Bob,
MA4B2
MA3B3
MA4BC
MA3B2C
MA2B2C2
MA3BCD
All check out. I did not do all possible mismatches, but I did confirm
all possible matches, as well as the mismatch that existed whenever I
started a new isomer by changing one model. That leaves 3 classes to go,
but it's 2:30 AM. Also, Tom gets to do MABCDEF. He just doesn't know it yet.
When I got into this coordination stuff, I tried to find a reference to
SMILES comparisons. I sure couldn't find a reference. In fact, there was
disagreement as to how these things should be curated, hence my original
query to inorganic chemists.
Otis
Otis Rothenberger
chemagic.com
On 11/16/2010 12:53 AM, Robert Hanson wrote:
On Mon, Nov 15, 2010 at 8:28 PM, Otis Rothenberger
<osrot...@chemagic.com <mailto:osrot...@chemagic.com>> wrote:
Bob,
After being out all day, I'm back at work. My intent was to begin
a systematic slow trek through all of the octahedral isomer types.
Unfortunately, I did not get far - SX4Y2. It's a strange problem,
so I thought that I better check in with you. By the way, because
of this problem early on, I went back to collecting stddev:
var i = {*}.atomIndex.max + 1;var t = {*}.atomIndex.min;select
within(branch, {atomIndex = i}, {atomIndex=t});var j =
{selected}.find('SMILES');var x = compare({selected}, {not
selected}, @j, 'stddev');echo @x
Call this osrCompare below.
I loaded SF6; I duplicated it in the window to produce two
identical models of SF6: osrCompare ~0 ( 4.5E-8)
I made the trans Br isomer of both: osrCompare = NaN YIKES!
A quick look at the problem:
Original SMILES: [S@@]123456.F6.F1.F2.F3.F4.F5
Duplicated SMILES: [S@@]123456.F6.F1.F2.F3.*F5.F4*
Original SMILES (after Br's): [S@@]123456.F6.Br1.Br2.F3.F4.F5
Duplicated SMILES (after Br's): [S@@]123456.F6.Br1.Br2.F3.*F5.F4*
My duplication method is to do
jmolGetPropertyAsString("extractModel", "all") and then a load APPEND.
In the testing that I did, I never thought to test an obvious
match. I just decided that I should be thorough here.
Otis
Otis Rothenberger
chemagic.com <http://chemagic.com>
------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today
http://p.sf.net/sfu/msIE9-sfdev2dev
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
