Hi Jim, On Thu, Jan 10, 2019 at 11:59 PM James T. Metz via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote:
> > I would like to calculate and be able to visualize the atomic > contributions > to the total molecular polarizability of small organic molecules. > Apparently > there is a molecular descriptor, apol, that is the sum total from the > atomic > contributions to polarizability available in some programs e.g., CDK. > The CDK documentation doesn't include a citation for this (aside from a link to a web page that no longer exists), but since the code is there and this descriptor is super simple, it's easy to re-implement: https://gist.github.com/greglandrum/7936fcf631bfdae0041e298421554bec Does anyone have code that will compute and write out the atomic > contributions to molecular polarizability to either the b factor column or > perhaps the charge column of PDB or MOL2 files, respectively? I could > then use other programs to visualize the structures with those numbers. > Thank you. > The gist linked above shows how to store values in the temperature factors that end up in PDB output. It's worth pointing out that this descriptor is pretty crude: the atomic contribution is determined solely by the atomic number, not by atom environment. The RDKit includes a more complicated (presumably more accurate?) polarizability descriptor: the Molar Refractivity (MR) values. The gist also shows how to get the atomic contributions to this. I hope this helps, -greg
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