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 std::string sg)
void	SetSpaceGroup (const int sg)
void	SetLatticeType (const LatticeType lt)
double	GetA ()
double	GetB ()
double	GetC ()
double	GetAlpha ()
double	GetBeta ()
double	GetGamma ()
vector3	GetOffset ()
const std::string	GetSpaceGroup ()
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	_spaceGroup
int	_numericSpaceGroup
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 & )

~OBUnitCell ( ) [inline]

Member Function Documentation

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

Reimplemented from OBGenericData.

OBUnitCell & operator= ( const OBUnitCell & )

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 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.

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 std::string GetSpaceGroup ( ) [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)

vector< vector3 > GetCellVectors ( )

Implements blue-obelisk:convertNotionalIntoCartesianCoordinates.

matrix3x3 GetCellMatrix ( )

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

matrix3x3 GetOrthoMatrix ( )

Implements blue-obelisk:calculateOrthogonalisationMatrix.

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

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.

void SetOrigin ( const DataOrigin s ) [inline, inherited]

Set the origin of this data, which can be used to filter the data.

virtual const std::string& GetAttribute ( ) const [inline, virtual, inherited]

Returns:: The attribute (key), which can be used to retrieve this data

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, OBPairData, and OBPairTemplate.

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

Member Data Documentation

double _a [protected]

double _b [protected]

double _c [protected]

double _alpha [protected]

double _beta [protected]

double _gamma [protected]

vector3 _offset [protected]

offset for origin

vector3 _v1 [protected]

vector3 _v2 [protected]

vector3 _v3 [protected]

translation vectors

std::string _spaceGroup [protected]

int _numericSpaceGroup [protected]

LatticeType _lattice [protected]

std::string _attr [protected, inherited]

attribute tag (e.g., "UnitCell", "Comment" or "Author")

unsigned int _type [protected, inherited]

attribute type -- declared for each subclass

DataOrigin _source [protected, inherited]

source of data for accounting

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

OBUnitCell Class Reference

Public Types

Public Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation