And the thing I forgot in this discussion is that there is an MIT-licensed C implementation of a SASA calculator here: https://github.com/mittinatten/freesasa that would probably be reasonably easy to add an RDKit connector to.
On Thu, Aug 18, 2016 at 12:54 PM, Campbell J.E. <[email protected]> wrote: > Here it is. > > > > http://zhanglab.ccmb.med.umich.edu/EDTSurf/ > > > > > > Josh > > > > *From:* Paolo Tosco [mailto:[email protected]] > *Sent:* 18 August 2016 10:16 > *To:* Campbell J.E. > *Subject:* Re: [Rdkit-discuss] Polar surface areas > > > > Dear Josh, > > > > I have used EDTSurf in the past to compute surface areas. > > > > http://zhanglab.ccmb.med.umich.edu/EDTSurf/ > > > > It works very well and it has a C++ API. > > > > Cheers, > > p. > > > On 17 Aug 2016, at 15:17, 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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