Metadata-Version: 1.1
Name: cluspro-api
Version: 1.0.5
Summary: Library for submitting and downloading job data from ClusPro.
Home-page: https://bitbucket.org/bu-structure/cluspro_api
Author: Katie Porter
Author-email: kaporter@bu.edu
License: MIT
Description-Content-Type: UNKNOWN
Description: cluspro_api
        ===========
        
        Python library and associated scripts for submiting jobs and
        downloading results from ClusPro.
        
        Installation
        ------------
        
        Ensure you have ``pip``, then run:
        
        .. code-block:: bash
        
            pip install --user cluspro_api
        
        or
        
        .. code-block:: bash
        
           [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:
        
        .. code-block:: bash
        
            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: 
        
        .. code-block:: bash
        
            $ 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:
        
        .. code-block:: bash
        
            cluspro_download <jobid>
        
        You can download multiple jobs at once:
        
        .. code-block:: bash
        
            cluspro_download <jobid1> <jobid2> <jobid3> ...
        
        The results will be saved in the directory from which you ran the command.
        
Keywords: cluspro protein
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: MacOS
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
