Commit 794f14ee authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN
Browse files

docs: updated examples

parent d171f050
<a name="0.0.18"></a>
## <small>0.0.18 (2018-04-24)</small>
* docs: Added bpt1 setup in examples ([a76abff](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a76abff))
* docs: Added link to example archive in docs ([9ec966b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9ec966b))
* docs: Added MALE_ECOLI example data ([4877131](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4877131))
* docs: updated changelog ([ceececc](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ceececc))
* docs: updated changelog ([95d3f62](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/95d3f62))
* docs: Updated changelog (removed old tags) ([a59416d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a59416d))
* *: Fix bug during pdf generation in analysis command; Added analysis example for bpt1 ([e159414](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e159414))
* Added casp rr support when there is no header (pfrmatrr) ([d9d7349](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/d9d7349))
* Added coverage report in generated ci files ([476478c](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/476478c))
* Added future to setup ([6540e57](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6540e57))
......@@ -35,20 +30,20 @@
* Revert "Update Dockerfile" ([b4598c3](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/b4598c3))
* Revised documentation ([705ef9e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/705ef9e))
* Solved issue within analysis command. If the native and ensemble segids didn't correspond, the viola ([5071ec0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/5071ec0))
* Update .gitlab-ci.yml ([0fd6683](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0fd6683))
* Update .gitlab-ci.yml ([ef27cca](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ef27cca))
* Update .gitlab-ci.yml ([7d37392](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/7d37392))
* Update .gitlab-ci.yml ([8e679df](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8e679df))
* Update .gitlab-ci.yml ([33f9575](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/33f9575))
* Update .gitlab-ci.yml ([0fd6683](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/0fd6683))
* Update .gitlab-ci.yml ([9ddd3ba](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9ddd3ba))
* Update .gitlab-ci.yml ([6a84129](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6a84129))
* Update .gitlab-ci.yml ([ca8c15e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ca8c15e))
* Update .gitlab-ci.yml ([9ddd3ba](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9ddd3ba))
* Update .gitlab-ci.yml ([33f9575](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/33f9575))
* Update CONTRIBUTING.md ([64f0a8a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/64f0a8a))
* Update .gitlab-ci.yml ([8e679df](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/8e679df))
* Update .gitlab-ci.yml ([7d37392](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/7d37392))
* Update CONTRIBUTING.md ([3c6b9a2](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3c6b9a2))
* Update CONTRIBUTING.md ([64f0a8a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/64f0a8a))
* Update CONTRIBUTING.rst ([e000d1e](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/e000d1e))
* Update Dockerfile ([c650124](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c650124))
* Update Dockerfile ([ae12b86](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ae12b86))
* Update Dockerfile ([da41768](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/da41768))
* Update Dockerfile ([ae12b86](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ae12b86))
* Update README.md ([6ee017a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6ee017a))
* Updated API doc ([6c1b229](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6c1b229))
* Updated changelog ([6c72ac0](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/6c72ac0))
......@@ -65,6 +60,12 @@
* updated logo file ([774713a](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/774713a))
* Updated README.rst and installation doc ([aa67392](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/aa67392))
* Updated toctree & ariaec setup command within sphinx documentation ([3ee3140](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/3ee3140))
* docs: Added bpt1 setup in examples ([a76abff](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a76abff))
* docs: Added link to example archive in docs ([9ec966b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/9ec966b))
* docs: Added MALE_ECOLI example data ([4877131](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/4877131))
* docs: updated changelog ([ceececc](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/ceececc))
* docs: updated changelog ([95d3f62](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/95d3f62))
* docs: Updated changelog (removed old tags) ([a59416d](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/a59416d))
* feat: Automatic changelog ([23e095b](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/23e095b))
* fix: wrong installation order in dockerfile for husky npm module ([c83c314](https://gitlab.pasteur.fr/bis-aria/Ariaec/commit/c83c314))
......
