| defining molecule clusters after similarity analysis [message #1534] |
Mon, 07 March 2022 18:22  |
Xenia
Messages: 2
Registered: March 2022
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Junior Member |
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Hi,
I've run a similarity analysis based on the SkelSpheres descriptor on a set of 50k compounds with 80% similarity limit. Is there a way to obtain a list of all the molecules that are connected to each other? I would like to get a list of separate clusters similar to this:
Cluster 1: molecules A-B-C-D-E (each of them are connected because they have >80% similarity)
Cluster 2: molecules X-Y-Z
...
I can see the neighbor identifiers for each molecule (e.g. molecule B is connected to A and C) but I can't figure out a way to obtain this kind of list. In a small set of molecules I can do it by manually selecting the connected molecules in the neighbor tree view but I would like to find a way to obtain a list of clusters automatically.
Thank you for your help and for developing such an amazing software!
Xènia
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| Re: defining molecule clusters after similarity analysis [message #1579 is a reply to message #1534] |
Tue, 05 April 2022 15:03  |
thomas
Messages: 715
Registered: June 2014
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Senior Member |
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Hi Xènia,
you are not the first to ask for that. Thus, I have updated the similarity/activity-cliff-analysis to generate two more columns: a cluster number and the cluster member count. You can download the updated DataWarrior file (dev version) from the link in the fine-print that appears when clicking the 'read and understood' checkbox on the DataWarrior download page.
Hope this solves the issue for you,
Thomas
[Updated on: Tue, 05 April 2022 15:03] Report message to a moderator |
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