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annotate align-it_create_db.xml @ 0:c021d69c8e2e draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
author bgruening
date Mon, 22 May 2017 03:02:09 -0400
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0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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1 <tool id="ctb_alignit_create_db" name="Pharmacophore" version="0.1">
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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2 <description>generation (Align-it)</description>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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3 <requirements>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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4 <requirement type="package" version="1.0.3">align_it</requirement>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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5 </requirements>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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6 <command detect_errors="aggressive">
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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7 <![CDATA[
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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8 align-it
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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9 --dbType '${database.ext}'
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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10 --dbase '$database'
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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11 --pharmacophore '$pharmacophores'
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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12 $merge
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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13 $noHybrid
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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14 ]]>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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15 </command>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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16 <inputs>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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17 <param name="database" type="data" format='mol,mol2,sdf,smi'
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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18 label="Defines the database of molecules that will be converted to pharmacophores" />
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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19 <param name='merge' type='boolean' truevalue='--merge' falsevalue=''
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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20 label='Merge pharmacophore points' />
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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21 <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue=''
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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22 label='Disable the use of hybrid pharmacophore points'
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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23 help="Using this flag will increase the number of pharmacophore points."/>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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24 </inputs>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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25 <outputs>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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26 <data name="pharmacophores" format="txt" label="${tool.name} on ${on_string} (scores)"/>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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27 </outputs>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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28 <tests>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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29 <test>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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30 <param name="database" ftype="sdf" value="6mol.sdf"/>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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31 <output name="pharmacophores" file="alignit_Create_Phar_DB_6mol.phar" />
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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32 </test>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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33 </tests>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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34 <help>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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35 <![CDATA[
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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36
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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37 .. class:: infomark
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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38
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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39 **What this tool does**
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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40
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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41 Align-it_ is a tool to align molecules according to their pharmacophores.
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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42 A pharmacophore is an abstract concept based on the specific interactions
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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43 observed in drug-receptor interactions: hydrogen bonding,
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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44 charge transfer, electrostatic and hydrophobic interactions.
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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45 Molecular modeling and/or screening based on pharmacophore similarities
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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46 has been proven to be an important and useful method in drug discovery.
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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47
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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48 The functionality of Align-it_ consists mainly of two parts.
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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49 The first functionality is the generation of pharmacophores from molecules
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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50 (the function of this tool). Secondly, pairs of pharmacophores
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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51 can be aligned (use the tool **Pharmacophore Alignment**). The resulting
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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52 score is calculated from the volume overlap resulting of the alignments.
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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53
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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54 .. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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55
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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56 -----
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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57
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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58 .. class:: infomark
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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59
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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60 **Input**
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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61
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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62 * Example::
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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63
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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64 - database
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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65
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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66 30 31 0 0 0 0 0 0 0999 V2000
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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67 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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68 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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69 -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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70 -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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71 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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72 -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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73 -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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74 -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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75 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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76 -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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77 -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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78 -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
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79 -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
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80 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
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81 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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82 -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
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83 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
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84 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
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85 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
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86 -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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87 -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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88 -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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89 -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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90 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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91 -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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92 -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
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93 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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94 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
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95 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
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96 -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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97
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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98 - cutoff : 0.0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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99
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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100 -----
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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101
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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102 .. class:: infomark
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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103
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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104 **Output**
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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105
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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106 * Example::
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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107
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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108 - aligned Pharmacophores
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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109
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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110 3033
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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111 HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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112 HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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113 HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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114 HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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115 HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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116 $$$$
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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117
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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118
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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119 ]]>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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120 </help>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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121 <citations>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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122 <citation type="doi">10.1016/j.jmgm.2008.04.003</citation>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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123 </citations>
c021d69c8e2e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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124 </tool>