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
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