OBUnitCell Class Reference

Used for storing information about periodic boundary conditions with conversion to/from translation vectors and (a, b, c, alpha, beta, gamma). More...

#include <openbabel/generic.h>

Inheritance diagram for OBUnitCell:

[legend]

List of all members.

Public Types

enum LatticeType {
Undefined, Triclinic, Monoclinic, Orthorhombic,
Tetragonal, Rhombohedral, Hexagonal, Cubic
}

Public Member Functions

OBUnitCell ()

OBUnitCell (const OBUnitCell &)

virtual OBGenericData * Clone (OBBase *) const

~OBUnitCell ()

OBUnitCell & operator= (const OBUnitCell &)

void SetData (const double a, const double b, const double c, const double alpha, const double beta, const double gamma)

void SetData (const vector3 v1, const vector3 v2, const vector3 v3)

void SetOffset (const vector3 v1)

void SetSpaceGroup (const SpaceGroup *sg)

void SetSpaceGroup (const std::string sg)

void SetSpaceGroup (const int sg)

void SetLatticeType (const LatticeType lt)

void FillUnitCell (OBMol *)

double GetA ()

double GetB ()

double GetC ()

double GetAlpha ()

double GetBeta ()

double GetGamma ()

vector3 GetOffset ()

const SpaceGroup * GetSpaceGroup ()

const std::string GetSpaceGroupName ()

LatticeType GetLatticeType (int spacegroup)

LatticeType GetLatticeType ()

std::vector< vector3 > GetCellVectors ()

matrix3x3 GetCellMatrix ()

matrix3x3 GetOrthoMatrix ()

matrix3x3 GetFractionalMatrix ()

int GetSpaceGroupNumber (std::string name="")

double GetCellVolume ()

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

Protected Attributes

double _a

double _b

double _c

double _alpha

double _beta

double _gamma

vector3 _offset

vector3 _v1

vector3 _v2

vector3 _v3

std::string _spaceGroupName

const SpaceGroup * _spaceGroup

LatticeType _lattice

std::string _attr

unsigned int _type

DataOrigin _source

Detailed Description

Used for storing information about periodic boundary conditions with conversion to/from translation vectors and (a, b, c, alpha, beta, gamma).

Member Enumeration Documentation

enum LatticeType

Enumerator:

Undefined
Triclinic
Monoclinic
Orthorhombic
Tetragonal
Rhombohedral	also called trigonal
Hexagonal
Cubic

Constructor & Destructor Documentation

OBUnitCell ( )

public constructor

OBUnitCell ( const OBUnitCell & src )

~OBUnitCell ( ) [inline]

Member Function Documentation

virtual OBGenericData* Clone ( OBBase * ) const [inline, virtual]

Reimplemented from OBGenericData.

OBUnitCell & operator= ( const OBUnitCell & src )

void SetData	(	const double	a,
		const double	b,
		const double	c,
		const double	alpha,
		const double	beta,
		const double	gamma
	)			`[inline]`

Sets the vectors and angles of the unitcell.

Parameters:

	a	The length a
	b	The length b
	c	The length c
	alpha	The angle alpha
	beta	The angle beta
	gamma	The angle gamma

void SetData	(	const vector3	v1,
		const vector3	v2,
		const vector3	v3
	)

Sets the vectors, angles and lengths of the unitcell.

The angles and lengths of the unitcell will be calculated from the vectors v1, v2 and v3. Those vectors will as well be stored internally. Implements blue-obelisk:convertCartesianIntoNotionalCoordinates

Parameters:

	v1	The x-vector
	v2	The y-vector
	v3	The z-vector

See also:: OBUnitCell::GetCellVectors

void SetOffset ( const vector3 v1 ) [inline]

Set the offset to the origin to v1.

void SetSpaceGroup ( const SpaceGroup * sg ) [inline]

Set the space group for this unit cell. Does not create an OBSymmetryData entry

void SetSpaceGroup ( const std::string sg ) [inline]

Set the space group symbol for this unit cell. Does not create an OBSymmetryData entry or attempt to convert between different symbol notations

void SetSpaceGroup ( const int sg ) [inline]

