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:[email protected]]
> 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 <[email protected]> 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:[email protected]]
> > Sent: Monday, September 28, 2009 11:58 AM
> > To: [email protected]
> > 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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> >
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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
>
>
>
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