#include <openbabel/atom.h>

Inheritance diagram for OBAtom:

Public Types
enum	StereoFlag

Public Member Functions
	OBAtom ()

virtual	~OBAtom ()

OBAtom &	operator= (OBAtom &)

bool	operator== (const OBAtom *other) const

void	Duplicate (OBAtom *)

bool	Clear ()

double	GetDistance (int index)

double	GetDistance (OBAtom *)

double	GetDistance (vector3 *v)

double	GetAngle (int b, int c)

double	GetAngle (OBAtom b, OBAtom c)

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 *)

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	SetImplicitHCount (unsigned int val)

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 (bool value=true)

void	SetInRing (bool value=true)

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	GetExplicitDegree () const

unsigned int	GetTotalDegree () const

unsigned int	GetExplicitValence () const

unsigned int	GetTotalValence () const

unsigned int	GetHyb () const

unsigned char	GetImplicitHCount () const

unsigned int	GetHvyDegree () const

unsigned int	GetHeteroDegree () const

char *	GetType ()

double	GetX () const

double	GetY () const

double	GetZ () const

double	x () const

double	y () const

double	z () const

double *	GetCoordinate ()

vector3 &	GetVector ()

const vector3 &	GetVector () const

double	GetPartialCharge ()

OBResidue *	GetResidue ()

OBMol *	GetParent ()

bool	GetNewBondVector (vector3 &v, double length)

OBBond *	GetBond (OBAtom *)

Iterator methods
OBBondIterator	BeginBonds ()

OBBondIterator	EndBonds ()

OBBond *	BeginBond (OBBondIterator &i)

OBBond *	NextBond (OBBondIterator &i)

OBAtom *	BeginNbrAtom (OBBondIterator &i)

OBAtom *	NextNbrAtom (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)

Property information
unsigned int	CountFreeOxygens () const

unsigned int	CountFreeSulfurs () const

unsigned int	ExplicitHydrogenCount (bool ExcludeIsotopes=false) const

unsigned int	MemberOfRingCount () const

unsigned int	MemberOfRingSize () const

unsigned int	CountRingBonds () const

double	SmallestBondAngle ()

double	AverageBondAngle ()

std::pair< int, int >	LewisAcidBaseCounts () const

bool	HasResidue ()

bool	IsHetAtom ()

bool	IsAromatic () const

bool	IsInRing () const

bool	IsInRingSize (int) const

bool	IsHeteroatom ()

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	IsHbondAcceptor ()

bool	IsHbondAcceptorSimple ()

bool	IsHbondDonor ()

bool	IsHbondDonorH ()

bool	IsMetal ()

bool	HasAlphaBetaUnsat (bool includePandS=true)

bool	HasBondOfOrder (unsigned int bo)

int	CountBondsOfOrder (unsigned int bo)

int	HighestBondOrder ()

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

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
int	GetFlag () const

void	SetFlag (int flag)

void	UnsetFlag (int flag)

bool	HasFlag (int flag)

Protected Attributes
unsigned char	_ele

unsigned char	_imph

char	_type [OBATOM_TYPE_LEN]

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

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

◆ StereoFlag

enum StereoFlag

Constructor & Destructor Documentation

◆ OBAtom()

OBAtom ( )

Constructor.

◆ ~OBAtom()

~OBAtom ( )

virtual

Destructor.

Member Function Documentation

◆ GetFlag()

int GetFlag ( ) const

inlineprotected

Returns: All flags

◆ SetFlag()

void SetFlag ( int flag )

inlineprotected

Sets the bitwise flag.

◆ UnsetFlag()

void UnsetFlag ( int flag )

inlineprotected

Unsets the bitwise flag.

◆ HasFlag()

bool HasFlag ( int flag )

inlineprotected

Returns: True of the atom has the flag

◆ operator=()

OBAtom & operator= ( OBAtom & src )

Assignment.

◆ operator==()

bool operator== ( const OBAtom * other ) const

inline

Equivalence.

◆ Duplicate()

void Duplicate ( OBAtom * src )

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

Since: version 2.2

Referenced by OBUnitCell::FillUnitCell().

◆ Clear()

bool Clear ( void )

virtual

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

Returns: True if successful.

Reimplemented from OBBase.

Referenced by OpenBabel::addFragment().

◆ SetIdx()

void SetIdx ( int idx )

inline

Set atom index (i.e., in an OBMol)

Referenced by OBMol::AddAtom(), OBMol::DeleteAtom(), OBMol::DeleteHydrogen(), OBMol::EndModify(), and OBMol::NewAtom().

◆ SetId()

void SetId ( unsigned long id )

inline

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

◆ SetHyb()

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().

◆ SetAtomicNum()

void SetAtomicNum ( int atomicnum )

inline

Set atomic number.

Referenced by OpenBabel::addFragment(), OBMol::AddHydrogens(), OBMol::AddNewHydrogens(), OBChemTsfm::Apply(), AliasData::Expand(), OBAtom::HtoMethyl(), and OBAtom::SetHybAndGeom().

◆ SetIsotope()

void SetIsotope ( unsigned int iso )

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

Referenced by AliasData::Expand().

◆ SetImplicitHCount()

void SetImplicitHCount ( unsigned int val )

inline

Set the implicit hydrogen count to val.

Referenced by OBMol::AddHydrogens(), OBMol::AddNewHydrogens(), OBChemTsfm::Apply(), OBMol::DeleteHydrogens(), and OpenBabel::OBAtomAssignTypicalImplicitHydrogens().

◆ SetFormalCharge()

void SetFormalCharge ( int fcharge )

inline

Set the formal charge of the atom to fcharge.

