SP3 carbon count in the mol properties node?

[dsmithso]

Hi

I was wondering if it would be difficult to add an SP3 carbon count to the mol properties node - it would be useful for calculating the fraction SP3 score as a partial capture of molecular complexity.

 

Thanks

-Dave

[richards99]

An sp3 carbon count wouldnt tell the full picture of sp3 character in the molecule. You should consider other heavy atoms too so a "Heavy Atom sp3 Count" would be more suitable.

You can calculate the degree of aliphatic character in a molecule by using the Indigo Molecule Properties node and retrieving properties on; Number of Aliphatic Atoms and Number of Heavy Atoms. Then simply use a Maths node to calculate the percentage to give you the overall aliphatic character percentage in the molecule, which although not fully accounting for all the sp3 character, will give a good idea.

Simon.

[dsmithso]

Thanks for the advice - it would be interesting to compare the results from that approach to one that is grabbing the full SP3 nature. Still, it should work for what I need for now. I just need a decent complexity score for a LDA I'm trying to run on our libraries.

-Dave

[s.roughley]

You can use a table creator node to define some SMARTS queries (leave the column as a string type) - e.g [C;X4] for sp3 C (I don't think the Indigo nodes understand the [C^3] hybridisation notation), [#6] for all C etc, and then pass these directly into the Indigo substructure match counter node query molecules port, and set the 'strings as SMARTS' option.  Then you can use the Math node to calculate the ratio (which Lovering refers to as Fsp3) - I assume this is what you were aiming for.