VMD-L Mailing List

From: MD Simulation (mdsimulationgroup_at_gmail.com)
Date: Mon Jul 03 2017 - 14:27:23 CDT

Hi All,

I ended up figuring out the problem: TCL dict syntax.

I had: "dict set $empirical_formula $atom $value"

but it should have been: "dict set empirical_formula $atom $value"

Here's a procedure to get the empirical formula of a fragment:

proc get_empirical_formula {frag_number} {
> set frag_sel [atomselect top "fragment $frag_number"]
> set atoms [$frag_sel get element]
>
> set empirical_formula [dict create]
> foreach atom $atoms {
> if {[dict exists $empirical_formula $atom]} {
> set value [expr {[dict get $empirical_formula $atom] + 1}]
> } else {
> set value 1
> }
> dict set empirical_formula $atom $value
> }
>
> $frag_sel delete
> return $empirical_formula
> }
>

Thanks for the help and suggestions

On Mon, Jul 3, 2017 at 3:19 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Sat, Jul 1, 2017 at 9:12 PM, MD Simulation
> <mdsimulationgroup_at_gmail.com> wrote:
> > Hello,
> >
> > I'm trying to write a procedure that will determine the empirical
> formula of
> > a fragment:
> >
> >> proc get_empirical_formula {frag_number} {
> >> set frag_sel [atomselect top "fragment $frag_number"]
> >> set atoms [$frag_sel get element]
> >>
> >> set empirical_formula [dict create]
> >> foreach atom $atoms {
> >> if {[dict exists $empirical_formula $atom]} {
> >> set value [expr {[dict get $empirical_formula $atom] + 1}]
> >> dict set $empirical_formula $atom $value
> >> } else {
> >> dict set $empirical_formula $atom 1
> >> }
> >> }
> >> puts $empirical_formula
> >> }
> >
> >
> > The idea is that when you get the elements of the frag_sel, you'll get a
> > list, for instance "C C H H H H H H". I then try to foreach the atom
> list
> > and increment a dictionary value. When I try to print the dictionary,
> all I
> > get is empty.
>
> you could do a simpler strategy. when you get the list of elements,
> also sort it.
> then define a "hold" variable and initialize it to a dummy element
> (XXX), also define a counter and have a loop over the list of sorted
> elements.
> whenever the current element is different from the hold element (and
> the hold element is different from the dummy value), output the
> counter. then initialize the counter to 1 and set the hold element to
> the current element. when the current element is the same as the hold
> element, just increment the counter. when you reach the end of the
> list, print the current counter value. with that, you should easily
> get your fragment formula.
>
> axel.
>
> >
> > Any help would be appreciated. Thanks
> >
>
>
>
> --
> 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.
>