Otis,
Sure enough -- I forgot about (all trans)-XA2B2C2 and trans-XA2B4. You would
think you wouldn't need @ or @@ for cases like that, but you do. Even though
@ and @@ are the same! Because they still represent specific stereoisomers,
and that is the only way with SMILES that you can specify the ordering of
the bonds around the central atom. As far as I can tell, the only cases you
do NOT need @ for are XA6, XA5B, and XA5. Even though it is not necessary
for XA5B, it's too much of a trouble to figure out that is what it is, so
I'm just letting Jmol indicate @ for XA5B as well. At least for now.
Wow, this is really going to be something when the bugs are worked out! I'll
bet you anything this has never been done before.
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.jar
should take care of that. Please check. Uploading now...
After being up all day, I'm back to bed!
Bob
On Mon, Nov 15, 2010 at 8:28 PM, Otis Rothenberger <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 Rothenbergerchemagic.com
>
>
> On 11/15/2010 10:19 AM, Otis Rothenberger wrote:
>
> Bob,
>
> For the time being, I'm simply trapping and replacing the responses from
> your Jmol compare/isomer routine when coordination compounds are loaded. I
> can automate this change over in JavaScript. The response replacements allow
> identical/not identical/not same formula responses for coordination
> compounds. This will allow me to do some quick checking.
>
> I've played a bit, and this approach seems to work. Square planar is fine.
> Octahedral will take more testing. I'll get back to you on this.
>
> Otis
>
> Otis Rothenbergerchemagic.com
>
>
> On 11/15/2010 6:53 AM, Robert Hanson wrote:
>
> Otis, I've also started the same thread at <
> blueobelisk-smi...@lists.sourceforge.net>, and I'm hoping it can be
> explained to me how you do this with T-shaped, see-saw, and square pyramidal
> shapes. I think perhaps the answer is going to be that you just leave out
> the missing groups and use explicit [...@tbn] or [...@ohn] stereochemical
> descriptors (and possibly [...@thn] for trigonal pyramidal). But I'm not
> sure about that, because, for example:
>
> [...@oh2]1234.c1.br2.cl3.n4
>
> gives the warning:
>
> WARNING: Chiral center has wrong connectivity -- ignored
>
>
>
> at the Daylight Depict site. Hope to hear about that soon.
>
> On Mon, Nov 15, 2010 at 12:44 AM, Otis Rothenberger <
> osrot...@chemagic.com> wrote:
>
>> Bob,
>>
>> I think I see it. If I'm analyzing @ or @@, group 1 is toward me. Is that
>> correct?
>>
>> Yes, group 1 is toward you, and the rotation about the others is the
> same as depicted in the @ symbol itself -- CCW for "@" . The first and last
> groups must be axial. The ones in between are the ones that are checked for
> rotation order.
>
> Notice that the way this works for SMILES generation in Jmol is that Jmol
> will now first list all "components" based on atoms that have more than four
> attachments. For example, a particular isomer of SF3IBrCl might be:
>
> [...@]123456.i5.f1.br6.f4.f3.cl2
>
> and a ferrocene model I have returns:
>
> [fe]123456789%10...@h]1%11[c@h]...@h]4[c@H]3[C@@h]%112...@h]6%12[c@H
> ]%1...@h]9[c@h]...@h]7%12
>
> That is, we're creating a "generic" n-coordinate center and then just
> listing the attached components. The nice thing about this is that there's
> no significance to the order of groups in the individual components -- it's
> just the connection numbers 1-10 that determines the stereochemistry, and
> you can have as many of these connected inorganic components as you need to
> get the job done.
>
> The success here is based on not requiring any sort of "canonical" or
> "unique" SMILES description for our purposes. Jmol can match structures to
> stereochemical SMILES strings as well as stereochemical SMILES strings to
> stereochemical SMILES strings without any need for canonicalization. So
> that's all we need.
>
> Except for your finding a bug possibly, Jmol should now be able to match
> any stereochemical SMILES involving allenyl, tetrahedral, trigonal
> bipyramidal, or octahedral stereochemistry descriptors, and it will generate
> stereochemical SMILES strings for structures with all of these shapes
> automatically.
>
>
>
>
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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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