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diff PLIDflow/pdb2pqr_plidflow.xml @ 0:6fcfa4756040 draft

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author bitlab
date Tue, 14 Jan 2020 06:09:42 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PLIDflow/pdb2pqr_plidflow.xml	Tue Jan 14 06:09:42 2020 -0500
@@ -0,0 +1,18 @@
+<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) ;
+	  python2.7 \$swpath --ff=amber --ffout=amber --verbose --chain --ph-calc-method=propka --with-ph=7.0 --drop-water ${receptor_pdb} ${pdb_processed}.pqr ;
+	  
+	  ${__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>