Re: [Rdkit-discuss] Polar surface areas

[Campbell J.E. <je...@so...>]

Thanks for the replies guys. You’re right Greg I was looking for a 3D version, I am always surprised by the amount of functionality present in RDKit so I thought I better ask first. I will investigate the program Paolo linked.

Thanks again,

Josh

From: Greg Landrum [mailto:gre...@gm...]
Sent: 18 August 2016 10:03
To: Campbell J.E.
Cc: rdk...@li...
Subject: Re: [Rdkit-discuss] Polar surface areas

Hi Josh,

Adrian already answered about the 2D version of the TPSA that's available in the RDKit.

I suspect, however, that you're more interested in a 3D version of PSA.
Unfortunately the RDKit does not currently have any method for calculation surface areas in 3D. This, of course, means that there's no PSA implementation.

This isn't an area that I've spent much time thinking about, so I don't really know what the standard algorithm(s) is/are for calculating molecular surfaces/surface areas or how difficult they are to implement. Perhaps someone else out there can comment on this?

In the meantime, your best bet may be to find another open-source (or otherwise) PSA calculator and feed it with conformations generated from the RDKit.

Best,
-greg







On Wed, Aug 17, 2016 at 4:17 PM, Campbell J.E. <je...@so...<mailto:je...@so...>> wrote:
Hi RDKitters,

I’d like to be able to calculate polar surface areas on some molecules using RDKit as a torsion changes. I’ve dug into the code and found the MolSurf.py and some of the functions but as I understand it these are mostly for a 2Dish representation of the molecule. So what’s the best way to go about this? I can supply 3D coordinates for the conformations and partial charges. Is there also a way to increase the accuracy of the surface area calculated?

Cheers,

Josh Campbell



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