Reading molecular coordinates in standard orientation

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Reading molecular coordinates in standard orientation

Mohammad Mehdi Ghahremanpour
Hello OpenBabel developers,

Greetings!

I am coding to read the coordinates from gaussian log file using OpenBabel libraries. Having the coordinates, I calculate molecular electric moments up to quadrupoles.
To compare my results to QM, particularly for quadrupoles, I need to have the "Standard Orientation” as Gaussian does Population analysis in the Standard Orientation.

My question is that when I use OpenBabel to extract the coordinate, does it return the Standard Orientation?  

Thanks,
Mohammad
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Re: Reading molecular coordinates in standard orientation

David van der Spoel
On 20/06/17 18:32, Mohammad Mehdi Ghahremanpour wrote:
> Hello OpenBabel developers,
>
> Greetings!
>
> I am coding to read the coordinates from gaussian log file using OpenBabel libraries. Having the coordinates, I calculate molecular electric moments up to quadrupoles.
> To compare my results to QM, particularly for quadrupoles, I need to have the "Standard Orientation” as Gaussian does Population analysis in the Standard Orientation.
>
> My question is that when I use OpenBabel to extract the coordinate, does it return the Standard Orientation?

You can try to use GetConformers to access all the coordinates that
Gaussian prints, however it is only of either the standard orientation
or of the input orientation. This you can check by comparing to the log
file manually for a few cases.

http://openbabel.org/dev-api/classOpenBabel_1_1OBMol.shtml#a5246a44bf82aa31c2f428665db94bfb8

>
> Thanks,
> Mohammad
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> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> OpenBabel-Devel mailing list
> [hidden email]
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--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se

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