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========
Tutorial
========

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.. note::

  Even if data for this tutorial are already in the ``docs/examples`` folder. You
  have to change at least ``cns_executable`` and ``host_executable`` with the
  path of your CNS_ executable (not supplied in this package) in the
  configuration file . Otherwise, this example will not work.
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Structure calculation with EC restraints
========================================
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We show here an example of *de novo* structure prediction from GREMLIN_ contacts
combined with secondary structure prediction with the ``ariaec`` Command Line
Interface (CLI) is the tool for converting and analyze contact map information.
. The files related to this example can be found in the ``docs`` folder
or :download:`here <../../examples.tar.gz>`.
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Configuration file
------------------

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All the parameters for ``ariaec`` commands are encapsulated on a configuration
file in INI format. Each time you need to overwrite the default parameters,
another configuration file can be used with the updated parameters. There is
no need to give all the parameters in order to have a correct configuration
file.

A more detailed description of the parameters is in :doc:`configuration`
section.
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Restraints & project conversion
-------------------------------
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The main command of this interface is ``ariaec setup`` which convert EC data
and create an ARIA project XML file. Then we can follow the usual steps like an
usual ARIA project.

.. code-block:: console

    (venv) [user@host tmp] > ariaec setup bpt1/data/BPT1_BOVIN.fa bpt1/data/BPT1_BOVIN_contacts.gremlin.out -t gremlin -s bpt1/data/BPT1_BOVIN.indextableplus -o /tmp -c bpt1/data/config.ini
    ================================================================================

                             ARIA Evolutive Contact toolbox

    ================================================================================

    INFO     Initialize settings
    INFO     Updating settings according to config file
    INFO     Making output directories
    INFO     Reading fasta file /tmp/bpt1/data/bpt1_bovin.fa
    INFO     Amino acid sequence:   FCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG
    INFO     Checking if file /tmp/bpt1/data/BPT1_BOVIN.indextableplus correspond to indextableplus format
    INFO     Format type correct (indextableplus)
    INFO     Reading secondary structure file /tmp/bpt1/data/BPT1_BOVIN.indextableplus [indextableplus]
    INFO     Loading ss dist file
    INFO     Reading distance file /.conda/envs/aria/lib/python2.7/site-packages/aria/conbox/data/ss_dist.txt
    INFO     Align secondary structure sequence with protein sequence
    INFO     Reading /tmp/bpt1/data/BPT1_BOVIN_contacts.gremlin.out file
    INFO     Filtering gremlin contact map
    INFO     ...Position filter
    INFO     Removed 21 contacts.
    INFO     ...Conservation filter
    INFO     Conservation filter only works with indextableplus files !
    INFO     ...Secondary structure clash filter
    INFO     Removed 1 contacts.
    INFO     ...Disulfure bridge unicity filter
    INFO     Removed 11 contacts.
    INFO     Setting contact number with treshold 1.0
    INFO     Update gremlin maplot
    INFO     Update gremlin scoremap
    INFO     Select top 53 contacts according to scoremap
    writing to the file: /tmp/etc/BPT1_BOVIN.seq
    INFO     Load molecule file and convert it into xml format
    INFO     [SequenceList]: reading sequence /tmp/etc/BPT1_BOVIN.seq

                             reading /tmp/etc/BPT1_BOVIN.seq
    INFO     Writing tbl files ...
    INFO        Dihedral restraints for secondary structures (/tmp/tbl/BPT1_BOVIN_dihed.tbl)
    INFO        Secondary structure restraints (/tmp/tbl/BPT1_BOVIN_ssdist.tbl)
    INFO        Helix bond restraints (/tmp/tbl/BPT1_BOVIN_hbond.tbl)
    INFO     Writing gremlin ARIA XML distance restraints
    INFO     Using contact scores as selection criteria
    INFO     Selecting 53 contacts
    INFO     0%|          | 0/53 [00:00<?, ?it/s]
    INFO     100%|##########| 53/53 [00:00<00:00, 2549.17it/s]
    INFO     Write 53 xml distance restraints in /tmp/xml/BPT1_BOVIN_gremlin.xml
    INFO     Loading aria template file /.conda/envs/aria/lib/python2.7/site-packages/aria/conbox/templates/aria_project_v2.3.7.xml
    INFO     Writing ARIA project file (/tmp/ariaproject.xml)
    INFO     Generate contact file (/tmp/etc/BPT1_BOVIN_gremlin_filtered.contact.txt)


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Build infrastructure
--------------------
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Before running the structure calculation pipeline, ARIA needs to build the whole
infrastructure of the project.

