[PyMOL] Fwd: Iterate Script Over States

... This should've gone to the list ... :S

TAW

---------- Forwarded message ----------


Hi Warren (e.a.),

First, as a side note, your first post had 'for state in
cmd.count_states():' whereas it seems it should read 'for state in
range(cmd.count_states()):'.

I find myself doing something similar to Sean now, accumulating
coordinates over different frames for each of the atoms. The question
is how to do that fastest. At this moment I'm doing the following,
which is painstakingly slow (but it works :)). Aside from that it has
a nasty hack adding to globals(), as cmd.alter executes in its own
scope.

class AtomVar:
   sum = None
   ssq = None
   N   = None
   cov = None
   var = None

   def __init__( self ):
       self.sum = [ 0,0,0 ]       #  x,  y,  z
       self.ssq = [ 0,0,0,0,0,0 ] # xx, yy, zz, xy, xz, yz
       self.N   = 0

   def inc( self, x ):
       self.sum = [ self.sum[i] + x[i] for i in range(3) ]
       squares  = [ x[0]*x[0], x[1]*x[1], x[2]*x[2], x[0]*x[1],
x[0]*x[2], x[1]*x[2] ]
       self.ssq = [ self.ssq[i] + squares[i] for i in range(6) ]
       self.N = self.N + 1

   def purge( self ):
       s = self.sum
       squares = [ s[0]*s[0], s[1]*s[1], s[2]*s[2], s[0]*s[1],
s[0]*s[2], s[1]*s[2] ]
       self.cov = [ (squares[i] - self.ssq[i]/self.N)/self.N for i in
range(6) ]
       self.var = self.cov[0] + self.cov[1] + self.cov[2]

def molVar( sele="all" ):
   model = cmd.get_model( sele )
   globals()["M"] = {}
   for i in model.atom:
       M[ i.id ] = AtomVar()
   for state in range(cmd.count_states()):
       cmd.iterate_state( state, sele, "M[ ID ].inc( (x,y,z) )" )
   for i in M.keys():
       M[ i ].purge()
   cmd.alter( sele, "b = M[ ID ].var" )

Any suggestions are welcome :)

Cheers,

Tsjerk


On Mon, Sep 28, 2009 at 9:05 PM, Warren DeLano <wa...@de...> wrote:
> Sean,
>
>
>
> Yes, that is an alternate route.  cmd.get_model is likely slower than
> cmd.iterate_state, but should work regardless.
>
>
>
> Cheers
>
> Warren
>
>
>
> ________________________________
>
> From: Sean Law [mailto:mag...@ho...]
> Sent: Monday, September 28, 2009 11:58 AM
> To: pym...@li...
> Subject: Re: [PyMOL] Iterate Script Over States
>
>
>
> I think I figured it out (though, it wasn't documented).  What I needed was
> to use:
>
> cmd.get_model(selection, STATE)
>
> I think that's the correct usage?  What I needed was to loop through a
> selection and then to calculate the sugar pucker information.  However, not
> all atoms from the selection are required for the calculation so some
> pre-parsing of the residue is needed.  It appears that I can specify the
> state to obtain atom objects from via the get_model command.  I hope that is
> right?
>
> Sean
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623