RE: [PyMOL] how to get minimum distances in script?

[Warren L. D. <wa...@de...>]

Seth,

	PyMOL is definitely behind other packages right now when it
comes to geometric measurement, which is shame since Python is such a
good tool for working up this stuff.  We'll get there eventually
though...

	I think a brute-force approach is currently necessary, and here
is a little code to get you started:

# define interface

cmd.select("query", ...)
cmd.select("target", ...)

# example depends on "query" and "target" selections

from pymol import cmd
import pymol

result_list = []
for a in cmd.index("query"):

   # for each query atom, generate a list of 
   # neighbors within 8 angstroms, including  
   # attributes and xyz coordinates

   q_sel = "%s`%d"%a
   print q_sel

   cmd.iterate(q_sel,
"stored.qry_info = (chain,resn,resi,name)")

   cmd.iterate_state(1,q_sel,
"stored.qry_xyz = (x,y,z)")

   pymol.stored.nbr_info = []
   pymol.stored.nbr_xyz = []

   cmd.iterate("target and (%s expand 8)"%q_sel,
"stored.nbr_info.append((chain,resn,resi,name))")

   cmd.iterate_state(1,"target and (%s expand 8)"%q_sel,
"stored.nbr_xyz.append((x,y,z))")

   result_list.append((
	((stored.qry_info), (stored.qry_xyz)),
	map(None,stored.nbr_info, stored.nbr_xyz)))	

# the rest of the task is just pure Python math, using the
# values stored in result_list.

for a in result_list:
   print "Query:",a[0]
   if len(a[1]):
      print "Neighbors:"
      for b in a[1]:
         print "  ",b

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Seth Harris
> Sent: Friday, July 11, 2003 5:37 PM
> To: pym...@li...
> Subject: [PyMOL] how to get minimum distances in script?
> 
> Hello all,
> 
> I am trying to write a script that will go through each residue in a
> dimer interface and determine for each one how close it is to the
> partner monomer.
> 
> I can interactively plot all the distances within a certain cutoff
> using the handy:
> distance chosen, residue_selected_on_first_chain,
> partner_monomer_selection, cutoff
> 
> For atom selections Warren earlier explained how to parse into its
> components (using list=[]; iterate
> (selection),list.append((resi,resn))).  However, the selection
> created by the distance command (i.e. "chosen") does not behave the
> same way it seems and I haven't been able to iterate over it to get
> at the info.
> 
> I see from "help distance" that in the API cmd.distance returns the
> average, so it suggested that perhaps minimum and maximum or even
> each individual value might also be accessible, giving me hope that
> the more elegant solution was close at hand and limited more by my
> ignorance than the chosen approach.
> 
> Otherwise I suppose there's the more brute-force avenue of going
> through each residue, selecting atoms from the partner monomer within
> a certain distance if any, and then explicitly measuring the distance
> to each atom one by one, but I thought I'd check with the community
> before launching such an ugly attack on the problem, having walked
> that road before!
> 
> Also, not to push my luck, but if you'd like to write your
> suggestions in both English and Python, my less-than-rudimentary
> knowledge of Python will thank you(!)
> 
> Cheers and thanks,
> Seth
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Seth F. Harris, PhD
> Agard Laboratory
> University of California, San Francisco
> Mission Bay Genentech Hall
> 600 16th St. Suite S416
> San Francisco, CA 94143-2240
> 415.502.2930
> 
> 
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