No preview for this file type
BPT1_BOVIN structure prediction with EC map
===========================================
Here we show an example of *de novo* structure prediction from GREMLIN contacts
We show an example of *de novo* structure prediction from GREMLIN_ contacts
combined with secondary structure prediction. The files related to this example
can be found in the ``docs`` folder or :download:`here <docs/examples.tar.gz>`.
can be found in the ``docs`` folder or :download:`here <../../examples.tar.gz>`.
.. note::
Even if data for this example is already in the ``docs/examples`` folder. You
Even if data for this example 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). Otherwise,
you cannot run this example.
path of your CNS_ executable (not supplied in this package) in the
configuration file . Otherwise, this example will not work.
Contact map analysis
--------------------
......@@ -37,7 +37,7 @@ Contact map analysis
INFO Format type correct (indextableplus)
INFO Reading secondary structure file examples/bpt1/data/BPT1_BOVIN.indextableplus [indextableplus]
INFO Loading ss dist file
INFO Reading distance file /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/aria/conbox/data/ss_dist.txt
INFO Reading distance file ss_dist.txt
INFO Align secondary structure sequence with protein sequence
INFO Reader focused on file(s) ['examples/bpt1/data/BPT1_BOVIN.native.aligned.pdb', 'examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out'] ['pdb', 'gremlin']
INFO Reading examples/bpt1/data/BPT1_BOVIN.native.aligned.pdb file
......@@ -116,7 +116,7 @@ Setup
INFO 0%| | 0/53 [00:00<?, ?it/s]
INFO 100%|##########| 53/53 [00:00<00:00, 1485.97it/s]
INFO Write 53 xml distance restraints in examples/bpt1/out/xml/BPT1_BOVIN_gremlin.xml
INFO Loading aria template file /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/aria/conbox/templates/aria_project_v2.3.4.xml
INFO Loading aria template file aria_project_v2.3.4.xml
INFO Directory /tmp/BPT1_BOVIN/gremlin doesn't exist.
INFO Create new directory /tmp/BPT1_BOVIN/gremlin
INFO Writing ARIA project file (examples/bpt1/out/ariaproject.xml)
......@@ -204,8 +204,7 @@ ARIA Run
MESSAGE [CNS]: Starting analyses...
MESSAGE [CNS]: Analyses done. Results are in examples/bpt1/out/run1/structures/
it8/analysis
MESSAGE [Project]: Temporary directory "/baycells/scratch/fallain/tmp/
BPT1_BOVIN/gremlin/aria_temp.tmpRNyO3Q1524493463" removed.
MESSAGE [Project]: Temporary directory "tmp/BPT1_BOVIN/gremlin/aria_temp.tmpRNyO3Q1524493463" removed.
MESSAGE [Project]: ARIA run completed at Mon Apr 23 17:25:08 2018
......@@ -247,6 +246,7 @@ Violation analysis for the last iteration
.. _CNS: http://cns-online.org/v1.3/
.. _ARIA: http://aria.pasteur.fr
.. _GREMLIN: http://gremlin.bakerlab.org/gremlin_faq.php
.. raw:: html
<style>
......
This diff is collapsed.
