Hi Gregori,
Many thanks
I will look into this.
Best regards,
Richard
From: Grégori Gerebtzoff [mailto:greg...@gerebtzoff.com]
Sent: 19 February 2018 21:30
To: Richard Marchese Robinson <r.l.marcheserobin...@leeds.ac.uk>
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Calculating the MOE vsa_acc descriptor using the
rdkit (or other Open Source software)?
Hi Richard,
Have you thought about an implementation similar to the way TPSA has been
designed?
https://doi.org/10.1021/jm000942e
Best,
Grégori
On 19 Feb 2018, at 19:36, Richard Marchese Robinson
<r.l.marcheserobin...@leeds.ac.uk<mailto:r.l.marcheserobin...@leeds.ac.uk>>
wrote:
Dear Rdkit Team,
Please excuse me if I am overlooking something, but it does not seem possible
to calculate the MOE vsa_acc descriptor using the Rdkit. Is that correct?
[https://www.chemcomp.com/journal/descr.htm#VSA][http://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-descriptors]
I did wonder whether it might be possible to implement the descriptor in Python
using the Rdkit, but there seems to be no obvious way to do that. (I can see
how it would be possible to use the Rdkit to identify all “pure hydrogen bond
acceptors”, as defined in the MOE documentation, using SMARTS patterns, but
identifying the contribution of each atom to the van der Waals surface area
seems decidedly non-trivial, based on my reading of Labute
[http://www.chemcomp.com/journal/vsadesc.htm].)
Whilst I appreciate I may need to simply persevere, I would be grateful if any
guidance could be provided as to how this descriptor might be calculated using
the rdkit (e.g. is there a straightforward way of getting those van der Waals
surface area contributions that I have embarrassingly overlooked) or some other
Open Source tool that I may have overlooked?
Otherwise, are there any plans to implement this descriptor in a forthcoming
version of the rdkit?
As ever, the efforts of the Rdkit Team in making this great resource available
to the community are much appreciated.
Best regards,
Richard
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