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Commit a76abff1 authored by Fabrice Allain's avatar Fabrice Allain
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docs: Added bpt1 setup in examples

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aria/conbox/conf/config.ini
View file @ a76abff1
......@@ -36,7 +36,7 @@ default_cutoff: 8.0
;ca_ca:
;cb_cb:
;sc_sc:
bool
[setup]
; ------------------------------ TBL parameters ------------------------------ #
; longrange_hb : True, False [False]
......@@ -150,7 +150,7 @@ nd_alpha: 1.0
runid: 1
cpus: 100
host_command: "sbatch -t 02:00:00"
host_executable: bin/cns1.21_aria_logn_linux_x86_64_intel.exe
host_executable:
temp_root: examples/tmp
parameter_definition: automatic
ss_dist_format: tbl
......@@ -166,7 +166,7 @@ dist_calibrate: no
dist_run_network_anchoring: no
dist_filter_contributions: yes
dist_avg_exponent: 6
cns_executable: bin/cns1.21.exe
cns_executable:
cns_keep_output: no
unambiguous_restraints_k_cool1_initial: 10.0
unambiguous_restraints_k_cool1_final: 50.0
......
aria/conbox/protmap.py
View file @ a76abff1
......@@ -1017,7 +1017,6 @@ class ResAtmMap(ProteinMap):
Returns
-------
"""
if self._sequence:
# If non empty string
......@@ -1128,14 +1127,14 @@ class ResAtmMap(ProteinMap):
def contact_map(self, contactdef, scsc_min=None, def_cut=5.0):
"""
Contact map generator from all atoms distance map. There's a contact
with 2 residues iff dist between 2 atoms are below the given treshold
with 2 residues iff distance between 2 atoms are below the given treshold
Parameters
----------
def_cut :
(Default value = 5.0)
def_cut : float
Default cutoff (Default value = 5.0)
contactdef :
for all atom pair
Contact definition for all atom pair
scsc_min :
(Default value = None)
......
docs/configuration.rst
View file @ a76abff1
This diff is collapsed.
docs/examples/bpt1/bpt1.rst
View file @ a76abff1
BPT1_BOVIN structure prediction with EC map
===========================================
Setup
-----
Here we show an example of setup with GREMLIN contacts with secondary structure
prediction
.. 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
The output should look like this
.. 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 /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/data/BPT1_BOVIN.indextableplus correspond to indextableplus format
INFO Format type correct (indextableplus)
INFO Reading secondary structure file /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/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 Align secondary structure sequence with protein sequence
INFO Reader focused on file(s) ['/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out'] ['gremlin']
INFO Reading /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/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: /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/etc/BPT1_BOVIN.seq
INFO Load molecule file and convert it into xml format
MESSAGE [SequenceList]: reading sequence /baycells/home/fallain/Projects/ariaec/
bin/python/Ariaec/docs/examples/bpt1/out/etc/BPT1_BOVIN.
seq
reading /baycells/home/fallain/Projects/ariaec/bin/
python/Ariaec/docs/examples/bpt1/out/etc/BPT1_BOVIN.seq
INFO Writing tbl files ...
INFO Dihedral restraints for secondary structures (/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/tbl/BPT1_BOVIN_dihed.tbl)
INFO Secondary structure restraints (/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/tbl/BPT1_BOVIN_ssdist.tbl)
INFO Helix bond restraints (/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/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 /baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/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 Directory /tmp/BPT1_BOVIN/gremlin doesn't exist.
