|
2
|
1 <tool id="Ab_haddock_format" name="Ab_haddock_format" version="2.0">
|
|
1
|
2 <description>Using ab_haddock_format.py after ANARCI.</description>
|
|
|
3 <command detect_errors="exit_code"><![CDATA[
|
|
2
|
4 source /home/galaxy/data/_conda/bin/activate Ab-HADDOCK;
|
|
|
5 python2.7 /home/galaxy/HADDOCK-antibody-antigen/ab_haddock_format.py '${input}' '${output}' ${chain};
|
|
|
6 source /home/galaxy/data/_conda/bin/deactivate
|
|
1
|
7 ]]></command>
|
|
|
8 <inputs>
|
|
|
9 <param name="input" format="pdb" type="data" label="Select your PDB file."/>
|
|
|
10 <param name="chain" type="text" label="Chain id to use." help="Chain id to use for the HADDOCK-formatted PDB structure."/>
|
|
|
11 </inputs>
|
|
|
12 <outputs>
|
|
|
13 <data name="output" format="pdb" />
|
|
|
14 </outputs>
|
|
|
15 <help>
|
|
|
16 usage: ab_haddock_format.py [-h] pdb out chain
|
|
|
17
|
|
|
18 Formats the antibody to fit the HADDOCK requirements with the
|
|
|
19 specified chain id and returns the list of residues belonging
|
|
|
20 to the HV loops defined according to the HADDOCK friendly format.
|
|
|
21
|
|
|
22 *** The antibody has to be numbered according to the Chothia scheme ***
|
|
|
23
|
|
|
24 Usage:
|
|
|
25 python haddock-format.py <chothia numbered antibody> <output .pdb file> <chain_id>
|
|
|
26
|
|
|
27 Example:
|
|
|
28 python 4G6K_ch.pdb 4G6K-HADDOCK.pdb A
|
|
|
29
|
|
|
30 Author: Francesco Ambrosetti
|
|
|
31 Email: ambrosetti.francesco@gmail.com
|
|
|
32
|
|
|
33 positional arguments:
|
|
|
34 pdb Path to the Chothia numbered antibody PDB structure
|
|
|
35 out Path to the output PDB file
|
|
|
36 chain Chain id to use for the HADDOCK-formatted PDB structure
|
|
|
37
|
|
|
38 optional arguments:
|
|
|
39 -h, --help show this help message and exit
|
|
|
40 </help>
|
|
|
41 </tool>
|
|
|
42
|