Set the space group for this unit cell. Each spacegroup-symbol has a numeric equivalent which is easier to use to convert between notations. Does not create an OBSymmetryData entry or attempt to convert between different symbol notations

void SetLatticeType ( const LatticeType lt ) [inline]

Set the Bravais lattice type for this unit cell.

void FillUnitCell ( OBMol * mol )

Duplicate symmetry-unique atoms to fill out the unit cell of the molecule, based on the known space group

double GetA ( ) [inline]

Returns:: vector a

double GetB ( ) [inline]

Returns:: vector b

double GetC ( ) [inline]

Returns:: vector c

double GetAlpha ( ) [inline]

Returns:: angle alpha

double GetBeta ( ) [inline]

Returns:: angle beta

double GetGamma ( ) [inline]

Returns:: angle gamma

vector3 GetOffset ( ) [inline]

Returns:: any offset in the origin of the periodic boundaries

const SpaceGroup* GetSpaceGroup ( ) [inline]

Returns:: the text representation of the space group for this unit cell

Referenced by OBUnitCell::FillUnitCell().

const std::string GetSpaceGroupName ( ) [inline]

Returns:: the text representation of the space group for this unit cell

OBUnitCell::LatticeType GetLatticeType ( int spacegroup )

Returns:: lattice type (based on the spacegroup)

OBUnitCell::LatticeType GetLatticeType ( )

Returns:: lattice type (based on angles and distances)

Referenced by OBUnitCell::GetCellVolume().

vector< vector3 > GetCellVectors ( )

Implements blue-obelisk:convertNotionalIntoCartesianCoordinates.

Returns:: v1, v2, v3 cell vectors

matrix3x3 GetCellMatrix ( )

Returns:: v1, v2, v3 cell vectors as a 3x3 matrix

matrix3x3 GetOrthoMatrix ( )

Implements blue-obelisk:calculateOrthogonalisationMatrix.

Returns:: The orthogonalization matrix, used for converting from fractional to Cartesian coords.

Referenced by OBUnitCell::FillUnitCell(), OBUnitCell::GetCellMatrix(), and OBUnitCell::GetCellVectors().

matrix3x3 GetFractionalMatrix ( )

Returns:: The fractionalization matrix, used for converting from Cartesian to fractional coords.

Matrix to convert from Cartesian to fractional Implements blue-obelisk:convertCartesianIntoFractionalCoordinates

Referenced by OBUnitCell::FillUnitCell().

int GetSpaceGroupNumber ( std::string name = "" )

Returns:: The numeric value of the given spacegroup

double GetCellVolume ( )

Returns:: The cell volume (in Angstroms^3)

void SetAttribute ( const std::string & v ) [inline, inherited]

Set the attribute (key), which can be used to retrieve this data.

Referenced by OBGastChrg::AssignPartialCharges(), OBForceField::GetAtomTypes(), OBMol::GetFormula(), OBForceField::GetPartialCharges(), 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::FindAngles(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBMol::GetFormula(), 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 OBDescriptor::FilterCompare(), and OBDescriptor::GetValues().

virtual DataOrigin GetOrigin ( ) const [inline, virtual, inherited]

Member Data Documentation

double _a [protected]

Referenced by OBUnitCell::GetCellVolume(), OBUnitCell::GetFractionalMatrix(), OBUnitCell::GetLatticeType(), OBUnitCell::GetOrthoMatrix(), OBUnitCell::operator=(), and OBUnitCell::SetData().

double _b [protected]

Referenced by OBUnitCell::GetCellVolume(), OBUnitCell::GetFractionalMatrix(), OBUnitCell::GetLatticeType(), OBUnitCell::GetOrthoMatrix(), OBUnitCell::operator=(), and OBUnitCell::SetData().

double _c [protected]

Referenced by OBUnitCell::GetCellVolume(), OBUnitCell::GetFractionalMatrix(), OBUnitCell::GetLatticeType(), OBUnitCell::GetOrthoMatrix(), OBUnitCell::operator=(), and OBUnitCell::SetData().