INFO Create new directory /tmp/BPT1_BOVIN/gremlin
INFO Writing ARIA project file (/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/ariaproject.xml)
INFO Generate contact file (/baycells/home/fallain/Projects/ariaec/bin/python/Ariaec/docs/examples/bpt1/out/etc/BPT1_BOVIN_gremlin_filtered.contact.txt)
Run
---
docs/examples/bpt1/data/BPT1_BOVIN.fa 0 → 100644
View file @ a76abff1
>sp|P00974|BPT1_BOVIN Pancreatic trypsin inhibitor OS=Bos taurus PE=1 SV=2
FCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCG
docs/examples/bpt1/data/BPT1_BOVIN.indextableplus 0 → 100644
View file @ a76abff1
up_index up_residue ss_pred ss_conf msa_index msa_cons% msa_cons in_const pdb_atom pdb_chain pdb_index pdb_residue pdb_x_pos pdb_y_pos pdb_z_pos
1 M C 9 - - - - - - - - - - -
2 K C 3 - - - - - - - - - - -
3 M H 2 - - - - - - - - - - -
4 S H 6 - - - - - - - - - - -
5 R H 7 - - - - - - - - - - -
6 L H 9 - - - - - - - - - - -
7 C H 9 - - - - - - - - - - -
8 L H 9 - - - - - - - - - - -
9 S H 9 - - - - - - - - - - -
10 V H 9 - - - - - - - - - - -
11 A H 9 - - - - - - - - - - -
12 L H 9 - - - - - - - - - - -
13 L H 9 - - - - - - - - - - -
14 V H 9 - - - - - - - - - - -
15 L H 9 - - - - - - - - - - -
16 L H 8 - - - - - - - - - - -
17 G H 6 - - - - - - - - - - -
18 T H 5 - - - - - - - - - - -
19 L H 1 - - - - - - - - - - -
20 A C 2 - - - - - - - - - - -
21 A C 7 - - - - - - - - - - -
22 S C 9 - - - - - - - - - - -
23 T C 9 - - - - - - - - - - -
24 P C 8 - - - - - - - - - - -
25 G C 9 - - - - - - - - - - -
26 C C 8 - - - - - - - - - - -
27 D C 7 - - - - - - - - - - -
28 T C 7 - - - - - - - - - - -
29 S C 6 - - - - - - - - - - -
30 N C 6 - - - - - - - - - - -
31 Q C 4 - - - - - - - - - - -
32 A C 1 - - - - - - - - - - -
33 K C 1 - - - - - - - - - - -
34 A C 4 - - - * - - - - - - -
35 Q C 9 - - - * - - - - - - -
36 R C 9 - - - * 2 A 1 R 32.184 14.697 -11.772
37 P C 9 - - - * 28 A 2 P 34.897 13.603 -9.390
38 D C 9 - - - * 42 A 3 D 35.837 10.014 -9.507
39 F C 7 35 12 * * 54 A 4 F 34.975 9.704 -5.855
40 C C 7 36 86 * * 74 A 5 C 31.286 10.029 -6.794
41 L C 6 37 13 * * 84 A 6 L 31.467 6.583 -8.351
42 E C 8 38 34 * * 103 A 7 E 32.663 4.924 -5.112
43 P C 9 39 52 * * 127 A 8 P 30.224 2.852 -3.086
44 P C 8 40 19 * * 141 A 9 P 29.160 4.238 0.321
45 Y C 7 44 29 * * 155 A 10 Y 31.512 3.320 3.156
46 T C 5 45 15 * * 176 A 11 T 30.045 2.720 6.641
47 G C 6 46 82 * * 190 A 12 G 33.523 2.128 8.130
48 P C 8 52 30 * * 197 A 13 P 34.519 0.168 11.227
49 C C 7 56 85 * * 211 A 14 C 32.817 2.337 13.956
50 K C 5 57 23 * * 221 A 15 K 29.455 1.371 15.454
51 A C 3 63 30 * * 243 A 16 A 27.519 4.598 15.454
52 R C 1 82 13 * * 253 A 17 R 24.373 4.865 13.248
53 I E 5 83 15 * * 277 A 18 I 24.709 8.341 11.537
54 I E 6 91 19 * * 296 A 19 I 22.472 8.852 8.467
55 R E 5 92 54 * * 315 A 20 R 24.442 10.455 5.670
56 Y E 4 93 45 * * 339 A 21 Y 23.980 10.950 1.898
