* 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))
* 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))
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/
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
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.
...
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@@ -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.
...
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@@ -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)
