VMD-L Mailing List

From: J T (jtibbitt_at_odu.edu)
Date: Tue Aug 21 2007 - 18:54:08 CDT

> > Try instead
> > set nwatlist [lsort -unique -index 1 $wlist]

I've also tried that. Elements of the list may have the same residue
number, but the distance is still different, which renders the -
unique option void. I've even setting the elements of the list with:

lset wlist $i [list $d $wresnum]

instead of

lset wlist $i "$d $wresnum"

Jeff Tibbitt

------------------------------------------------------------------------
----------------------------------------------------
On Aug 21, 2007, at 5:34 PM, Nuno Loureiro Ferreira wrote:

> J T wrote:
>>> > 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 ;-)
> Try instead
> set nwatlist [lsort -unique -index 1 $wlist]
>
> This way you will sort by uniqueness on the second element, in your
> case, the residue number.
>
>
>> 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]
>>>> }
>>>> -------------------------------------------------------------------
>>>> -----
>>>>
>>>> No virus found in this incoming message.
>>>> Checked by AVG Free Edition. Version: 7.5.484 / Virus Database:
>>>> 269.12.0/961 - Release Date: 19-08-2007 7:27
>>>>
>>>
>>
>>
>>
>