..
   Copyright 2026 SIB - Swiss Institute of Bioinformatics and Biozentrum -
   University of Basel
   Copying and distribution of this file, with or without modification, are
   permitted provided the copyright notice and this notice are preserved.

Handling ModelCIF (:mod:`modelarchive.modelcif`)
================================================

The :mod:`~modelarchive.modelcif` module assists the `ModelArchive`_ team to prepare deposition data before storing in the database. For the most part this involves converting files from PDB legacy format into ModelCIF, as well as refining submitted mmCIF/ ModelCIF files.

Functionality can be broadly divided into :mod:`accessing <modelarchive.modelcif.access>` and :mod:`editing <modelarchive.modelcif.edit>` ModelCIF files.

One note on performance: by the nature of the task addressed here, code clarity is preferred over raw efficiency. Scripts that translate user data into ModelCIF for a deposition, are run once and offline, so it does not matter if execution takes one minute or five. In general, preparing data usually takes far longer than running the code itself.

Keep this in mind when implementing ModelCIF support in your own tool, you may prefer to draw inspiration from this module rather than use it directly... or use the |python-modelcif|_ package straight away.


Accessing ModelCIF (:mod:`modelarchive.modelcif.access`)
--------------------------------------------------------

.. automodule:: modelarchive.modelcif.access
   :members:
   :member-order: alphabetical
   :undoc-members:
   :show-inheritance:


Editing ModelCIF (:mod:`modelarchive.modelcif.edit`)
----------------------------------------------------

.. automodule:: modelarchive.modelcif.edit
   :members:
   :member-order: alphabetical
   :undoc-members:
   :show-inheritance:

Fixing AlphaFold 3 ModelCIF files (:mod:`modelarchive.modelcif.fix_af3`)
------------------------------------------------------------------------

.. automodule:: modelarchive.modelcif.fix_af3
   :members:
   :member-order: alphabetical
   :undoc-members:
   :show-inheritance:


..  LocalWords:  modelarchive modelcif automodule