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Command Line Interface
======================

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Two :abbr:`Command Line Interface CLI)` are accessible after the installation.
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    * :command:`aria2`: interface for setting up and running an ARIA project
    * :command:`ariaec` [1]_: interface for converting and analyze contact maps

ARIA2
-----

Please refer to the `ARIA documentation <http://aria.pasteur.fr/>`_ for more
explanations.

ARIAEC
------
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.. code-block:: shell
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    ariaec COMMAND [OPTIONS] ARGS
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**Commands**

.. rst-class:: table-hover

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.. list-table::
    :header-rows: 1
    :widths: 25 60

    *   - Name
        - Short Description
    *   - `setup <Setup_>`_
        - Setup ARIA project with EC data
    *   - `bbconv <BBconv_>`_
        - Translate BBcontacts as distance restraints
    *   - `maplot <Maplot_>`_
        - Contact map visualisation tool
    *   - `pdbqual <PDBQual_>`_
        - Call PDB quality tools
    *   - `analysis <Analysis_>`_
        - Analyze results from an ARIA project
    *   - `tbl2xml <TBL2XML_>`_
        - Convert TBL restraints in ARIA XML format
    *   - `pdbdist <PDBDist_>`_
        - Extract distance from a culled list of PDBs
    *   - `pdbstat <PDBStat_>`_
        - Statistical analysis of ``pdbdist`` results
    *   - `iniconv <Iniconv_>`_
        - Convert a INI file as csv for easy readability
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**Options**


.. rst-class:: table-hover

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.. list-table::
    :header-rows: 1
    :widths: 25 60
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    *   - Name
        - Short Description
    *   - ``-h``, ``--help``
        - show help message and exit
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Setup
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Translate contact maps as distance restraints and initialize a new ARIA XML project.
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.. code-block:: shell
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    ariaec setup [OPTIONS] SEQFILE INFILE [INFILE ...] -o OUTPUT_DIRECTORY -t INTYPE [INTYPE ...]
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**Arguments**

.. rst-class:: table-hover

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.. list-table::
    :header-rows: 1
    :widths: 25 60
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    *   - Name
        - Short Description
    *   - ``seq``
        - Sequence file [``FASTA``]
    *   - ``infile [infile ...]``
        - Contact or pdb file(s) used to build aria distance restraints
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.. _ConKit: http://www.conkit.org/en/latest/


**Options**


.. rst-class:: table-hover

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.. list-table::
    :header-rows: 1
    :widths: 25 60
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    *   - Name
        - Short Description
    *   - ``-h``, ``--help``
        - show help message and exit
    *   - ``-d``, ``--debug``
        - Increase output verbosity (default: False)
    *   - ``--nolog``
        - Don't generate log files (default: False)
    *   - ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY``
        - Output directory (default: None)
    *   - ``-c CONF_FILE``, ``--conf CONF_FILE``
        - configuration file (default: None)
    *   - ``-t intype [intype ...]``
        - Contact Map file format:sup:`*`
    *   - ``-d DISTFILE``, ``--distfile DISTFILE``
        - Pdb or distance matrix iif distance_type set to distfile in conf file, use distances in the given file as target distance to build distance restraints
    *   - ``-s SSPRED``, ``--ssfile SSPRED``
        - Secondary structure prediction file. Supported formats are psipred, psipred2, psipred3, ss2 and indextableplus
    *   - ``-p ARIAPROJECT``, ``--ariaproject ARIAPROJECT``
        - ARIA project file. This project will be updated with data generated during the ``ariaec setup`` call
    *   - ``-r SEQRANGE``, ``--range SEQRANGE``
        - Index range if we don't want tu use the whole sequence and map
    *   - ``-n REF``, ``--native REF``
        - Native pdb. Allow TP/FP detection
    *   - ``--hb HB``
        - H-bonds contact file (eg: metapsicov.hb)
    *   - ``--no-filter``
        - Do not filter contact map
    *   - ``--extract-all``
        - Extract data or all data and parameters if an ARIA project is defined with ``-p`` option
    *   - ``--ssidx``
        - :sup:`*` Accepted contact map formats combining formats supported by ConKit_ with few supplementary formats: ``gremlin``, ``pconsc1``, ``pconsc3``, ``pconsc2``, ``bbcontacts``, ``metapsicov_stg1``, ``membrain``, ``metapsicovhb``, ``comsat``, ``casprr``, ``ccmpred``, ``plm``, ``bclcontact``, ``epcmap``, ``evfold``, ``native``, ``pconsc``, ``psicov``, ``freecontact``, ``genericstructure``, ``ncont``, ``plmc``, ``plmdca``, ``metapsicov_stg2``, ``native_full``, ``metapsicov``, ``evcoupling``, ``contactlist``, ``plmev``, ``mmcif``, ``casp``, ``pdb``, ``flib``
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Bbconv
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Translate BBcontacts as distance restraints which can be used during
`setup <Setup_>`_.

