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Comparing Structure Files [message #1470] Wed, 12 January 2022 13:42 Go to next message
biolive31!! is currently offline  biolive31!!
Messages: 2
Registered: January 2022
Junior Member
Good morning I'am Olivier a new datawarior user !
I tried to use the "Find similar compound in other file" tool but it doesnt work.

I know that some molecule are similar to those in the "other file " and the tool did not find it . Any molecule is find similar. I try both comparison method , even to 70% of similarity any similar molecule is find .
Could you help me ?

Thank you

Olivier
Re: Comparing Structure Files [message #1471 is a reply to message #1470] Thu, 13 January 2022 23:44 Go to previous messageGo to next message
nbehrnd is currently offline  nbehrnd
Messages: 96
Registered: June 2019
Member
Dear Oliver,

your question contains little material to replicate your finding. Thus, it is difficult to identify a plausible cause for your observation.

On the other hand, I created two tiny libraries of drug-like molecules (chemistry -> generate random molecules) where the defaults were modified slightly (instead of 1000, I opted for 100 molecules each). Subsequently, while reading set_b.dwar, I selected set_a.dwar for a comparison. With a structureFp threshold lowered to 70%, DW identified 13 molecules as similar enough. Raw data, set up of the parameters, and result files in the attachement below. Perhaps the threshold set by you was too high? The criterion «structure exact» isn't a restraint, it is meant as a constraint*); any variation in the molecule to check vs. the reference molecule and the test assigns the two as dissimilar.

*) which may be weakened in regard of stereochemistry, tautomers, or application on the largest fragment only.

Norwid
Re: Comparing Structure Files [message #1473 is a reply to message #1471] Mon, 17 January 2022 14:39 Go to previous message
biolive31!! is currently offline  biolive31!!
Messages: 2
Registered: January 2022
Junior Member
Dear Norwid,
Thank you for your help.
I tired to compare the set a and seb . I found 16 similar compounds.

My first conclusion is that DW I installed work well. Smile

Now I wondering if my files are, in someway, unanalysable by similarity tool in DW.
These files are sdf files with structures.

I tried an other tool to compare molecule of my files (chemdiff) and it wasn't able to identify similar structure like DW.
Do you know what is the file type required to perform a similarity analysis ?

thank you for your help.

Olivier
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