57 F E 5 96 49 * * 360 A 22 F 25.997 9.344 -0.804
58 Y E 5 97 61 * * 380 A 23 Y 25.779 9.725 -4.634
59 N E 5 98 44 * * 401 A 24 N 24.473 6.511 -6.126
60 A C 4 111 17 * * 415 A 25 A 25.937 6.771 -9.710
61 K C 9 112 12 * * 425 A 26 K 23.844 3.843 -10.944
62 A C 9 113 28 * * 447 A 27 A 20.576 5.701 -10.043
63 G C 9 114 25 * * 457 A 28 G 21.970 9.249 -10.618
64 L C 1 115 18 * * 464 A 29 L 20.589 10.458 -7.271
65 C E 5 116 99 * * 483 A 30 C 21.875 11.033 -3.734
66 Q E 4 117 24 * * 493 A 31 Q 20.508 8.474 -1.259
67 T E 7 121 15 * * 510 A 32 T 20.941 7.836 2.490
68 F E 8 122 85 * * 524 A 33 F 23.207 5.275 4.060
69 V E 7 125 19 * * 544 A 34 V 24.349 4.496 7.646
70 Y E 2 127 73 * * 560 A 35 Y 27.814 5.860 8.458
71 G C 4 131 54 * * 581 A 36 G 29.544 4.252 11.487
72 G C 6 149 86 * * 588 A 37 G 31.172 7.377 12.736
73 C C 7 151 86 * * 595 A 38 C 34.813 7.212 11.868
74 R C 9 155 37 * * 605 A 39 R 37.025 7.056 8.805
75 A C 9 157 80 * * 629 A 40 A 34.631 8.632 6.385
76 K C 9 161 80 * * 639 A 41 K 35.456 8.549 2.638
77 R C 8 165 14 * * 661 A 42 R 34.659 11.372 0.167
78 N C 9 173 95 * * 685 A 43 N 31.235 10.157 -1.075
79 N C 9 174 49 * * 699 A 44 N 29.680 10.998 2.281
80 F C 3 175 90 * * 713 A 45 F 27.732 14.188 2.696
81 K C 0 176 18 * * 733 A 46 K 25.670 15.810 5.399
82 S C 3 177 48 * * 755 A 47 S 23.068 17.191 3.061
83 A H 9 178 20 * * 766 A 48 A 21.452 16.202 -0.192
84 E H 9 179 35 * * 776 A 49 E 22.235 19.620 -1.652
85 D H 9 180 37 * * 791 A 50 D 25.961 19.288 -1.082
86 C H 9 185 98 * * 803 A 51 C 25.822 15.753 -2.493
87 M H 9 186 27 * * 813 A 52 M 23.975 16.860 -5.592
88 R H 9 187 13 * * 838 A 53 R 26.111 19.970 -6.044
89 T H 7 188 24 * * 862 A 54 T 29.317 17.889 -5.933
90 C C 0 189 97 * * 876 A 55 C 28.337 14.779 -7.839
91 G C 7 190 10 * * 886 A 56 G 25.221 15.180 -9.791
92 G C 7 - - - * 893 A 57 G 23.532 16.179 -13.038
93 A C 9 - - - * 900 A 58 A 20.058 15.148 -14.143
94 I C 9 - - - * - - - - - - -
95 G C 9 - - - * - - - - - - -
96 P C 9 - - - * - - - - - - -
97 W C 9 - - - - - - - - - - -
98 E C 8 - - - - - - - - - - -
99 N C 9 - - - - - - - - - - -
100 L C 9 - - - - - - - - - - -
docs/examples/bpt1/data/BPT1_BOVIN_contacts.gremlin.out 0 → 100644
View file @ a76abff1
i j i_id j_id r_sco s_sco prob
11 35 11_C 35_C 1.8751 4.951 1.000
17 41 17_R 41_N 1.2690 3.351 1.000
21 28 21_N 28_Q 1.2309 3.250 1.000
45 49 45_A 49_M 1.0435 2.755 1.000
24 28 24_A 28_Q 0.8186 2.161 1.000
14 31 14_R 31_V 0.8011 2.115 1.000
6 19 6_P 19_F 0.7280 1.922 1.000
18 45 18_Y 45_A 0.6058 1.600 0.998
17 43 17_R 43_K 0.6022 1.590 0.998
4 42 4_E 42_F 0.5441 1.437 0.995
10 33 10_P 33_G 0.5022 1.326 0.991
44 47 44_S 47_D 0.4921 1.299 0.990
4 39 4_E 39_R 0.4679 1.235 0.985
48 52 48_C 52_C 0.4673 1.234 0.985
49 53 49_M 53_G 0.4665 1.232 0.984
43 47 43_K 47_D 0.4617 1.219 0.983
1 39 1_F 39_R 0.4528 1.196 0.981
