OBAtom Class Reference

Atom class. More...

#include <openbabel/atom.h>

Inheritance diagram for OBAtom:

List of all members.

Public Member Functions

 OBAtom ()
virtual ~OBAtom ()
OBAtomoperator= (OBAtom &)
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 > *)
template<class T>
T * CastAndClear (bool clear=true)
Methods to set atomic information
void SetIdx (int idx)
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 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 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)
unsigned int 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

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

Constructor & Destructor Documentation

OBAtom (  ) 

Constructor.

~OBAtom (  )  [virtual]

Destructor.


Member Function Documentation

int GetFlag (  )  const [inline, protected]

Returns:
All flags

Referenced by OBAtom::Duplicate().

void SetFlag ( int  flag  )  [inline, protected]

Sets the bitwise flag.

bool HasFlag ( int  flag  )  [inline, protected]

Returns:
True of the atom has the flag

Referenced by OBAtom::IsAromatic(), OBAtom::IsChiral(), OBAtom::IsInRing(), and OBAtom::IsInRingSize().

OBAtom & operator= ( OBAtom src  ) 

Assignment.

void Duplicate ( OBAtom src  ) 

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

Since:
version 2.2

Referenced by OBUnitCell::FillUnitCell(), and OBAtom::operator=().

bool Clear ( void   )  [virtual]

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

Returns:
True if successful.

Reimplemented from OBBase.

Referenced by OBAtom::OBAtom().

void SetIdx ( int  idx  )  [inline]

void SetHyb ( int  hyb  )  [inline]

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

Referenced by OBResidueData::AssignBonds(), OBAtomTyper::AssignHyb(), OBAtom::HtoMethyl(), OBMol::PerceiveBondOrders(), and OBAtom::SetHybAndGeom().

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 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]

Mark atom as having SMILES clockwise stereochemistry (i.e., "@@").

Referenced by OpenBabel::CorrectChirality().

void SetAntiClockwiseStereo (  )  [inline]

Mark atom as having SMILES anticlockwise stereochemistry (i.e., "@").

Referenced by OpenBabel::CorrectChirality().

void SetPositiveStereo (  )  [inline]

Mark an atom as having + chiral volume.

void SetNegativeStereo (  )  [inline]

Mark an atom as having - chiral volume.

void UnsetStereo (  )  [inline]

Clear all stereochemistry information.

Referenced by OpenBabel::CorrectChirality().

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.

Referenced by OBMol::FindChiralCenters().

void ClearCoordPtr (  )  [inline]

Clear the internal coordinate pointer.

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

unsigned short int GetIsotope (  )  const [inline]

Returns:
the isotope for this atom, if specified, or 0 for unspecified

Referenced by OBAtom::Duplicate(), OpenBabel::EvalAtomExpr(), and OBAtom::ExplicitHydrogenCount().

int GetSpinMultiplicity (  )  const [inline]

Returns:
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(), OBAtom::Duplicate(), OBMol::GetTotalSpinMultiplicity(), and OBAtom::ImplicitHydrogenCount().

double GetAtomicMass (  )  const

Returns:
the atomic mass of this atom given by standard IUPAC average molar mass

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

double GetExactMass (  )  const

Returns:
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]

