Mercurial > repos > bgruening > openbabel_spectrophore_search
comparison ob_spectrophore_search.xml @ 0:7133973beaf0 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
| author | bgruening |
|---|---|
| date | Sat, 20 May 2017 08:40:10 -0400 |
| parents | |
| children | f93f3e01abe8 |
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| -1:000000000000 | 0:7133973beaf0 |
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| 1 <tool id="openbabel_spectrophore_search" name="Spectrophores(TM) search:" version="@VERSION@.0"> | |
| 2 <description>similarity search based on 1D chemical features</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"> | |
| 7 <requirement type="package" version="1.7.1">numpy</requirement> | |
| 8 </expand> | |
| 9 <command detect_errors="aggressive"> | |
| 10 <![CDATA[ | |
| 11 python '$__tool_directory__/ob_spectrophore_search.py' | |
| 12 --target '$target' | |
| 13 --library '$library' | |
| 14 --output '$outfile' | |
| 15 --column $column | |
| 16 ]]> | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param name="target" type="data" format="sdf" | |
| 20 label="Target molecule in SDF format (it must contain its Spectrophores(TM) stored as meta-data)"/> | |
| 21 <param name="library" type="data" format="tabular" | |
| 22 label="Tabular file with pre-computed Spectrophores(TM) in one column"/> | |
| 23 <param name="column" label="Specify the column number containing the Spectrophores(TM) descriptors" | |
| 24 type="data_column" data_ref="library" accept_default="true" /> | |
| 25 </inputs> | |
| 26 <outputs> | |
| 27 <data format="tabular" name="outfile"/> | |
| 28 </outputs> | |
| 29 <tests> | |
| 30 <test> | |
| 31 <param name="target" ftype="sdf" value="CID2244_with_spectrophore.sdf"/> | |
| 32 <param name="library" value="lib.tabular" /> | |
| 33 <param name="column" value="8" /> | |
| 34 <output name="outfile" ftype="tabular" file="ob_spectrophore_search.tabular" /> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help> | |
| 38 <![CDATA[ | |
| 39 | |
| 40 .. class:: infomark | |
| 41 | |
| 42 **What does this tool do?** | |
| 43 | |
| 44 This tool computes the Euclidean distance between the Spectrophores(TM) descriptors of the target to each molecule stored in the library. | |
| 45 | |
| 46 |Spectrophores (TM)| search | |
| 47 |Spectrophores (TM)| is a screening technology by Silicos_ which converts three-dimensional molecular property data into one-dimensional spectra. Typical characteristics that can be converted include electrostatic potentials, molecular shape, lipophilicity, hardness and softness potentials. The computation is independent of the position and orientation of a molecule and allows an easy comparison of |Spectrophores (TM)| of different molecules. | |
| 48 | |
| 49 Molecules with similar three-dimensional properties and shape, and therefore also similar biological activities, always have similar |Spectrophores (TM)|. As a result this technique is a very powerful tool to investigate the similarity of molecules and can be applied as a screening tool for molecular databases, virtual screening, and database characterisations. | |
| 50 | |
| 51 *Advantages:* | |
| 52 | |
| 53 - |Spectrophores (TM)| can realistically compute ligand-protein interactions based on aforementioned molecular descriptors | |
| 54 - |Spectrophores (TM)| can be applied in both a ligand- or target-based setting | |
| 55 - |Spectrophores (TM)| can distinguish, if needed, between the different enantiomers of stereo-selective compounds | |
| 56 - |Spectrophores (TM)| can be computed fast | |
| 57 | |
| 58 .. |Spectrophores (TM)| unicode:: Spectrophores U+2122 | |
| 59 | |
| 60 ----- | |
| 61 | |
| 62 .. class:: warningmark | |
| 63 | |
| 64 **Hint** this tool is useful to select compounds with similar chemical features to a target, but accounting for the discovery of diverse scaffolds. This is in contrast to the results expected in a similarity search based on atom connectivity. | |
| 65 | |
| 66 ----- | |
| 67 | |
| 68 .. class:: infomark | |
| 69 | |
| 70 **Input** | |
| 71 | |
| 72 The target molecule must be a SD formatted file with the |Spectrophores (TM)| descriptors stored as metadata. Such files can be generated using the *Compute physico-chemical properties* tool. | |
| 73 | |
| 74 ----- | |
| 75 | |
| 76 .. class:: infomark | |
| 77 | |
| 78 **Output** | |
| 79 | |
| 80 The library of compounds is a tabular file with one line per compound. One column contains the |Spectrophores (TM)| descriptors. | |
| 81 | |
| 82 ----- | |
| 83 | |
| 84 .. class:: infomark | |
| 85 | |
| 86 **Cite** | |
| 87 | |
| 88 N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_ | |
| 89 | |
| 90 Silicos_ - |Spectrophores (TM)| is a registered tool implemented in the open-source OpenBabel. | |
| 91 | |
| 92 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf | |
| 93 .. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html | |
| 94 | |
| 95 ]]> | |
| 96 </help> | |
| 97 <expand macro="citations"> | |
| 98 <citation type="doi">10.1186/1752-153X-2-5</citation> | |
| 99 </expand> | |
| 100 </tool> |