Referenced by OpenBabel::addFragment(), OBChemTsfm::Apply(), OBBondTyper::AssignFunctionalGroupBonds(), OBMol::ConvertDativeBonds(), OBMol::ConvertZeroBonds(), AliasData::Expand(), OBMol::MakeDativeBonds(), and OBMol::PerceiveBondOrders().

◆ SetSpinMultiplicity()

void SetSpinMultiplicity ( short spin )

inline

Set the atomic spin to spin. See _spinmultiplicity.

Referenced by OpenBabel::addFragment(), and AliasData::Expand().

◆ SetType() [1/2]

void SetType ( const char * type )

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

Referenced by OBMol::AddHydrogens(), OBMol::AddNewHydrogens(), OBResidueData::AssignBonds(), OBAtomTyper::AssignTypes(), OBForceField::GetGrid(), OBAtom::HtoMethyl(), and OBAtom::SetHybAndGeom().

◆ SetType() [2/2]

void SetType ( const std::string & type )

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

◆ SetPartialCharge()

void SetPartialCharge ( double pcharge )

inline

Set the partial charge to pcharge.

Referenced by OBGastChrg::AssignPartialCharges(), OBPhModel::AssignSeedPartialCharge(), OBForceField::GetGrid(), and OBAtom::GetPartialCharge().

◆ SetVector() [1/3]

void SetVector ( const vector3 & v )

Set the coordinate vector for this atom to v as a vector3.

Referenced by OpenBabel::addFragment(), OBMol::AddNewHydrogens(), OBMol::Align(), OpenBabel::ApplyRotMatToBond(), OBMol::BeginModify(), OBBuilder::Build(), OBMol::Center(), OBBuilder::Connect(), OBDepict::DrawMolecule(), AliasData::Expand(), OBUnitCell::FillUnitCell(), OpenBabel::generateDiagram(), OBForceField::GetCoordinates(), OpenBabel::groupRedraw(), OBAtom::HtoMethyl(), OpenBabel::InternalToCartesian(), OBBuilder::IsSpiroAtom(), OBForceField::LineSearch(), OBForceField::NumericalDerivative(), OBForceField::NumericalSecondDerivative(), OBForceField::SetConformers(), OBForceField::SetCoordinates(), OBAtom::SetHybAndGeom(), OBBond::SetLength(), OBPointGroup::Symmetrize(), OBForceField::ValidateConjugateGradients(), OBForceField::ValidateLineSearch(), and OBForceField::ValidateSteepestDescent().

◆ SetVector() [2/3]

void SetVector	(	const double	x,
		const double	y,
		const double	z
	)

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

◆ SetCoordPtr()

void SetCoordPtr ( double ** c )

inline

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

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

◆ SetVector() [3/3]

void SetVector ( )

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

◆ SetResidue()

void SetResidue ( OBResidue * res )

inline

Attach an OBResidue res as containing this atom.

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

◆ SetParent()

void SetParent ( OBMol * ptr )

inline

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

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

◆ SetAromatic()

void SetAromatic ( bool value = true )

inline

Mark atom as being aromatic.

Referenced by OBAromaticTyper::AssignAromaticFlags(), and OpenBabel::AssignOBAromaticityModel().

◆ SetInRing()

void SetInRing ( bool value = true )

inline

Mark an atom as belonging to at least one ring.

Referenced by OpenBabel::FindRings().

◆ ClearCoordPtr()

void ClearCoordPtr ( )

inline

Clear the internal coordinate pointer.

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

◆ GetFormalCharge()

int GetFormalCharge ( ) const

inline

◆ GetAtomicNum()

unsigned int GetAtomicNum ( ) const

inline

Returns: the atomic number for this atom

Referenced by OBMol::AddHydrogens(), OBMol::AddNewHydrogens(), OpenBabel::alternate(), OBAromaticTyper::AssignAromaticFlags(), OBResidueData::AssignBonds(), OBBondTyper::AssignFunctionalGroupBonds(), OpenBabel::AssignOBAromaticityModel(), OBGastChrg::AssignPartialCharges(), OpenBabel::AssignRadicalDots(), OpenBabel::AtomIsNSOP(), OpenBabel::ComparePairSecond(), OBBuilder::Connect(), OBMol::ConnectTheDots(), OBMol::ConvertZeroBonds(), OBAtom::CountFreeOxygens(), OBAtom::CountFreeSulfurs(), OBMol::DeleteAtom(), OBMol::DeleteHydrogen(), OBMol::DeleteHydrogens(), OBDepict::DrawMolecule(), OBSmartsMatcher::EvalAtomExpr(), OBAtom::ExplicitHydrogenCount(), OpenBabel::findMetalloceneBonds(), OBMol::FindTorsions(), OpenBabel::GetCorrectedBondVector(), OpenBabel::GetDFFVector(), OBBond::GetEquibLength(), OBMol::GetGIVector(), OBMol::GetGTDVector(), OpenBabel::GetHeavyAtomCoords(), OBAtom::GetHvyDegree(), OBRing::GetRootAtom(), OBRotorRules::GetRotorIncrements(), OBMol::GetTotalSpinMultiplicity(), OBAtom::HasAlphaBetaUnsat(), OpenBabel::HasExocyclicBondToOxygenMinus(), OBAtom::HtoMethyl(), OpenBabel::intToStr(), OBAtom::IsAromaticNOxide(), OpenBabel::isFerroceneBond(), OBStericConformerFilter::IsGood(), OBAtom::IsHbondDonor(), OBAtom::IsNonPolarHydrogen(), OpenBabel::IsNotCorH(), OBAtom::IsPolarHydrogen(), OpenBabel::IsSpecialCase(), OpenBabel::IsSulfoneOxygen(), OBMol::MakeDativeBonds(), OBQueryAtom::Matches(), OpenBabel::NeedsDoubleBond(), OBMol::NumHvyAtoms(), OpenBabel::OBAtomAssignTypicalImplicitHydrogens(), OBMol::PerceiveBondOrders(), OBChainsParser::PerceiveChains(), OBRotorList::RemoveSymVals(), OBAtom::SetHybAndGeom(), OBAlign::SetRefMol(), OBAlign::SetTargetMol(), OpenBabel::validAdditionalBond(), and OBChainsParser::~OBChainsParser().

