httk.io.cif
===========

.. py:module:: httk.io.cif


Submodules
----------

.. toctree::
   :maxdepth: 1

   /reference/autoapi/httk/io/cif/cif_parser/index
   /reference/autoapi/httk/io/cif/cif_reader/index
   /reference/autoapi/httk/io/cif/cif_writer/index
   /reference/autoapi/httk/io/cif/expand_asu/index
   /reference/autoapi/httk/io/cif/mcif_parser/index
   /reference/autoapi/httk/io/cif/symops_utils/index


Functions
---------

.. autoapisummary::

   httk.io.cif.asus_from_cif_file
   httk.io.cif.single_asu_from_cif_file
   httk.io.cif.read_cif
   httk.io.cif.cif_to_struct
   httk.io.cif.mag_asus_from_mcif_file
   httk.io.cif.single_mag_asu_from_mcif_file


Package Contents
----------------

.. py:function:: asus_from_cif_file(fs)

.. py:function:: single_asu_from_cif_file(fs)

.. py:function:: 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 :class:`os.PathLike`) is opened through
   :class:`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.


.. py:function:: cif_to_struct(fs, *, separate_noneq_atoms=False, tol=1e-06)

   Read a CIF file, expand the asymmetric unit, and return the result.

   ``fs`` is a filename or file-like object (anything accepted by the ``read_cif``
   layer). When ``separate_noneq_atoms`` is true, unique numbers are assigned by CIF
   label (even for the same element); otherwise numbers are assigned by element
   symbol. ``tol`` controls the expansion consistency tolerance. Returns a dict with
   the expanded structure data.


.. py:function:: mag_asus_from_mcif_file(fs, *, error_on_nonmag=False)

.. py:function:: single_mag_asu_from_mcif_file(fs, *, error_on_nonmag=False)