double _alpha [protected]

Referenced by OBUnitCell::GetCellVolume(), OBUnitCell::GetFractionalMatrix(), OBUnitCell::GetLatticeType(), OBUnitCell::GetOrthoMatrix(), OBUnitCell::operator=(), and OBUnitCell::SetData().

double _beta [protected]

Referenced by OBUnitCell::GetCellVolume(), OBUnitCell::GetFractionalMatrix(), OBUnitCell::GetLatticeType(), OBUnitCell::GetOrthoMatrix(), OBUnitCell::operator=(), and OBUnitCell::SetData().

double _gamma [protected]

Referenced by OBUnitCell::GetCellVolume(), OBUnitCell::GetFractionalMatrix(), OBUnitCell::GetLatticeType(), OBUnitCell::GetOrthoMatrix(), OBUnitCell::operator=(), and OBUnitCell::SetData().

vector3 _offset [protected]

offset for origin

Referenced by OBUnitCell::operator=().

vector3 _v1 [protected]

Referenced by OBUnitCell::GetCellMatrix(), OBUnitCell::GetCellVectors(), OBUnitCell::operator=(), and OBUnitCell::SetData().

vector3 _v2 [protected]

Referenced by OBUnitCell::GetCellMatrix(), OBUnitCell::GetCellVectors(), OBUnitCell::operator=(), and OBUnitCell::SetData().

vector3 _v3 [protected]

translation vectors

Referenced by OBUnitCell::GetCellMatrix(), OBUnitCell::GetCellVectors(), OBUnitCell::operator=(), and OBUnitCell::SetData().

std::string _spaceGroupName [protected]

Referenced by OBUnitCell::GetSpaceGroupNumber(), and OBUnitCell::operator=().

const SpaceGroup* _spaceGroup [protected]

Referenced by OBUnitCell::GetLatticeType(), OBUnitCell::GetSpaceGroupNumber(), and OBUnitCell::operator=().

LatticeType _lattice [protected]

Referenced by OBUnitCell::GetLatticeType(), and OBUnitCell::operator=().

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 files:


Public Types
enum	LatticeType { Undefined, Triclinic, Monoclinic, Orthorhombic, Tetragonal, Rhombohedral, Hexagonal, Cubic }
Public Member Functions
	OBUnitCell ()
	OBUnitCell (const OBUnitCell &)
virtual OBGenericData *	Clone (OBBase *) const
	~OBUnitCell ()
OBUnitCell &	operator= (const OBUnitCell &)
void	SetData (const double a, const double b, const double c, const double alpha, const double beta, const double gamma)
void	SetData (const vector3 v1, const vector3 v2, const vector3 v3)
void	SetOffset (const vector3 v1)
void	SetSpaceGroup (const SpaceGroup *sg)
void	SetSpaceGroup (const std::string sg)
void	SetSpaceGroup (const int sg)
void	SetLatticeType (const LatticeType lt)
void	FillUnitCell (OBMol *)
double	GetA ()
double	GetB ()
double	GetC ()
double	GetAlpha ()
double	GetBeta ()
double	GetGamma ()
vector3	GetOffset ()
const SpaceGroup *	GetSpaceGroup ()
const std::string	GetSpaceGroupName ()
LatticeType	GetLatticeType (int spacegroup)
LatticeType	GetLatticeType ()
std::vector< vector3 >	GetCellVectors ()
matrix3x3	GetCellMatrix ()
matrix3x3	GetOrthoMatrix ()
matrix3x3	GetFractionalMatrix ()
int	GetSpaceGroupNumber (std::string name="")
double	GetCellVolume ()
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
Protected Attributes
double	_a
double	_b
double	_c
double	_alpha
double	_beta
double	_gamma
vector3	_offset
vector3	_v1
vector3	_v2
vector3	_v3
std::string	_spaceGroupName
const SpaceGroup *	_spaceGroup
LatticeType	_lattice
std::string	_attr
unsigned int	_type
DataOrigin	_source