◆ GetIsotope()

unsigned short int GetIsotope ( ) const

inline

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

Referenced by OBDepict::DrawMolecule(), OBSmartsMatcher::EvalAtomExpr(), OBAtom::ExplicitHydrogenCount(), OpenBabel::findMetalloceneBonds(), and OpenBabel::IsSuppressibleHydrogen().

◆ GetSpinMultiplicity()

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 OpenBabel::alternate(), OpenBabel::AssignRadicalDots(), OpenBabel::findMetalloceneBonds(), OBMol::GetTotalSpinMultiplicity(), and OpenBabel::intToStr().

◆ GetAtomicMass()

double GetAtomicMass ( ) const

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

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

◆ GetExactMass()

double GetExactMass ( ) const

Returns: the atomic mass of this atom given by the isotope (default of 0 gives the most abundant isotope)

Referenced by OBMol::GetExactMass().

◆ GetIdx()

unsigned int GetIdx ( ) const

inline

Returns: the internal atom index (e.g., inside an OBMol)

Referenced by OBMol::AddAtom(), OBMol::AddHydrogens(), OBMol::AddNewHydrogens(), OBMol::Align(), OpenBabel::ApplyRotMatToBond(), OBMol::AreInSameRing(), OBAromaticTyper::AssignAromaticFlags(), OBResidueData::AssignBonds(), OpenBabel::AssignOBAromaticityModel(), OBGastChrg::AssignPartialCharges(), OBBuilder::Build(), OpenBabel::BuildOBRTreeVector(), OpenBabel::CanonicalLabels(), OpenBabel::CartesianToInternal(), OpenBabel::ComparePairSecond(), OBBuilder::Connect(), OBMol::ConnectTheDots(), OBMol::ContigFragList(), OBMol::CopySubstructure(), OBBuilder::CorrectStereoAtoms(), OpenBabel::CreateNewClassVector(), OBMolAtomBFSIter::CurrentDepth(), OBMol::DeleteAtom(), OBMol::DeleteHydrogen(), OBSmartsMatcher::EvalAtomExpr(), AliasData::Expand(), OBSmartsMatcher::FastSingleMatch(), OBMol::FindChildren(), OBMol::FindLargestFragment(), OpenBabel::FindRings(), OBBond::GetBeginAtomIdx(), OpenBabel::GetDFFVector(), OBBond::GetEndAtomIdx(), OpenBabel::getFragment(), OBBuilder::GetFragment(), OBForceField::GetGradient(), OBForceField::GetGrid(), OBMol::GetGTDVector(), OBBond::GetNbrAtomIdx(), OBMol::GetNextFragment(), OBRotorRules::GetRotorIncrements(), OBGraphSym::GetSymmetry(), OBGrid::Init(), OpenBabel::InternalToCartesian(), OBRotorList::IsFixedBond(), OBForceField::IsInSameRing(), OBRing::IsMember(), OBBuilder::IsSpiroAtom(), OBSSMatch::Match(), OBAtom::MatchesSMARTS(), OpenBabel::NeedsDoubleBond(), OBMol::NewAtom(), OpenBabel::OBBondGetSmallestRingSize(), OBMolAtomBFSIter::OBMolAtomBFSIter(), OBMolAtomDFSIter::OBMolAtomDFSIter(), OBMolPairIter::OBMolPairIter(), OBMolAtomDFSIter::operator++(), OBMolAtomBFSIter::operator++(), OBMolPairIter::operator++(), OBAtom::operator=(), OBMol::operator=(), OBAtom::operator==(), OBChainsParser::PerceiveChains(), OBRotorList::RemoveSymVals(), OBMol::RenumberAtoms(), OBRotorList::SetEvalAtoms(), OBAtom::SetHybAndGeom(), OBBond::SetLength(), OBMol::SetTorsion(), OBProxGrid::Setup(), OBSmartsMatcher::SetupAtomMatchTable(), OBFFCalculation2::SetupPointers(), OBFFCalculation3::SetupPointers(), OBFFCalculation4::SetupPointers(), and OBForceField::UpdatePairsSimple().

◆ GetIndex()

unsigned int GetIndex ( ) const

inline

Referenced by OpenBabel::findMetalloceneBonds(), OpenBabel::GetAtomSymClass(), and OBIsomorphismMapper::GetInstance().

◆ GetId()

unsigned long GetId ( ) const

inline

Referenced by OBMol::AddAtom(), OBMol::AddHydrogens(), OBMol::AddNewHydrogens(), OpenBabel::CanonicalLabels(), OBBuilder::CorrectStereoAtoms(), OBMol::DeleteAtom(), OBMol::DeleteHydrogen(), OBBuilder::GetNewBondVector(), OBSmartsMatcher::match(), and OBMol::operator+=().

◆ GetCoordinateIdx()

unsigned int GetCoordinateIdx ( ) const

inline

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

Referenced by OBMol::DeleteHydrogen(), OpenBabel::SetRotorToAngle(), and OBMol::SetTorsion().

◆ GetExplicitDegree()

unsigned int GetExplicitDegree ( ) const

inline

Returns: The number of explicit bonds to this atom

Referenced by OBMol::AddBond(), OBResidueData::AssignBonds(), OBAtomTyper::AssignHyb(), OpenBabel::AssignOBAromaticityModel(), OBGastChrg::AssignPartialCharges(), OBMol::ConnectTheDots(), OBDepict::DrawMolecule(), OBSmartsMatcher::EvalAtomExpr(), OpenBabel::GetLabelAlignment(), OBBuilder::GetNewBondVector(), OBRing::GetRootAtom(), OpenBabel::isFerroceneBond(), OBMol::PerceiveBondOrders(), and OBRotorList::RemoveSymVals().

