Apparently Paolo forgot to include the list on that email, would you please let us know which program he mentioned?
Thanks, -greg On Thu, Aug 18, 2016 at 12:45 PM, Campbell J.E. <[email protected]> wrote: > 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:[email protected]] > *Sent:* 18 August 2016 10:03 > *To:* Campbell J.E. > *Cc:* [email protected] > *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. <[email protected]> > 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 > > > > > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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