Re: Extracting data

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Feb 04 2015 - 08:39:33 CST

[molinfo top set frame $i] does indeed update the frame index for the
selections. All of the scripts that I use everyday work like this.

–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Wed, Feb 4, 2015 at 8:24 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> please note that setting the current frame for the molecule does not
> update the frame index for selections (at least that is what i
> recall).
> in any case, this can be done in a simpler fashion with just two
> selections. this kind of loop construct is particularly useful, if the
> selection strings are complex expressions that need to be updated, so
> the number of costly selections updates is minimized.
>
> that all being said, i am not convinced that the creation of the
> selections is the time critical factor. since we don't know what is
> done with the data in the loop body. that may be more performance
> critical than the creation of selections.
>
> axel.
>
> p.s.: here is the (untested and from the top of my head) suggested
> optimized script framework.
>
> # please note that the script below assumes that these lists are sorted in
> # numerical ascending order. otherwise first apply "lsort -integer -increasing"
> set from {1 10 20 30}
> set to {40 50 60 70}
> set steps_start 101
>
> set fromsel [atomselect top "index $from"]
> set tosel [atomselect top "index $to"]
>
> set num_steps [molinfo top get numframes]
> # Step through each frame.
> for {set i $steps_start} {$i < $num_steps} {incr i} {
> $fromsel frame $i
> $tosel frame $i
>
> # adjust the get lines here to whatever is needed. x y z is used for
> illustration
> set fromdata [$fromsel get {x y z}]
> set todata [$tosel get {x y z}]
>
> for {set j 0} {$j < $fromsel num} {incr j} {
> set fromidx [lindex $from $j]
> set fromxyz [lindex $fromdata $j]
>
> for {set k 0} {$k < $tosel num} {incr k} {
> set toidx [lindex $to $k]
> set toxyz [lindex $todata $k]
>
> # now do something with the data
> }
> }
>
> $fromsel delete
> $tosel delete
>
>>
>> foreach fromSel $fromSelList {
>> foreach toSel $toSelList {
>> # Do something with the selections $toSel and $fromSel.
>> }
>> }
>> }
>
> On Wed, Feb 4, 2015 at 8:56 AM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
>> Hi Stephan,
>>
>> You are making a new selection 16 times per frame. Since your
>> selections don't change, I think it would be faster to make the
>> selections outside of the loop. Something like:
>>
>> set from {1 10 20 30}
>> set to {40 50 60 70}
>> set steps_start 101
>>
>> # Make lists of selections.
>> set fromSelList {}
>> foreach ind $from {
>> lappend fromSelList [atomselect top "index $ind"]
>> }
>> set toSelList {}
>> foreach ind $to {
>> lappend toSelList [atomselect top "index $ind"]
>> }
>>
>> set num_steps [molinfo top get numframes]
>> # Step through each frame.
>> for {set i $steps_start} {$i < $num_steps} {incr i} {
>> molinfo top set frame $i
>>
>> foreach fromSel $fromSelList {
>> foreach toSel $toSelList {
>> # Do something with the selections $toSel and $fromSel.
>> }
>> }
>> }
>>
>> # Delete the selections
>> foreach fromSel $fromSelList {
>> $fromSel delete
>> }
>> foreach toSel $toSelList {
>> $toSel delete
>> }
>>
>>
>> –––––––––––––––––––––––––––––––––––———————
>> Jeffrey Comer, PhD
>> Assistant Professor
>> Institute of Computational Comparative Medicine
>> Nanotechnology Innovation Center of Kansas State
>> Kansas State University
>> Office: P-213 Mosier Hall
>> Phone: 785-532-6311
>>
>>
>> On Wed, Feb 4, 2015 at 5:55 AM, Stephan Grein
>> <grein_at_informatik.uni-frankfurt.de> wrote:
>>> Dear NAMD users,
>>>
>>> i want to extract information from my DCD file as follows:
>>>
>>> set from {1 10 20 30}
>>> set to {40 50 60 70}
>>> set from_len [lindex $from]
>>> set to_len [lindex $to]
>>> set steps_start 101
>>>
>>> for {set i $steps_start} {$i < $num_steps} {incr i} {
>>> for {set j 0} {$j < $from_len} {incr j} {
>>> for {set k 0} {$k < $from_len} {incr k} {
>>> set mysel1 [atomselect top "index [lindex $from $j]"]
>>> set mysel2 [atomselect top "index [lindex $to $k]"]
>>> # do something with the selection, then delete it
>>> $mysel1 delete
>>> $mysel2 delete
>>> }
>>> }
>>> animate goto $i
>>> }
>>>
>>> But for me, this is horribly slow.
>>> Is there any obvious failure in my snippet?
>>>
>>> Would be glad, if someone could point it out.
>>>
>>> Best regards,
>>> Stephan
>>>
>>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.

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