Re: [PyMOL] Iterate Script Over States

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

Tsjerk,

This will only provide a minor speedup, but the alter* and iterate* commands do take a "space" argument with a dictionary to use in lieu of PyMOL globals().

my_dict = {'L':[]}

cmd.iterate_state(1, 'all', 'L.append( (x,y,z) )', space=my_dict)

print len(my_dict['L'])

etc.

Cheers,
Warren


> -----Original Message-----
> From: Tsjerk Wassenaar [mailto:ts...@gm...]
> Sent: Tuesday, September 29, 2009 7:40 AM
> To: Warren DeLano
> Subject: Re: [PyMOL] Iterate Script Over States
> 
> 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
> 
> 
>