Hi Alan, Thank you for pointing that out. Somehow I missed the part about the logarithms while going through the article and your explanation makes much more sense now.
-- Best, Ganesh On Wed, Apr 1, 2020 at 11:59 AM Alan Kerstjens Medina < alankerstj...@hotmail.com> wrote: > Hi Ganesh, > > > > To delve a bit deeper into this, if I recall correctly, SA score is > calculated based on both: > > 1. The prevalence of your molecule’s chemical motifs in a virtual > library of synthesizable compounds. > 2. A set of logarithmic formulas that take as parameters molecular > features associated with chemical complexity, like the ring complexity or > number of stereocenters. > > Consequently, like Axel and Nils have pointed out before me, the sum of > fragment SA scores shouldn’t be the same as that of a whole molecule. This > is because you have more chemical motifs in your larger molecule (think of > how fingerprints are generated) and because you can’t sum logarithms in the > same way you sum real numbers. > > > > You can find the details in the original publication: > > Ertl, P., & Schuffenhauer, A. (2009). Estimation of synthetic > accessibility score of drug-like molecules based on molecular complexity > and fragment contributions. *Journal of Cheminformatics*, *1*(1), 1–11. > https://doi.org/10.1186/1758-2946-1-8 > > *From: *Nils Weskamp <nils.wesk...@gmail.com> > *Sent: *01 April 2020 12:48 > *To: *Ganesh Shahane <ganesh7shah...@gmail.com> > *Cc: *rdkit-discuss@lists.sourceforge.net > *Subject: *Re: [Rdkit-discuss] Synthetic Accessibility (SA) score > > > > Hi Ganesh, > > > > I would like to challenge your premise. Why do you think that synthetic > accessibility should add up like that? > > > > Theoretically, I would expect that the combination of A,B and C to ABC > will require some synthetic effort - so should be SA(A) + SA(B) + SA(C) < > SA(ABC). > > > > Technically, the combination of the three fragments will change the > properties and environment of at least some atoms in the molecule, so that > should have an influence on the result. I suspect it will be difficult to > define a score with the desired properties without making use of the > fragmentation scheme you are using. > > > > Best regards, > > Nils > > > > > > On Wed, Apr 1, 2020 at 12:36 PM Ganesh Shahane <ganesh7shah...@gmail.com> > wrote: > > Hi Axel, > > > > Thank you for your response. > > > > Yes, I tried to implement the aforementioned script. It works very well on > whole molecules. > > > > However, I am trying to implement the script on fragments. For example, if > I have fragments: A, B and C that makes up a whole molecule "ABC", then the > sum of SA scores of the fragments should be equal to SA score of the whole > molecule. > > > > Right now, the summation doesn't add up. > > > > I was wondering if there is a correction that needs to be made to the sum > of SA scores such that it is equal to the SA score of the whole molecule. > > > > -- > > Best, > > Ganesh > > > > > > On Mon, Mar 30, 2020 at 4:30 PM Axel Pahl <axelp...@gmx.de> wrote: > > Hi Ganesh, > > are you aware that the SA Score IS implemented in RDKit: > > https://github.com/rdkit/rdkit/tree/master/Contrib/SA_Score > > Kind regards, > Axel > > > On 30.03.20 16:55, Ganesh Shahane wrote: > > Dear RDKitters, > > > > I am trying a to find a way to implement the SA score as a sum of > fragments contributions from this paper: > > > > Ertl, Peter, and Ansgar Schuffenhauer. 2009. “Estimation of Synthetic > Accessibility Score of Drug-like Molecules Based on Molecular Complexity > and Fragment Contributions.” *Journal of Cheminformatics* 1 (1): 8. > > > > For example, if I have three different fragments: A, B and C and their > respective SA scores, then the SA score of molecule "A+B+C" should be the > sum of all three fragment SA scores. > > > > In practice though, the fragment SA scores do not add up. > > > > I was wondering if anyone across the cheminformatics community has > successfully implemented this or a similar strategy? > > > > -- > > Best, > > Ganesh > > > > > _______________________________________________ > > Rdkit-discuss mailing list > > Rdkit-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > >
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