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.. code-block:: shell

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    ariaec bbconv [OPTIONS] CONTACTFILE SSPRED SEQ [MSA] -t CONTACTYPE
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**Arguments**

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+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|  Name                   | Short description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+=========================+========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
| ``contactfile``         | contacts file                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``sspred``              | PSIPRED secondary structure prediction file                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``seq``                 | sequence file [FASTA]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``msa``                 | MSA [FASTA] used to compute diversityvalue (optional)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+


**Options**

.. rst-class:: table-hover

+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|  Name                                                  | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
+========================================================+=========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
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| ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY`` | Output directory (default: None)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-c CONF_FILE``, ``--conf CONF_FILE``                 | configuration file (default: None)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--nolog``                                            | Don't generate log files (default: False)                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-d``, ``--debug``                                    | Increase output verbosity (default: False)                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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| ``-t intype``                                          | Contact Map file format:sup:`*`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| :sup:`*` Accepted contact map formats combining formats supported by ConKit_ with few supplementary formats: ``gremlin``, ``pconsc1``, ``pconsc3``, ``pconsc2``, ``bbcontacts``, ``metapsicov_stg1``, ``membrain``, ``metapsicovhb``, ``comsat``, ``casprr``, ``ccmpred``, ``plm``, ``bclcontact``, ``epcmap``, ``evfold``, ``native``, ``pconsc``, ``psicov``, ``freecontact``, ``genericstructure``, ``ncont``, ``plmc``, ``plmdca``, ``metapsicov_stg2``, ``native_full``, ``metapsicov``, ``evcoupling``, ``contactlist``, ``plmev``, ``mmcif``, ``casp``, ``pdb``, ``flib`` |
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+


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Maplot
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Contactmap analysis and visualisation tool.

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.. code-block:: shell

    ariaec maplot [-h] [--filter] [--onlyreport] [--no-filter] [--ssidx] [--prefix] [--prefixname PREFIXNAME] seq sspred infile [infile ...] -t intype [intype ...] --merge mergetype [mergetype ...]

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**Arguments**

.. rst-class:: table-hover

+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|  Name                   | Short description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+=========================+========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
| ``seq``                 | Sequence file [``FASTA``]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``sspred``              | Secondary structure prediction file                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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| ``infile [infile ...]`` | Contact or pdb file(s) used to build aria distance restraints                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
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+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+

**Options**

.. rst-class:: table-hover

+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|  Name                                                  | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
+========================================================+=========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
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| ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY`` | Output directory (default: None)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-c CONF_FILE``, ``--conf CONF_FILE``                 | configuration file (default: None)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--nolog``                                            | Don't generate log files (default: False)                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-d``, ``--debug``                                    | Increase output verbosity (default: False)                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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| ``-t intype [intype ...]``                             | Contact Map file format:sup:`*`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
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+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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| ``--merge mergetype [mergetype ...]``                  | Merge given contact types with other maps                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
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+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--filter``                                           | Use contact list filter and top n contacts selection                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--onlyreport``                                       | Generate only report file                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--no-filter``                                        | Do not filter contact map                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--ssidx``                                            | Use secondary structure index                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--prefix``                                           | Generate prefix for file names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--prefixname PREFIXNAME``                            | Prefix name for file names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| :sup:`*` Accepted contact map formats combining formats supported by ConKit_ with few supplementary formats: ``gremlin``, ``pconsc1``, ``pconsc3``, ``pconsc2``, ``bbcontacts``, ``metapsicov_stg1``, ``membrain``, ``metapsicovhb``, ``comsat``, ``casprr``, ``ccmpred``, ``plm``, ``bclcontact``, ``epcmap``, ``evfold``, ``native``, ``pconsc``, ``psicov``, ``freecontact``, ``genericstructure``, ``ncont``, ``plmc``, ``plmdca``, ``metapsicov_stg2``, ``native_full``, ``metapsicov``, ``evcoupling``, ``contactlist``, ``plmev``, ``mmcif``, ``casp``, ``pdb``, ``flib`` |
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+

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Analysis
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Supplementary analysis results for a specific iteration from an ARIA project.

