Mercurial > repos > bitlab > plidflow
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/pdb2pqr_plidflow.xml Wed Apr 22 06:12:00 2020 -0400 @@ -0,0 +1,23 @@ +<tool id="pdb2pqr_plidflow" name="PLIDflow: PDB2PQR"> + <description>Converts a pdb to pqr</description> + <inputs> + <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."/> + </inputs> + <command><![CDATA[ + swpath=\$(which pdb2pqr.py) ; + + ${__tool_directory__}/scripts/preparePDB2PQR_plidflow.sh ${receptor_pdb} ${receptor_pdb}.prepdb ; + + (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 ; + + rm ${receptor_pdb}.prepdb ; + + ${__tool_directory__}/scripts/includeAtom3.sh ${__tool_directory__}/scripts/table ${pdb_processed}.pqr > ${pdb_processed} ; + + rm ${pdb_processed}.pqr ; + + ]]></command> + <outputs> + <data name="pdb_processed" format="pdb" label="${receptor_pdb.name}_processed"/> + </outputs> +</tool>