Returns:
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(), OpenBabel::BreakChiralTies(), OBBuilder::Build(), OpenBabel::BuildOBRTreeVector(), OpenBabel::CalcSignedVolume(), OpenBabel::CalculateSymmetry(), OpenBabel::CartesianToInternal(), OBAromaticTyper::CheckAromaticity(), OBMol::ConnectTheDots(), OBMol::ContigFragList(), OBBuilder::CorrectStereoAtoms(), OpenBabel::CreateNewClassVector(), OBMolAtomBFSIter::CurrentDepth(), OBMol::DeleteAtom(), OBMol::DeleteHydrogen(), OpenBabel::EvalAtomExpr(), OBAromaticTyper::ExcludeSmallRing(), OBMol::expand_kekulize(), OBMol::expandcycle(), OpenBabel::ExpandKekule(), OpenBabel::FastSingleMatch(), OBMol::FindChildren(), OBMol::FindChiralCenters(), OpenBabel::FindConjugatedEZBonds(), OBMol::FindLargestFragment(), OpenBabel::FixCisTransBonds(), OBRTree::GetAtomIdx(), OpenBabel::GetDFFVector(), OBBuilder::GetFragment(), OpenBabel::GetGIVector(), OBForceField::GetGradient(), OBForceField::GetGrid(), OBMol::GetGTDVector(), OpenBabel::GetGTDVector(), OpenBabel::GetHvyBondSum(), OpenBabel::GetHvyValence(), OBAtom::GetNextAtom(), OBRotorRules::GetRotorIncrements(), OpenBabel::GetValence(), OBAtom::HtoMethyl(), OBGrid::Init(), OpenBabel::InternalToCartesian(), OBBond::IsClosure(), OBRotorList::IsFixedBond(), OBAtom::IsInRingSize(), OBForceField::IsInSameRing(), OBRing::IsMember(), OpenBabel::KekulePropagate(), OBSSMatch::Match(), OBAtom::MatchesSMARTS(), OBAtom::MemberOfRingCount(), OBAtom::MemberOfRingSize(), OBMol::NewAtom(), OBMolAtomBFSIter::OBMolAtomBFSIter(), OBMolAtomDFSIter::OBMolAtomDFSIter(), OBMolPairIter::OBMolPairIter(), OBMolPairIter::operator++(), OBMolAtomBFSIter::operator++(), OBMolAtomDFSIter::operator++(), OBMol::operator=(), OBAtom::operator=(), OBMol::PerceiveKekuleBonds(), OBAromaticTyper::PropagatePotentialAromatic(), OBMol::RenumberAtoms(), OBAromaticTyper::SelectRootAtoms(), OBRotorList::SetEvalAtoms(), OBAtom::SetHybAndGeom(), OBBond::SetLength(), OBMol::SetTorsion(), OBProxGrid::Setup(), OpenBabel::SetupAtomMatchTable(), OBMol::start_kekulize(), and OBAromaticTyper::TraverseCycle().

unsigned int GetCoordinateIdx (  )  const [inline]

Returns:
the index into a pointer-driven array as used by GetCoordPtr() or SetCoordPtr()

unsigned int GetCIdx (  )  const [inline]

unsigned int GetHeteroValence (  )  const

Returns:
The number of heteroatoms connected to an atom

char * GetType (  ) 

Returns:
the atomic type (e.g., for molecular mechanics)

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

double GetX (  )  const [inline]

Returns:
the x coordinate

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

double GetY (  )  const [inline]

Returns:
the y coordinate

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

double GetZ (  )  const [inline]

Returns:
the z coordinate

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

double z (  )  const [inline]

double* GetCoordinate (  )  [inline]

Returns:
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

Returns:
the coordinates as a vector3 object

double GetPartialCharge (  ) 

Returns:
the partial charge of this atom, calculating a Gasteiger charge if needed

Referenced by OBGastChrg::AssignPartialCharges(), and OBAtom::Duplicate().

OBResidue * GetResidue (  ) 

Returns:
the residue which contains this atom, or NULL if none exists

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

OBResidue * GetResidue ( bool  perception  ) 

Parameters:
perception implies whether chain perception should occur
Returns:
the residue which contains this atom, or NULL if none exists

bool GetNewBondVector ( vector3 v,
double  length 
)

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

Returns:
success or failure

Referenced by OBAtom::HtoMethyl(), and OBAtom::SetHybAndGeom().

OBBond * GetBond ( OBAtom nbr  ) 

Returns:
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::CorrectStereoBonds(), OBMol::expand_kekulize(), and OBMol::PerceiveBondOrders().

OBAtom * GetNextAtom (  ) 

Returns:
a pointer to the "next" atom (by atom index) in the parent OBMol, or NULL if no such atom exists.
Deprecated:
Use any of the other iterator methods. This method will be removed in the future.

OBBondIterator BeginBonds (  )  [inline]

Returns:
An iterator to the beginning of the bonds to this atom

Referenced by OBResidueData::AssignBonds().

OBBondIterator EndBonds (  )  [inline]

Returns:
An iterator to the end of the bonds to this atom

OBAtom * BeginNbrAtom ( OBBondIterator i  ) 

double GetDistance ( int  index  ) 

Returns:
the distance to the atom defined by OBMol::GetAtom()

Referenced by OBBondTyper::AssignFunctionalGroupBonds().

double GetDistance ( OBAtom b  ) 

Returns:
the distance to the supplied OBAtom

double GetAngle ( int  b,
int  c 
)

Returns:
the angle defined by this atom -> b (vertex) -> c

Referenced by OBMol::GetAngle().

double GetAngle ( OBAtom b,
OBAtom c 
)

Returns:
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.