34 37 34_G 37_A 0.4515 1.192 0.980
8 33 8_T 33_G 0.4497 1.188 0.980
37 41 37_A 41_N 0.4362 1.152 0.975
16 29 16_I 29_T 0.4345 1.147 0.974
38 41 38_K 41_N 0.4193 1.107 0.968
7 37 7_Y 37_A 0.4172 1.102 0.967
19 28 19_F 28_Q 0.4127 1.090 0.964
32 37 32_Y 37_A 0.4055 1.071 0.960
46 50 46_E 50_R 0.3972 1.049 0.955
10 36 10_P 36_R 0.3778 0.998 0.939
47 51 47_D 51_T 0.3735 0.986 0.935
9 37 9_G 37_A 0.3652 0.964 0.926
9 41 9_G 41_N 0.3635 0.960 0.925
25 53 25_G 53_G 0.3470 0.916 0.904
30 38 30_F 38_K 0.3295 0.870 0.878
1 51 1_F 51_T 0.3260 0.861 0.872
16 31 16_I 31_V 0.3187 0.842 0.859
1 42 1_F 42_F 0.3148 0.831 0.850
15 31 15_I 31_V 0.3107 0.820 0.842
3 22 3_L 22_A 0.3057 0.807 0.831
3 45 3_L 45_A 0.2994 0.791 0.818
11 33 11_C 33_G 0.2955 0.780 0.808
32 40 32_Y 40_N 0.2914 0.769 0.797
20 25 20_Y 25_G 0.2876 0.759 0.787
13 34 13_A 34_G 0.2867 0.757 0.785
8 12 8_T 12_K 0.2854 0.754 0.782
14 33 14_R 33_G 0.2763 0.730 0.757
32 41 32_Y 41_N 0.2761 0.729 0.756
3 51 3_L 51_T 0.2701 0.713 0.738
46 49 46_E 49_M 0.2698 0.712 0.737
18 28 18_Y 28_Q 0.2615 0.691 0.713
32 38 32_Y 38_K 0.2612 0.690 0.711
5 23 5_P 23_K 0.2551 0.674 0.692
18 29 18_Y 29_T 0.2549 0.673 0.691
50 53 50_R 53_G 0.2540 0.671 0.688
36 39 36_R 39_R 0.2507 0.662 0.677
12 33 12_K 33_G 0.2468 0.652 0.664
22 28 22_A 28_Q 0.2353 0.621 0.623
25 28 25_G 28_Q 0.2341 0.618 0.618
13 33 13_A 33_G 0.2299 0.607 0.603
9 19 9_G 19_F 0.2286 0.604 0.599
14 36 14_R 36_R 0.2260 0.597 0.590
9 34 9_G 34_G 0.2240 0.592 0.583
3 25 3_L 25_G 0.2200 0.581 0.567
12 20 12_K 20_Y 0.2184 0.577 0.562
23 29 23_K 29_T 0.2132 0.563 0.542
20 27 20_Y 27_C 0.2089 0.552 0.526
23 26 23_K 26_L 0.2037 0.538 0.507
27 52 27_C 52_C 0.2036 0.538 0.507
4 23 4_E 23_K 0.2036 0.538 0.507
12 31 12_K 31_V 0.2023 0.534 0.501
25 46 25_G 46_E 0.1989 0.525 0.488
30 37 30_F 37_A 0.1986 0.524 0.487
23 43 23_K 43_K 0.1985 0.524 0.487
22 25 22_A 25_G 0.1900 0.502 0.456
27 48 27_C 48_C 0.1895 0.500 0.454
4 49 4_E 49_M 0.1872 0.494 0.445
19 29 19_F 29_T 0.1832 0.484 0.432
36 50 36_R 50_R 0.1802 0.476 0.421
4 38 4_E 38_K 0.1800 0.475 0.420
3 47 3_L 47_D 0.1798 0.475 0.420
8 31 8_T 31_V 0.1765 0.466 0.408
30 33 30_F 33_G 0.1755 0.463 0.404
docs/examples/bpt1/data/config.ini
View file @ a76abff1
......@@ -10,7 +10,7 @@ n_factor: 1.0
host_command: sbatch -t 06:00:00
host_executable: /path/to/cns1.21.exe
cns_executable: /path/to/cns1.21.exe
temp_root: /path/to/tempdir
temp_root: /tmp
# Protocol parameters
# -------------------
rama_potential_enabled: yes
......
docs/tutorial/analysis.rst
View file @ a76abff1
Analysis
========
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)
docs/tutorial/run.rst
View file @ a76abff1
Run
===
Cette étape se résume en deux partie,
L'initialisation du projet ARIA généré durant le setup
L'exécution du projet
=> NB vérifier la commande utilisée pour exécuter le projet si elle correspond au gestionnaire de job utilisé par votre cluster