◆ GetTotalDegree()

unsigned int GetTotalDegree ( ) const

inline

Returns: The total number of bonds to this atom including bonds to implicit hydrogens

Referenced by OpenBabel::ComparePairSecond(), OBSmartsMatcher::EvalAtomExpr(), OBBond::IsAmide(), OBBond::IsPrimaryAmide(), OBBond::IsSecondaryAmide(), OpenBabel::IsSpecialCase(), OBBond::IsTertiaryAmide(), and OpenBabel::NeedsDoubleBond().

◆ GetExplicitValence()

unsigned int GetExplicitValence ( ) const

Returns: The sum of the bond orders of the explicit bonds to this atom

Referenced by OpenBabel::AssignOBAromaticityModel(), OBMol::ConnectTheDots(), OBRing::GetRootAtom(), OBMol::MakeDativeBonds(), OpenBabel::OBAtomAssignTypicalImplicitHydrogens(), OBMol::PerceiveBondOrders(), and OpenBabel::validAdditionalBond().

◆ GetTotalValence()

unsigned int GetTotalValence ( ) const

Returns: The sum of the bond orders of all bonds to this atom including bonds to implicit hydrogens

Referenced by OpenBabel::AssignRadicalDots(), and OBSmartsMatcher::EvalAtomExpr().

◆ GetHyb()

unsigned int GetHyb ( ) const

Returns: The hybridization of this atom: 1 for sp, 2 for sp2, 3 for sp3, 4 for sq. planar, 5 for trig. bipy, 6 for octahedral

Referenced by OBMol::AddHydrogens(), OBMol::AddNewHydrogens(), OBAtomTyper::AssignHyb(), OBGastChrg::AssignPartialCharges(), OBBuilder::Build(), OBBuilder::Connect(), OBSmartsMatcher::EvalAtomExpr(), OBBond::GetEquibLength(), OBBuilder::GetNewBondVector(), OBRotorRules::GetRotorIncrements(), OBAtom::HtoMethyl(), OBAtom::IsAxial(), OBMol::PerceiveBondOrders(), OBRotorList::RemoveSymVals(), and OBAtom::SetHybAndGeom().

◆ GetImplicitHCount()

unsigned char GetImplicitHCount ( ) const

inline

Returns: The number of implicit hydrogens attached to this atom

Referenced by OBMol::AddHydrogens(), OBMol::AddNewHydrogens(), OBChemTsfm::Apply(), OpenBabel::AssignOBAromaticityModel(), OBMol::ConvertZeroBonds(), OBMol::DeleteHydrogens(), OBDepict::DrawMolecule(), OBSmartsMatcher::EvalAtomExpr(), OBMol::GetExactMass(), OBMol::GetGIVector(), OBMol::GetMolWt(), and OpenBabel::TotalHydrogenCount().

◆ GetHvyDegree()

unsigned int GetHvyDegree ( ) const

Returns: The number of non-hydrogens connected to this atom

Referenced by OBGastChrg::AssignPartialCharges(), OBAtom::CountFreeOxygens(), OBAtom::CountFreeSulfurs(), OBMol::GetGIVector(), OBBond::IsPrimaryAmide(), OBBond::IsSecondaryAmide(), OBBuilder::IsSpiroAtom(), OpenBabel::IsSulfoneOxygen(), OpenBabel::IsSuppressibleHydrogen(), OBBond::IsTertiaryAmide(), and OBChainsParser::PerceiveChains().

◆ GetHeteroDegree()

unsigned int GetHeteroDegree ( ) const

Returns: The number of heteroatoms connected to an atom

◆ GetType()

char * GetType ( )

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

Referenced by OBGastChrg::AssignPartialCharges(), and OBAtomTyper::AssignTypes().

◆ GetX()

double GetX ( ) const

inline

Returns: the x coordinate

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

◆ GetY()

double GetY ( ) const

inline

Returns: the y coordinate

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

◆ GetZ()

double GetZ ( ) const

inline

Returns: the z coordinate

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

◆ x()

double x ( ) const

inline

Returns: the x coordinate

Referenced by OBMol::Center(), OBMol::Has2D(), OBMol::Has3D(), OBMol::ToInertialFrame(), OBForceField::ValidateConjugateGradients(), OBForceField::ValidateLineSearch(), and OBForceField::ValidateSteepestDescent().

◆ y()

double y ( ) const

inline

Returns: the y coordinate

Referenced by OBMol::Center(), OBMol::Has2D(), OBMol::Has3D(), OBMol::ToInertialFrame(), OBForceField::ValidateConjugateGradients(), OBForceField::ValidateLineSearch(), and OBForceField::ValidateSteepestDescent().

◆ z()

double z ( ) const

inline

Returns: the z coordinate

Referenced by OBMol::Center(), OBMol::Has2D(), OBMol::Has3D(), OBMol::ToInertialFrame(), and OBForceField::ValidateConjugateGradients().

◆ GetCoordinate()

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(), OBFFCalculation2::SetupPointers(), OBFFCalculation3::SetupPointers(), OBFFCalculation4::SetupPointers(), and OBForceField::UpdatePairsSimple().

