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comparison xcos.xml @ 1:9b6210854c8c draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
author bgruening
date Mon, 27 Jul 2020 11:30:49 -0400
parents 73164cea9b60
children
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0:73164cea9b60 1:9b6210854c8c
29 <test> 29 <test>
30 <param name="poses" ftype='sdf' value="poses.sdf" /> 30 <param name="poses" ftype='sdf' value="poses.sdf" />
31 <param name="fragments" ftype='sdf' value="hits-17.sdf" /> 31 <param name="fragments" ftype='sdf' value="hits-17.sdf" />
32 <output name="output" ftype='sdf'> 32 <output name="output" ftype='sdf'>
33 <assert_contents> 33 <assert_contents>
34 <has_text text="XCos_Score3" /> 34 <has_text text="XCos_RefMols" />
35 <has_n_lines n="818" /> 35 <has_text text="XCos_NumHits" />
36 <has_text text="XCos_Score1" />
37 <has_n_lines n="734" />
36 </assert_contents> 38 </assert_contents>
37 </output> 39 </output>
38 </test> 40 </test>
39 </tests> 41 </tests>
40 <help> 42 <help>
47 XCos is a reverse shape and feature overlap score for a pose compared to a set of ligands that identifies which ligands 49 XCos is a reverse shape and feature overlap score for a pose compared to a set of ligands that identifies which ligands
48 best overlap. 50 best overlap.
49 The molecule is fragmented using the BRICS algorithm and each fragment (bit) is compared to the ligands using the SuCOS 51 The molecule is fragmented using the BRICS algorithm and each fragment (bit) is compared to the ligands using the SuCOS
50 methodology. The resulting scores are the combined scores of the bits. 52 methodology. The resulting scores are the combined scores of the bits.
51 53
52 XCoseScore1 - 54 XCos_RefMols - The fragments that the ligand overlays
53 XCoseScore2 - 55 XCos_NumHits - the number of fragments the ligand overlays
54 XCoseScore3 - 56 XCos_Score1 - The sum of each bit's feature and shape overlay score scaled by the number of heavy bit atoms.
55 57
56 XCos was conceived and implemented by Warren Thompson <warren.thompson@diamond.ac.uk>. 58 XCos was conceived and implemented by Warren Thompson <warren.thompson@diamond.ac.uk>.
57 The original code can be found here: https://github.com/Waztom/xchem-notebooks/blob/master/XCOS.ipynb 59 The original code can be found here: https://github.com/Waztom/xchem-XCOS
58 60
59 ----- 61 -----
60 62
61 .. class:: infomark 63 .. class:: infomark
62 64