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TPSA [message #1025] Mon, 03 August 2020 13:13 Go to next message
sansun is currently offline  sansun
Messages: 26
Registered: April 2019
Junior Member
I found disagreement between TPSA values calculated from DW and RDKit although both seem to follow same methodology by Peter Ertl et al. in J. Med. Chem. 43, 3714-3717 (2000).

In some case the difference is quite large e.g. 87 vs 252

However, Spearman correlation is > 0.9 for my data set (N > 20000).
Re: TPSA [message #1028 is a reply to message #1025] Tue, 04 August 2020 11:24 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 360
Registered: June 2014
Senior Member
One reason may be that DataWarrior considers the largest fragment only by removing counter ions, water molecules and other small fragments from the main ingredient before the calculation.
Re: TPSA [message #1029 is a reply to message #1028] Tue, 04 August 2020 12:20 Go to previous messageGo to next message
sansun is currently offline  sansun
Messages: 26
Registered: April 2019
Junior Member
I performed calculations after extracting the largest fragments and used the same file for both programs.
However, I find useful information on the following link which says RDkit doesn't use P and S atoms for TPSA calculation.

Does DW uses these atoms?

https://www.rdkit.org/docs/RDKit_Book.html



Re: TPSA [message #1046 is a reply to message #1029] Mon, 17 August 2020 14:01 Go to previous message
thomas is currently offline  thomas
Messages: 360
Registered: June 2014
Senior Member
DataWarrior sticks to the original publication, which includes contributions for S and P
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