Library for submitting and downloading job data from ClusPro.
Project description
Python library and associated scripts for submiting jobs and downloading results from ClusPro.
Installation
Ensure you have pip, then run:
pip install --user cluspro_api
or
[sudo] pip install cluspro_api
sudo is only needed if you are installing globally. If --user option is used, binaries will be in $HOME/.local/bin. We recommend use of Anaconda (https://www.continuum.io).
Usage
Submitting Jobs
To submit a docking job to ClusPro:
cluspro_submit --receptor <path to receptor pdb file> --ligand <path to ligand pdb file>
This will prompt you for your username and API secret, which can be found on the API tab after logging into ClusPro. These will be stored in a .clusprorc file in your home directory.
Options:
$ cluspro_submit --help
Usage: cluspro_submit [OPTIONS]
Jobs are expected to be in one of four "modes": docking with a provided
ligand PDB ID or PDB file, docking in multimer mode (using --multimer), or
peptide docking (using --pepmot and --pepseq). If using multimer mode add
--multimer and specify dimer or trimer (ex. --multimer dimer or --multimer
trimer). If using peptide mode supply both the peptide motif and sequence
(ex. --pepmot KXRRL --pepseq KGRRL). If using dimer classification mode add
--dcmode and provide the chain(s) that define the potential dimer interface
(ex. --rec-chains and --lig-chains). Mixing options from these four modes
is not supported and will result in an error message.
Options:
--username TEXT
--secret TEXT
--coeffs PATH Coefficients file [Advanced]
--rotations PATH Rotations file [Advanced]
-j, --jobname TEXT Will default to job number
-a, --antibodymode Use Antibody mode [Advanced]
-o, --othersmode Use Others mode [Advanced]
--receptor PATH Upload a PDB file
--ligand PATH Upload a PDB file
--recpdb TEXT 4-letter PDB code
--ligpdb TEXT 4-letter PDB code
--pepmot TEXT Peptide motif
--pepseq TEXT Peptide sequence
--pepexclusion TEXT List of PDB ids to exclude from motif
search
--rec-chains TEXT Chains to use, for example "A B" (in double
quotes)
--lig-chains TEXT Chains to use, for example "A B" (in double
quotes)
--rec-mask PATH Receptor mask [Advanced]
--lig-mask PATH Ligand mask [Advanced]
--rec-attraction PATH Receptor attraction [Advanced]
--lig-attraction PATH Ligand attraction [Advanced]
--rec-dssp Remove unstructured terminal residues in
receptor [Advanced]
--lig-dssp Remove unstructured terminal residues in ligand [Advanced]
--restraints PATH Upload restraints file [Advanced]
--saxs-file PATH Upload SAXS profile [Advanced]
--masknoncdr Automatically mask non-CDR region, Antibody mode only [Advanced]
--multimers [dimer|trimer] Multimer mode [Advanced]
--dcmode Use Dimer Classification mode
--help Show this message and exit
If you write a script which submits the jobs in a loop, please submit no more than 50 jobs per batch (and then wait until these jobs finish before submitting more). Please pause for 5-10 seconds between job submissions within each batch.
Running cluspro_submit will print out the cluspro job id, which you should record and use later to download your job results.
Downloading Results
To download results from a finished job:
cluspro_download <jobid>
You can download multiple jobs at once:
cluspro_download <jobid1> <jobid2> <jobid3> ...
The results will be saved in the directory from which you ran the command.
Project details
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