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.
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:
var sm = {*}.find('SMILES');
var i = {*}.atomIndex.max + 1;
select within(branch, {atomIndex = i}, {atomIndex=0});
27 atoms selected
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');
script ERROR:
Otis
--
Otis Rothenberger
chemagic.com
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