<!DOCTYPE project SYSTEM "project1.0.dtd">
<project name="MALE_ECOLI" version="1.0" author="" date="" description="" comment="" references="" working_directory="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI" temp_root="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI" run="1" file_root="MALE_ECOLI" cache="yes" cleanup="yes">
<project name="MALE_ECOLI" version="1.0" author="" date="" description="" comment="" references="" working_directory="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data" temp_root="/baycells/scratch/fallain/tmp" run="1" file_root="MALE_ECOLI" cache="yes" cleanup="yes">
<data>
<ccpn_model filename=""/>
<molecule file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/sequence.xml" format="xml" ccpn_id="">
<molecule file="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data/xml/sequence.xml" format="xml" ccpn_id="">
<linkage_definition name="automatic" filename=""/>
<parameter_definition name="automatic" filename=""/>
<topology_definition name="automatic" filename=""/>
</molecule>
<spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no" filter_diagonal_peaks="yes" filter_unassigned_peaks="no">
<shifts file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/n20_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/n20_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="0.025" freq_window_hetero1="0.3" freq_window_proton2="0.04" freq_window_hetero2="0.5" use_bounds="no">
<shifts file="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data/xml/n20_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data/xml/n20_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="0.025" freq_window_hetero1="0.3" freq_window_proton2="0.04" freq_window_hetero2="0.5" use_bounds="no">
<lower_bound_correction value="0.0" enabled="no"/>
<upper_bound_correction value="6.0" enabled="no"/>
</peaks>
<experiment_data molecule_correlation_time="0.0" spectrum_mixing_time="0.0" spectrometer_frequency="0.0" ambiguity_type="intra"/>
</spectrum>
<spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no" filter_diagonal_peaks="yes" filter_unassigned_peaks="no">
<shifts file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/c_redo_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/c_redo_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="0.025" freq_window_hetero1="0.3" freq_window_proton2="0.04" freq_window_hetero2="0.5" use_bounds="no">
<shifts file="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data/xml/c_redo_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data/xml/c_redo_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="0.025" freq_window_hetero1="0.3" freq_window_proton2="0.04" freq_window_hetero2="0.5" use_bounds="no">
<lower_bound_correction value="0.0" enabled="no"/>
<upper_bound_correction value="6.0" enabled="no"/>
</peaks>
<experiment_data molecule_correlation_time="0.0" spectrum_mixing_time="0.0" spectrometer_frequency="0.0" ambiguity_type="intra"/>
</spectrum>
<spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no" filter_diagonal_peaks="yes" filter_unassigned_peaks="no">
<shifts file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/cc20_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/cc20_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="999.0" freq_window_hetero1="0.3" freq_window_proton2="0.03" freq_window_hetero2="0.3" use_bounds="no">
<shifts file="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data/xml/cc20_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data/xml/cc20_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="999.0" freq_window_hetero1="0.3" freq_window_proton2="0.03" freq_window_hetero2="0.3" use_bounds="no">
<lower_bound_correction value="0.0" enabled="no"/>
<upper_bound_correction value="6.0" enabled="no"/>
</peaks>
<experiment_data molecule_correlation_time="0.0" spectrum_mixing_time="0.0" spectrometer_frequency="0.0" ambiguity_type="intra"/>
</spectrum>
<spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no" filter_diagonal_peaks="yes" filter_unassigned_peaks="no">
<shifts file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/nn20_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/nn20_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="999.0" freq_window_hetero1="0.3" freq_window_proton2="0.03" freq_window_hetero2="0.3" use_bounds="no">
