Sean Law
Mon, 26 Oct 2009 11:07:36 -0700
Warren, I was trying to write a script that would read in CHARMM trajectory files (DCD) specifically for users who do not have access to the most current version of PyMOL. I have written a Python script that will interpret a DCD file and load it into the corresponding object but this process is definitely not as fast as the C implementation already available in version 1.2. I can see where it would be difficult to access the coordinates in the C array via Python. This is not a pressing need of mine by any means as it was something that I am revisiting (if you recall, I had tried this in the past) as I definitely made some mistakes earlier that made the script very slow and inefficient. Now, I have an "optimized" version of the Python script with the limitation being the replacement of the coordinates.
Sean Subject: RE: [PyMOL] Replace Coordinates in State Date: Mon, 26 Oct 2009 10:54:39 -0700 From: war...@delsci.com To: magic...@hotmail.com; pymol-users@lists.sourceforge.net Sean, Unfortunately, there isn’t any way at present to directly expose PyMOL’s internal C coordinate array to Python in an accessible form. Yes, iterate_state and alter_state are highly inefficient – it would make more sense to provide a means of exporting and re-importing coordinate sets via either native Python lists or, even better, NumPy arrays. In what form do you have the current coordinate data? Cheers, Warren From: Sean Law [mailto:magic...@hotmail.com] Sent: Friday, October 23, 2009 4:54 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Replace Coordinates in State Hi All, I was wondering if there was a faster way to replace all coordinates. I've used commands such as iterate_state and alter_state before but they are far too slow since they have to iterate over each atom. Instead, I want to replace one set of coordinates that correspond to a specific state with a different set. Here's what I have to work with: I have a list that contains x, y, z coordinates. Of course, this list can be manipulated and/or separated if necessary. I'm assuming that the coordinates for a specific state are stored somewhere in memory and I would basically like to replace one set of coordinates with the other. I would think that something like "pointers or references" would work a lot faster than having to copy the coordinates over (which is typically slow and is likely what alter_state is doing?). In addition, I am dealing with 100+ states using alter_state for each state would be far too slow. Any suggestions would be greatly appreciated. Thanks in advance! Sean Save up to 84% on Windows 7 until Jan 3-eligible CDN College or University students only. Hurry-buy it now for $39.99! _________________________________________________________________ Save up to 84% on Windows 7 until Jan 3—eligible CDN College & University students only. Hurry—buy it now for $39.99! http://go.microsoft.com/?linkid=9691635
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