.. code-block:: console

    (venv) [user@host tmp] > aria2 -s bpt1/out/ariaproject.xml
    Loading project "ariaproject.xml"...
    Setting-up bpt1/out/ariaproject.xml (run: 1)
    INFO     [Project]: Protocols copied.
    INFO     [Project]: Directory tree created.
    INFO     [Project]: Copying data files into local data-directory...

    Done.

    For running ARIA: aria2 bpt1/out/ariaproject.xml

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Running ARIA
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------------

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We use `aria2` command without the ``-s`` flag to launch structure calculations

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.. code-block:: console

    (venv) [user@host tmp] > aria2 --no-test bpt1/out/ariaproject.xml
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    .. .......................................................................... ..
    ..          ARIA -- Ambiguous Restraints for Iterative Assignment             ..
    ..                                                                            ..
    ..                A software for automated NOE assignment                     ..
    ..                                                                            ..
    ..                               Version 2.3                                  ..
    ..                                                                            ..
    ..                                                                            ..
    .. Copyright (C) Benjamin Bardiaux, Michael Habeck, Therese Malliavin,        ..
    ..              Wolfgang Rieping, and Michael Nilges                          ..
    ..                                                                            ..
    .. All rights reserved.                                                       ..
    ..                                                                            ..
    .. NO WARRANTY. This software package is provided 'as is' without warranty of ..
    .. any kind, expressed or implied, including, but not limited to the implied  ..
    .. warranties of merchantability and fitness for a particular purpose or      ..
    .. a warranty of non-infringement.                                            ..
    ..                                                                            ..
    .. Distribution of substantively modified versions of this module is          ..
    .. prohibited without the explicit permission of the copyright holders.       ..
    ..                                                                            ..
    .. .......................................................................... ..
    Loading project "ariaproject.xml"...
    INFO     [Project]: Temporary directory has been set to /tmp/BPT1_BOVIN/gremlin/
                        aria_temp.tmpAVTAwy1562832135
    INFO     [Project]: Host list check has been disabled.
    INFO     [Project]: -------------------- Reading data --------------------
    INFO     [Project]: Cache is enabled.
    INFO     [Project]: Cache file does not exist. Creating new file.
    INFO     [Project]: Reading molecule definition /tmp/bpt1/out/
                        run1/data/sequence/BPT1_BOVIN.xml.
    INFO     [Project]: Data files read.
    INFO     [Project]: Data files cached.
    INFO     [Project]: ------------------- Filtering input data -------------------
    INFO     [NOESYSpectrumFilter.TP]: Spectrum filter report written to file "/tmp
                                       /bpt1/out/run1/data/spectra/peak_list.filtered"
    INFO     [Project]: ---------------- Preparing structure engine ----------------
    INFO     [CNS]: Sequence PDB-file written.
    INFO     [CNS]: PSF-file has been created.
    INFO     [CNS]: Template PDB-file has been created.
    INFO     [Project]: Starting ARIA main protocol on ...
    INFO     [Project]: -------------------- Assigning spectra --------------------
    INFO     [Protocol]: ---------------------- Iteration 0 -----------------------
    INFO     [Protocol]: Calibrating spectrum "gremlin"...
    INFO     [Protocol]: Waiting for completion of structure calculation...
    ...
    INFO    [Project]: ARIA run completed at ...
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.. warning::

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    Most of the time the ``--no-test`` flags needs to be activated in order to
    disables the initial dry run of the commands (specified in the host
    list) used to launch a structure calculation. Those dry run are not
    compatible with several hosts.

Structure calculation with EC & NMR restraints
==============================================

Another possibility is to use an already existing ARIA project with NMR
restraints and use ``ariaec setup`` with the ``-p`` flag to update it with EC
restraints.

