diff --git a/docs/configuration.rst b/docs/configuration.rst
index 810e196cb87dd12987891fa5c872858eea5dde1f..cfb1b27925b8dd1be115cb2f25dd74bef48b5b14 100644
--- a/docs/configuration.rst
+++ b/docs/configuration.rst
@@ -1,4 +1,4 @@
- Configuration
+Configuration
=============
The following tables list the available parameters with the corresponding
diff --git a/docs/contents.rst b/docs/contents.rst
index 4e7e833e11b4517781612af047571e69f1908b19..5f3ed27ae9d8bb125cf29a7b13c19c12ff86e734 100644
--- a/docs/contents.rst
+++ b/docs/contents.rst
@@ -6,20 +6,8 @@
installation
configuration
usage
- contributing
-
-.. toctree::
- :maxdepth: 2
- :caption: Tutorial
-
tutorial
-
-.. toctree::
- :maxdepth: 2
- :caption: Examples
-
- examples/bpt1/bpt1
- examples/malecoli/malecoli
+ contributing
.. toctree::
:maxdepth: 4
diff --git a/docs/examples/bpt1/bpt1.rst b/docs/examples/bpt1/bpt1.rst
deleted file mode 100644
index a2c97e5c1310674f55798140ddace103bd61c438..0000000000000000000000000000000000000000
--- a/docs/examples/bpt1/bpt1.rst
+++ /dev/null
@@ -1,271 +0,0 @@
-BPT1_BOVIN structure prediction with EC map
-===========================================
-
-
-
-
-Contact map analysis
---------------------
-
-**Input**
-
-.. code-block:: console
-
- (venv) [user@host examples] > 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
-
-**Output**
-
-.. code-block:: console
-
- ================================================================================
-
- ARIA Evolutive Contact toolbox
-
- ================================================================================
-
- INFO Initialize settings
- INFO Making output directories
- INFO Reading fasta file /c7/home/fallain/tmp/bpt1/data/bpt1_bovin.fa
- INFO Amino acid sequence: FCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG
- INFO Checking if file /c7/home/fallain/tmp/bpt1/data/BPT1_BOVIN.indextableplus correspond to indextableplus format
- INFO Format type correct (indextableplus)
- INFO Reading secondary structure file /c7/home/fallain/tmp/bpt1/data/BPT1_BOVIN.indextableplus [indextableplus]
- INFO Loading ss dist file
- INFO Reading distance file /c7/home/fallain/.conda/envs/aria/lib/python2.7/site-packages/aria/conbox/data/ss_dist.txt
- INFO Align secondary structure sequence with protein sequence
- INFO Reading /c7/home/fallain/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 /c7/home/fallain/tmp/bpt1/data/BPT1_BOVIN_contacts.gremlin.out file
- INFO Pdb map set as reference
- INFO Generate contact map plot (/c7/home/fallain/tmp/bpt1/out/BPT1_BOVIN.maplot.pdf)
- INFO Generate map report file (/c7/home/fallain/tmp/bpt1/out/mapreport)
- INFO Generate roc file (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.roc.csv)
- INFO Generate roc plot (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.roc.pdf)
- INFO Generate precall file (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.roc.csv)
- INFO Generate precall plot (/c7/home/fallain/tmp/bpt1/out/graphics/maplot.precall.pdf)
- INFO Generate contact file (/c7/home/fallain/tmp/bpt1/out/BPT1_BOVIN_contacts_gremlin.contact.txt)
- INFO Generate stat file (/c7/home/fallain/tmp/bpt1/out/maplot.contactcmp.csv)
- 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 (/c7/home/fallain/tmp/bpt1/out/.maplot.pdf)
- INFO Generate contact file (/c7/home/fallain/tmp/bpt1/out/BPT1_BOVIN_native_aligned.contact.txt)
-
-
-
-Setup
------
-
-.. code-block:: console
-
- > ariaec -o examples/bpt1/out -c examples/bpt1/data/config.ini setup examples/bpt1/data/BPT1_BOVIN.fa examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out -t gremlin -s examples/bpt1/data/BPT1_BOVIN.indextableplus
-
-**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/bpt1/data/BPT1_BOVIN.fa
- INFO Amino acid sequence: FCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG
- INFO Checking if file examples/bpt1/data/BPT1_BOVIN.indextableplus correspond to indextableplus format
- 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 aria/conbox/data/ss_dist.txt
- INFO Align secondary structure sequence with protein sequence
- INFO Reader focused on file(s) ['examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out'] ['gremlin']
- INFO Reading examples/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: examples/bpt1/out/etc/BPT1_BOVIN.seq
- INFO Load molecule file and convert it into xml format
- MESSAGE [SequenceList]: reading sequence examples/bpt1/out/etc/BPT1_BOVIN.seq
- reading examples/bpt1/out/etc/BPT1_BOVIN.seq
- INFO Writing tbl files ...
