httk.io.cif¶
Submodules¶
Functions¶
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Generic cif reader, given a filename / ioadapter it places all data in a python dictionary. |
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Read a CIF file, expand the asymmetric unit, and return the result. |
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Package Contents¶
- httk.io.cif.read_cif(fs, pragmatic=True, allow_cif2=False, use_types=False)[source]¶
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 (
stroros.PathLike) is opened throughhttk.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.cif_to_struct(fs, *, separate_noneq_atoms=False, tol=1e-06)[source]¶
Read a CIF file, expand the asymmetric unit, and return the result.
fsis a filename or file-like object (anything accepted by theread_ciflayer). Whenseparate_noneq_atomsis true, unique numbers are assigned by CIF label (even for the same element); otherwise numbers are assigned by element symbol.tolcontrols the expansion consistency tolerance. Returns a dict with the expanded structure data.