cluspro_api

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 three "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). Mixing options from these three 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 [Advanced]
  --pepseq TEXT               Peptide sequence [Advanced]
  --pepexclusion TEXT         List of PDB ids to exclude from motif
                              search [Advanced]
  --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]
  --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.