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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