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CSYM library

File list

• csymlib.h - contains details of the C/C++ API
• ccp4_spg.h - contains details of the spacegroup data structure

Overview

The CSYM library is centred around a data file syminfo.lib which is auto-generated from sgtbx (the Space Group Toolbox of cctbx). A description of the contents of this file is given in the documentation of the Fortran API.

A particular spacegroup in a particular setting is loaded into an in-memory data structure by requesting a particular spacegroup name, number, or set of operators. See the functions ccp4spg_load_by_standard_num, ccp4spg_load_by_ccp4_num, ccp4spg_load_by_spgname, ccp4spg_load_by_ccp4_spgname and ccp4_spgrp_reverse_lookup. Information on the in-memory data structure is given in ccp4_spg.h The memory can be freed by the function ccp4spg_free.

Functions are provided to:

• Query the data structure, e.g. ccp4spg_symbol_Hall, etc. (members of the structure can of course be obtained directly)
• Check reciprocal space indices for a particular spacegroup, e.g. ccp4spg_is_in_asu, ccp4spg_is_centric, ccp4spg_get_multiplicity, ccp4spg_is_sysabs, etc.
• Set appropriate grids for FFT, e.g. set_fft_grid

Symmetry operators

Symmetry operators are expressed in a variety of ways:

• Using the struct ccp4_symop, which consists of a 3 x 3 rotation matrix and a translation vector.
• As a 4 x 4 matrix, in which the rotation matrix is in the top-left-hand corner and the translation vector is in elements [*][3]. Element [3][3] is set to 1.0
• As a string, such as "-x+1/2,-y,z+1/2"

Check the function description for which form is expected. Often, there are alternative functions if you wish to supply the operators in a different form. There are also the following conversion functions:

• rotandtrn_to_mat4
• rotandtrn_to_symop
• mat4_to_rotandtrn
• mat4_to_symop
• mat4_to_recip_symop
• symop_to_rotandtrn
• symop_to_mat4

Note that the order of symmetry operators may be important in some cases, for example in MTZ files with a M/ISYM column where ISYM encodes the symmetry operation used.

Examples

See examples on ftp area