Mercurial > repos > p.lucas > abhaddock

<tool id="ABHADDOCK" name="ABHADDOCK" version="1">
  <description>Using ab_haddock_format.py after ANARCI.</description>
  <command detect_errors="exit_code"><![CDATA[
    source /home/galaxy/data/_conda/bin/activate Ab-HADDOCK;
    python2.7 /home/galaxy/HADDOCK-antibody-antigen/ab_haddock_format.py '${input}' '${output1}' ${chain} > '${output2}';
    source /home/galaxy/data/_conda/bin/deactivate
  ]]></command>
  <inputs>
    <param name="input" format="pdb" type="data" label="Select your PDB file."/>
    <param name="chain" type="text" label="Chain id to use." help="Chain id to use for the HADDOCK-formatted PDB structure."/>
  </inputs>
  <outputs>
    <data name="output1" format="pdb" />
    <data name="output2" format="txt" />
  </outputs>
  <help>
usage: ab_haddock_format.py [-h] pdb out chain

Formats the antibody to fit the HADDOCK requirements with the
specified chain id and returns the list of residues belonging
to the HV loops defined according to the HADDOCK friendly format.

*** The antibody has to be numbered according to the Chothia scheme ***

Usage:
    python haddock-format.py 'chothia numbered antibody' 'output .pdb file' 'chain_id'

Example:
    python 4G6K_ch.pdb 4G6K-HADDOCK.pdb A

Author: Francesco Ambrosetti
Email: ambrosetti.francesco@gmail.com

positional arguments:
  pdb         Path to the Chothia numbered antibody PDB structure
  out         Path to the output PDB file
  chain       Chain id to use for the HADDOCK-formatted PDB structure

optional arguments:
  -h, --help  show this help message and exit
  </help>
</tool>
author	p.lucas
date	Thu, 06 May 2021 09:34:40 +0000
parents	9a64e7a9c3aa
children