diff search/ob_spectrophore_search.xml @ 0:527ecd2fc500 draft

Uploaded

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+++ b/search/ob_spectrophore_search.xml	Thu Aug 15 03:25:06 2013 -0400
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+<tool id="ctb_spectrophore_search" name="Spectrophores(TM) search:" version="1.0">
+  <description>similarity search based on 1D chemical features</description>
+  <requirements>
+    <requirement type="package" version="2.3.2">openbabel</requirement>
+    <requirement type="package" version="1.7.1">numpy</requirement>
+  </requirements>
+  <command interpreter="python">
+    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>
+
+.. 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>
+</tool>