docs/tutorial/setup.rst
View file @ a76abff1
Setup
=====
Modifier les paramètres indiquant le chemin de CNS et du ou des programmes d'analyse qu'on souhaite utiliser
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
docs/usage.rst
View file @ a76abff1
......@@ -27,7 +27,7 @@ ARIAEC
+-------------------------+-----------------------------------------------------+
| Name | Short description |
+-------------------------+-----------------------------------------------------+
+=========================+=====================================================+
| `setup <Setup_>`_ | Setup ARIA project with EC data |
+-------------------------+-----------------------------------------------------+
| `bbconv <BBconv_>`_ | Translate BBcontacts as distance restraints |
......@@ -56,7 +56,7 @@ ARIAEC
+--------------------------------------------------------+-----------------------------------------------------+
| Name | Description |
+--------------------------------------------------------+-----------------------------------------------------+
+========================================================+=====================================================+
| ``-h``, ``--help`` | show help message and exit |
+--------------------------------------------------------+-----------------------------------------------------+
| ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY`` | Output directory (default: None) |
......@@ -86,7 +86,7 @@ Translate contact maps as distance restraints and setup ARIA infrastructure.
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Name | Short description |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+=========================+========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================+
| ``seq`` | Sequence file [``FASTA``] |
+-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``infile`` | Contact or pdb file(s) used to build aria distance restraints |
......@@ -107,7 +107,7 @@ Translate contact maps as distance restraints and setup ARIA infrastructure.
+--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
| Name | Description |
+--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
+========================================================+========================================================================================================================================================+
| ``-d DISTFILE``, ``--distfile DISTFILE`` | Pdb or distance matrix iif distance_type set to distfile in conf file, use distances in the given file as target distance to build distance restraints |
+--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``-s SSPRED``, ``--ssfile SSPRED`` | Secondary structure prediction file |
......
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