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question about 'analyse similarity/activity cliffs' function [message #588] Thu, 04 July 2019 11:44 Go to next message is currently offline
Messages: 1
Registered: July 2019
Location: Cambridge
Junior Member
I'm new to DataWarrior and finding it very nice.
I've tried the 'Analyse similarity/activity cliffs' function, and it has made a nice plot showing the molecules as dots.
I can select a molecule and see other similar molecules coloured according to how similar they are to my molecule of interest, using the FragFP score (green: very similar, red: not similar).
I'm wondering is there a way to list the other molecules by their FragFP score from my molecule of interest? The plot I've made contains thousands of molecules, so it's a little hard to see ones that are a bit greenish in the huge plot.
Any advice will be much appreciated!
Re: question about 'analyse similarity/activity cliffs' function [message #595 is a reply to message #588] Tue, 09 July 2019 14:12 Go to previous message
thomas is currently offline  thomas
Messages: 219
Registered: June 2014
Senior Member
Hi Avril,
the easiest way would be to use a structure filter: right mouse click on a molecule marker of the view, then select 'New Structure Filter From -> this structure'. Then you may adjust the similarity slider in the filter and see the similar molecules in the Table view. To avoid always creating new filters, you may within a view do a right mouse click and 'Copy->Structure as->2D-Structure' and in an existing structure filter double-click the structure and use 'paste' in the editor.

You may also sort the Table/Structure view by a right mouse click on a structure, then 'Sort by->XXX-similarity to this molecule.

Tip: If you calculate the SkeletonSpheres descriptor from your chemical structures with 'Chemistry->From Chemical Structure->Calculate Descriptor->SkelSpheres', you may use this for all chemical similarity functionality, which usually gives better results than the FragFp descriptor.

Hope this helps, Thomas
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