segmentation.geostas
====================

.. py:module:: segmentation.geostas

.. autoapi-nested-parse::

   Bio3D is an R package that encapsulates different tools for biological
   structure analysis. The GeoStaS domain finder tries to locate rigid domains
   based on trajectory movements. The generated files come from a custom script
   written in R, so their format is controlled by our workflow rather than by the
   external project itself.

   Documentation can be found at:
   http://thegrantlab.org/bio3d/reference/geostas.html





Module Contents
---------------

.. py:class:: Parser(pdb_path, clustering_directory_path)

   Bases: :py:obj:`segmentation.SegmentationParser`


   The base class for all segmentation parsers.


   .. py:method:: parse() -> collections.abc.Iterator[Tuple[str, int, str]]

      The return value is a collection of items of the form::

          ("<method name>", <number of domains>, "<chopping>")

      They could be collected into a list or yield-ed. The
      :func:`write_segmentations` function only expects that this method
      returns an iterable object.



   .. py:method:: _translate_atoms_to_residues(atom_data, atom_groups)

      The output of GeoStaS is (alpha carbon) atom indices (1-indexed) while
      the output of the parser is in residues. This method translates the
      sequential atom indices into the residues they correspond to by using
      an MDAnalysis universe.



   .. py:method:: _generate_chopping(residue_groups)

      Input: ``[[1, 2, 3], [10, 11, 20, 21], ...]``
      Output: ``1-3,10-11_20,21,...``