Is there any way currently using Avogadro 2 to calculate the size of a molecule? I know that it will calculate things like solvent-accessible and solvent-excluded areas, however I’d like to actually get back a number for the volume of a molecule. From my understanding most programs use GEPOL to calculate the volume of a molecule, is it possible to implement this into Avogadro?
Well, it will calculate the surfaces, but at the moment, it doesn’t populate the surface area or volume.
I have a branch to generate the numbers from the surface, but haven’t added the “plumbing” to add them to the UI.
Basically the hold-up would be expanding the “molecule properties” dialog to include more of a table for other properties.
In the short term, I can certainly put up a pull request that will calculate the surface area and volume of the surfaces once generated (e.g. as debugging information onto the terminal / console).
If you have a good idea where to put the numbers, I’m happy to hear it.
@brockdyer03 Side note: some time ago, I became aware about MoloVol by Maglic and Lavendomme (see J. Appl. Cryst.) which may be of interest for you. Either .cif, .pdb, or .xyz is an input format acceptable to the program.
I think that the molecular properties dialog box is probably the right spot, although if you can make a part of the Analysis tab that is something along the lines of “Physical Properties” then that might be a good spot for it.
On a side note, I have been wanting to contribute to the development of Avogadro 2 for quite some time, especially given that I often raise bugs and feel like it is possible that I can figure out how to fix them myself. I am familiar with a fair bit of Python, but I have no idea what the process is for working on GitHub, I know that there is a thing called a “pull request” but I have no clue what that means. Is there somewhere or someone I can ask that can walk me through that stuff?
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I’m less certain about the “Physical Properties” because this would, in principle, be a property of the surface. I’ll probably go create a small “surface property” dialog with surface area and volume of the current surface (if available).
Of course:
Also useful:
Thanks! Hopefully I’ll be fixing the bugs I find myself soon enough, until then I will be sure to report them here.
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