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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Preparation]-->
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4 <tool id="Ligand3DGenerator" name="Ligand3DGenerator" version="1.1.0">
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5 <description>generate 3D coordinates for small molecules</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">Ligand3DGenerator</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="stdio"/>
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11 <expand macro="requirements"/>
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12 <command>Ligand3DGenerator
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13
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14 #if $param_i:
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15 -i $param_i
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16 #end if
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17 #if $param_o:
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18 -o $param_o
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19 #end if
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20 #if $param_ph:
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21 -ph $param_ph
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22 #end if
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23 #if $param_ff:
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24 -ff "$param_ff"
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25 #end if
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26 #if $param_rm:
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27 -rm $param_rm
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28 #end if
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29 #if $param_k:
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30 -k $param_k
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31 #end if
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32 #if $param_kp:
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33 -kp $param_kp
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34 #end if
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35 </command>
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36 <inputs>
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37 <param name="param_i" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file" help="(-i) "/>
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38 <param name="param_ph" type="float" value="7.0" label="pH-value for pH-dep. protonation" help="(-ph) "/>
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39 <param name="param_ff" type="text" size="30" value="MMFF94" label="Forcefield to use for optimization (any available OpenBabel plugin)" help="(-ff) ">
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40 <sanitizer>
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41 <valid initial="string.printable">
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42 <remove value="'"/>
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43 <remove value="""/>
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44 </valid>
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45 </sanitizer>
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46 </param>
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47 <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/>
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48 <param name="param_k" type="integer" min="0" max="1" optional="True" value="0" label="keep existing 3D coordinates (flag precedes '-kp')" help="(-k) "/>
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49 <param name="param_kp" type="integer" min="0" max="1" optional="True" value="0" label="keep existing 3D coordinates but re-protonate compound in a pH dependent manner (flag is preceded by '-k')" help="(-kp) "/>
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50 </inputs>
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51 <expand macro="advanced_options"/>
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52 <outputs>
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53 <data name="param_o" metadata_source="param_i" format="input"/>
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54 </outputs>
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55 <help>This tool takes input molecules and generates a single 3D conformation which is ready for docking. The input has to be a chemical file
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56 containing valid topologies and conistent bond order assignements. 2D coordinates in the input file are overwritten, 3D coordinates can be kept ('-k' or '-kp').
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57
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58 '-k': 3D coordinates are tried to be kept. Molecules with non-zero coordinates in all three dimensions are passed through without modifications.
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59 However, if a molecule is not ready for docking (i.e. unusual bond leghts, unusual charges), the molecule will be rebuild and new
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60 3D coordinates are assigned. If only hydrogens are missing, the coordinates of non-hydrogen atoms are kept but the molecule gets newly protonated.
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61 '-kp': 3D coordinates are tried to be kept as for the '-k' flag but the molecule will be newly protonated.
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62
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63 Please note that the main purpose of this tool is to generate valid starting conformations for docking or other optimization procedures.
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64 Therefore, the generated 3D coordinates for each fragment should be all right, but in extreme cases (i.e. very large and/or complex molecules)
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65 different fragments might still overlap with each other.
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66
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67 Supported formats are mol2,sdf,drf,pdb,ac,ent,brk,hin,mol,xyz,mol2.gz,sdf.gz,drf.gz,pdb.gz,ac.gz,ent.gz,brk.gz,hin.gz,mol.gz,xyz.gz.
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68
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69 </help>
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70 </tool>
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