sorry -- was at the BCCE conference....
var i = {*}.atomIndex.max + 1;
select within(branch, {atomIndex = i}, {atomIndex=0});
What is the intent of that, Otis? I'm pretty sure that's the same as
select molecule=1
right?
Bob
On Wed, Aug 4, 2010 at 10:16 AM, Otis Rothenberger <osrot...@chemagic.com>wrote:
> The following Jmol script works flawlessly with two small (C6 ish)
> molecules as they undergo model kit editing in the same frame:
>
> var sm = {*}.find('SMILES');var i = {*}.atomIndex.max + 1;select
> within(branch, {atomIndex = i}, {atomIndex=0});var x =
> {selected}.size;var y={*}.size;var z = y - x;var w = 'The models are
> identical.';if (z != 0){var i = compare({selected},{not
> selected},'SMILES',sm,'stddev');if (i == 'NAN'){w = 'The models are NOT
> identical.'};echo @w;}
>
> I mean flawlessly, including stereochemistry.
>
> With large models (e.g. some monoterpenes), the behavior of the script
> is erratic - works once and stops; does not work at all, throwing a
> script error after if (i == 'NAN'), or reporting incorrect comparison
> results. To make sure that the assumption that I was making with the
> opening var sm = {*}.find('SMILES') was correct, I rearranged the script
> to place this fragment in a more certain position:
>
> var i = {*}.atomIndex.max + 1;select within(branch, {atomIndex = i},
> {atomIndex=0});var sm = {selected}.find('SMILES');var x =
> {selected}.size;var y={*}.size;var z = y - x;var w = 'The models are
> identical.';if (z != 0){var i = compare({selected},{not
> selected},'SMILES',sm,'stddev');if (i == 'NAN'){w = 'The models are NOT
> identical.'};echo @w;}
>
> Same result.
>
> Is this a matter of the compare function inherently "stressing out"
> with model size, or is there a logic error in my script code. Things
> seem to go erratic at about 20-30 total atoms.
>
definitely not. I've compared the entire ribosomal large subunit.
>
> By way of example with two pulegone models, the first run of the script
> produces the models identical echo. After the edit of one model (H to Cl
> back to H, just to do an edit back to identical), I get the following
> history:
>
>
sounds like a good test.
> var sm = {*}.find('SMILES');
>
..SMILES for both models as though one...
> var i = {*}.atomIndex.max + 1;
> select within(branch, {atomIndex = i}, {atomIndex=0});
>
...same as select molecule=1, I think
> 27 atoms selected
> var x = {selected}.size;
> var y={*}.size;
> var z = y - x;
> var w = 'The models are identical.';
> if (z != 0);
>
... true if there is more than one molecule, I think...
> var i = compare({selected},{not selected},'SMILES',sm,'stddev');
> script ERROR:
>
> Otis
>
>
OK, one thing is that Jmol isn't numbering molecules correctly after atoms
are deleted. But that's not the problem here. What you seem to be doing is
using the compare command with SMILES -- meaning a conformational search. A
value of 0.0 for i would mean the two models have the same configuration AND
conformation. "NAN" would mean they failed the SMILES match and so are
nonidentical.
The way I was thinking to categorize two models is this:
var m1 = {molecule=1} # or whatever
var m2 = {molecule=2} # or whatever
# check molecular formulas
var sameMF = (m1.find("MF") == m2.find("MF"))
# get SMILES string for molecule 1
var smiles = m1.find("SMILES")
var smiles_enantiomer =
sm.replace("@@","!@").replace("@","@@").replace("!@@","@")
var smiles_nostereo = smiles.replace("@","")
# note: we can't just compare SMILES strings like we can molecular formulas
# because SMILES strings here are not "cannonical" - but that is no problem
at all
# instead, we "find" the SMILES string for one model in the other. Using
"SMILES"
# here instead of "SMARTS" guarantees an exact search and not a substructure
search
var identical = sameMF && (m2.find("SMILES",smiles)> 0)
var configurationalIsomers = sameMF && !identical &&
(m2.find("SMILES",sm_nostereo) > 0)
var enantiomers = configurationalIsomers &&
(m2.find("SMILES",smiles_enantiomer) > 0)
var diastereomers = configurationalIsomers && !enantiomers
var constitutionalIsomers = sameMF && !identical && !configurationalIsomers
...but "molecule=2" won't work right now after you delete atoms. It's fixed
for Jmol 12.1.2 and Jmol 12.0.4
Bob
> --
> Otis Rothenberger
> chemagic.com
>
>
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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