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1 <tool id="Ab_haddock_format" name="Ab_haddock_format" version="1.0">
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2 <description>Using ab_haddock_format.py after ANARCI.</description>
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3 <command detect_errors="exit_code"><![CDATA[
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4 conda activate Ab-HADDOCK;
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5 python2.7 ab_haddock_format.py '${input}' '${output}' '${chain}'
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6 conda deactivate
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7 ]]></command>
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8 <inputs>
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9 <param name="input" format="pdb" type="data" label="Select your PDB file."/>
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10 <param name="chain" type="text" label="Chain id to use." help="Chain id to use for the HADDOCK-formatted PDB structure."/>
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11 </inputs>
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12 <outputs>
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13 <data name="output" format="pdb" />
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14 </outputs>
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15 <help>
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16 usage: ab_haddock_format.py [-h] pdb out chain
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17
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18 Formats the antibody to fit the HADDOCK requirements with the
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19 specified chain id and returns the list of residues belonging
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20 to the HV loops defined according to the HADDOCK friendly format.
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21
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22 *** The antibody has to be numbered according to the Chothia scheme ***
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23
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24 Usage:
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25 python haddock-format.py <chothia numbered antibody> <output .pdb file> <chain_id>
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26
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27 Example:
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28 python 4G6K_ch.pdb 4G6K-HADDOCK.pdb A
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29
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30 Author: Francesco Ambrosetti
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31 Email: ambrosetti.francesco@gmail.com
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32
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33 positional arguments:
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34 pdb Path to the Chothia numbered antibody PDB structure
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35 out Path to the output PDB file
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36 chain Chain id to use for the HADDOCK-formatted PDB structure
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37
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38 optional arguments:
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39 -h, --help show this help message and exit
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40 </help>
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41 </tool>
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42
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