diff --git a/CHANGELOG b/CHANGELOG
index 624d2079e4cfe8b7740e2449767ce99eaf24f757..21b3f5b01be0ac5e61ba602e1e52d494755738d0 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,12 +1,7 @@
<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))
diff --git a/docs/examples.tar.gz b/docs/examples.tar.gz
index 87ddc8c27863bc8c5a9fab3836b0c8aa7427be9d..e5a27e5160615ef21290d9b8ea8c55960f78aa13 100644
Binary files a/docs/examples.tar.gz and b/docs/examples.tar.gz differ
diff --git a/docs/examples/bpt1/bpt1.rst b/docs/examples/bpt1/bpt1.rst
index ba3c9b6446f838f68dff47e7f46c3e250114e486..113342db06d7237236ec0a8613b2272ea77dab9f 100644
--- a/docs/examples/bpt1/bpt1.rst
+++ b/docs/examples/bpt1/bpt1.rst
@@ -1,16 +1,16 @@
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>
diff --git a/docs/examples/malecoli/data/MALE_ECOLI_contacts.evfold.out b/docs/examples/malecoli/data/MALE_ECOLI_contacts.evfold.out
new file mode 100644
index 0000000000000000000000000000000000000000..86ebbe679cbdb2d4afbe0eb1cf89daa29aa55886
--- /dev/null
+++ b/docs/examples/malecoli/data/MALE_ECOLI_contacts.evfold.out
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+141,94,9.661e-05,0,35,15,0,0,0,L,G
+260,196,9.5595e-05,0,10,17,0,0,0,N,K
+293,244,9.5593e-05,0,24,23,0,0,0,N,N
+393,282,9.5245e-05,0,7,29,0,0,0,R,K
+226,199,9.478e-05,0,21,22,0,0,0,K,N
+377,328,9.4507e-05,0,14,18,0,0,0,A,V
+104,58,9.3655e-05,0,36,49,0,0,0,E,G
+310,129,9.334e-05,0,36,19,0,0,0,L,L
+176,104,9.1623e-05,0,18,36,0,0,0,N,E
+245,93,9.0893e-05,0,17,23,0,0,0,K,F
+315,119,9.0462e-05,0,16,16,0,0,0,G,T
+129,55,9.0153e-05,0,19,39,0,0,0,L,K
+221,53,8.4521e-05,0,32,66,0,0,0,L,F
+239,37,8.4246e-05,0,18,15,0,0,0,A,I
+355,70,8.2681e-05,0,15,17,0,0,0,I,E
+117,6,8.0378e-05,0,39,9,0,0,0,P,G
+271,233,7.9519e-05,0,24,13,0,0,0,T,D
+124,58,7.936e-05,0,23,49,0,0,0,R,G
+161,85,7.8805e-05,0,18,40,0,0,0,L,I
+222,206,7.5722e-05,0,21,9,0,0,0,V,D
+320,231,7.5646e-05,0,24,17,0,0,0,N,N
+72,29,7.3246e-05,0,34,15,0,0,0,K,E
+54,41,7.2384e-05,0,39,13,999,0,0,E,K
+355,78,7.1519e-05,0,15,30,0,0,0,I,A
+267,58,6.9578e-05,0,21,49,0,0,0,N,G
+243,143,6.8859e-05,0,43,65,0,0,0,F,Y
+312,250,6.7985e-05,0,36,30,0,0,0,T,M
+358,236,6.6357e-05,0,9,12,0,0,0,N,Y
+381,208,6.4379e-05,0,10,10,0,0,0,Q,G
+339,313,6.4262e-05,0,13,33,0,0,0,K,D
+356,335,6.2612e-05,0,7,17,0,0,0,M,E
+252,138,5.7667e-05,0,20,24,0,0,0,I,A
+310,154,5.748e-05,0,36,52,0,0,0,L,T
+175,81,5.125e-05,0,15,15,0,0,0,F,D
+126,40,5.1191e-05,0,37,21,0,0,0,N,D
+281,116,4.3022e-05,0,14,14,0,0,0,S,Y
+259,230,4.0556e-05,0,16,14,0,0,0,S,M
+198,146,3.9842e-05,0,15,43,0,0,0,E,D
+263,159,3.8404e-05,0,14,16,0,0,0,T,P
+112,72,3.6752e-05,0,16,34,0,0,0,Q,K
+165,97,3.5923e-05,0,32,25,0,0,0,L,A
