VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Feb 10 2017 - 16:17:49 CST

In terms of fully compiled builds, I'm afraid the answer is no, and those aren't even useful if they need to link into python, since the system pythons are probably different. Compiling VMD from source is not as easy as it could be, but its also not impossible (although it definitely feels that way the first time)! The two best sources that explain the process in all the gory detail that is required to get python-enabled VMD working that I've found are http://robinbetz.com/blog/2015/01/08/compiling-vmd-with-python-support/ (for linux) or http://nuweb5.neu.edu/bardhan/?p=104 (for mac).

In terms of the data itself, volmap gives you a bunch of voxel values, 1 value per voxel. The value of the voxel depends on what analysis you asked for. Here it would probably be informative to look at what a dx file looks like, just for a small synthetic test set. The data is fundamentally stored the same way.

-Josh

On 02/10/2017 02:51 PM, Karl Decker wrote:
Thank you for including that command in the VMD CVS, Joshua Vermaas. I've gotten an account, checked out VMD through CVS, and found the py_molecule.C source file that contains the definition of the python object mol_get_volumetric(). I'm in the process of assessing how I would use the mol_get_volumetric in my plugin. Thanks very much for the help.

I do have another question, though. Are fully compiled builds from the source code on CVS available for download? If not, it may be difficult to use the features available through CVS, as I have not been able to compile VMD on my machine.

Also, what format does the VolMap data take? It's not clear from the sources I've seen.

Thanks,
Karl

On Tue, Feb 7, 2017 at 3:51 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
Hi Karl,

It sounds like you want to interact with volume maps already loaded into VMD. When I needed to do this for my own purposes, I dug into VMD internals and wrote something to access volumetric datasets and make it accessible to VMD's python interface (this is now in the VMD CVS as molecule.get_volumetric). From there, you can access the data itself in python and do whatever you want. This does not expose a pointer to VMD's internal data structure directly (which isn't even useful, since its stored out of order as far as numpy is concerned), however since the copy never went to disk, it was fast enough to be efficient.

-Josh

On 02/07/2017 02:15 PM, Karl Decker wrote:
Is it possible to share memory between two processes, one of which is VMD? I'm aware this is generally messy and dangerous, but it's one way to avoid writing large files to disk and slowing down the execution of the plugin we're designing. It would obviously take some effort to write the code for sharing the memory between two processes, but first I want to know: can VMD even be made to share its memory with another process?

Alternatively, we are considering implementing a python plugin to VMD. Can VMD be made to share memory with a plugin?

The memory we want to share is from VolMap, specifically a distance map generated in VolMap. The idea is to sidestep writing the map to disk because it takes too long.

Thanks,
Karl