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	SetData (const matrix3x3 m)
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	GetA () const
double	GetB ()
double	GetB () const
double	GetC ()
double	GetC () const
double	GetAlpha ()
double	GetAlpha () const
double	GetBeta ()
double	GetBeta () const
double	GetGamma ()
double	GetGamma () const
vector3	GetOffset ()
vector3	GetOffset () const
const SpaceGroup *	GetSpaceGroup ()
const SpaceGroup *	GetSpaceGroup () const
const std::string	GetSpaceGroupName ()
const std::string	GetSpaceGroupName () const
LatticeType	GetLatticeType (int spacegroup)
LatticeType	GetLatticeType (int spacegroup) const
LatticeType	GetLatticeType ()
LatticeType	GetLatticeType () const
std::vector< vector3 >	GetCellVectors ()
std::vector< vector3 >	GetCellVectors () const
matrix3x3	GetCellMatrix ()
matrix3x3	GetCellMatrix () const
matrix3x3	GetOrthoMatrix ()
matrix3x3	GetOrthoMatrix () const
matrix3x3	GetOrientationMatrix ()
matrix3x3	GetOrientationMatrix () const
matrix3x3	GetFractionalMatrix ()
matrix3x3	GetFractionalMatrix () const
vector3	FractionalToCartesian (vector3 frac)
vector3	FractionalToCartesian (vector3 frac) const
vector3	CartesianToFractional (vector3 cart)
vector3	CartesianToFractional (vector3 cart) const
vector3	WrapCartesianCoordinate (vector3 cart)
vector3	WrapCartesianCoordinate (vector3 cart) const
vector3	WrapFractionalCoordinate (vector3 frac)
vector3	WrapFractionalCoordinate (vector3 frac) const
int	GetSpaceGroupNumber (std::string name="")
int	GetSpaceGroupNumber (std::string name="") const
double	GetCellVolume ()
double	GetCellVolume () 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
Protected Attributes
matrix3x3	_mOrtho
matrix3x3	_mOrient
vector3	_offset
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
	)

Constructs the cell matrix in lower triangular form from the values supplied.

Implements blue-obelisk:calculateOrthogonalisationMatrix

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

Referenced by OBUnitCell::SetData().

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

Constructs the cell matrix using the supplied row vectors.

Implements blue-obelisk:calculateOrthogonalisationMatrix

Parameters:

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

See also:: OBUnitCell::GetCellVectors

void SetData ( const matrix3x3 m )

Sets the unit cell matrix.

Implements blue-obelisk:calculateOrthogonalisationMatrix

Parameters:

m

The unit cell matrix (row vectors)

See also:: OBUnitCell::GetCellMatrix

void SetOffset ( const vector3 v1 )

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

Referenced by OBUnitCell::FillUnitCell().

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 ( )

Todo:: Remove nonconst overloads in OBUnitCell on next version bump

Returns:: vector a

Referenced by OBUnitCell::GetLatticeType().

double GetA ( ) const

double GetB ( )

Returns:: vector b

Referenced by OBUnitCell::GetLatticeType().

double GetB ( ) const

double GetC ( )

Returns:: vector c

Referenced by OBUnitCell::GetLatticeType().

double GetC ( ) const

double GetAlpha ( )

Returns:: angle alpha

Referenced by OBUnitCell::GetLatticeType().

double GetAlpha ( ) const

double GetBeta ( )

Returns:: angle beta

Referenced by OBUnitCell::GetLatticeType().

double GetBeta ( ) const

double GetGamma ( )

Returns:: angle gamma

Referenced by OBUnitCell::GetLatticeType().

double GetGamma ( ) const

vector3 GetOffset ( )

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

vector3 GetOffset ( ) const

const SpaceGroup* GetSpaceGroup ( ) [inline]

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

Referenced by OBUnitCell::FillUnitCell().

const SpaceGroup* GetSpaceGroup ( ) const [inline]

const std::string GetSpaceGroupName ( ) [inline]

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

const std::string GetSpaceGroupName ( ) const [inline]

LatticeType GetLatticeType ( int spacegroup )

Returns:: lattice type (based on the spacegroup)

OBUnitCell::LatticeType GetLatticeType ( int spacegroup ) const

LatticeType GetLatticeType ( )

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

Referenced by OBUnitCell::GetLatticeType().

OBUnitCell::LatticeType GetLatticeType ( ) const

std::vector<vector3> GetCellVectors ( )

Returns:: v1, v2, v3 cell vectors

vector< vector3 > GetCellVectors ( ) const

Implements blue-obelisk:convertNotionalIntoCartesianCoordinates

matrix3x3 GetCellMatrix ( )

Access to the cell matrix as row vectors, useful for writing input files. Equivalent to the transpose of GetOrientationMatrix() * GetOrthoMatrix()

Returns:: The cell matrix with row vectors.

