Mercurial > repos > bitlab > plidflow
comparison PLIDflow/pdb2pqr_plidflow.xml @ 6:795e11fac81b draft default tip
Included new tools for standardization
| author | bitlab |
|---|---|
| date | Wed, 22 Apr 2020 06:12:00 -0400 |
| parents | |
| children |
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| 5:97f12f7cc852 | 6:795e11fac81b |
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| 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 | |
| 9 ${__tool_directory__}/scripts/preparePDB2PQR_plidflow.sh ${receptor_pdb} ${receptor_pdb}.prepdb ; | |
| 10 | |
| 11 (python2.7 \$swpath --ff=amber --ffout=amber --verbose --chain --ph-calc-method=propka --with-ph=7.0 --drop-water ${receptor_pdb}.prepdb ${pdb_processed}.pqr ) &> /dev/null ; | |
| 12 | |
| 13 rm ${receptor_pdb}.prepdb ; | |
| 14 | |
| 15 ${__tool_directory__}/scripts/includeAtom3.sh ${__tool_directory__}/scripts/table ${pdb_processed}.pqr > ${pdb_processed} ; | |
| 16 | |
| 17 rm ${pdb_processed}.pqr ; | |
| 18 | |
| 19 ]]></command> | |
| 20 <outputs> | |
| 21 <data name="pdb_processed" format="pdb" label="${receptor_pdb.name}_processed"/> | |
| 22 </outputs> | |
| 23 </tool> |