.. _file_formats:

Table of available file formats
===============================

.. note::

   If you would like your data format to appear in the table below, please contact us via `GitHub <https://github.com/rigdenlab/conkit/issues>`_.


The following table contains the various different file formats currently implemented in ConKit.

*Type*
    The type of information the file contains
*Format*
    The source of the file
*Keyword*
    The keyword to be used in ConKit


.. rst-class:: table-hover

+--------------------+------------------------+-----------------------------------------------------------+
| Type               | Format                 | Keyword                                                   |
+====================+========================+===========================================================+
| Contact Prediction | Bbcontacts             | ``bbcontacts``:sup:`*`                                    |
+                    +------------------------+-----------------------------------------------------------+
|                    | BCLContacts            | ``bclcontacts``:sup:`*`                                   |
+                    +------------------------+-----------------------------------------------------------+
|                    | Casp RR                | ``casp``, ``casprr``                                      |
+                    +------------------------+-----------------------------------------------------------+
|                    | CCMpred                | ``ccmpred``                                               |
+                    +------------------------+-----------------------------------------------------------+
|                    | COMSAT                 | ``comsat``                                                |
+                    +------------------------+-----------------------------------------------------------+
|                    | EPCMap                 | ``epcmap``                                                |
+                    +------------------------+-----------------------------------------------------------+
|                    | EVfold (EVcouplings)   | ``evfold``                                                |
+                    +------------------------+-----------------------------------------------------------+
|                    | Flib                   | ``flib``                                                  |
+                    +------------------------+-----------------------------------------------------------+
|                    | FreeContact            | ``freecontact``                                           |
+                    +------------------------+-----------------------------------------------------------+
|                    | GREMLIN                | ``gremlin``                                               |
+                    +------------------------+-----------------------------------------------------------+
|                    | MemBrain               | ``membrain``                                              |
+                    +------------------------+-----------------------------------------------------------+
|                    | mmCIF                  | ``mmcif``:sup:`*`                                         |
+                    +------------------------+-----------------------------------------------------------+
|                    | Ncont                  | ``ncont``:sup:`*`                                         |
+                    +------------------------+-----------------------------------------------------------+
|                    | Pcons[C|C2|C3]         | ``pconsc``, ``pconsc2``, ``pconsc3``                      |
+                    +------------------------+-----------------------------------------------------------+
|                    | Protein DataBank (PDB) | ``pdb``:sup:`*`                                           |
+                    +------------------------+-----------------------------------------------------------+
|                    | plmDCA                 | ``plmdca``                                                |
+                    +------------------------+-----------------------------------------------------------+
|                    | [Meta]PSICOV           | ``psicov``, ``metapsicov``                                |
+--------------------+------------------------+-----------------------------------------------------------+
| Sequence Alignment | A3M                    | ``a3m``, ``a3m-inserts``:sup:`a`                          |
+                    +------------------------+-----------------------------------------------------------+
|                    | FASTA                  | ``fasta``                                                 |
+                    +------------------------+-----------------------------------------------------------+
|                    | Jones                  | ``jones`` :sup:`b`                                        |
+                    +------------------------+-----------------------------------------------------------+
|                    | Stockholm              | ``stockholm``                                             |
+--------------------+------------------------+-----------------------------------------------------------+
| :sup:`*` These formats do not have a :func:`write() <conkit.io.write>` function.                        |
|                                                                                                         |
| :sup:`a` The ``a3m-inserts`` keyword stores the alignment including insert states.                      |
|                                                                                                         |
| :sup:`b` The ``jones`` format corresponds to one sequence per line without sequence header information. |
|                                                                                                         |
+--------------------+------------------------+-----------------------------------------------------------+