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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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