#include <crystal_orientation.h>
Public Member Functions | |
| crystal_orientation () | |
| Default constructor. Some data members are not initialized! | |
| crystal_orientation (oc_mat3 const &, bool const &) | |
| Constructor using a direct or reciprocal space matrix. | |
| cctbx::uctbx::unit_cell | unit_cell () const |
| Access to direct space unit cell. | |
| cctbx::uctbx::unit_cell | unit_cell_inverse () const |
| Access to reciprocal space unit cell. | |
| oc_mat3 | direct_matrix () const |
| Access to direct space orientation matrix. | |
| oc_mat3 | reciprocal_matrix () const |
| Access to reciprocal space orientation matrix. | |
| crystal_orientation | change_basis (cctbx::sgtbx::change_of_basis_op const &) const |
| Change of basis. Return value gives mutated orientation. | |
| crystal_orientation | change_basis (oc_mat3 const &) const |
| Change of basis. Return value gives mutated orientation. | |
| template<typename FloatType> | |
| crystal_orientation | rotate_thru (oc_vec3 const &unit_axis, FloatType const &angle) |
| Rotation mutator. | |
| double | direct_mean_square_difference (crystal_orientation const &other) const |
| Simple measure for the similarity of two orientatons. | |
| double | difference_Z_score (crystal_orientation const &other) const |
| Simple measure for the similarity of two orientatons. | |
| oc_mat3 | best_similarity_transformation (crystal_orientation const &other, double const &fractional_length_tolerance, int unimodular_generator_range=1) const |
| Best change of basis for superimposing onto another orientation. | |
All dimensions are in Angstroms (direct space) and inverse Angstroms (reciprocal space).
The reciprocal space matrix is a generalization of the fractionalization matrix:
/ A*x B*x C*x \
Matrix A* = | A*y B*y C*y |
\ A*z B*z C*z /
The direct space matrix is a generalization of the orthogonalization matrix:
/ Ax Ay Az \
Matrix A = | Bx By Bz |
\ Cx Cy Cz /
| crystal_orientation | ( | ) | [inline] |
Default constructor. Some data members are not initialized!
Not available in Python.
Referenced by crystal_orientation::rotate_thru().
| crystal_orientation | ( | oc_mat3 const & | , | |
| bool const & | ||||
| ) | [explicit] |
Constructor using a direct or reciprocal space matrix.
basis type flag: false=direct space; true=reciprocal space
| crystal_orientation change_basis | ( | cctbx::sgtbx::change_of_basis_op const & | ) | const |
Change of basis. Return value gives mutated orientation.
Input is the change of basis operator for transforming direct space vectors from the current setting to a reference setting.
| crystal_orientation change_basis | ( | oc_mat3 const & | ) | const |
Change of basis. Return value gives mutated orientation.
Input is a rotation matrix, assumed to be the matrix for transforming direct space vectors from the current setting to a reference setting.
| crystal_orientation rotate_thru | ( | oc_vec3 const & | unit_axis, | |
| FloatType const & | angle | |||
| ) | [inline] |
Rotation mutator.
Right-hand rotation of the crystal about a laboratory vector through an angle expressed in radians.
References crystal_orientation::crystal_orientation(), mat3::get_column(), mat3::set_column(), and cctbx::vector_rotate_thru().
| double direct_mean_square_difference | ( | crystal_orientation const & | other | ) | const [inline] |
Simple measure for the similarity of two orientatons.
The result is the mean of the squared differences between basis vectors. The basis vectors are taken in direct space. DEPRECATED 7/19/2009.
References crystal_orientation::direct_matrix().
| double difference_Z_score | ( | crystal_orientation const & | other | ) | const [inline] |
Simple measure for the similarity of two orientatons.
The result is a sum of mock Z-scores for the three basis vectors of the other orientation. It assumes that the direct space vectors of this crystal orientation are distributed normally with a standard deviation of 1% of the basis vector length. Introduced 8/13/2009.
References crystal_orientation::direct_matrix(), mat3::get_row(), and vec3::length().
| oc_mat3 best_similarity_transformation | ( | crystal_orientation const & | other, | |
| double const & | fractional_length_tolerance, | |||
| int | unimodular_generator_range = 1 | |||
| ) | const |
Best change of basis for superimposing onto another orientation.
Used for aligning two orientations determined independently from the same crystal sample. The rotation part of an inverse cb_op is returned.
1.5.6