◆ GetVector() [1/2]

vector3 & GetVector ( )

Returns: the coordinates as a vector3 object

Referenced by OBMol::Align(), OpenBabel::ApplyRotMatToBond(), OBAtom::AverageBondAngle(), OBBuilder::Build(), OpenBabel::CartesianToInternal(), OBMol::Center(), OBBuilder::Connect(), OBMol::ConnectTheDots(), OBDepict::DrawMolecule(), OBAtom::Duplicate(), OBMol::EndModify(), AliasData::Expand(), OBAlign::GetAlignment(), OBAtom::GetAngle(), OBAtom::GetDistance(), OpenBabel::GetLabelAlignment(), OBBuilder::GetNewBondVector(), OBMol::GetTorsion(), OBMol::HasNonZeroCoords(), OBBond::IsDoubleBondGeometry(), OBBuilder::IsSpiroAtom(), OBForceField::LineSearch(), OBForceField::NumericalDerivative(), OBForceField::NumericalSecondDerivative(), OBAtom::SetHybAndGeom(), OBBond::SetLength(), OBAlign::SetRefMol(), OBAlign::SetTargetMol(), OBMol::SetTorsion(), OBAtom::SmallestBondAngle(), OBBuilder::Swap(), and OBForceField::ValidateLineSearch().

◆ GetVector() [2/2]

const vector3 & GetVector ( ) const

Returns: the coordinates as a vector3 object

◆ GetPartialCharge()

double GetPartialCharge ( )

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

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

◆ GetResidue()

OBResidue * GetResidue ( )

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

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

◆ GetParent()

OBMol* GetParent ( )

inline

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

Referenced by OpenBabel::addNbrs(), OpenBabel::BuildOBRTreeVector(), OBSmartsMatcher::EvalAtomExpr(), OpenBabel::findMetalloceneBonds(), OpenBabel::GetAtomSymClass(), OBBuilder::GetNewBondVector(), and OBBond::SetLength().

◆ GetNewBondVector()

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

◆ GetBond()

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(), OBBuilder::GetNewBondVector(), and OBMol::PerceiveBondOrders().

◆ BeginBonds()

OBBondIterator BeginBonds ( )

inline

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

Referenced by OBResidueData::AssignBonds().

◆ EndBonds()

OBBondIterator EndBonds ( )

inline

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

◆ BeginBond()

OBBond * BeginBond ( OBBondIterator & i )

Set the iterator i to the beginning of the bonds

Returns: The first bond to this atom (or NULL if none exist)

Referenced by OpenBabel::ComparePairSecond(), OBMol::ConnectTheDots(), OBMol::ContigFragList(), OBMol::ConvertDativeBonds(), OBMol::FindLargestFragment(), OpenBabel::FindRings(), OBResidue::GetBonds(), OpenBabel::GetDFFVector(), OBMol::GetGTDVector(), OBBond::IsAmide(), OBAtom::IsAmideNitrogen(), OBBond::IsEster(), OBAtom::IsOneFour(), OBAtom::IsOneThree(), OBBond::IsPrimaryAmide(), OBBond::IsSecondaryAmide(), OpenBabel::IsSulfoneOxygen(), OBBond::IsTertiaryAmide(), and OBMol::MakeDativeBonds().

◆ NextBond()

OBBond * NextBond ( OBBondIterator & i )

Increment the iterator i

Returns: The next bond to this atom (or NULL if none exist)

Referenced by OpenBabel::ComparePairSecond(), OBMol::ConnectTheDots(), OBMol::ContigFragList(), OBMol::ConvertDativeBonds(), OBMol::FindLargestFragment(), OpenBabel::FindRings(), OBResidue::GetBonds(), OpenBabel::GetDFFVector(), OBMol::GetGTDVector(), OBBond::IsAmide(), OBAtom::IsAmideNitrogen(), OBBond::IsEster(), OBAtom::IsOneFour(), OBAtom::IsOneThree(), OBBond::IsPrimaryAmide(), OBBond::IsSecondaryAmide(), OpenBabel::IsSulfoneOxygen(), OBBond::IsTertiaryAmide(), and OBMol::MakeDativeBonds().

◆ BeginNbrAtom()

OBAtom * BeginNbrAtom ( OBBondIterator & i )

Set the iterator i to the beginning of the bonds

Returns: The first neighboring atom (or NULL if none exist)

Referenced by OBMol::AddBond(), OBAromaticTyper::AssignAromaticFlags(), OBAtomTyper::AssignTypes(), OpenBabel::BuildOBRTreeVector(), OpenBabel::ComparePairSecond(), OBMol::DeleteAtom(), OBMol::DeleteHydrogen(), OBMol::DeleteHydrogens(), AliasData::Expand(), OBSmartsMatcher::FastSingleMatch(), OBMol::FindChildren(), OBMol::FindTorsions(), OBMol::GetBond(), OpenBabel::GetLabelAlignment(), OBBuilder::GetNewBondVector(), OBRotorRules::GetRotorIncrements(), OBAtom::HasAlphaBetaUnsat(), OBAtom::IsAxial(), OBBond::IsDoubleBondGeometry(), OBRotorList::IsFixedBond(), OBSSMatch::Match(), OBMolAtomBFSIter::OBMolAtomBFSIter(), OBMolAtomDFSIter::OBMolAtomDFSIter(), OBMolAtomDFSIter::operator++(), OBMolAtomBFSIter::operator++(), OBMol::PerceiveBondOrders(), OBChainsParser::PerceiveChains(), and OBRotorList::SetEvalAtoms().