.. code-block:: console

    (venv) [user@host tmp] > ariaec setup malecoli/data/MALE_ECOLI.fa malecoli/data/MALE_ECOLI_contacts.evfold.out -t evcoupling -o malecoli/out -c malecoli/data/config.ini -p malecoli/data/ariaproject_nmr.xml
    ================================================================================

                             ARIA Evolutive Contact toolbox
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    ================================================================================

    INFO     Initialize settings
    INFO     Updating settings according to config file
    INFO     Making output directories
    INFO     Reading fasta file /c7/home/fallain/tmp/malecoli/data/male_ecoli.fa
    INFO     Amino acid sequence:   KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK
    INFO     The file format evcoupling is not supported by the conkit plugin. Switching to homemade parsers.
    INFO     Checking if file /c7/home/fallain/tmp/malecoli/data/MALE_ECOLI_contacts.evfold.out correspond to our definition of evcoupling format
    INFO     Reading /c7/home/fallain/tmp/malecoli/data/MALE_ECOLI_contacts.evfold.out file
    INFO     Loading contact file
    INFO     Alignment of sequence in contact file (evcoupling) with reference (MALE_ECOLI.fa)
    ****TGARILALSALTTMMFSASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKY***DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLE*YLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRI--
                              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||.||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
    --------------------------KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK
      Score=364

    WARNING  Found a shift of 26 residues in positions given within contact list
    INFO     Update index in contact list and remove unassigned contacts
    INFO     Remove contacts outside sequence bonds
    INFO     Filtering evcoupling contact map
    INFO     ...Position filter
    INFO     ...Conservation filter
    WARNING  No conservation information. Can't use related filter
    INFO     ...Secondary structure clash filter
    WARNING  No secondary structure information. Can't use secondary structure filter
    INFO     ...Disulfure bridge unicity filter
    INFO     Setting contact number with treshold 1.0
    INFO     Update evcoupling maplot
    INFO     Update evcoupling scoremap
    INFO     Select top 370 contacts according to scoremap
    writing to the file: /c7/home/fallain/tmp/malecoli/out/etc/MALE_ECOLI.seq
    INFO     Load molecule file and convert it into xml format
    INFO     [SequenceList]: reading sequence /c7/home/fallain/tmp/malecoli/out/etc/
                             MALE_ECOLI.seq
                             reading /c7/home/fallain/tmp/malecoli/out/etc/
                             MALE_ECOLI.seq
    INFO     Writing tbl files ...
    INFO     Writing evcoupling ARIA XML distance restraints
    INFO     Using contact scores as selection criteria
    INFO     Selecting 370 contacts
    INFO     0%|          | 0/370 [00:00<?, ?it/s]
    INFO     100%|##########| 370/370 [00:00<00:00, 1245.07it/s]
    INFO     Write 370 xml distance restraints in /c7/home/fallain/tmp/malecoli/out/xml/MALE_ECOLI_evcoupling.xml
    INFO     Loading aria template file /c7/home/fallain/Projects/ariaec/src/ariaec/src/aria/conbox/templates/aria_project_v2.3.4.xml
    INFO     Directory /baycells/scratch/fallain/tmp/MALE_ECOLI/evcoupling doesn't exist.
    INFO     Create new directory /baycells/scratch/fallain/tmp/MALE_ECOLI/evcoupling
    INFO     Writing ARIA project file (/c7/home/fallain/tmp/malecoli/out/ariaproject.xml)
    INFO     Reading ARIA project file
    INFO     Update spectrum data in project
    INFO     Update sequence data in project
    INFO     Update dihedrals data in project
    INFO     Update rdcs data in project
    INFO     Update rdcs annealing parameters
    INFO     Writing new ARIA xml file (/c7/home/fallain/tmp/malecoli/out/ariaproject.xml)
    INFO     Generate contact file (/c7/home/fallain/tmp/malecoli/out/etc/MALE_ECOLI_evcoupling_filtered.contact.txt)


.. warning::

    The ARIA project file is mandatory during the setup step if we want to mix
    evolutionary with experimental restraints. Only the data section is
    conserved actually. You still needs to give a configuration file for the
    other project parameters.
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Analysis
========

Configuration file
------------------
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A possible way to analyze different output according to their initial parameters
in a configuration file is to use the `iniconv` command. It will convert the
file into a comma separated value file which can be more practical for an
analysis pipeline.