Returns:
success or failure

bool SetHybAndGeom ( int  hyb  ) 

Change the hybridization of this atom and modify the geometry accordingly

Returns:
success or failure

void ForceNoH (  )  [inline]

Mark that atom has no hydrogens attached.

bool HasNoHForced (  )  [inline]

Returns:
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)

Since:
version 2.2

bool HasImplHForced (  )  [inline]

Returns:
if atom has been marked as having no hydrogens attached
Since:
version 2.2

Referenced by OBMol::AssignSpinMultiplicity().

unsigned int CountFreeOxygens (  )  const

Returns:
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

Returns:
The number of hydrogens needed to fill the implicit valence of this atom

Referenced by OpenBabel::EvalAtomExpr(), OBMol::GetExactMass(), and OBMol::GetMolWt().

unsigned int ExplicitHydrogenCount ( bool  ExcludeIsotopes = false  )  const

Returns:
The number of hydrogens explicitly bound to this atom, optionally excluding D,T and isotope explicitly set to 1

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

unsigned int MemberOfRingCount (  )  const

Returns:
The number of rings that contain this atom

Referenced by OpenBabel::EvalAtomExpr().

unsigned int MemberOfRingSize (  )  const

Returns:
The size of the smallest ring that contains this atom (0 if not in a ring)

Referenced by OBAtom::SetHybAndGeom().

unsigned int CountRingBonds (  )  const

Returns:
The number of explicit ring connections to this atom

Referenced by OpenBabel::EvalAtomExpr().

double SmallestBondAngle (  ) 

Returns:
The smallest angle of bonds to this atom

Referenced by OBMol::ConnectTheDots().

double AverageBondAngle (  ) 

Returns:
The average angle of bonds to this atom

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

unsigned int BOSum (  )  const

Returns:
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

Returns:
The sum of the bond orders of bonds to the atom, considering only KDouble, KTriple bonds
Deprecated:
Use BOSum() instead

Referenced by OpenBabel::EvalAtomExpr().

bool HasResidue (  )  [inline]

Returns:
Is there any residue information?

Referenced by OBMol::AddHydrogens().

bool IsCarbon (  )  [inline]

bool IsPhosphorus (  )  [inline]

Returns:
Is the atom phosphorus?

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

bool IsInRingSize ( int  size  )  const

Returns:
Is the atom in a ring of a given size?

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

bool IsHeteroatom (  ) 

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

Referenced by OBAtom::GetHeteroValence().

bool IsNotCorH (  ) 

Returns:
Is this atom any element except carbon or hydrogen?

bool IsConnected ( OBAtom a1  ) 

bool IsOneThree ( OBAtom a1  ) 

Returns:
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  ) 

Returns:
Is this atom related to the supplied OBAtom in a 1,4 bonding pattern?

bool IsCarboxylOxygen (  ) 

Returns:
Is this atom an oxygen in a carboxyl (-CO2 or CO2H) group?

bool IsPhosphateOxygen (  ) 

Returns:
Is this atom an oxygen in a phosphate (R-PO3) group?

bool IsSulfateOxygen (  ) 

Returns:
Is this atom an oxygen in a sulfate (-SO3) group?

bool IsNitroOxygen (  ) 

Returns:
Is this atom an oxygen in a nitro (-NO2) group?

bool IsAmideNitrogen (  ) 

Returns true if nitrogen is part of an amide.

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

Referenced by OBMol::getorden().

bool IsPolarHydrogen (  ) 

Returns:
Is this atom a hydrogen connected to a polar atom (i.e., N, O, P, S)

bool IsNonPolarHydrogen (  ) 

Returns:
Is this atom a hydrogen connected to a non-polar atom (i.e., C)

Referenced by OBMol::DeleteNonPolarHydrogens().

bool IsAromaticNOxide (  ) 

Returns:
Is this atom an aromatic nitrogen with at least one double bond to an oxygen atom

bool IsChiral (  ) 

Returns:
Is this atom chiral?

Referenced by OpenBabel::EvalAtomExpr(), OBMol::FindChiralCenters(), and OBMol::IsChiral().

bool IsAxial (  ) 

Returns:
Is this atom an axial atom in a ring

bool IsClockwise (  )  [inline]

Returns:
Does this atom have SMILES-specified clockwise "@@" stereochemistry?

Referenced by OpenBabel::CorrectChirality(), and OpenBabel::EvalAtomExpr().

bool IsAntiClockwise (  )  [inline]

Returns:
Does this atom have SMILES-specified anticlockwise "@" stereochemistry?