◆ NextNbrAtom()

OBAtom * NextNbrAtom ( OBBondIterator & i )

Increment the iterator i

Returns: The next neighboring atom (or NULL if none exist)

Referenced by OBAromaticTyper::AssignAromaticFlags(), OBAtomTyper::AssignTypes(), OpenBabel::BuildOBRTreeVector(), OpenBabel::ComparePairSecond(), OBMol::DeleteAtom(), OBMol::DeleteHydrogen(), OBMol::DeleteHydrogens(), AliasData::Expand(), OBAtom::ExplicitHydrogenCount(), OBSmartsMatcher::FastSingleMatch(), OBMol::FindChildren(), OBMol::FindTorsions(), OBMol::GetBond(), OpenBabel::GetLabelAlignment(), OBBuilder::GetNewBondVector(), OBRotorRules::GetRotorIncrements(), OBAtom::HasAlphaBetaUnsat(), OBAtom::IsAxial(), OBRotorList::IsFixedBond(), OBSSMatch::Match(), OBMolAtomBFSIter::OBMolAtomBFSIter(), OBMolAtomDFSIter::OBMolAtomDFSIter(), OBMolAtomDFSIter::operator++(), OBMolAtomBFSIter::operator++(), OBMol::PerceiveBondOrders(), OBChainsParser::PerceiveChains(), and OBRotorList::SetEvalAtoms().

◆ GetDistance() [1/3]

double GetDistance ( int index )

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

Referenced by OBBondTyper::AssignFunctionalGroupBonds().

◆ GetDistance() [2/3]

double GetDistance ( OBAtom * b )

Returns: the distance to the supplied OBAtom

◆ GetDistance() [3/3]

double GetDistance ( vector3 * v )

Returns: the distance to the coordinates of the supplied vector3

Since: version 2.4

◆ GetAngle() [1/2]

double GetAngle	(	int	b,
		int	c
	)

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

Referenced by OBMol::GetAngle().

◆ GetAngle() [2/2]

double GetAngle	(	OBAtom *	b,
		OBAtom *	c
	)

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

◆ NewResidue()

void NewResidue ( )

inline

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

◆ AddResidue()

void AddResidue ( OBResidue * res )

inline

Add (set) the residue for this atom.

◆ DeleteResidue()

void DeleteResidue ( )

inline

Delete any residue associated with this atom.

◆ AddBond()

void AddBond ( OBBond * bond )

inline

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

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

◆ InsertBond()

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().

◆ DeleteBond()

bool DeleteBond ( OBBond * bond )

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

◆ ClearBond()

void ClearBond ( )

inline

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

◆ HtoMethyl()

bool HtoMethyl ( )

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

Returns: success or failure

◆ SetHybAndGeom()

bool SetHybAndGeom ( int hyb )

Change the hybridization of this atom and modify the geometry accordingly

Returns: success or failure

Deprecated:: This will be removed in future versions of Open Babel

◆ CountFreeOxygens()

unsigned int CountFreeOxygens ( ) const

Returns: The number of oxygen atoms connected that only have one heavy valence

Referenced by OBGastChrg::AssignPartialCharges(), OBAtom::IsCarboxylOxygen(), OBAtom::IsNitroOxygen(), OBAtom::IsPhosphateOxygen(), OBAtom::IsSulfateOxygen(), and OpenBabel::IsSulfoneOxygen().

◆ CountFreeSulfurs()

unsigned int CountFreeSulfurs ( ) const

Returns: The number of sulfur atoms connected that only have one heavy valence

Since: version 2.4

Referenced by OBAtom::IsCarboxylOxygen().

◆ ExplicitHydrogenCount()

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 OBSmartsMatcher::EvalAtomExpr(), OBMol::PerceiveBondOrders(), and OpenBabel::TotalHydrogenCount().

◆ MemberOfRingCount()

unsigned int MemberOfRingCount ( ) const

Returns: The number of rings that contain this atom

Referenced by OBSmartsMatcher::EvalAtomExpr().

◆ MemberOfRingSize()

unsigned int MemberOfRingSize ( ) const

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

◆ CountRingBonds()

unsigned int CountRingBonds ( ) const

Returns: The number of explicit ring connections to this atom

Referenced by OBSmartsMatcher::EvalAtomExpr().

◆ SmallestBondAngle()

double SmallestBondAngle ( )

Returns: The smallest angle of bonds to this atom

Referenced by OBMol::ConnectTheDots().

◆ AverageBondAngle()

double AverageBondAngle ( )

Returns: The average angle of bonds to this atom

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

◆ LewisAcidBaseCounts()

pair< int, int > LewisAcidBaseCounts ( ) const

Lewis acid/base vacancies for this atom

Returns: A pair of integers, where first is acid count and second is base count

Since: version 2.3

The returned values count whole lone pairs, so the acid count is the number of electron pairs desired and the base count is the number of electron pairs available.

Algorithm from:
Clark, A. M. Accurate Specification of Molecular Structures: The Case for
Zero-Order Bonds and Explicit Hydrogen Counting. Journal of Chemical Information
and Modeling, 51, 3149-3157 (2011). http://pubs.acs.org/doi/abs/10.1021/ci200488k

Referenced by OBMol::ConvertZeroBonds().

◆ HasResidue()

bool HasResidue ( )

inline

Returns: Is there any residue information?

Referenced by OBMol::AddNewHydrogens().

◆ IsHetAtom()

bool IsHetAtom ( )

inline

Returns: Is this a HETATM in a residue (returns false if not in a residue)

Since: version 2.4

◆ IsAromatic()

bool IsAromatic ( ) const

Returns: Is the atom aromatic?

Referenced by OpenBabel::ComparePairSecond(), OBSmartsMatcher::EvalAtomExpr(), OBMol::GetGIVector(), OBQueryAtom::Matches(), and OpenBabel::NeedsDoubleBond().

◆ IsInRing()

bool IsInRing ( ) const

Returns: Is the atom in a ring?

Referenced by OBAromaticTyper::AssignAromaticFlags(), OpenBabel::AssignOBAromaticityModel(), OBBuilder::Connect(), OBSmartsMatcher::EvalAtomExpr(), OpenBabel::findMetalloceneBonds(), OBMol::GetGIVector(), OBAtom::IsAxial(), OBQueryAtom::Matches(), and OBMol::PerceiveBondOrders().

