diff options
| -rw-r--r-- | doc/reference/CrystFEL-docs.sgml | 5 | ||||
| -rw-r--r-- | doc/reference/CrystFEL-sections.txt | 50 | ||||
| -rw-r--r-- | libcrystfel/src/cell-utils.c | 17 | ||||
| -rw-r--r-- | libcrystfel/src/integer_matrix.c | 2 |
4 files changed, 71 insertions, 3 deletions
diff --git a/doc/reference/CrystFEL-docs.sgml b/doc/reference/CrystFEL-docs.sgml index 2f42f5e7..ffff9e9f 100644 --- a/doc/reference/CrystFEL-docs.sgml +++ b/doc/reference/CrystFEL-docs.sgml @@ -48,6 +48,11 @@ </chapter> <chapter> + <title>Integer Matrices</title> + <xi:include href="xml/integer_matrix.xml"><xi:fallback /></xi:include> + </chapter> + + <chapter> <title>Simulation</title> <xi:include href="xml/simulation.xml"><xi:fallback /></xi:include> </chapter> diff --git a/doc/reference/CrystFEL-sections.txt b/doc/reference/CrystFEL-sections.txt index 3ccc1511..8da5798c 100644 --- a/doc/reference/CrystFEL-sections.txt +++ b/doc/reference/CrystFEL-sections.txt @@ -60,11 +60,16 @@ read_reflections read_reflections_from_file asymmetric_indices res_cutoff +check_list_symmetry +copy_reflist +find_equiv_in_list </SECTION> <SECTION> <FILE>unitcell</FILE> UnitCell +LatticeType +UnitCellTransformation <SUBSECTION> cell_new cell_new_from_cell @@ -77,7 +82,9 @@ cell_get_cartesian cell_get_parameters cell_get_pointgroup cell_get_reciprocal -cell_get_spacegroup +cell_get_centering +cell_get_lattice_type +cell_get_unique_axis <SUBSECTION> cell_set_cartesian cell_set_cartesian_a @@ -86,14 +93,22 @@ cell_set_cartesian_c cell_set_parameters cell_set_pointgroup cell_set_reciprocal -cell_set_spacegroup +cell_set_centering +cell_set_lattice_type +cell_set_unique_axis <SUBSECTION> +cell_transform +cell_transform_inverse tfn_combine tfn_identity +tfn_from_intmat tfn_inverse tfn_print tfn_vector tfn_free +<SUBSECTION> + +cell_rep </SECTION> <SECTION> @@ -110,6 +125,9 @@ uncenter_cell bravais_lattice right_handed str_lattice +uncenter_cell +forbidden_reflection +load_cell_from_pdb </SECTION> <SECTION> @@ -213,6 +231,7 @@ index_pattern run_dirax run_mosflm indexingprivate +map_all_peaks </SECTION> <SECTION> @@ -238,11 +257,35 @@ is_centrosymmetric </SECTION> <SECTION> +<FILE>integer_matrix</FILE> +IntegerMatrix +<SUBSECTION> +intmat_new +intmat_copy +intmat_free +<SUBSECTION> +intmat_get +intmat_set +<SUBSECTION> +intmat_intmat_mult +intmat_intvec_mult +intmat_det +intmat_inverse +<SUBSECTION> +intmat_equals +intmat_is_identity +intmat_is_inversion +<SUBSECTION> +intmat_print +</SECTION> + +<SECTION> <FILE>detector</FILE> copy_geom fill_in_values free_detector_geometry get_detector_geometry +write_detector_geometry find_panel find_panel_by_name find_panel_number @@ -252,6 +295,9 @@ get_pixel_extents get_q get_q_for_panel get_tt +smallest_q +reverse_2d_mapping +largest_q </SECTION> <SECTION> diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c index 74f33bb2..174240b6 100644 --- a/libcrystfel/src/cell-utils.c +++ b/libcrystfel/src/cell-utils.c @@ -71,6 +71,8 @@ * * Rotate a %UnitCell using a %quaternion. * + * Deprecated: 0.4.3. Use tfn_random_rotation() and cell_transform() instead. + * * Returns: a newly allocated rotated copy of @in. * */ @@ -1045,6 +1047,21 @@ void cell_fudge_gslcblas() } +/** + * rotate_cell: + * @in: A %UnitCell to rotate + * @omega: Euler angle about +z + * @phi: Euler angle about +x + * @rot: Euler angle about new +z + * + * Rotate a %UnitCell using Euler angles + * + * Deprecated: Deprecated since 0.4.3. Use tfn_random_rotation() and + * cell_transform() instead. + * + * Returns: a newly allocated rotated copy of @in. + * + */ UnitCell *rotate_cell(UnitCell *in, double omega, double phi, double rot) { UnitCell *out; diff --git a/libcrystfel/src/integer_matrix.c b/libcrystfel/src/integer_matrix.c index ad38a9fe..32784f20 100644 --- a/libcrystfel/src/integer_matrix.c +++ b/libcrystfel/src/integer_matrix.c @@ -47,7 +47,7 @@ * @include: "integer_matrix.h" * @Image: * - * Routines to handle integer matrix + * An integer matrix library */ |