Referenced by OpenBabel::CorrectChirality(), and OpenBabel::EvalAtomExpr().

bool IsPositiveStereo (  )  [inline]

Returns:
Does this atom have a positive chiral volume?

bool IsNegativeStereo (  )  [inline]

Returns:
Does this atom have a negative chiral volume?

bool HasChiralitySpecified (  )  [inline]

Returns:
Does this atom have SMILES-specified stereochemistry?

Referenced by OpenBabel::CorrectChirality(), and OpenBabel::EvalAtomExpr().

bool HasChiralVolume (  )  [inline]

Returns:
Does this atom have a specified chiral volume?

bool IsHbondAcceptor (  ) 

Returns:
Is this atom a hydrogen-bond acceptor (receptor)?

bool IsHbondDonor (  ) 

Returns:
Is this atom a hydrogen-bond donor?

Referenced by OBAtom::IsHbondDonorH().

bool IsHbondDonorH (  ) 

Returns:
Is this a hydrogen atom attached to a hydrogen-bond donor?

bool HasAlphaBetaUnsat ( bool  includePandS = true  ) 

Returns:
Whether a neighboring atom (alpha) has an unsaturated bond to a third atom (beta).
Parameters:
includePandS Whether to include phosphorus and sulfur neighbors in this determination (or to exclude them)
This can be sketched as follows
              '*'
                 \
                  a=b
where a and b are the 'apha' and 'beta' atoms, respectively and '*' indicates the current atom.

Referenced by OBAtom::GetNewBondVector().

bool HasBondOfOrder ( unsigned int  bo  ) 

Returns:
Whether this atom is connected to any bond with order == bo

Referenced by OBMol::PerceiveBondOrders().

int CountBondsOfOrder ( unsigned int  bo  ) 

Returns:
The count of bonds connected to this atom with order == bo

bool HasNonSingleBond (  ) 

Returns:
Whether this atom is connected to any bond with order >1

Referenced by OBMol::PerceiveBondOrders().

bool HasSingleBond (  )  [inline]

Returns:
Does this atom have a single bond

bool HasDoubleBond (  )  [inline]

Returns:
Does this atom have a double bond

Referenced by OBBondTyper::AssignFunctionalGroupBonds(), and OpenBabel::FindConjugatedEZBonds().

bool HasAromaticBond (  )  [inline]

Returns:
Does this atom have an aromatic bond

Referenced by OBMol::NewPerceiveKekuleBonds().

bool MatchesSMARTS ( const char *  pattern  ) 

Returns:
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()

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.

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

unsigned int 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 ( 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

OBDataIterator BeginData (  )  [inline, inherited]

Returns:
An iterator pointing to the beginning of the data

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


Member Data Documentation

char _ele [protected]

char _impval [protected]

char _type[6] [protected]

short _fcharge [protected]

formal charge

Referenced by OBAtom::Clear(), and OBAtom::Duplicate().

short _spinmultiplicity [protected]

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

Referenced by OBAtom::Clear(), and OBAtom::Duplicate().

unsigned int _idx [protected]

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

Referenced by OBAtom::Clear(), and OBAtom::operator=().

OBMol* _parent [protected]

parent molecule (if any)

Referenced by OBAtom::OBAtom().

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

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

Referenced by OBAtom::BeginBond(), OBAtom::BeginNbrAtom(), OBAtom::Clear(), OBAtom::DeleteBond(), OBAtom::NextBond(), and OBAtom::NextNbrAtom().

unsigned int _cidx [protected]

index into coordinate array

Referenced by OBAtom::Clear(), OBAtom::GetVector(), and OBAtom::SetVector().

unsigned short _hyb [protected]

hybridization

Referenced by OBAtom::Clear(), OBAtom::Duplicate(), and OBAtom::GetHyb().

unsigned short _flags [protected]

bitwise flags (e.g. aromaticity)

Referenced by OBAtom::Clear(), and OBAtom::Duplicate().

double _pcharge [protected]

partial charge

Referenced by OBAtom::Clear(), OBAtom::Duplicate(), and OBAtom::GetPartialCharge().

double** _c [protected]

vector3 _v [mutable, protected]

coordinate vector

Referenced by OBAtom::Duplicate(), OBAtom::GetVector(), and OBAtom::SetVector().

OBResidue* _residue [protected]

parent residue (if applicable)

Referenced by OBAtom::Clear(), OBAtom::Duplicate(), OBAtom::GetResidue(), and OBAtom::~OBAtom().

bool Visit

Used internally by graph traversal algorithms.


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