- INFO Dihedral restraints for secondary structures (examples/bpt1/out/tbl/BPT1_BOVIN_dihed.tbl)
- INFO Secondary structure restraints (examples/bpt1/out/tbl/BPT1_BOVIN_ssdist.tbl)
- INFO Helix bond restraints (examples/bpt1/out/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, 1485.97it/s]
- INFO Write 53 xml distance restraints in examples/bpt1/out/xml/BPT1_BOVIN_gremlin.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)
- INFO Generate contact file (examples/bpt1/out/etc/BPT1_BOVIN_gremlin_filtered.contact.txt)
-
-ARIA Setup
-----------
-
-.. code-block:: console
-
- > aria2 -s examples/bpt1/out/ariaproject.xml
-
-**Output**
-
-.. code-block:: console
-
- ARIA Version 2.3.2. Authors: Benjamin Bardiaux, Michael Habeck, Jens Linge,
- Therese Malliavin, Sean O'Donoghue, Wolfgang Rieping, and Michael Nilges.
-
- If you use this software, please quote the following reference(s):
-
- Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,
- Nilges M.(2007) ARIA2: automated NOE assignment and data integration in NMR
- structure calculation. Bioinformatics 23:381-382
-
-
- Loading project "ariaproject.xml"...
- Setting-up examples/bpt1/out/ariaproject.xml (run: 1)
- MESSAGE [Project]: Protocols copied.
- MESSAGE [Project]: Directory tree created.
- MESSAGE [Project]: Copying data files into local data-directory...
-
- Done.
-
- For running ARIA: aria2 examples/bpt1/out/ariaproject.xml
-
-ARIA Run
---------
-
-.. code-block:: console
-
- > aria2 examples/bpt1/out/ariaproject.xml
-
-**Output**
-
-.. code-block:: console
-
- ARIA Version 2.3.2. Authors: Benjamin Bardiaux, Michael Habeck, Jens Linge,
- Therese Malliavin, Sean O'Donoghue, Wolfgang Rieping, and Michael Nilges.
-
- If you use this software, please quote the following reference(s):
-
- Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E.,
- Nilges M.(2007) ARIA2: automated NOE assignment and data integration in NMR
- structure calculation. Bioinformatics 23:381-382
-
-
- Loading project "ariaproject.xml"...
- MESSAGE [Project]: Temporary directory has been set to /tmp/BPT1_BOVIN/gremlin/
- aria_temp.tmpw0BTnZ1524489605
- MESSAGE [Project]: Host list check has been disabled.
- MESSAGE [Project]: -------------------- Reading data --------------------
- MESSAGE [Project]: Cache is enabled.
- MESSAGE [Project]: Cache file does not exist. Creating new file.
- MESSAGE [Project]: Reading molecule definition examples/bpt1/out/run1/data/
- sequence/BPT1_BOVIN.xml.
- MESSAGE [Project]: Data files read.
- MESSAGE [Project]: Data files cached.
- MESSAGE [Project]: ------------------- Filtering input data -------------------
- MESSAGE [NOESYSpectrumFilter.TP]: Spectrum filter report written to file "
- examples/bpt1/out/run1/data/spectra/
- peak_list.filtered"
- MESSAGE [Project]: ---------------- Preparing structure engine ----------------
- MESSAGE [CNS]: Sequence PDB-file written.
- MESSAGE [CNS]: PSF-file has been created.
- MESSAGE [CNS]: Template PDB-file has been created.
- MESSAGE [Project]: Starting ARIA main protocol on Mon Apr 23 15:20:31 2018
- MESSAGE [Project]: -------------------- Assigning spectra --------------------
- MESSAGE [Protocol]: ---------------------- Iteration 0 -----------------------
-
- MESSAGE [Protocol]: Calibrating spectrum "gremlin"...
- MESSAGE [Job]: Submitted batch job 18432586 (run_cns_99)
- MESSAGE [Job]: Submitted batch job 18432587 (run_cns_96)
- ...
- MESSAGE [CNS]: Starting analyses...
- MESSAGE [CNS]: Analyses done. Results are in examples/bpt1/out/run1/structures/
- it8/analysis
- 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
-
-
-Violation analysis
-------------------
-
-Violation analysis for the last iteration
-
-.. code-block:: console
-
- > ariaec -c examples/bpt1/data/config.ini -o examples/bpt1/out/run1/structures/it8 analysis -r examples/bpt1/data/BPT1_BOVIN.native.aligned.pdb examples/bpt1/out/ariaproject.xml examples/bpt1/out/run1/structures/it8 gremlin
-
-
-**Output**
-
-.. code-block:: console
-
- ================================================================================
-
- ARIA Evolutive Contact toolbox
-
- ================================================================================
-
- INFO Initialize settings
- INFO Updating settings according to config file
- INFO Reading distance restraints file(s)
- INFO Wrote 143 xml distance restraints in examples/bpt1/out/run1/structures/it0/unambig_restraints.xml
- INFO Reading native structure
- MESSAGE [StructureEnsemble]: Reading PDB files ...
