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2 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
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3 <tool id="pdbcutter" name="PDBCutter" version="1.6">
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4 <description>separate ligand and receptor</description>
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5 <command interpreter="bash"><![CDATA[../../PDBCutter
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6 #if str( $i ) != '' and str( $i ) != 'None' :
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7 -i "$i"
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8 #end if
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9 #if str( $rec ) != '' and str( $rec ) != 'None' :
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10 -rec "$rec"
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11 #end if
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12 #if str( $lig ) != '' and str( $lig ) != 'None' :
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13 -lig "$lig"
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14 #end if
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15 #if str( $lig_chain ) != '' and str( $lig_chain ) != 'None' :
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16 -lig_chain "$lig_chain"
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17 #end if
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18 #if str( $lig_name ) != '' and str( $lig_name ) != 'None' :
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19 -lig_name "$lig_name"
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20 #end if
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21 #if str( $rm_ch ) != '' and str( $rm_ch ) != 'None' :
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22 -rm_ch "$rm_ch"
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23 #end if
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24 #if str( $id ) != '' and str( $id ) != 'None' :
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25 -id "$id"
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26 #end if
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27 #if str( $p ) != '' and str( $p ) != 'None' :
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28 -p "$p"
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29 #end if
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30 #if str( $rm_res ) != '' and str( $rm_res ) != 'None' :
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31 -rm_res "$rm_res"
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32 #end if
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33 #if str( $auto ) != '' and str( $auto ) != 'None' :
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34 -auto
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35 #end if
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36 | tail -n 5
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37 ]]></command>
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38 <inputs>
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39 <param name="i" optional="false" label="input pdb-file" type="data" format="pdb"/>
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40 <param name="lig_chain" optional="false" label="chain-name of ligand" area="true" type="text" size="1x15"/>
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41 <param name="lig_name" optional="false" label="ligand name" area="true" type="text" size="1x15"/>
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42 <param name="rm_ch" optional="true" label="Optional: protein chains that are to be deleted" area="true" type="text" size="1x15"/>
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43 <param name="id" optional="true" label="Optional: PDB ID for download of ligand as sdf from PDB server, if desired" area="true" type="text" size="1x15"/>
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44 <param name="p" optional="true" label="Optional: proxy for ligand download, if required" area="true" type="text" size="1x15"/>
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45 <param name="rm_res" optional="true" label="Optional: pdb-residues that are to be deleted (e.g. water or ions)" area="true" type="text" size="1x15"/>
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46 <param name="auto" optional="true" label="extract largest heterosystem as ligand (ignore specified lig. def.)" type="boolean" truevalue="true" falsevalue=""/>
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47 </inputs>
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48 <outputs>
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49 <data name="rec" format="pdb"/>
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50 <data name="lig" format="pdb"/>
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51 </outputs>
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52 <help>This tool splits a given pdb-file into two files containing receptor and reference ligand, respectively.
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53
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54 The name of the reference ligand (exactly as it appears in the pdb-file) and the name of its chain need to be specified by '-lig_name' and '-lig_chain'.
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55 If desired, the correct topology of the reference ligand can be downloaded by this tool from the Protein Data Bank as an sd-file and stored in the specified ligand output file.
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56 Optionally, chains (e.g. in case of multimers) or pdb-residues (e.g. water or ions) that you don't need can be deleted from the receptor. In this case, specify their names with '-rm_ch' or '-rm_res'.
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57
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58 Output of this tool is one pdb-file containing the receptor-structure, i.e. the protein w/o reference ligand and w/o undesired chains/residues (if any were specified), and one file containing the reference ligand.</help>
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59 </tool> |
