OBBase Class Reference

#include <openbabel/base.h>

Inheritance diagram for OBBase:

Public Member Functions
virtual	~OBBase ()
virtual bool	Clear ()
virtual OBBase *	DoTransformations (const std::map< std::string, std::string > *, OBConversion *)
template<class T >
T *	CastAndClear (bool clear=true)
virtual const char *	GetTitle (bool replaceNewlines=true) const
virtual void	SetTitle (const char *)
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 * >	GetAllData (const unsigned int type)
std::vector< OBGenericData * > &	GetData ()
std::vector< OBGenericData * >	GetData (DataOrigin source)
OBDataIterator	BeginData ()
OBDataIterator	EndData ()

Static Public Member Functions
static const char *	ClassDescription ()

Protected Attributes
std::vector< OBGenericData * >	_vdata

Detailed Description

Base Class.

The various classes (Atom, Bond, Molecule) inherit from base classes– OBBase is largely a placeholder class. It also allows adding, deleting, and retrieving OBGenericData objects, which are ways to store arbitrary data for any atom, bond, molecule, or residue.

For example, a graphics program may want to allow users to add labels to individual atoms:

string atomLabel; // e.g., from the user adding annotation to an atom
if (!atom.HasData("UserLabel")) // stored textual data as an OBPairData
{
 OBPairData *label = new OBPairData;
 label->SetAttribute("UserLabel");
 label->SetValue(atomLabel);
 label->SetOrigin(userInput); // set by user, not by Open Babel

 atom.SetData(label);
}

This class is also important in the OBConversion class. Any derived class of OBBase can be supported in reading or writing data. While most OBFormat "translators" are designed around reading molecular data, the OBConversion framework can support any base object. For example OBReaction supports reading and writing reaction files, OBGrid supports reading and writing 2D or 3D "grids" of numeric data.

Therefore if you want to expand the range of input or output via the OBConversion and OBFormat classes, you will also need to make sure you define an appropriate derived class from OBBase.

Constructor & Destructor Documentation

~OBBase()

virtual ~OBBase ( )

inlinevirtual

Member Function Documentation

Clear()

bool Clear ( void  )

virtual

Clear any and all data associated with this object.

This method can be called by OBConversion::Read() before reading data. Derived classes should be sure to call OBBase::Clear() to remove inherited generic data.

Returns

Whether the call was successful.

Since

version 2.1.

Reimplemented in OBMol, OBAtom, OBReaction, and OBResidue.

Referenced by OBResidue::Clear().

DoTransformations()

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

inlinevirtual

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 ( )

inlinestatic

Returns

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

CastAndClear()

T* CastAndClear ( bool  clear = true )

inline

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

GetTitle()

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

inlinevirtual

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 *  )

inlinevirtual

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

HasData() [1/3]

bool HasData

(

const std::string &

s

)

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

)

Returns

whether the generic attribute/value pair exists

HasData() [3/3]

bool HasData

(

const unsigned int

type

)

Returns

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

DeleteData() [1/4]

void DeleteData

(

unsigned int

type

)

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

)

Delete the given generic data from this object.

DeleteData() [3/4]

void DeleteData

(

std::vector< OBGenericData *> &

vg

)

Delete all of the given generic data from this object.

DeleteData() [4/4]

bool DeleteData

(

const std::string &

s

)

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

SetData()

void SetData ( OBGenericData *  d )

inline

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

)

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

inline

Returns

the number of OBGenericData items attached to this molecule.

GetData() [1/5]

OBGenericData * GetData

(

const unsigned int

type

)

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

)

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

)

Returns

any data matching the given attribute name or NULL if nothing matches

the value given an attribute name

GetAllData()

std::vector< OBGenericData * > GetAllData

(

const unsigned int

type

)

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+=().

GetData() [4/5]

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

inline

Returns

all data, suitable for iterating

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

GetData() [5/5]

std::vector< OBGenericData * > GetData

(

DataOrigin

source

)

Returns

all data with a specific origin, suitable for iterating

BeginData()

OBDataIterator BeginData ( )

inline

Returns

An iterator pointing to the beginning of the data

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

EndData()

OBDataIterator EndData ( )

inline

Returns

An iterator pointing to the end of the data

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

Member Data Documentation

_vdata

std::vector<OBGenericData*> _vdata

protected

Custom data.

Referenced by OBMol::OBMol().

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

• base.h
• base.cpp