◆ IsInRingSize()

bool IsInRingSize ( int size ) const

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

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

◆ IsHeteroatom()

bool IsHeteroatom ( )

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

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

◆ IsConnected()

bool IsConnected ( OBAtom * a1 )

Returns: Is this atom directly connected to the supplied OBAtom?

Referenced by OBAromaticTyper::AssignAromaticFlags(), OBMol::ConnectTheDots(), OBStericConformerFilter::IsGood(), OBMolPairIter::OBMolPairIter(), and OBMolPairIter::operator++().

◆ IsOneThree()

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++().

◆ IsOneFour()

bool IsOneFour ( OBAtom * a1 )

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

◆ IsCarboxylOxygen()

bool IsCarboxylOxygen ( )

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

Referenced by OBGastChrg::AssignPartialCharges(), and OBBuilder::GetNewBondVector().

◆ IsPhosphateOxygen()

bool IsPhosphateOxygen ( )

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

Referenced by OBGastChrg::AssignPartialCharges().

◆ IsSulfateOxygen()

bool IsSulfateOxygen ( )

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

Referenced by OBGastChrg::AssignPartialCharges().

◆ IsNitroOxygen()

bool IsNitroOxygen ( )

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

◆ IsAmideNitrogen()

bool IsAmideNitrogen ( )

Returns true if nitrogen is part of an amide.

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

◆ IsPolarHydrogen()

bool IsPolarHydrogen ( )

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

Referenced by OBMol::DeletePolarHydrogens().

◆ IsNonPolarHydrogen()

bool IsNonPolarHydrogen ( )

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

Referenced by OBMol::DeleteNonPolarHydrogens().

◆ IsAromaticNOxide()

bool IsAromaticNOxide ( )

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

◆ IsChiral()

bool IsChiral ( )

Returns: Is this atom chiral?

Todo:

◆ IsAxial()

bool IsAxial ( )

Returns: Is this atom an axial atom in a ring

◆ IsHbondAcceptor()

bool IsHbondAcceptor ( )

Returns: Is this atom a hydrogen-bond acceptor (considering also atom surrounding)

◆ IsHbondAcceptorSimple()

bool IsHbondAcceptorSimple ( )

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

◆ IsHbondDonor()

bool IsHbondDonor ( )

Returns: Is this atom a hydrogen-bond donor?

Referenced by OBAtom::IsHbondDonorH().

◆ IsHbondDonorH()

bool IsHbondDonorH ( )

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

◆ IsMetal()

bool IsMetal ( )

Returns: Is this atom a metal?

Since: version 2.4

◆ HasAlphaBetaUnsat()

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.

◆ HasBondOfOrder()

bool HasBondOfOrder ( unsigned int bo )

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

Referenced by OBMol::PerceiveBondOrders().

◆ CountBondsOfOrder()

int CountBondsOfOrder ( unsigned int bo )

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

◆ HighestBondOrder()

int HighestBondOrder ( )

Returns: The maximum bond order for this atom

◆ HasNonSingleBond()

bool HasNonSingleBond ( )

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

Referenced by OBMol::PerceiveBondOrders().

◆ HasSingleBond()

bool HasSingleBond ( )

inline

Returns: Does this atom have a single bond

◆ HasDoubleBond()

bool HasDoubleBond ( )

inline

Returns: Does this atom have a double bond

Referenced by OBBondTyper::AssignFunctionalGroupBonds().

◆ HasAromaticBond()

bool HasAromaticBond ( )

inline

Returns: Does this atom have an aromatic bond

◆ MatchesSMARTS()

bool MatchesSMARTS ( const char * pattern )

Returns: Whether this atom matches the first atom in a given SMARTS pattern

◆ DoTransformations()

virtual OBBase* DoTransformations	(	const std::map< std::string, std::string > *	,
		OBConversion *
	)

inlinevirtualinherited

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.

◆ ClassDescription()

static const char* ClassDescription ( )

inlinestaticinherited

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

◆ CastAndClear()

T* CastAndClear ( bool clear = true )

inlineinherited

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

◆ GetTitle()

virtual const char* GetTitle ( bool replaceNewlines = true ) const

inlinevirtualinherited

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

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

◆ SetTitle()

virtual void SetTitle ( const char * )

inlinevirtualinherited

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

◆ HasData() [1/3]

bool HasData ( const std::string & s )

inherited

Returns: whether the generic attribute/value pair exists

Referenced by OBDepict::AddAtomLabels(), OBDepict::DrawMolecule(), AliasData::Expand(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBForceField::GetPartialCharges(), OBDescriptor::MatchPairData(), OBMoleculeFormat::ReadChemObjectImpl(), and OBMol::SetEnergies().

◆ HasData() [2/3]

bool HasData ( const char * s )

inherited

Returns: whether the generic attribute/value pair exists

◆ HasData() [3/3]

bool HasData ( const unsigned int type )

inherited

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

◆ DeleteData() [1/4]

void DeleteData ( unsigned int type )

inherited

Delete any data matching the given OBGenericDataType.

Referenced by OpenBabel::CanonicalLabels(), OBDescriptor::DeleteProperties(), OpenBabel::DeleteStereoOnAtom(), and OBMol::RenumberAtoms().

◆ DeleteData() [2/4]

void DeleteData ( OBGenericData * gd )

inherited

Delete the given generic data from this object.

◆ DeleteData() [3/4]

void DeleteData ( std::vector< OBGenericData *> & vg )

inherited

Delete all of the given generic data from this object.

◆ DeleteData() [4/4]

bool DeleteData ( const std::string & s )

inherited

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

◆ SetData()

void SetData ( OBGenericData * d )

inlineinherited

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

Referenced by OBGastChrg::AssignPartialCharges(), OBMol::CopySubstructure(), AliasData::Expand(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBForceField::GetPartialCharges(), OBMoleculeFormat::MakeCombinedMolecule(), OBDescriptor::PredictAndSave(), AliasData::RevertToAliasForm(), and OBMol::SetEnergies().

