VMD-L Mailing List

From: Peter C. Lai (pcl_at_uab.edu)
Date: Wed Jan 25 2012 - 16:51:49 CST

A couple of tips: since you're not using counter k for anything other than
loop control, and you are looping across the whole lists why not use foreach.

foreach atom1 $atom1_list {
  set atom2_select [atomselect top "resname SOL and pbwithin 5.00 of index $atom1"]
  set $atom2_list [ $atom2_select get index ]
  foreach atom2 $atom2_list {
     lappend duplist $atom2
     #append each atom found from the $atom2_select to a list called duplist
  }
}

#duplist should now contain every occurence of the duplicate atom index

set duplist_index [ lsort -unique $duplist ]
#sort and remove duplicates so you have a unique index of the duplist

foreach dupatom $duplist_index {
 puts "$dupatom : " [ llength [ lsearch -exact -all $duplist $dupatom ] ]
#search for all instances of $atom2 in $duplist. this returns a list of
#list indices which is then parsed by llength.
}

On 2012-01-25 02:48:18PM -0500, jeela keel wrote:
> Dear Alex and VMD users,
>
> Thank you for your help and I am sorry if I was not clear earlier. I am
> looking for a way of counting a molecule for example with an index 452, how
> many times does this molecule appear in the selection or how many times it
> is in the list of the molcules that are selected.
>
> Based on your suggestion , started writing the following :
>
> So I make the selection of the atom atom_select
> then get the index of the atom selected set atom1_list [$atom1_select get
> index]
> get the number of the atoms in the list atoms1_number [llength
> [$atom1_select list]]
> for {set k 0} {$k < $atoms1_number } {incr k} {
> set atom1 [lindex $atom1_list $k]
> set atom2_select [atomselect top "resname SOL and pbwithin
> 5.00 of index $atom1"]
> set atom2_index [$atom2_select get index]
> set atom2_list [ $atom2_index list ]
> set num_atom2 [ llength $atom2_list]
>
> puts " atoms: $atom2_list and
> num_atoms : $num_atom2
> "
>
> *so I get something like this for one single frame. in the list there are
> three atoms with index 452 and two atoms of index 1942 and nine atoms of
> index 1855.*
>
> atom : 1855 num_atoms 1
> atom : 1855 num_atoms 1
> atom : 452 num_atoms 1
> atom : 452 num_atoms 1
> atom : 1855 num_atoms 1
> atom : 1855 num_atoms 1
> atom : 1942 num_atoms 1
> atom : 1855 num_atoms 1
> atom : 1855 num_atoms 1
> atom : 1855 num_atoms 1
> atom : 1942 num_atoms 1
> atom : 1855 num_atoms 1
> atom : 452 num_atoms 1
> atom : 1855 num_atoms 1
>
> the question I am trying to solve, is* how do I count how many atoms are
> that have same index* ( meaning how many times the same atom is selected).
> and create a new list that has something like this
>
> index 452 3
> index 1855 9
> index 1942 2
>
> Thank you for any suggestions or sharing scripts that are solving similar
> question.
>
> Jeela
>
>
>
> On Wed, Jan 25, 2012 at 10:12 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> > On Wed, Jan 25, 2012 at 9:39 AM, jeela keel <jeela22_at_gmail.com> wrote:
> > > Hello VMD users,
> > >
> > > Is possible to count how many of same atomselect is in a list or how
> > many
> > > times atomselect is selected? Using VMD , selected molecules that are
> > close
> > > to different parts of protein and selected some molecules more than once
> > and
> > > want to know how many times the same atomselect is been selected or how
> > many
> > > of them are in the list per each frame.
> > >
> > > for example in frame 1 there are 4 of atomselect2345 (same molecule) and
> > 5
> > > of atomselect8509 and so on.
> >
> > your wording is a bit confusing. lets first see whether we are on the same
> > page.
> >
> > an "atom selection", i.e. the procedure that is created by the
> > atomselect command,
> > is in essence a list of atoms that is generated based on a rule (the
> > selection text).
> >
> > from what i gather, you are now looking for the *intersection*
> > of two atom selections, right?
> >
> > there are multiple ways to do that. for example, create a new
> > selection that contains
> > the first selection text combined with the section selection text via
> > an "and" condition.
> >
> > if you want to do that in an automated fashion, there should be
> > something like this:
> >
> > set selintersect [atomselect top "([$sel1 text]) and ([$sel2 text])"]
> >
> > you could also write a small proc that computes the intersection of
> > [$sel1 get index] and [$sel2 get index]. there is an 'intersect' command
> > in TclX that does this automatically, but VMD does not contain TclX.
> >
> > it should also be straightforward to write a small proc to do this.
> > you can write the proc fairly efficiently, since you can rely on the
> > fact that index lists are always pre-sorted with increasing index.
> >
> > a good place to look for Tcl script hacks and existing solutions
> > is the Tcl/Tk wiki at: http://wiki.tcl.tk
> >
> > axel.
> >
> >
> > > I have used the command llength and num before that counts how many atoms
> > > are in a list, but this time I need to count how many times each specific
> > > atomselect is selected in the same frame. then move to next frame where
> > > there are different atomselect that again change with next frame.
> > >
> > > I am trying to write a script to do the above but I am wondering if
> > there is
> > > a command that can be useful to use in the script . Did anybody wrote
> > > something similar to what am trying to do or have any suggestion. Thank
> > you
> > > for your help and suggestions.
> > >
> > > jeela
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer
> > akohlmey_at_gmail.com http://goo.gl/1wk0
> >
> > College of Science and Technology
> > Temple University, Philadelphia PA, USA.
> >
> > 

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