Mercurial > repos > bitlab > plidflow
annotate PLIDflow/pdb2pqr_plidflow.xml @ 0:6fcfa4756040 draft
Uploaded
| author | bitlab |
|---|---|
| date | Tue, 14 Jan 2020 06:09:42 -0500 |
| parents | |
| children |
| rev | line source |
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| 0 | 1 <tool id="pdb2pqr_plidflow" name="PLIDflow: PDB2PQR"> |
| 2 <description>Converts a pdb to pqr</description> | |
| 3 <inputs> | |
| 4 <param name="receptor_pdb" type="data" format="pdb" label="Receptor PDB file" help="Preparing the receptor involves adding gasteiger charges and adding hydrogens. First it will be processed by pdb2pqr."/> | |
| 5 </inputs> | |
| 6 <command><![CDATA[ | |
| 7 swpath=\$(which pdb2pqr.py) ; | |
| 8 python2.7 \$swpath --ff=amber --ffout=amber --verbose --chain --ph-calc-method=propka --with-ph=7.0 --drop-water ${receptor_pdb} ${pdb_processed}.pqr ; | |
| 9 | |
| 10 ${__tool_directory__}/scripts/includeAtom3.sh ${__tool_directory__}/scripts/table ${pdb_processed}.pqr > ${pdb_processed} ; | |
| 11 | |
| 12 rm ${pdb_processed}.pqr | |
| 13 | |
| 14 ]]></command> | |
| 15 <outputs> | |
| 16 <data name="pdb_processed" format="pdb" label="${receptor_pdb.name}_processed"/> | |
| 17 </outputs> | |
| 18 </tool> |