Accessing volumetric data as numpy arrays

[OleinikovasV]

Accessing volumetric data as numpy arrays

[Eigenstate]

I do need to update the code to 1.9.4... the main obstacle to this is I need to upstream all of my Python 3 compatibility stuff and now everything is so out of sync it'll take me a while... This is on my to-do list :)

I do work with volumetric data a lot and use gridDataFormats from mdanalysis which lets me work with volumetric data as numpy arrays: https://www.mdanalysis.org/GridDataFormats/. It'll both read and write dx files.

[jvermaas]

I think you'll want to look at the output of "help(atomsel)" after you've imported the atomsel interface in python. There is a mdffsim command that will get you the data directly. There is also a "get_volumetric" command within the "molecule" module that will get you a loaded volumetric dataset into a numpy friendly format.

[jvermaas]

Whoops, my bad. I introduced both of those features after 1.9.3 was released, so those features aren't included in these builds. In principle all you'd need to do is copy over py_molecule.C and py_atomsel.C from an alpha version of VMD or the public CVS repository.

[OleinikovasV]

In principle all you'd need to do is copy over py_molecule.C and py_atomsel.C from an alpha version of VMD or the public CVS repository.

@jvermaas , thanks, I have found now the previous thread about this in VMD mailing-list.
The source code of the post 1.9.3 (alpha) release is still not available on the website. I have requested a CVS account, however..
Still hoping that you will be able to patch it here soonish :)
Thanks a lot to you both!

[jvermaas]

Ok, I've updated the fork I've got of this, and added the updated version of py_molecule.C there. I'm not entirely positive that it works with python 3, mostly since I never tried.