httk.io.cif

Submodules

• httk.io.cif.cif_parser
• httk.io.cif.cif_reader
• httk.io.cif.cif_writer
• httk.io.cif.mcif_parser
• httk.io.cif.symops_utils

Functions

asus_from_cif_file(fs)
read_cif_asus(fs)	Read a CIF and return its asymmetric units as a neutral, tagged payload.
single_asu_from_cif_file(fs)
read_cif(fs[, pragmatic, allow_cif2, use_types])	Generic cif reader, given a filename / ioadapter it places all data in a python dictionary.
mag_asus_from_mcif_file(fs, *[, error_on_nonmag])
single_mag_asu_from_mcif_file(fs, *[, error_on_nonmag])

Package Contents

httk.io.cif.asus_from_cif_file(fs)

httk.io.cif.read_cif_asus(fs)

Read a CIF and return its asymmetric units as a neutral, tagged payload.

This is what httk.core.load returns for a .cif file: a mapping with format set to "cif", blocks holding one asymmetric-unit mapping per data block that describes a structure, and header the file’s leading comment. The tag lets a consumer dispatch on the file type without knowing which reader produced the payload.

Loading never fails on account of a block that is not a structure. CIF is a general-purpose format and a file may hold bibliographic entries, powder patterns, or an incomplete draft alongside — or instead of — anything crystallographic. Blocks without atom sites are simply not structures and are passed over; blocks that have atom sites but cannot be interpreted are collected in unparsed, each with the reason, so that nothing is dropped silently and the failure surfaces when a structure is actually asked for.

The mapping stays neutral — plain lists, strings, and exact Fraction symmetry operations, with no domain objects — so httk-io need not know about httk-atomistic. Turning it into a structure is httk.atomistic.asu_structure_from_cif.

httk.io.cif.single_asu_from_cif_file(fs)

httk.io.cif.read_cif(fs, pragmatic=True, allow_cif2=False, use_types=False)

Generic cif reader, given a filename / ioadapter it places all data in a python dictionary.

It returns a tuple: (header, list) Where list are pairs of data blocks names and data blocks

Each data block is a dictionary with tag_name:value

For loops, value is another dictionary with format column_name:value

The optional parameter pragmatic regulates handling of some counter-intuitive aspects of the cif specification, where the default pragmatic=True handles these features the way people usually use them, whereas pragmatic=False means to read the cif file precisely according to the spec. For example, in a multiline text field:

;
some text
;

Means the string ‘nsome text’. For this specific case pragmatic=True removes the leading newline.

set use_types to True to convert things that look like floats and integers to those respective types

A filename (str or os.PathLike) is opened through httk.core.TextstreamFileView, so a compressed file (.cif.bz2, .cif.gz, …) is decompressed transparently. An already-open text stream or a plain iterable of lines is consumed as-is and left open for the caller.

httk.io.cif.mag_asus_from_mcif_file(fs, *, error_on_nonmag=False)

httk.io.cif.single_mag_asu_from_mcif_file(fs, *, error_on_nonmag=False)