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1 <tool id="stripit" name="Strip-it">
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2 <description> extracts predefined scaffolds from molecules</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.0">silicos_it</requirement>
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5 </requirements>
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6 <command >
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7 strip-it --inputFormat ${infile.ext} --input $infile --output $outfile 2>&1
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8 </command>
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9 <inputs>
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10 <param name="infile" type="data" format='sdf,mol,mol2,smi' label="Molecule file" />
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11 </inputs>
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12 <outputs>
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13 <data name="outfile" format="tabular" />
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="infile" type='sdf' value="CID_3037.sdf"/>
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18 <data name="output" type="tabular" file="Strip-it_on_CID3037.tabular" />
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19 </test>
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20 </tests>
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21 <help>
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22
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23 **What it does**
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24
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25 Strip-it is a program that extracts predefined scaffolds from organic
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26 molecules
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27
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28 The program comes with a number of predefined molecular scaffolds for
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29 extraction. These scaffolds include, amongst others
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30
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31 - Molecular frameworks as originally described by Bemis and
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32 Murcko;1
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33 - Molecular frameworks and the reduced molecular frameworks as
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34 described by Ansgar Schuffenhauer and coworkers;2
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35 - Scaffold topologies as described by Sara Pollock and coworkers.3
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36
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37 -----
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38
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39 **Example**
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40
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41 * input ::
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42
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43 - input
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44 27 28 0 0 0 0 0 0 0999 V2000
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45 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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46 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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47 -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0
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48 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0
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49 -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0
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50 -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0
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51 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0
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52 -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0
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53 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0
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54 -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
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55 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
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56 -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0
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57 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0
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58 -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0
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59 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0
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60 -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0
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61 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0
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62 -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0
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63 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0
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64 -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0
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65 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0
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66 -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0
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67 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0
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68 -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0
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69 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0
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70 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0
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71 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0
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72 1 14 1 0 0 0 0
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73 2 15 1 0 0 0 0
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74 3 8 1 0 0 0 0
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75 3 26 1 0 0 0 0
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76 4 9 1 0 0 0 0
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77 4 27 1 0 0 0 0
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78 5 6 1 0 0 0 0
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79
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80
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81
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82 * output ::
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83
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84 NAME MOLECULE RINGS_WITH_LINKERS_1 RINGS_WITH_LINKERS_2 MURCKO_1 MURCKO_2 OPREA_1 OPREA_2 OPREA_3 SCHUFFENHAUER_1 SCHUFFENHAUER_2 SCHUFFENHAUER_3 SCHUFFENHAUER_4 SCHUFFENHAUER_5
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85 3037 Oc1ccc(cc1Cc1cc(Cl)ccc1O)Cl c1ccc(cc1)Cc1ccccc1 c1ccc(cc1)Cc1ccccc1 C1CCC(CC1)CC1CCCCC1 C1CCC(CC1)C1CCCCC1 C1CC1C1CC1 C1CC1C1CC1 C1CC1C1CC1 c1ccccc1
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86
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87 </help>
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88 </tool>
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