openmolecules.org Forum: Cheminformatics

Home » DataWarrior » Cheminformatics » sp3 count

Show: Today's Messages :: Polls :: Message Navigator

sp3 count [message #1369]

Tue, 10 August 2021 00:22

mvamos
Messages: 24
Registered: January 2015
Location: US

Junior Member

I'm curious about the sp3-Atoms count from the Calculate Properties->Atom Counts section. Generally for fraction sp3 calculations, it's # of sp3 carbon atoms divided by total carbon atoms. The sp3-Atoms count from DW seems to over-count, just not sure what else it's including.

In the attached photo, for the compound I count 3 sp3 carbon atoms, but DW returns 5.

Feature request: it might be more useful for users if it calculated the fraction of sp3 carbons instead of just # of sp3 atoms, as it's common to report the fraction for druglike compounds.
https://pubs.acs.org/doi/10.1021/jm901241e

Thanks and keep up the good work!

Attachment: Untitled9.png
(Size: 25.98KB, Downloaded 611 times)

Report message to a moderator

Re: sp3 count [message #1370 is a reply to message #1369]

Tue, 10 August 2021 22:24

nbehrnd
Messages: 234
Registered: June 2019

Senior Member

Dear mvamos,

based on the SMILES string generated by DW for this very structure, yet submitted to RDKit (2020.09.4) suggests different programs assign sp3-hybridization differently. In the case of RDKit, including fluorine [sic!], a total of 6.

Norwid

Attachment: test_case.zip
(Size: 140.57KB, Downloaded 582 times)

Report message to a moderator

Re: sp3 count [message #1380 is a reply to message #1370]

Thu, 19 August 2021 21:23

thomas
Messages: 736
Registered: June 2014

Senior Member

Dear Mvamos,

DataWarrior considers C,N,O,P,S as potential sp3 atoms. In your case the 2 oxygen atoms are considered to be sp3 in addition to the 3 obvious carbon atoms. I agree that an ether-oxygen doesn't contribute much to the 3D-shape of a molecule, but the same is true for an (sp3) methyl group. It is a formal number. sp3 fraction in carbon atoms is simple and I will add it...

Thomas

Report message to a moderator

Re: sp3 count [message #1381 is a reply to message #1369]

Fri, 20 August 2021 12:05

thomas
Messages: 736
Registered: June 2014

Senior Member

I just deployed an update with 'sp3-Carbon Fraction', which is the count of sp3 carbons devided by all carbons as proposed in the 'Escape from flatland' paper.

Report message to a moderator

Previous Topic:	Mean value in category function
Next Topic:	Integration with KNIME or Python

Goto Forum:

-=] Back to Top [=-

[ Syndicate this forum (XML) ] [

] [

]

Current Time: Wed Oct 29 08:47:54 CET 2025

Total time taken to generate the page: 1.19138 seconds