See also:: OBUnitCell::GetOrthoMatrix; OBUnitCell::GetFractionalMatrix; OBUnitCell::GetOrientationMatrix; OBUnitCell::FractionalToCartesian; OBUnitCell::CartesianToFractional

Referenced by OBUnitCell::GetCellVectors(), and OBUnitCell::GetCellVolume().

matrix3x3 GetCellMatrix ( ) const

matrix3x3 GetOrthoMatrix ( )

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

See also:: OBUnitCell::GetCellMatrix; OBUnitCell::GetFractionalMatrix; OBUnitCell::GetOrientationMatrix; OBUnitCell::FractionalToCartesian; OBUnitCell::CartesianToFractional

matrix3x3 GetOrthoMatrix ( ) const

matrix3x3 GetOrientationMatrix ( )

Used to convert fractional and cartesian coordinates if the cell is not oriented in standard form (a parallel to x axis, b in xy plane)

Returns:: The orientation matrix

See also:: OBUnitCell::GetOrthoMatrix; OBUnitCell::GetCellMatrix; OBUnitCell::GetFractionalMatrix; OBUnitCell::FractionalToCartesian; OBUnitCell::CartesianToFractional

matrix3x3 GetOrientationMatrix ( ) const

matrix3x3 GetFractionalMatrix ( )

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

See also:: OBUnitCell::GetOrthoMatrix; OBUnitCell::GetCellMatrix; OBUnitCell::GetOrientationMatrix; OBUnitCell::FractionalToCartesian; OBUnitCell::CartesianToFractional

matrix3x3 GetFractionalMatrix ( ) const

vector3 FractionalToCartesian ( vector3 frac )

Convenience function to convert fractional coordinates to cartesian coordinates. Returns

GetOrientationMatrix() * GetOrthoMatrix() * frac + GetOffset()

Parameters:

frac

Vector of fractional coordinates

Returns:: Cartesian coordinates

Referenced by OBUnitCell::FillUnitCell(), and OBUnitCell::WrapCartesianCoordinate().

vector3 FractionalToCartesian ( vector3 frac ) const

vector3 CartesianToFractional ( vector3 cart )

Convenience function to convert cartesian coordinates to fractional coordinates. Returns

GetFractionalMatrix() * GetOrientationMatrix().inverse() * (cart - GetOffset())

Parameters:

cart

Vector of cartesian coordinates

Returns:: Fractional coordinates

Referenced by OBUnitCell::FillUnitCell(), and OBUnitCell::WrapCartesianCoordinate().

vector3 CartesianToFractional ( vector3 cart ) const

vector3 WrapCartesianCoordinate ( vector3 cart )

Wraps cartesian coordinate to fall within the unit cell.

Parameters:

cart

Vector of cartesian coordinates

Returns:: Cartesian coordinates within cell boundaries.

vector3 WrapCartesianCoordinate ( vector3 cart ) const

vector3 WrapFractionalCoordinate ( vector3 frac )

Wraps fractional coordinate to fall within the unit cell.

Parameters:

frac

Vector of fractional coordinates

Returns:: Fractional coordinates within cell boundaries (between 0 and 1).

Todo:: Make OBUnitCell::WrapFractionalCoordinate static in the next ABI break

Referenced by OBUnitCell::FillUnitCell(), and OBUnitCell::WrapCartesianCoordinate().

vector3 WrapFractionalCoordinate ( vector3 frac ) const

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

Returns:: The numeric value of the given spacegroup

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

double GetCellVolume ( )

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

double GetCellVolume ( ) const

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

matrix3x3 _mOrtho [protected]

Referenced by OBUnitCell::CartesianToFractional(), OBUnitCell::FractionalToCartesian(), OBUnitCell::GetA(), OBUnitCell::GetAlpha(), OBUnitCell::GetB(), OBUnitCell::GetBeta(), OBUnitCell::GetC(), OBUnitCell::GetCellMatrix(), OBUnitCell::GetFractionalMatrix(), OBUnitCell::GetGamma(), OBUnitCell::GetOrthoMatrix(), OBUnitCell::operator=(), and OBUnitCell::SetData().

matrix3x3 _mOrient [protected]

Referenced by OBUnitCell::CartesianToFractional(), OBUnitCell::FractionalToCartesian(), OBUnitCell::GetCellMatrix(), OBUnitCell::GetOrientationMatrix(), OBUnitCell::operator=(), and OBUnitCell::SetData().

vector3 _offset [protected]

Referenced by OBUnitCell::CartesianToFractional(), OBUnitCell::FractionalToCartesian(), OBUnitCell::GetOffset(), OBUnitCell::operator=(), and OBUnitCell::SetOffset().

std::string _spaceGroupName [protected]

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

const SpaceGroup* _spaceGroup [protected]

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

LatticeType _lattice [protected]

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

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:

OBUnitCell Class Reference

Public Types

Public Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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