<shifts file="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data/xml/nn20_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data/xml/nn20_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="999.0" freq_window_hetero1="0.3" freq_window_proton2="0.03" freq_window_hetero2="0.3" use_bounds="no">
<lower_bound_correction value="0.0" enabled="no"/>
<upper_bound_correction value="6.0" enabled="no"/>
</peaks>
<experiment_data molecule_correlation_time="0.0" spectrum_mixing_time="0.0" spectrometer_frequency="0.0" ambiguity_type="intra"/>
</spectrum>
<spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no" filter_diagonal_peaks="yes" filter_unassigned_peaks="no">
<shifts file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/cn0_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/cn0_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="999.0" freq_window_hetero1="0.3" freq_window_proton2="0.03" freq_window_hetero2="0.3" use_bounds="no">
<shifts file="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data/xml/cn0_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data/xml/cn0_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="999.0" freq_window_hetero1="0.3" freq_window_proton2="0.03" freq_window_hetero2="0.3" use_bounds="no">
<lower_bound_correction value="0.0" enabled="no"/>
<upper_bound_correction value="6.0" enabled="no"/>
</peaks>
<experiment_data molecule_correlation_time="0.0" spectrum_mixing_time="0.0" spectrometer_frequency="0.0" ambiguity_type="intra"/>
</spectrum>
<spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no" filter_diagonal_peaks="yes" filter_unassigned_peaks="no">
<shifts file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/nc0_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/xml/nc0_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="999.0" freq_window_hetero1="0.3" freq_window_proton2="0.03" freq_window_hetero2="0.3" use_bounds="no">
<shifts file="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data/xml/nc0_cs.xml" format="xml" ccpn_id="" default_shift_error="0.0" use_shift_error="yes"/>
<peaks file="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data/xml/nc0_peaks.xml" format="xml" ccpn_id="" peak_size="volume" freq_window_proton1="999.0" freq_window_hetero1="0.3" freq_window_proton2="0.03" freq_window_hetero2="0.3" use_bounds="no">
<lower_bound_correction value="0.0" enabled="no"/>
<upper_bound_correction value="6.0" enabled="no"/>
</peaks>
<experiment_data molecule_correlation_time="0.0" spectrum_mixing_time="0.0" spectrometer_frequency="0.0" ambiguity_type="intra"/>
</spectrum>
<rdcs file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/gel_exp.tbl" format="tbl" ccpn_id="" enabled="yes" parameter_class="1"/>
<dihedrals file="/baycells/home/fallain/Workspace/These/data/2017-04-ECNMR/MALE_ECOLI/talos.tbl" format="tbl" ccpn_id="" enabled="yes" data_type="standard"/>
<rdcs file="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data/tbl/gel_exp.tbl" format="tbl" ccpn_id="" enabled="yes" parameter_class="1"/>
<dihedrals file="/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/malecoli/data/tbl/talos.tbl" format="tbl" ccpn_id="" enabled="yes" data_type="standard"/>
<symmetry enabled="no" method="standard" n_monomers="1" symmetry_type="None" ncs_enabled="no" packing_enabled="no"/>
<initial_structure file="" format="iupac" ccpn_id="" enabled="no"/>
</data>
......@@ -85,7 +85,7 @@
<md_parameters dynamics="torsion" random_seed="89764443" tad_temp_high="10000.0" tad_timestep_factor="9.0" cartesian_temp_high="2000.0" cartesian_first_iteration="0" timestep="0.003" temp_cool1_final="1000.0" temp_cool2_final="50.0" steps_high="20000" steps_refine="4000" steps_cool1="30000" steps_cool2="30000"/>
</cns>
<job_manager default_command="csh -f">
<host enabled="yes" command="qsub -@ /Bis/home/bardiaux/sge_options.sge" executable="" n_cpu="60" use_absolute_path="yes"/>
<host enabled="yes" command="sbatch -t 12:00:00" executable="" n_cpu="60" use_absolute_path="yes"/>
</job_manager>
</structure_generation>
<protocol floating_assignment="yes">
......
MALE_ECOLI folding with EC and NMR restraints
=============================================
The files related to this example can be found in the ``docs`` folder or
:download:`here <docs/examples.tar.gz>`
We show an example of structure calculation combining sparse NMR data and
evolutionary restraints from EVFold_ server. The files related to this example
can be found in the ``docs`` folder or :download:`here <../../examples.tar.gz>`
Setup
-----
.. warning::
We actually need an ARIA project file in 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.
