yes, it's an integer code, not the actual charge. This is explained in the
CtFile format document.
http://www.symyx.com/downloads/public/ctfile/ctfile.pdf
*0 = uncharged or value other than these, 1 = +3, 2 = +2, 3 = +1,
4 = doublet radical, 5 = -1, 6 = -2, 7 = -3
so '3" there is "+1"
*
On Mon, Jan 10, 2011 at 1:15 PM, Otis Rothenberger <osrot...@chemagic.com>wrote:
> 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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--
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Professor of Chemistry
St. Olaf College
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Northfield, MN 55057
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