.. code-block:: console

    (venv) [user@host tmp] > ariaec iniconv bpt1/data/config.ini -o bpt1/out
    ================================================================================

                             ARIA Evolutive Contact toolbox

    ================================================================================

    INFO     Initialize settings
    INFO     Reading configuration file(s)
    INFO     Generate output csv file (configs.csv)


Contact map analysis
--------------------

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Aside ConKit_  :abbr:`Command Line Interface CLI)` tools, the
:ref:`maplot <./usage>` command line has been implemented to show statistics
between contact maps and the reference which can be a structure in PDB_ format.
The first argument in this command will always be set as the reference map/pdb
for the contact map, ROC or precision-recall plots.
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.. code-block:: console

    (venv) [user@host tmp] > ariaec maplot bpt1/data/BPT1_BOVIN.fa bpt1/data/BPT1_BOVIN.indextableplus  bpt1/data/BPT1_BOVIN.native.aligned.pdb bpt1/data/BPT1_BOVIN_contacts.gremlin.out -o bpt1/out -t pdb gremlin
    ================================================================================

                             ARIA Evolutive Contact toolbox

    ================================================================================

    INFO     Initialize settings
    INFO     Making output directories
    INFO     Reading fasta file /tmp/bpt1/data/bpt1_bovin.fa
    INFO     Amino acid sequence:   FCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG
    INFO     Checking if file /tmp/bpt1/data/BPT1_BOVIN.indextableplus correspond to indextableplus format
    INFO     Format type correct (indextableplus)
    INFO     Reading secondary structure file /tmp/bpt1/data/BPT1_BOVIN.indextableplus [indextableplus]
    INFO     Loading ss dist file
    INFO     Reading distance file /tmp/venv/lib/python2.7/site-packages/aria/conbox/data/ss_dist.txt
    INFO     Align secondary structure sequence with protein sequence
    INFO     Reading /tmp/bpt1/data/BPT1_BOVIN.native.aligned.pdb file
    INFO     Updating distance map with pdb file
    INFO     Generate contact map using contact definition defaultdict(None, {'default_cutoff': 8.0})
    INFO     Using default cutoff
    INFO     Reading /tmp/bpt1/data/BPT1_BOVIN_contacts.gremlin.out file
    INFO     Pdb map set as reference
    INFO     Generate contact map plot (/tmp/bpt1/out/BPT1_BOVIN.maplot.pdf)
    INFO     Generate map report file (/tmp/bpt1/out/mapreport)
    INFO     Generate roc file (/tmp/bpt1/out/graphics/maplot.roc.csv)
    INFO     Generate roc plot (/tmp/bpt1/out/graphics/maplot.roc.pdf)
    INFO     Generate precall file (/tmp/bpt1/out/graphics/maplot.roc.csv)
    INFO     Generate precall plot (/tmp/bpt1/out/graphics/maplot.precall.pdf)
    INFO     Generate contact file (/tmp/bpt1/out/BPT1_BOVIN_contacts_gremlin.contact.txt)
    INFO     Generate stat file (/tmp/bpt1/out/cmp.contactcmp.csv)
    INFO
    INFO     Contact list: [(1, 39), (1, 42), (1, 51), (3, 22), (3, 25), (3, 45), (3, 47), (3, 51), (4, 23), (4, 38), (4, 39), (4, 42), (4, 49), (5, 23), (6, 19), (7, 37), (8, 12), (8, 31), (8, 33), (9, 19), (9, 34), (9, 37), (9, 41), (10, 33), (10, 36), (11, 33), (11, 35), (12, 8), (12, 20), (12, 31), (12, 33), (13, 33), (13, 34), (14, 31), (14, 33), (14, 36), (15, 31), (16, 29), (16, 31), (17, 41), (17, 43), (18, 28), (18, 29), (18, 45), (19, 6), (19, 9), (19, 28), (19, 29), (20, 12), (20, 25), (20, 27), (21, 28), (22, 3), (22, 25), (22, 28), (23, 4), (23, 5), (23, 26), (23, 29), (23, 43), (24, 28), (25, 3), (25, 20), (25, 22), (25, 28), (25, 46), (25, 53), (26, 23), (27, 20), (27, 48), (27, 52), (28, 18), (28, 19), (28, 21), (28, 22), (28, 24), (28, 25), (29, 16), (29, 18), (29, 19), (29, 23), (30, 33), (30, 37), (30, 38), (31, 8), (31, 12), (31, 14), (31, 15), (31, 16), (32, 37), (32, 38), (32, 40), (32, 41), (33, 8), (33, 10), (33, 11), (33, 12), (33, 13), (33, 14), (33, 30), (34, 9), (34, 13), (34, 37), (35, 11), (36, 10), (36, 14), (36, 39), (36, 50), (37, 7), (37, 9), (37, 30), (37, 32), (37, 34), (37, 41), (38, 4), (38, 30), (38, 32), (38, 41), (39, 1), (39, 4), (39, 36), (40, 32), (41, 9), (41, 17), (41, 32), (41, 37), (41, 38), (42, 1), (42, 4), (43, 17), (43, 23), (43, 47), (44, 47), (45, 3), (45, 18), (45, 49), (46, 25), (46, 49), (46, 50), (47, 3), (47, 43), (47, 44), (47, 51), (48, 27), (48, 52), (49, 4), (49, 45), (49, 46), (49, 53), (50, 36), (50, 46), (50, 53), (51, 1), (51, 3), (51, 47), (52, 27), (52, 48), (53, 25), (53, 49), (53, 50)]
    INFO     Generate contact map plot (/tmp/bpt1/out/ref.maplot.pdf)
    INFO     Generate contact file (/tmp/bpt1/out/BPT1_BOVIN_native_aligned.contact.txt)