.. code-block:: console
> ariaec -o examples/malecoli/out -c examples/malecoli/data/config.ini setup examples/malecoli/data/MALE_ECOLI.fa examples/malecoli/data/MALE_ECOLI_contacts.evfold.out -t plmev -p examples/malecoli/data/ariaproject_nmr.xml
**Output**
.. code-block:: console
================================================================================
ARIA Evolutive Contact toolbox
================================================================================
INFO Initialize settings
INFO Updating settings according to config file
INFO Making output directories
reading FASTA file examples/malecoli/data/MALE_ECOLI.fa
INFO Amino acid sequence: KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK
INFO Reader focused on file(s) ['examples/malecoli/data/MALE_ECOLI_contacts.evfold.out'] ['evcoupling']
INFO Conkit doesn't support evcoupling
INFO Checking if file examples/malecoli/data/MALE_ECOLI_contacts.evfold.out correspond to evcoupling format
INFO Format type correct
INFO Reading examples/malecoli/data/MALE_ECOLI_contacts.evfold.out file
INFO Loading contact file
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: examples/malecoli/out/etc/MALE_ECOLI.seq
INFO Load molecule file and convert it into xml format
MESSAGE [SequenceList]: reading sequence examples/malecoli/out/etc/
MALE_ECOLI.seq
reading examples/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, 855.92it/s]
INFO Write 370 xml distance restraints in examples/malecoli/out/xml/MALE_ECOLI_evcoupling.xml
INFO Loading aria template file aria/conbox/templates/aria_project_v2.3.4.xml
INFO Directory /tmp/MALE_ECOLI/evcoupling doesn't exist.
INFO Create new directory /tmp/MALE_ECOLI/evcoupling
WARNING No output file defined in host_command. You should add the output option (-o) to your command.
INFO Writing ARIA project file (examples/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 (examples/malecoli/out/ariaproject.xml)
INFO Generate contact file (examples/malecoli/out/etc/MALE_ECOLI_evcoupling_filtered.contact.txt)
.. _EVFold: http://evfold.org/evfold-web/evfold.do
\ No newline at end of file
......@@ -4,9 +4,8 @@ Analysis
Contact map
-----------
Since ConKit_ is installed as a dependency, all the contact map analysis tools
should be available in the terminal. Aside these tools, an extra command line
has been implemented to show several statistics between residu contact maps
Aside ConKit_ :abbr:`Command Line Interface CLI)` tools, the `maplot <../usage.rst#Maplot_>`_
command line has been implemented to show statistics between residu contact maps
and the reference which can be a structure in PDB_ format.
......@@ -19,7 +18,9 @@ Here is a brief list of files you should look at when all the iteration are fini
* ``report`` (and ``report.clustering`` if clustering is activated) related to ensemble of generated structure
* ``itY/analysis`` folder with all structure quality reports generated with Procheck, molprobity, whatif & prosa (iff the executable path are correct in the initial configuration file)
A more detailed explanation of an ARIA output is on the main ARIA_ website.
You can find a more detailed explanation of ARIA output files on the ARIA_
website.
......@@ -27,3 +28,6 @@ Analyse des cartes de contacts via la commande maplot
Analyse de structures au format PDB via la commande pdbqual (en ayant précisé les chemins des programmes dans le fichier de configuration)
.. _ConKit: http://www.conkit.org/en/0.9/
.. _PDB: ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf
.. _ARIA: http://aria.pasteur.fr/
\ No newline at end of file
......@@ -9,7 +9,6 @@ L'exécution du projet
=> NB vérifier la commande utilisée pour exécuter le projet si elle correspond au gestionnaire de job utilisé par votre cluster
.. warning::
Depending on your environment, you probably have to give ``--no-test`` option
......@@ -18,5 +17,4 @@ L'exécution du projet
.. _ARIA: http://aria.pasteur.fr
......@@ -5,3 +5,4 @@ Modifier les paramètres indiquant le chemin de CNS et du ou des programmes d'an
Lancer la commande setup en prenant en compte l'ensemble des fichiers qu'on souhaite convertir
Lister les différents fichiers générés
Verifier dans les log si les étapes se sont correctement déroulé
Command Line Interface
======================
Two CLI:abbr:`Command Line Interface` are accessible after the installation.
Two :abbr:`Command Line Interface CLI)` are accessible after the installation.
* :command:`aria2`: interface for setting up and running an ARIA project
* :command:`ariaec` [1]_: interface for converting and analyze contact maps
......@@ -170,6 +170,7 @@ Translate BBcontacts as distance restraints which can be used during
Maplot
++++++
Contactmap analysis and visualisation tool.
.. code-block:: shell
......
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