scipion-chem / scipion-chem-fpocket

Plugin of fpocket software, integrated in the scipion framework

CHEM scipion plugin

Documentation under development, sorry for the inconvenience

Base Scipion plugin defining objects and protocols for CHEMoinformatics and virtual drug screening

Full documentation can be found in the Scipion Chem official documentation page.

Install this plugin

You will need to use 3.0.0 version of Scipion to run these protocols. To install the plugin, you have two options:

• Stable version (Currently not available)

scipion3 installp -p scipion-chem

OR

• through the plugin manager GUI by launching Scipion and following Configuration >> Plugins

• Developer's version

1. Download repository:

git clone https://github.com/scipion-chem/scipion-chem.git

2. Switch to the desired branch (master or devel):

Scipion-chem is constantly under development. If you want a relatively older an more stable version, use master branch (default). If you want the latest changes and developments, user devel branch.

cd scipion-chem
git checkout devel

3. Install: The following comand will launch the installation of the plugin, together with some third-party programs

scipion3 installp -p path_to_scipion-chem --devel

• External software

External software currently installed by scipion-chem:

• OpenBabel and RDKit: the main small molecule handlers and converters
• MGLTools: additional utils for small molecules, docking, ... (includes AutoDockTools)
• JChemPaint: Java program to manually draw small molecules.
• PyMol: main viewer of Scipion-Chem for small molecules and structures
• VMD: secondary viewer of Scipion-Chem for structures and Molecular Dynamics
• AliView: main viewer for sequences
• PLIP: specialized viewer for docking interactions in PyMol

Buildbot status

Status devel version:

Status production version:

scipion-chem-fpocket's Issues

Find pockets unexpected crush

00001:   Logging configured. STDOUT --> Runs/000155_FpocketFindPockets/logs/run.stdout , STDERR --> Runs/000155_FpocketFindPockets/logs/run.stderr
00002:   RUNNING PROTOCOL -----------------
00003:   Protocol starts
00004:   Hostname: ruben-GL502VSK
00005:   PID: 14459
00006:   pyworkflow: 3.0.17
00007:   plugin: fpocket
00008:   currentDir: /home/ruben/ScipionUserData/projects/chemoinfo
00009:   workingDir: Runs/000155_FpocketFindPockets
00010:   runMode: Restart
00011:             MPI: 1
00012:         threads: 1
00013:    Starting at step: 1
00014:    Running steps 
00015:   STARTED: convertInputStep, step 1, time 2021-10-26 11:56:03.861915
00016:   FINISHED: convertInputStep, step 1, time 2021-10-26 11:56:03.932502
00017:   STARTED: fPocketStep, step 2, time 2021-10-26 11:56:04.032080
00018:   fpocket - Find pockets
00019:    /home/ruben/app/scipion3/software/em/fpocket-3.0/bin/fpocket "-f" "/home/ruben/ScipionUserData/projects/chemoinfo/Runs/000155_FpocketFindPockets/extra/nsp13-x0020_0B_apo-desolv.pdb" "-m" "3.4" "-M" "6.2" "-i" "15" "-p" "0.0" "-A" "3" "-C" "s" "-e" "e" "-D" "2.4" "-v" "300"
00020:   ***** POCKET HUNTING BEGINS ***** 
00021:   ***** POCKET HUNTING ENDS ***** 
00022:   FINISHED: fPocketStep, step 2, time 2021-10-26 11:56:05.608947
00023:   STARTED: createOutputStep, step 3, time 2021-10-26 11:56:05.733832
00024:   Protocol failed: expected str, bytes or os.PathLike object, not NoneType
00025:   FAILED: createOutputStep, step 3, time 2021-10-26 11:56:06.135884
00026:   *** Last status is failed 
00027:   ------------------- PROTOCOL FAILED (DONE 3/3)
``
[nsp13-x0020_0B_apo-desolv.pdb.zip](https://github.com/scipion-chem/scipion-chem-fpocket/files/7418071/nsp13-x0020_0B_apo-desolv.pdb.zip)
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