.. code-block:: shell

    ariaec analysis [-h] [-r REF] [-d RESTRAINT] [-p PREFIXNAME] project iteration_path list_name

**Arguments**

.. rst-class:: table-hover

+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|  Name                   | Short description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+=========================+========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
| ``project``             | ARIA project file [XML]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``iteration_path``      | Iteration path used to run violation analysis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``list_name``           | Name of restraint list analyzed in the tbl file                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+


**Options**

.. rst-class:: table-hover

+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|  Name                                                  | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
+========================================================+=========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
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| ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY`` | Output directory (default: None)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-c CONF_FILE``, ``--conf CONF_FILE``                 | configuration file (default: None)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--nolog``                                            | Don't generate log files (default: False)                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-d``, ``--debug``                                    | Increase output verbosity (default: False)                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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| ``-r REF, --ref REF``                                  | Native pdb. Allow TP/FP detection.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-d RESTRAINT``                                       | Distance restraint file (XML) used for violation analysis. Otherwise, use restraints of the current iteration                                                                                                                                                                                                                                                                                                                                                                                                           |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-p PREFIXNAME, --prefixname PREFIXNAME``             | Prefix name for file names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
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PDBQual
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Call PDB quality tools.


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.. code-block:: shell

    ariaec pdbqual [-h] infile [infile ...]

**Arguments**

.. rst-class:: table-hover

+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|  Name                   | Short description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+=========================+========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
| ``infile [infile ...]`` | PDB file(s) used to run quality tools with aria API                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+



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TBL2XML
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Convert TBL restraints in ARIA XML format.

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.. code-block:: shell

    ariaec tbl2xml [-h] molecule.xml list_name infile.tbl [infile.tbl ...]

**Arguments**

.. rst-class:: table-hover

+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|  Name                   | Short description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+=========================+========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
| ``molecule.xml``        | ARIA molecule file [XML]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``list_name``           | Restraint list name in the tbl file                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``infile.tbl``          | TBL distance restraint file(s)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+


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PDBDist
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Extract distance from a culled list of PDBs.

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.. code-block:: shell

    ariaec pdbdist [-h] [--cullist CULLED_PDB_LIST] [--pdbdir PDB_FOLDER]


**Options**

.. rst-class:: table-hover

+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|  Name                                                  | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
+========================================================+=========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
| ``--cullist CULLED_PDB_LIST``                          | Culled list of pdb files from PISCES server  :sup:`*`                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--pdbdir PDB_FOLDER``                                | Folder containing pdb file entries                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| :sup:`*` : G. Wangand R. L. Dunbrack, Jr. PISCES: a protein sequence culling server. Bioinformatics, 19:1589-1591, 2003.                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+


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PDBStat
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Statistical analysis of `pdbdist <PDBDist>`_ results.
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.. code-block:: shell

    ariaec pdbstat [-h] [-j N_JOBS] [--min] pdbdists

**Arguments**

.. rst-class:: table-hover

+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|  Name                   | Short description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+=========================+========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
| ``pdbdists``            | PDB distance file in csv format                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+


**Options**

.. rst-class:: table-hover

+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|  Name                                                  | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
+========================================================+=========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
| ``-j N_JOBS``                                          | Number of cpus used to run mixture in parallel. By default, use max of available cpus                                                                                                                                                                                                                                                                                                                                                                                                                                   |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``--min``                                              | Compute stats only on a minimized list of atom (CA, CB and 1 SC)                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
+--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+


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IniConv
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Convert a configuration file (INI format) as csv for readability purpose.


.. code-block:: shell

    ariaec iniconv [-h] confile [confile ...]

**Arguments**

.. rst-class:: table-hover

+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|  Name                    | Short description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+==========================+========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
| ``confile [confile ...]``| configuration file(s)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
+--------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+

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.. Hyperlinks
.. [1] :command:`ec2aria` for older versions