Mercurial > repos > p.lucas > abhaddock
changeset 1:40ccca3fac6d draft
Uploaded wrapper
| author | p.lucas |
|---|---|
| date | Thu, 06 May 2021 08:47:16 +0000 |
| parents | 6a4d5446c123 |
| children | a8cda1a4b9ea |
| files | abhaddock_wrapper.xml |
| diffstat | 1 files changed, 42 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abhaddock_wrapper.xml Thu May 06 08:47:16 2021 +0000 @@ -0,0 +1,42 @@ +<tool id="Ab_haddock_format" name="Ab_haddock_format" version="1.0"> + <description>Using ab_haddock_format.py after ANARCI.</description> + <command detect_errors="exit_code"><![CDATA[ + conda activate Ab-HADDOCK; + python2.7 ab_haddock_format.py '${input}' '${output}' '${chain}' + conda 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="output" format="pdb" /> + </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> +