Bob,
I see that version 12.1.30_dev produces a more structured molfile on
Extract that includes charge data. That's neat.
This did break one of my scripts, and I can't find the problem. The broken
script involves a single model duplication. In this script, first the data
is extracted:
var modTxt = 'echo Copying model data...;mod1 = "' +
jmolGetPropertyAsString("extractModel", "all") + '";javascript
"dupMod2()";';
jmolScript(modTxt);
dupMod2() then does the following:
var scpt = 'delay 1;echo;var i = {*}.atomIndex.max + 1;var t =
{*}.atomIndex.min;select within(branch, {atomIndex = i}, {atomIndex=t});var
x = {selected}.size;var y={*}.size;var z = y - x;';
scpt += 'if (y > 40 || z != 0){echo This feature is limited to a single
model with|less than 40 atoms.;delay 3;echo;}';
scpt += 'else{var sz = 5;if (y > 8){sz = 6};if (y > 11){sz = 7};if (y >
30){sz = 9};set appendNew false;';
scpt += 'select *;translateSelected {...@sz @sz 0};load APPEND "@mod1";';
scpt += 'mod1="";hover off;' + loadScpt + 'select *;wireframe
0.15;spacefill 23%;boundbox {*};centerat boundbox;javascript
"getFormula();lnkSwitch()";}';
jmolScript(scpt);
The global variable loadScpt is just some echo and label settings. For
neutral models the above still works, but if I have an original ion, I end
up with charge problem. By way of example duplicating the 2-propyl cation
results in the following (end of email) extracted molfile for the two
models. Note the duplicated cation is now +3.
I've run into conflicting standards for charges in the molfile atom block
before. Some standards use actual charges while others use an integer
code!!! Is that what's going on here, or do you see a problem with my
code??
Otis
string
__Jmol-12_01101114153D 1 1.00000 0.00000 0
Jmol version 12.1.30_dev 2010-12-06 22:36 EXTRACT: ({0:5 8:21})
20 18 0 0 0 0 1 V2000
-5.25897 2.94760 -5.22727 C 0 0 0 0 0 0
-6.40696 3.88045 -4.97901 C 0 1 0 0 0 0
-5.19679 2.67627 -6.29968 H 0 0 0 0 0 0
-5.40453 2.03269 -4.62526 H 0 0 0 0 0 0
-4.32125 3.44406 -4.91922 H 0 0 0 0 0 0
-6.57636 4.30536 -3.56545 C 0 0 0 0 0 0
-5.64464 4.81988 -3.22194 H 0 0 0 0 0 0
-6.73390 3.40107 -2.92615 H 0 0 0 0 0 0
-7.43260 4.98898 -3.43879 H 0 0 0 0 0 0
-7.07100 4.22428 -5.77467 H 0 0 0 0 0 0
-0.31570 0.36779 0.60032 C 0 0 0 0 0 0
0.29552 -0.34440 -0.56970 C 0 3 0 0 0 0
0.12635 0.01278 1.55223 H 0 0 0 0 0 0
-1.40380 0.17640 0.60730 H 0 0 0 0 0 0
-0.13472 1.45247 0.49351 H 0 0 0 0 0 0
-0.23199 0.06232 -1.89775 C 0 0 0 0 0 0
-0.05836 1.15762 -2.04269 H 0 0 0 0 0 0
-1.33430 -0.12533 -1.92861 H 0 0 0 0 0 0
0.25017 -0.49061 -2.72136 H 0 0 0 0 0 0
1.07055 -1.10543 -0.45844 H 0 0 0 0 0 0
1 2 1 0 0 0
1 3 1 0 0 0
1 4 1 0 0 0
1 5 1 0 0 0
2 6 1 0 0 0
7 6 1 0 0 0
8 6 1 0 0 0
9 6 1 0 0 0
10 2 1 0 0 0
11 12 1 0 0 0
11 13 1 0 0 0
11 14 1 0 0 0
11 15 1 0 0 0
12 16 1 0 0 0
17 16 1 0 0 0
18 16 1 0 0 0
19 16 1 0 0 0
20 12 1 0 0 0
M END
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
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