VMD-L Mailing List

From: J T (jtibbitt_at_odu.edu)
Date: Tue Aug 21 2007 - 16:10:03 CDT

> > Instead of
> > set nwatlist [lsort $wlist]
> >
> > try,
> > set nwatlist [lsort -unique $wlist]

Tried it. Since the list elements are double valued (distance and
residue number) the -unique does not work. Is a different way to set
the list up so the -unique option would filter out all double residue
numbers. Right now the ith list element is created with the command:

  lset wlist $i "$d $wres"

where $d is the distance and $wres is the water residue number,

On Aug 21, 2007, at 4:55 PM, Nuno Loureiro Ferreira wrote:

> 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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>> 269.12.0/961 - Release Date: 19-08-2007 7:27
>>
>