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1 <tool id="ctb_stripit" name="Strip-it" version="1.0.1">
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2 <description> extracts predefined scaffolds from molecules</description>
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3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism>
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4 <requirements>
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5 <requirement type="package" version="2.3.2">openbabel</requirement>
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6 <requirement type="package" version="1.0.1">silicos_it</requirement>
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7 </requirements>
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8 <command>
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9 strip-it --inputFormat ${infile.ext} --input $infile --output $outfile --noLog --noHeader 2>&1
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10 </command>
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11 <inputs>
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12 <param name="infile" type="data" format='sdf,mol,mol2,smi' label="Molecule file" />
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13 </inputs>
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14 <outputs>
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15 <data name="outfile" format="tabular" />
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="infile" type='sdf' value="CID_3037.sdf"/>
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20 <data name="output" type="tabular" file="Strip-it_on_CID3037.tabular" />
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21 </test>
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22 </tests>
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23 <help>
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24
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25
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26 .. class:: infomark
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27
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28 **What this tool does**
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29
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30 Strip-it is a program that extracts predefined scaffolds from organic small
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31 molecules.
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32
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33 The program comes with a number of predefined molecular scaffolds for
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34 extraction. These scaffolds include, amongst others
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35
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36 - `molecular frameworks`_ as originally described by Bemis and
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37 Murcko
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38 - `molecular frameworks and the reduced molecular frameworks`_ as
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39 described by Ansgar Schuffenhauer and coworkers
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40 - `scaffold topologies`_ as described by Sara Pollock and coworkers
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41
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42 .. _molecular frameworks: http://www.ncbi.nlm.nih.gov/pubmed/8709122
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43 .. _molecular frameworks and the reduced molecular frameworks: http://peter-ertl.com/reprints/Schuffenhauer-JCIM-47-47-2007.pdf
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44 .. _scaffold topologies: http://www.ncbi.nlm.nih.gov/pubmed/18605680
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45
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46 -----
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47
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48 .. class:: infomark
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49
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50
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51 **Input**
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52
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53 | - `SD-Format`_
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54 | - `SMILES Format`_
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55 | - `MOL2 Format`_
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56
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57 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
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58 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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59 .. _MOL2 Format: http://www.tripos.com/data/support/mol2.pdf
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60
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61
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62 -----
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63
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64 .. class:: infomark
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65
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66 **Output**
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67
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68 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
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69 | NAME | MOLECULE | RINGS_WITH_LINKERS_1 | RINGS_WITH_LINKERS_2 | MURCKO_1 | ... |
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70 +=============+================================+======================+========================+======================+=====+
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71 | Diclofenac | OC(=O)Cc1ccccc1Nc1c(Cl)cccc1Cl | c1ccc(cc1)Nc1ccccc1 | c1ccc(cc1)Nc1ccccc1 | C1CCC(CC1)CC1CCCCC1 | ... |
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72 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
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73 | Bupivacaine | CCCCN1CCCCC1C(=O)Nc1c(C)cccc1C | C1CCC(NC1)CNc1ccccc1 | O=C(C1CCCCN1)Nc1ccccc1 | C1CCC(CC1)CCC1CCCCC1 | ... |
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74 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
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75 | ... | ... | ... | ... | ... | ... |
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76 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
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77
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78 -----
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79
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80 .. class:: infomark
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81
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82 **Cite**
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83
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84 `Silicos-it`_ - strip-it
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85
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86 .. _Silicos-it: http://silicos-it.com/software/strip-it/1.0.2/strip-it.html
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87
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88
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89 </help>
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90 </tool>
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