Greg, Thank you for your response and for your GitHub site where you are generouslyproviding snippets of code to help others. I agree that the atomic number to polarizabilityapproach is crude. However, experimental polarizabilities for small organics are available in the CRC Handbook and other sources. Hence, the error of this approach can be readily estimated. Thanks again for your help - greatly appreciated. Regards, Jim Metz
-----Original Message----- From: Greg Landrum <greg.land...@gmail.com> To: James T. Metz <jamestm...@aol.com> Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net> Sent: Fri, Jan 11, 2019 1:51 am Subject: Re: [Rdkit-discuss] atomic contributions to molecular polarizability 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 contributionsto the total molecular polarizability of small organic molecules. Apparentlythere is a molecular descriptor, apol, that is the sum total from the atomiccontributions 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 orperhaps the charge column of PDB or MOL2 files, respectively? I couldthen 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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