+325,310,3.525e-05,0,25,36,0,0,0,L,L
+245,212,3.2317e-05,0,17,27,0,0,0,K,A
+233,43,3.1138e-05,0,13,9,0,0,0,D,Y
+301,89,3.0662e-05,0,35,18,0,0,0,L,A
+237,127,3.001e-05,0,17,64,0,0,0,S,G
+317,227,2.8082e-05,0,21,18,0,0,0,E,N
+155,112,2.7252e-05,0,55,16,0,0,0,W,Q
+369,282,2.6688e-05,0,14,29,0,0,0,V,K
+273,134,1.8321e-05,0,19,21,0,0,0,L,I
+153,54,1.7916e-05,0,26,39,0,0,0,K,E
+320,127,1.7693e-05,0,24,64,0,0,0,N,G
+248,188,1.7408e-05,0,25,18,0,0,0,T,A
+344,258,1.7407e-05,0,14,16,0,0,0,A,W
+367,169,1.7e-05,0,11,53,0,0,0,Y,G
+129,11,1.6711e-05,0,19,28,0,0,0,L,A
+246,26,1.1768e-05,0,76,26,0,0,0,G,A
+364,257,1.0247e-05,0,11,15,0,0,0,A,A
+153,38,9.2581e-06,0,26,23,0,0,0,K,N
+222,181,6.8736e-06,0,21,21,0,0,0,V,Y
+300,98,6.5364e-06,0,31,16,0,0,0,E,Q
+342,275,3.331e-06,0,8,15,0,0,0,R,T
+321,228,8.9202e-07,0,15,33,0,0,0,K,K
+374,342,5.5004e-08,0,12,8,0,0,0,I,R
diff --git a/docs/examples/malecoli/data/ariaproject_nmr.xml b/docs/examples/malecoli/data/ariaproject_nmr.xml
index f76e96e1b85f75eb775789423e9094291e90e8cf..f552d35768ff3bf03314939a19c3559cff7f437a 100644
--- a/docs/examples/malecoli/data/ariaproject_nmr.xml
+++ b/docs/examples/malecoli/data/ariaproject_nmr.xml
@@ -1,62 +1,62 @@
<!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">
diff --git a/docs/examples/malecoli/malecoli.rst b/docs/examples/malecoli/malecoli.rst
index 4567ad2412049a247d2f9825ccac6c5615595dfc..71339281ec4a6f9602d07fcfa44919913120c234 100644
--- a/docs/examples/malecoli/malecoli.rst
+++ b/docs/examples/malecoli/malecoli.rst
@@ -1,9 +1,82 @@
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
diff --git a/docs/tutorial/analysis.rst b/docs/tutorial/analysis.rst
index 9afeb0ab83270d9fb0b74af2123d780b9c5f3eeb..3f318ca8e1dc5021e669b2d8372ec88aff30c2c2 100644
--- a/docs/tutorial/analysis.rst
+++ b/docs/tutorial/analysis.rst
@@ -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
diff --git a/docs/tutorial/run.rst b/docs/tutorial/run.rst
index 21a10e42856611b474e9456346cf6c9cabbf21c7..686e540a9643e94d82fd1428660081631843af76 100644
--- a/docs/tutorial/run.rst
+++ b/docs/tutorial/run.rst
@@ -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
diff --git a/docs/tutorial/setup.rst b/docs/tutorial/setup.rst
index 5d0934b1e21803b131e789547a6ac957e4bdb10c..d73a59eca4eb2273a9367f1e25e1ebe096fb6d63 100644
--- a/docs/tutorial/setup.rst
+++ b/docs/tutorial/setup.rst
@@ -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
+
diff --git a/docs/usage.rst b/docs/usage.rst
index 0ca67d61915d2bc7cc0c56415cc77ac19512c3e6..b8a21546c72d65ff67fe8da434325bb2a17b2214 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -1,7 +1,7 @@
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