OBTetraPlanarStereo Class Reference

Base class for handling and storing planar stereochemistry with 4 reference atoms. More...

#include <openbabel/stereo/tetraplanar.h>

Inheritance diagram for OBTetraPlanarStereo:

List of all members.

Public Member Functions
	OBTetraPlanarStereo (OBMol *mol)
virtual	~OBTetraPlanarStereo ()
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
Static Public Member Functions
template<typename ConfigType >
static ConfigType	ToConfig (const ConfigType &cfg, unsigned long start, OBStereo::Shape shape=OBStereo::ShapeU)
Protected Attributes
std::string	_attr
unsigned int	_type
DataOrigin	_source

---

Detailed Description

Base class for handling and storing planar stereochemistry with 4 reference atoms.

Combinations

The four reference ids can be treated like a sequence of 4 numbers. Each element can only occur once. This means there are 4! = 24 combinations.

These are the 24 possible combinations or permutations.

 1234   2134   3124   4123
 1243   2143   3142   4132
 1324   2314   3214   4213
 1342   2341   3241   4231
 1423   2413   3412   4312
 1432   2431   3421   4321

Based on which reference ids are on opposite sides (180°), it is possible to divide these 24 combinations in three sets. For this it is also needed to make use of a shape to map the reference id indexes on the points in the plane. Without these shapes or a fixed meaning, these sequences have no meaning. The use of these shapes (U, Z & 4) is illustrated in the figure below:

In the figure, it can be seen the OBStereo::ShapeU implies the 1st reference id in the sequence is opposite to the 3th and the 2nd is opposite to the 4th. The same can be done for OBStereo::ShapeZ and OBStereo::Shape

Grouped by opposite reference ids using OBStereo::Shape4

 1-2, 3-4 : 1234, 1243, 2134, 2143, 3412, 3421, 4312, 4321
 1-3, 2-4 : 1324, 1242, 2413, 2431, 3124, 3142, 4213, 4231
 1-4, 2-3 : 1423, 1432, 2314, 2341, 3214, 3241, 4123, 4132

Internally the reference ids are stored in a U shape. The OBTetraPlanarStereo::ToInternal() and OBTetraPlanarStereo::ToShape() methods convert between the internally used U shape and the other shapes.

Like all stereo classes, errors, warnings or info is reported using OBMessageHandler.

Note:

U shaped ordering can also be considered circular and is the only shape that can be rotated lexicographically.

Since:

version 2.3

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Constructor & Destructor Documentation

OBTetraPlanarStereo

(

OBMol *

mol

)

virtual ~OBTetraPlanarStereo

(

)

[virtual]

---

Member Function Documentation

static ConfigType ToConfig	(	const ConfigType &	cfg,
		unsigned long	start,
		OBStereo::Shape	shape = OBStereo::ShapeU
	)			[inline, static]

OBMol* GetMolecule

(

)

const [inline, inherited]

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, inherited]

Reimplemented by subclasses to return the type defined in OBStereo::Type.

Implemented in OBCisTransStereo, OBSquarePlanarStereo, and OBTetrahedralStereo.

void SetSpecified

(

bool

specified

)

[inline, inherited]

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, inherited]

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]

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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=().

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

• tetraplanar.h