VMD-L Mailing List

From: sally cii (cii.sally_at_googlemail.com)
Date: Mon Jul 16 2007 - 07:12:14 CDT

Dear all,

Thank you for all your responses.

I have $sel1 and $sel2 imported before I loaded this script. By correcting
with set list1 [lsort -increasing $lists 0], I can get the list sorted and
saved into the file $f.

This script is small part of what I really need to do, what I really want is
a script that does:

For all the atoms in $sel1 there is a counter, every time an atom in $sel2
get within certain distance ($dist) to an atom in $sel1 during $nf frames,
the corresponding counter to that atom adds 1. And the final output I want
is the values of counter for every atom in $sel1. As I don't know how to
accomplish that in one script, therefore I tried the previous script to sort
the list of $sel1 and planned to count the index afterwards. I really
appreciate if anyone can shed some light on how to do the counting in the
script for me. Thank you.

Best regards,
Sally Cii

On 7/14/07, Nuno Loureiro Ferreira <nunolf_at_ci.uc.pt> wrote:
>
> Has Axel said, you should import those sel1 sel2 vars.
> But you say that you get the result on the console, so I deduce that you
> are feeding those vars some way to the proc.
>
> About the no output ... because your script reports an error before
> reaching the "puts $f".
> Specifically:
>
> set list1 [lsort -increasing $lists 0]
>
> What's the "0" doing there? ;-)
> And by the way, why are you sorting a list of 2 elements? Be sure you
> know what you are doing, since the results
> from the measure contacts command, are indices, you cannot sort these
> lists, since you the correct correspondence between the elements of both
> element lists.
>
> Probably you want to sort the pairs of contacts, using -increasing and
> -index 0?
> Check the following:
>
> vmd > set c [measure contacts 3 $sel1 $sel2]
> {25 25 21 22 21 22 34 22 22 34 34 35 35 23} {36 39 36 36 39 39 39 38 56
> 38 37 36 37 39}
> vmd > set a [lindex $c 0]
> 25 25 21 22 21 22 34 22 22 34 34 35 35 23
> vmd > set b [lindex $c 1]
> 36 39 36 36 39 39 39 38 56 38 37 36 37 39
> vmd > foreach i $a j $b {lappend nlist "$i $j"}
> vmd > puts $nlist
> {25 36} {25 39} {21 36} {22 36} {21 39} {22 39} {34 39} {22 38} {22 56}
> {34 38} {34 37} {35 36} {35 37} {23 39}
> vmd > lsort -increasing -index 0 $nlist
> {21 36} {21 39} {22 36} {22 39} {22 38} {22 56} {23 39} {25 36} {25 39}
> {34 39} {34 38} {34 37} {35 36} {35 37}
>
> Is this what you want?
>
> Cheers,
> Nuno
>
>
>
> sally cii wrote:
> > Dear all,
> > I want to write a tcl script that can return the list of atom index in
> > $sel1 that within a certain distance contact with atoms in $sel2
> > during a trajectory. Here is the trial script, after I load this
> > script, I got the atom index printed out in tcl console together with
> > complain about 'bad option', but not saved in the file I wanted.
> > Can anyone tell me how to return a list in a file? thank you in
> advance!
> >
> > #####################################################
> > proc num_contact {mol dist fname} {
> >
> > set nf [molinfo top get numframes]
> >
> > set f [open $fname "w"]
> >
> > for {set i 0} {$i < $nf} {incr i} {
> >
> > $sel1 frame $i
> >
> > $sel1 update
> >
> > $sel2 frame $i
> >
> > $sel2 update
> >
> > set lists [measure contacts $dist $sel1 $sel2]
> >
> > set list1 [lsort -increasing $lists 0]
> >
> > puts $f "$list1"}
> >
> > close $f
> >
> > $sel1 delete
> >
> > $sel2 delete
> >
> > }
> > ####################################################
> >
> > Sincerely,
> > Sally Cii
> > ------------------------------------------------------------------------
> >
> > No virus found in this incoming message.
> > Checked by AVG Free Edition.
> > Version: 7.5.476 / Virus Database: 269.10.4/898 - Release Date:
> 12-07-2007 16:08
> >
>
>