◆ CloneData()

void CloneData ( OBGenericData * d )

inherited

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

Since: version 2.2

Referenced by AliasData::Expand().

◆ DataSize()

size_t DataSize ( ) const

inlineinherited

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

◆ GetData() [1/5]

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 OBDepict::AddAtomLabels(), OBDepict::DrawMolecule(), OpenBabel::extract_thermochemistry(), OBDescriptor::FilterCompare(), OpenBabel::GetAtomSymClass(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBForceField::GetPartialCharges(), OBDescriptor::GetValues(), OpenBabel::IsSuppressibleHydrogen(), OBMoleculeFormat::MakeCombinedMolecule(), OBMolAngleIter::OBMolAngleIter(), OBMolRingIter::OBMolRingIter(), OBMolTorsionIter::OBMolTorsionIter(), and OBDescriptor::PredictAndSave().

◆ GetData() [2/5]

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

◆ GetData() [3/5]

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

◆ GetData() [4/5]

std::vector<OBGenericData*>& GetData ( )

inlineinherited

Returns: all data, suitable for iterating

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

◆ GetData() [5/5]

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

inherited

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

◆ GetAllData()

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(), OBMol::CopySubstructure(), OBBuilder::CorrectStereoAtoms(), OBBuilder::CorrectStereoBonds(), OpenBabel::DeleteStereoOnAtom(), and OBMol::operator+=().

◆ BeginData()

OBDataIterator BeginData ( )

inlineinherited

Returns: An iterator pointing to the beginning of the data

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

◆ EndData()

OBDataIterator EndData ( )

inlineinherited

Returns: An iterator pointing to the end of the data

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

Member Data Documentation

◆ _ele

unsigned char _ele

protected

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

Referenced by OBAtom::Duplicate().

◆ _imph

unsigned char _imph

protected

number of implicit hydrogens

Referenced by OBAtom::Duplicate().

◆ _type

char _type[OBATOM_TYPE_LEN]

protected

atomic type

Referenced by OBAtom::Duplicate().

◆ _fcharge

short _fcharge

protected

formal charge

Referenced by OBAtom::Duplicate().

◆ _isotope

unsigned short _isotope

protected

isotope (0 = most abundant)

Referenced by OBAtom::Duplicate().

◆ _spinmultiplicity

short _spinmultiplicity

protected

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

Referenced by OBAtom::Duplicate().

◆ _idx

unsigned int _idx

protected

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

◆ _parent

OBMol* _parent

protected

parent molecule (if any)

◆ _vbond

std::vector<OBBond*> _vbond

protected

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

◆ _cidx

unsigned int _cidx

protected

index into coordinate array

◆ _hyb

unsigned short _hyb

protected

hybridization

Referenced by OBAtom::Duplicate().

◆ _flags

unsigned short _flags

protected

bitwise flags (e.g. aromaticity)

Referenced by OBAtom::Duplicate().

◆ _pcharge

double _pcharge

protected

partial charge

Referenced by OBAtom::Duplicate().

◆ _c

double** _c

protected

coordinate array in double*

◆ _v

vector3 _v

mutableprotected

coordinate vector

◆ _residue

OBResidue* _residue

protected

parent residue (if applicable)

◆ _id

unsigned long _id

protected

unique id

Referenced by OBAtom::Duplicate().

◆ Visit

bool Visit

Used internally by graph traversal algorithms.

◆ _vdata

std::vector<OBGenericData*> _vdata

protectedinherited

Custom data.

Referenced by OBMol::OBMol().

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

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

◆ StereoFlag

Constructor & Destructor Documentation

◆ OBAtom()

◆ ~OBAtom()

Member Function Documentation

◆ GetFlag()

◆ SetFlag()

◆ UnsetFlag()

◆ HasFlag()

◆ operator=()

◆ operator==()

◆ Duplicate()

◆ Clear()

◆ SetIdx()

◆ SetId()

◆ SetHyb()

◆ SetAtomicNum()

◆ SetIsotope()

◆ SetImplicitHCount()

◆ SetFormalCharge()

◆ SetSpinMultiplicity()

◆ SetType() [1/2]

◆ SetType() [2/2]

◆ SetPartialCharge()

◆ SetVector() [1/3]

◆ SetVector() [2/3]

◆ SetCoordPtr()

◆ SetVector() [3/3]

◆ SetResidue()

◆ SetParent()

◆ SetAromatic()

◆ SetInRing()

◆ ClearCoordPtr()

◆ GetFormalCharge()

◆ GetAtomicNum()

◆ GetIsotope()

◆ GetSpinMultiplicity()

◆ GetAtomicMass()

◆ GetExactMass()

◆ GetIdx()

◆ GetIndex()

◆ GetId()

◆ GetCoordinateIdx()

◆ GetExplicitDegree()

◆ GetTotalDegree()

◆ GetExplicitValence()

◆ GetTotalValence()

◆ GetHyb()

◆ GetImplicitHCount()

◆ GetHvyDegree()

◆ GetHeteroDegree()

◆ GetType()

◆ GetX()

◆ GetY()

◆ GetZ()

◆ x()

◆ y()

◆ z()

◆ GetCoordinate()

◆ GetVector() [1/2]

◆ GetVector() [2/2]

◆ GetPartialCharge()

◆ GetResidue()

◆ GetParent()

◆ GetNewBondVector()

◆ GetBond()

◆ BeginBonds()

◆ EndBonds()

◆ BeginBond()

◆ NextBond()

◆ BeginNbrAtom()

◆ NextNbrAtom()