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comparison abhaddock_wrapper.xml @ 7:9a64e7a9c3aa draft

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author p.lucas
date Thu, 06 May 2021 09:21:22 +0000
parents 81d1ab123329
children 59e22a98a99f
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6:81d1ab123329 7:9a64e7a9c3aa
11 </inputs> 11 </inputs>
12 <outputs> 12 <outputs>
13 <data name="output" format="pdb" /> 13 <data name="output" format="pdb" />
14 </outputs> 14 </outputs>
15 <help> 15 <help>
16 <!--
17 usage: ab_haddock_format.py [-h] pdb out chain 16 usage: ab_haddock_format.py [-h] pdb out chain
18 17
19 Formats the antibody to fit the HADDOCK requirements with the 18 Formats the antibody to fit the HADDOCK requirements with the
20 specified chain id and returns the list of residues belonging 19 specified chain id and returns the list of residues belonging
21 to the HV loops defined according to the HADDOCK friendly format. 20 to the HV loops defined according to the HADDOCK friendly format.
22 21
23 *** The antibody has to be numbered according to the Chothia scheme *** 22 *** The antibody has to be numbered according to the Chothia scheme ***
24 23
25 Usage: 24 Usage:
26 python haddock-format.py <chothia numbered antibody> <output .pdb file> <chain_id> 25 python haddock-format.py 'chothia numbered antibody' 'output .pdb file' 'chain_id'
27 26
28 Example: 27 Example:
29 python 4G6K_ch.pdb 4G6K-HADDOCK.pdb A 28 python 4G6K_ch.pdb 4G6K-HADDOCK.pdb A
30 29
31 Author: Francesco Ambrosetti 30 Author: Francesco Ambrosetti
36 out Path to the output PDB file 35 out Path to the output PDB file
37 chain Chain id to use for the HADDOCK-formatted PDB structure 36 chain Chain id to use for the HADDOCK-formatted PDB structure
38 37
39 optional arguments: 38 optional arguments:
40 -h, --help show this help message and exit 39 -h, --help show this help message and exit
41 -->
42 </help> 40 </help>
43 </tool> 41 </tool>
44 42