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 >> listRdkit-discuss@lists.sourceforge.nethttps://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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