Mercurial > repos > bgruening > openbabel_spectrophore_search
view ob_spectrophore_search.xml @ 3:a1db432874e5 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c376ab981fafb25f0c04a2a313968fa2e55f5196
author | bgruening |
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date | Sat, 20 May 2017 20:06:43 -0400 |
parents | 7133973beaf0 |
children | f93f3e01abe8 |
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<tool id="openbabel_spectrophore_search" name="Spectrophores(TM) search:" version="@VERSION@.0"> <description>similarity search based on 1D chemical features</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="1.7.1">numpy</requirement> </expand> <command detect_errors="aggressive"> <![CDATA[ python '$__tool_directory__/ob_spectrophore_search.py' --target '$target' --library '$library' --output '$outfile' --column $column ]]> </command> <inputs> <param name="target" type="data" format="sdf" label="Target molecule in SDF format (it must contain its Spectrophores(TM) stored as meta-data)"/> <param name="library" type="data" format="tabular" label="Tabular file with pre-computed Spectrophores(TM) in one column"/> <param name="column" label="Specify the column number containing the Spectrophores(TM) descriptors" type="data_column" data_ref="library" accept_default="true" /> </inputs> <outputs> <data format="tabular" name="outfile"/> </outputs> <tests> <test> <param name="target" ftype="sdf" value="CID2244_with_spectrophore.sdf"/> <param name="library" value="lib.tabular" /> <param name="column" value="8" /> <output name="outfile" ftype="tabular" file="ob_spectrophore_search.tabular" /> </test> </tests> <help> <![CDATA[ .. class:: infomark **What does this tool do?** This tool computes the Euclidean distance between the Spectrophores(TM) descriptors of the target to each molecule stored in the library. |Spectrophores (TM)| search |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. 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. *Advantages:* - |Spectrophores (TM)| can realistically compute ligand-protein interactions based on aforementioned molecular descriptors - |Spectrophores (TM)| can be applied in both a ligand- or target-based setting - |Spectrophores (TM)| can distinguish, if needed, between the different enantiomers of stereo-selective compounds - |Spectrophores (TM)| can be computed fast .. |Spectrophores (TM)| unicode:: Spectrophores U+2122 ----- .. class:: warningmark **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. ----- .. class:: infomark **Input** 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. ----- .. class:: infomark **Output** The library of compounds is a tabular file with one line per compound. One column contains the |Spectrophores (TM)| descriptors. ----- .. class:: infomark **Cite** N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_ Silicos_ - |Spectrophores (TM)| is a registered tool implemented in the open-source OpenBabel. .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf .. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html ]]> </help> <expand macro="citations"> <citation type="doi">10.1186/1752-153X-2-5</citation> </expand> </tool>