VMD-L Mailing List

From: Nuno Loureiro Ferreira (nunolf_at_ci.uc.pt)
Date: Tue Aug 21 2007 - 15:55:13 CDT

Hi JT

Instead of
set nwatlist [lsort $wlist]

try,
set nwatlist [lsort -unique $wlist]
N.

J T wrote:
> Dear VMD Community,
>
> I've been working on a script that will select the N-closest waters to
> a specified atom selection by following the algorithm suggested by
> John Stone in an earlier post. It successfully returns a sorted list
> of increasing distances, but there are duplicate water residues. The
> script generates a list of all water indices within a max cutoff
> distance. Then each water index in that list is replaced with a
> double valued element containing the distance and the water residue.
> Is there a way I can use the -unique option somehow to fix this?
>
> Thank-you for reading,
> Jeff Tibbitt
> jtibbitt_at_odu.edu <mailto:jtibbitt_at_odu.edu>
>
>
> John Stone's algorithm:
> / 1) select all waters within the max cutoff distance M /
> / 2) calculate the distance D of each water molecule and add the index
> and //distance to a list or lists /
> / 3) sort the list(s) by the distance (keeping the water index and
> distance //assocation intact, if they are in separate lists..) /
> / 4) select the closest N waters from the sorted list// /
> /
> /
> /
> /
> /My Script:/
> proc nwat {n sel} {
> set lists [measure contacts 6 [atomselect top water] $sel]
> set wlist [lindex $lists 0]
> set slist [lindex $lists 1]
> set n [llength $wlist]
> for {set i 0} {$i < $n} {incr i} {
> set satom [lindex $slist $i]
> set watom [lindex $wlist $i]
> set wres [[atomselect top "index $watom"] get resid]
> set d [measure bond "$watom $satom"]
> lset wlist $i "$d $wres"
> }
> set nwatlist [lsort $wlist]
> }
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