Structure quality report
------------------------

The generated structures can be analyzed with procheck, whatif, clashlist or
prosa using ``ariaec pdbqual`` command. It will only need a configuration
file with the path to the executable of the quality tool.

.. code-block:: console

    (venv) [user@host tmp] > ariaec pdbqual run1/structures/it2/fitted.pdb -o bpt1/out/ -c bpt1/data/config.ini
    ================================================================================

                             ARIA Evolutive Contact toolbox

    ================================================================================
    INFO     Initialize settings
    INFO     Updating settings according to config file
    INFO     Starting quality runs with ['/tmp/run1/structures/it2/fitted.pdb'] file(s)
    INFO     Copying file(s) to output directory /tmp/bpt1/out
    ...
    QualityChecks.py finished.
    INFO     /tmp/bpt1/out/quality_checks generated
    INFO     Removing infile(s) in output directory /tmp/bpt1/out

.. note::

    If quality tools has been configured in the pipeline. There is no need to
    run this command after ARIA calculation.

Violation analysis
------------------
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Additionally, we can use the ``ariaec analysis`` command to generate
supplementary analysis file for a given ARIA iteration.

.. code-block:: console

    (venv) [user@host tmp] > ariaec analysis bpt1/out/ariaproject.xml bpt1/out/run1/structures/it8 gremlin -r bpt1/data/BPT1_BOVIN.native.aligned.pdb -c bpt1/data/config.ini -o bpt1/out/run1/structures/it8
    ================================================================================

                             ARIA Evolutive Contact toolbox

    ================================================================================

    INFO     Initialize settings
    INFO     Updating settings according to config file
    INFO     Ensemble analysis will be done on restraints and ensemble from it7 with violation criteria of it8
    INFO     Reading distance restraints file(s)
    INFO     Reading native structure
    INFO     [StructureEnsemble]: Reading PDB files ...
    INFO     [StructureEnsemble]: PDB files read.
    INFO     Reading structure ensemble(s)
    INFO     Clusters found in this iteration, compute analysis foreach generated cluster ensemble
    INFO     [StructureEnsemble]: Reading PDB files ...
    INFO     [StructureEnsemble]: PDB files read.
    INFO     [StructureEnsemble]: Reading PDB files ...
    INFO     [StructureEnsemble]: PDB files read.
    INFO     Violation analysis
    INFO     Writing violation analysis of clust 0 /tmp/bpt1/out/run1/structures/it8/violations.csv file
    INFO     Writing violation analysis of clust 1 /tmp/bpt1/out/run1/structures/it8/violations.csv file
    INFO     [StructureEnsemble]: Reading PDB files ...
    INFO     [StructureEnsemble]: PDB files read.