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1 <tool id="autodocktools_receptor_plidflow" name="PLIDflow: AutoDock Receptor">
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2 <description>AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure</description>
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3 <inputs>
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4 <param name="receptor_pdb" type="data" format="pdb" label="Receptor PDB file" help="Preparing the receptor involves adding gasteiger charges and adding hydrogens. The formatted receptor is written in a 'pdbqt' file."/>
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5 </inputs>
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6 <command><![CDATA[
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7
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8 swpath=\$(which prepare_receptor4.py) ;
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9 cp ${receptor_pdb} ${receptor_pdb}.pdb ;
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10 pythonsh \$swpath -r ${receptor_pdb}.pdb -A hydrogens -o $receptor_pdbqt;
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11 rm ${receptor_pdb}.pdb;
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12 Rscript ${__tool_directory__}/scripts/pdbqtcorrector2step.R ${receptor_pdbqt} ${receptor_pdbqt_modified2} ${receptor_types};
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13
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14 ]]></command>
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15
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16 <outputs>
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17 <data name="receptor_pdbqt" format="pdbqt" label="Receptor PDBQT file"/>
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18 <data name="receptor_pdbqt_modified" format="pdbqt" label="Receptor PDBQT file modified"/>
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19 <data name="receptor_pdbqt_modified2" format="pdbqt" label="Receptor PDBQT file modified 2"/>
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20 <data name="receptor_types" format="txt" label="Receptor types molecules"/>
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21 </outputs>
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22 </tool>
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