Hi
thanks for your reply. Yes it is the id.
I found out also that it takes a lot time because is looping in all
atoms and in the "active" site. So I fixed that.
Anyway more in general, I saw that the manual is lacking of some
information useful for who wants to program. I mean, sometimes it
doesn't say if a command returns a tuple or a list or a dictionary.
Ex:
cmd.index("selection") is a list?
thanks
Regards,
andrea
2005/7/6, Gilleain Torrance <gille...@hotmail.com>:
> Hi,
>
> I suppose that these numbers are the atom_ids. It's probably the same
> numbers returned by the cmd.index function.
>
> I guess you could test this by typing "select atom260, id 260" and see if
> that makes a selection with atom260...
>
> As for the speed question, I have no idea. More of a question for Mr DeLano
> :) Calculating pairwise like this is always going to be computationally
> expensive, but I don't know ways to speed this up.
>
> gilleain torrance
>
>
> On 5/7/05 15:17, "Andrea Spitaleri" <andrea.spital...@gmail.com> wrote:
>
> >> HBA = cmd.distance('HBA', '(lig and acc)','(active and don)', 3.2)
> > yes thanks for the trick. However, I edited my script to:
> > DistOutput.write(" %14s %14s %8s %8s\n"%("donor","acceptor","hba","hbd"))
> > DistOutput.write(" %14s %14s %8.3f %8.3f\n"%(Don,Acc,HBA,HBD))
> > but I cannot figure out the meaning of the output:
> > complex_1
> > donor acceptor hba hbd
> > 260 271 2.536 -1.000
> > complex_2
> > donor acceptor hba hbd
> > 391 409 2.489 -1.000
> > complex_3
> > donor acceptor hba hbd
> > 522 547 2.512 -1.000
> > complex_4
> > donor acceptor hba hbd
> > 653 685 2.456 -1.000
> > what the numbers under donor and acceptor are?
> >
> >>
> >> atoms_Don = cmd.index('don')
> >>
> >
> > I tried also this option and it works fine (more or less) excet that
> > it takes a lot time to calculate all the distance (quite weird on my
> > dual-cpu 3Gz intel)
> > this is the loop used:
> > for donor in atoms_Don:
> > for acceptor in atoms_Acc:
> > di = cmd.get_distance("%s`%d"%donor,"%s`%d"%acceptor)
> > DistOutput.write("%8s %8s %8.3f\n"%(donor,acceptor,di))
> >
> > thanks
> >
> > Regards
> >
> > andrea
> >
> >
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