- MESSAGE [StructureEnsemble]: PDB files read.
- INFO Reading structure ensemble(s)
- INFO Clusters found in this iteration, compute analysis foreach generated cluster ensemble
- INFO Violation analysis
- INFO Writing violation analysis of clust 0 examples/bpt1/out/run1/structures/it0/violations.csv file
- INFO Writing violation analysis of clust 1 examples/bpt1/out/run1/structures/it0/violations.csv file
- MESSAGE [StructureEnsemble]: Reading PDB files ...
- MESSAGE [StructureEnsemble]: PDB files read.
-
-
-.. _CNS: http://cns-online.org/v1.3/
-.. _ARIA: http://aria.pasteur.fr
-.. _GREMLIN: http://gremlin.bakerlab.org/gremlin_faq.php
-
-.. raw:: html
- <style>
- .panel {
- padding: 0 18px;
- background-color: white;
- max-height: 0;
- overflow: hidden;
- transition: max-height 0.2s ease-out;
- }
- </style>
-
- <script>
- var acc = document.getElementsByClassName("accordion");
- var i;
-
- for (i = 0; i < acc.length; i++) {
- acc[i].addEventListener("click", function() {
- this.classList.toggle("active");
- var panel = this.nextElementSibling;
- if (panel.style.maxHeight){
- panel.style.maxHeight = null;
- } else {
- panel.style.maxHeight = panel.scrollHeight + "px";
- }
- });
- }
- </script>
\ No newline at end of file
diff --git a/docs/examples/malecoli/malecoli.rst b/docs/examples/malecoli/malecoli.rst
deleted file mode 100644
index bbb9b2500f1e72be357b84fd300b7d2f9b7f9d04..0000000000000000000000000000000000000000
--- a/docs/examples/malecoli/malecoli.rst
+++ /dev/null
@@ -1,82 +0,0 @@
-MALE_ECOLI folding with EC and NMR restraints
-=============================================
-
-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 setup examples/malecoli/data/MALE_ECOLI.fa examples/malecoli/data/MALE_ECOLI_contacts.evfold.out -t plmev -o examples/malecoli/out -c examples/malecoli/data/config.ini -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
diff --git a/docs/tutorial.rst b/docs/tutorial.rst
index 1621f5ea2464d90f1d814b74d2ec113b05d22832..bd150017b7c4080adc201900f130feea42366217 100644
--- a/docs/tutorial.rst
+++ b/docs/tutorial.rst
@@ -1,3 +1,7 @@
+========
+Tutorial
+========
+
.. note::
Even if data for this tutorial are already in the ``docs/examples`` folder. You
@@ -113,15 +117,145 @@ infrastructure of the project.
Running ARIA
------------
+We use `aria2` command without the ``-s`` flag to launch structure calculations
+
.. code-block:: console
(venv) [user@host tmp] > aria2 --no-test bpt1/out/ariaproject.xml
+ .. .......................................................................... ..
+ .. 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 ...
.. warning::
- Most of the time the ``--no-test`` flags needs to be activated
+ 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
+ ================================================================================
+
+ 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.
Analysis
========
@@ -226,3 +360,34 @@ file with the path to the executable of the quality tool.
Violation analysis
------------------
+
+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.
diff --git a/src/aria/core/ariabase.py b/src/aria/core/ariabase.py
index fb57d1ae4b267df0b53aaa2198a3e152a12e605b..5b14163ce691713ca81ff8909937b17959bf0619 100644
--- a/src/aria/core/ariabase.py
+++ b/src/aria/core/ariabase.py
@@ -258,8 +258,8 @@ class AriaBaseClass:
d['logger'] = logging.getLogger(self.__module__)
self.__dict__.update(d)
- if self.__class__.display_debug:
- logging.getLogger().setLevel(logging.DEBUG)
+ # if self.__class__.display_debug:
+ # logging.getLogger().setLevel(logging.DEBUG)
def __getstate__(self):
"""
diff --git a/src/aria/core/tools.py b/src/aria/core/tools.py
index 2c8f8eacd7e350bdc28c0835c9a052b4cf3b37b7..efacf1f0ed1b270d02ea915748339c6aa46168d6 100644
--- a/src/aria/core/tools.py
+++ b/src/aria/core/tools.py
@@ -84,10 +84,13 @@ def Dump(this, filename, mode='w', as_string=0, gzip=0):
# Issues if we try to dump the logger since it contains the log file instance
# TODO: do better testing
def remove_logger(this):
- if hasattr(elt, "items"):
- for foo in elt.items():
+ if hasattr(this, "items"):
+ for foo in this.items():
if hasattr(foo, "logger"):
delattr(foo, "logger")
+ else:
+ if hasattr(this, "logger"):
+ delattr(this, "logger")
if type(this) == list:
for elt in this: