OBStereoBase Class Reference
[Stereochemistry]
Base class for all stereochemistry classes. More...
#include <openbabel/stereo/stereo.h>
Public Member Functions | |
| OBStereoBase (OBMol *mol) | |
| virtual | ~OBStereoBase () |
| virtual OBGenericData * | Clone (OBBase *) const |
| void | SetAttribute (const std::string &v) |
| void | SetOrigin (const DataOrigin s) |
| virtual const std::string & | GetAttribute () const |
| unsigned int | GetDataType () const |
| virtual const std::string & | GetValue () const |
| virtual DataOrigin | GetOrigin () const |
Geniric (for all OBStereo::Type) stereochemistry | |
| OBMol * | GetMolecule () const |
| virtual OBStereo::Type | GetType () const =0 |
| void | SetSpecified (bool specified) |
| bool | IsSpecified () const |
Protected Attributes | |
| std::string | _attr |
| unsigned int | _type |
| DataOrigin | _source |
Detailed Description
Base class for all stereochemistry classes.
All stereochemistry classes are derived from OBStereoBase. This class inherits from OBGenericData which allows the objects to be stored in the molecule. The attribute (OBGenericData::GetAttribute) is set to "StereoData" and the data type is OBGenericDataType::StereoData. The pure virtual OBStereoBase::GetType function must be implemented by derived classes to return a type defined in OBStereo::Type.
Use the OBStereoFacade for easy access to the derived classes.
OBStereoBase keeps track of the OBMol object. This must always be a valid (not 0 or deleted) pointer and can only be set using the constructor. Subclasses can use this to get more information on bonding for example. Finally, OBStereoBase also keeps track of the specified flag. By default, this is always set to true.
- See also:
- OBStereo OBStereoFacade
- Since:
- version 2.3
Constructor & Destructor Documentation
| OBStereoBase | ( | OBMol * | mol | ) | [inline] |
Constructor. By default, the stereochemistry is specified. Use SetSpecified(false) for unspecified/unknown stereochemistry.
- Parameters:
-
mol The molecule.
| virtual ~OBStereoBase | ( | ) | [inline, virtual] |
Destructor.
Member Function Documentation
| OBMol* GetMolecule | ( | ) | const [inline] |
Get the molecule. This can be used by subclasses when more information is needed (e.g. OBCisTransStereo::GetCisRef, ...).
| virtual OBStereo::Type GetType | ( | ) | const [pure virtual] |
Reimplemented by subclasses to return the type defined in OBStereo::Type.
Implemented in OBCisTransStereo, OBSquarePlanarStereo, and OBTetrahedralStereo.
| void SetSpecified | ( | bool | specified | ) | [inline] |
Set whether the stereochemistry is specified. Comparing a specified OBStereoBase derived class (or it's Config struct) with an unspecified one, always returns true.
| bool IsSpecified | ( | ) | const [inline] |
- Returns:
- True if the stereochemistry is specified.
| virtual OBGenericData* Clone | ( | OBBase * | ) | const [inline, virtual, inherited] |
Reimplemented in AliasData, OBAtomClassData, OBCommentData, OBExternalBondData, OBPairData, OBSetData, OBVirtualBond, OBRingData, OBUnitCell, OBConformerData, OBSymmetryData, OBTorsionData, OBAngleData, OBChiralData, OBSerialNums, OBVibrationData, OBDOSData, OBOrbitalData, OBElectronicTransitionData, OBRotationData, OBVectorData, OBMatrixData, OBRateData, OBNasaThermoData, OBRotamerList, OBCisTransStereo, OBSquarePlanarStereo, and OBTetrahedralStereo.
Referenced by OBBase::CloneData(), and OBMoleculeFormat::MakeCombinedMolecule().
| void SetAttribute | ( | const std::string & | v | ) | [inline, inherited] |
Set the attribute (key), which can be used to retrieve this data.
Referenced by OBGastChrg::AssignPartialCharges(), OBMol::DoTransformations(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBForceField::GetAtomTypes(), OBMol::GetFormula(), OBMol::GetLSSR(), OBForceField::GetPartialCharges(), OBMol::GetSSSR(), OBDescriptor::PredictAndSave(), and OBMol::SetFormula().
| void SetOrigin | ( | const DataOrigin | s | ) | [inline, inherited] |
Set the origin of this data, which can be used to filter the data.
Referenced by OBGastChrg::AssignPartialCharges(), OpenBabel::CalcSignedVolume(), OBMol::DoTransformations(), OBMol::FindAngles(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBMol::GetFormula(), OBMol::GetLSSR(), OBMol::GetSSSR(), OBDescriptor::PredictAndSave(), and OBMol::SetFormula().
| virtual const std::string& GetAttribute | ( | ) | const [inline, virtual, inherited] |
- Returns:
- The attribute (key), which can be used to retrieve this data
Referenced by OBMoleculeFormat::MakeCombinedMolecule().
| unsigned int GetDataType | ( | ) | const [inline, inherited] |
- Returns:
- the data type for this object as defined in OBGenericDataType
| virtual const std::string& GetValue | ( | ) | const [inline, virtual, inherited] |
Base class returns a default value (the attribute type) but should never be called.
Reimplemented in OBCommentData, and OBPairData.
Referenced by OBDepict::DrawMolecule(), OBDescriptor::FilterCompare(), and OBDescriptor::GetValues().
| virtual DataOrigin GetOrigin | ( | ) | const [inline, virtual, inherited] |
Member Data Documentation
std::string _attr [protected, inherited] |
attribute tag (e.g., "UnitCell", "Comment" or "Author")
Referenced by OBRotamerList::Clone(), and OBNasaThermoData::OBNasaThermoData().
unsigned int _type [protected, inherited] |
attribute type -- declared for each subclass
Referenced by OBRotamerList::Clone(), and OBNasaThermoData::OBNasaThermoData().
DataOrigin _source [protected, inherited] |
source of data for accounting
Referenced by OBChiralData::operator=(), OBTorsionData::operator=(), OBAngleData::operator=(), OBConformerData::operator=(), and OBSymmetryData::operator=().
The documentation for this class was generated from the following file:
