clipper::RTop_orth Class Reference

Orthogonal operator class. More...

#include <coords.h>

Inheritance diagram for clipper::RTop_orth:

List of all members.

Public Member Functions
	RTop_orth ()
	null constructor
	RTop_orth (const RTop<> &o)
	constructor: copy/convert
	RTop_orth (const Mat33<> &r)
	constructor: from rotation
	RTop_orth (const Mat33<> &r, const Vec3<> &t)
	constructor: from rotation and translation
	RTop_orth (const std::vector< Coord_orth > &src, const std::vector< Coord_orth > &tgt)
	constructor: from two vectors of Coord_orth
	RTop_orth (const std::vector< Coord_orth > &src, const std::vector< Coord_orth > &tgt, const std::vector< ftype > &wgt)
	constructor: from two vectors of Coord_orth
template<class T >
	RTop_orth (const T &src, const T &tgt)
	constructor: from two atom-list type objects
RTop_frac	rtop_frac (const Cell &cell) const
	orthogonal-fractional conversion
RTop_orth	inverse () const
	inverse operator
Coord_orth	axis_coordinate_near (const Coord_orth &centre) const
	return point on axis near the specified coordinate
Coord_orth	screw_translation () const
	return screw translation
Static Public Member Functions
static RTop_orth	identity ()
	return identity operator
static RTop_orth	null ()
	return null (uninitialised) operator

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Detailed Description

Orthogonal operator class.

This class is used for any RT-operator which operates on orthogonal coordinates. For a full list of methods, see clipper::RTop

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Constructor & Destructor Documentation

clipper::RTop_orth::RTop_orth	(	const std::vector< Coord_orth > &	src,
		const std::vector< Coord_orth > &	tgt
	)

constructor: from two vectors of Coord_orth

Construct the operator which give the least-squares fit of one set of coordinates onto another. The coodinates are stored as STL vectors of Coord_orth. The lists must be the same size, and each atom in the source list must correspond to the same atom in the target list. The algorithm employed is that of Kearsley, S.K. (1989) 'On the orthogonal transformation used for structural comparisons'. Acta Cryst. A45, 208-210.

Parameters:

src	The source list (i.e. the atoms to be transformed).
tgt	The target list (i.e. the fixed atoms).

References clipper::Matrix< T >::eigen(), clipper::Rotation::matrix(), clipper::Message::message(), clipper::Rotation::norm(), clipper::RTop<>::rot(), and RTop_orth().

clipper::RTop_orth::RTop_orth	(	const std::vector< Coord_orth > &	src,
		const std::vector< Coord_orth > &	tgt,
		const std::vector< ftype > &	wgt
	)

constructor: from two vectors of Coord_orth

Construct the operator which give the least-squares fit of one set of coordinates onto another. The coodinates are stored as STL vectors of Coord_orth. The lists must be the same size, and each atom in the source list must correspond to the same atom in the target list. The algorithm employed is that of Kearsley, S.K. (1989) 'On the orthogonal transformation used for structural comparisons'. Acta Cryst. A45, 208-210.

Parameters:

src	The source list (i.e. the atoms to be transformed).
tgt	The target list (i.e. the fixed atoms).
wgt	The weight to apply to each atom.

References clipper::Matrix< T >::eigen(), clipper::Rotation::matrix(), clipper::Message::message(), clipper::Rotation::norm(), clipper::RTop<>::rot(), and RTop_orth().

template<class T >

clipper::RTop_orth::RTop_orth	(	const T &	src,
		const T &	tgt
	)

constructor: from two atom-list type objects

Construct the operator which relates one atom-list like object onto another. The lists must be the same size, and have the following properties:

• a size() method.
• a [int] operator, with int ranging from 0 to size()-1.
• the object returned by the [] operator must have a coord_orth() method. Suitable objects include a vector of Atom, or an Atom_list.

References RTop_orth().

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Member Function Documentation

RTop_frac clipper::RTop_orth::rtop_frac

(

const Cell &

cell

)

const

orthogonal-fractional conversion

Parameters:

cell	The cell concerned

Returns:

The transformed coordinate.

References clipper::Cell::matrix_frac(), and clipper::Cell::matrix_orth().

RTop_orth clipper::RTop_orth::inverse

(

)

const

inverse operator

Returns:

The inverse of the operator.

Reimplemented from clipper::RTop<>.

References RTop_orth().

Coord_orth clipper::RTop_orth::axis_coordinate_near

(

const Coord_orth &

centre

)

const

return point on axis near the specified coordinate

Parameters:

centre

An arbitrary point.

Returns:

point on axis near the specified coordinate, 000 if rotation is zero

References clipper::Rotation::abs_angle(), clipper::Polar_ccp4::kappa(), clipper::Rotation::norm(), clipper::Rotation::polar_ccp4(), clipper::RTop<>::rot(), clipper::RTop<>::trn(), clipper::Rotation::x(), clipper::Rotation::y(), and clipper::Rotation::z().

Coord_orth clipper::RTop_orth::screw_translation

(

)

const

return screw translation

Returns:

screw translation, 000 if rotation is zero

References clipper::Rotation::abs_angle(), clipper::RTop<>::rot(), clipper::RTop<>::trn(), clipper::Rotation::x(), clipper::Rotation::y(), and clipper::Rotation::z().

RTop_orth clipper::RTop_orth::identity

(

)

[static]

return identity operator

Returns:

The identity operator.

Reimplemented from clipper::RTop<>.

References RTop_orth().

RTop_orth clipper::RTop_orth::null

(

)

[static]

return null (uninitialised) operator

Returns:

The null (uninitialised) operator.

Reimplemented from clipper::RTop<>.

References RTop_orth().

Referenced by clipper::CNXmap_operator< T >::CNXmap_operator(), and clipper::CNXmap_operator< T >::update().

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

• coords.h
• coords.cpp