticBond (  ) [inline]
Does this atom have an aromatic bond

Referenced by OBMol::NewPerceiveKekuleBonds().

bool MatchesSMARTS ( const char *  pattern )
Whether this atom matches the first atom in a given SMARTS pattern
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() Base type does nothing

Reimplemented in OBMol.

static const char* ClassDescription (  ) [inline, static, inherited]
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]
whether the generic attribute/value pair exists
bool HasData ( const unsigned int  type ) [inherited]
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

version 2.2
size_t DataSize (  ) const [inline, inherited]
the number of OBGenericData items attached to this molecule.
OBGenericData * GetData ( const std::string &  s ) [inherited]
any data matching the given attribute name or NULL if nothing matches
the value given an attribute name
OBGenericData * GetData ( const char *  s ) [inherited]
any data matching the given attribute name or NULL if nothing matches
the value given an attribute name
std::vector<OBGenericData*>& GetData (  ) [inline, inherited]
all data, suitable for iterating

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

std::vector< OBGenericData * > GetData ( DataOrigin  source ) [inherited]
all data with a specific origin, suitable for iterating
std::vector< OBGenericData * > GetAllData ( const unsigned int  type ) [inherited]
the all matching data for a given type from OBGenericDataType or an empty vector if nothing matches
version 2.2

Referenced by OpenBabel::CanonicalLabels(), OBBuilder::CorrectStereoAtoms(), and OBBuilder::CorrectStereoBonds().

OBDataIterator BeginData (  ) [inline, inherited]
An iterator pointing to the beginning of the data

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

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

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

Member Data Documentation

unsigned char _ele [protected]

atomic number (type unsigned char to minimize space -- allows for 0..255 elements)

char _impval [protected]

implicit valence

char _type[6] [protected]

atomic type

short _fcharge [protected]

formal charge

unsigned short _isotope [protected]

isotope (0 = most abundant)

short _spinmultiplicity [protected]

atomic spin, e.g., 2 for radical 1 or 3 for carbene

unsigned int _idx [protected]

unique node index (GetIdx(), SetIdx())

OBMol* _parent [protected]

parent molecule (if any)

std::vector<OBBond*> _vbond [protected]

bonds to this atom -- assumed to be one of the endpoints

unsigned int _cidx [protected]

index into coordinate array

unsigned short _hyb [protected]


unsigned short _flags [protected]

bitwise flags (e.g. aromaticity)

double _pcharge [protected]

partial charge

double** _c [protected]

coordinate array in double*

Referenced by OpenBabel::CartesianToInternal().

vector3 _v [mutable, protected]

coordinate vector

OBResidue* _residue [protected]

parent residue (if applicable)

unsigned long _id [protected]

unique id

bool Visit

Used internally by graph traversal algorithms.

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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