From: Robert H. <ha...@st...> - 2010-11-15 11:53:29
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Otis, I've also started the same thread at < blu...@li...>, 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 [Xx@TBn] or [Xx@OHn] stereochemical descriptors (and possibly [Xx@THn] for trigonal pyramidal). But I'm not sure about that, because, for example: [Fe@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 <osr...@ch...>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: [S@]123456.I5.F1.Br6.F4.F3.Cl2 and a ferrocene model I have returns: [Fe]123456789%10.[C@H]1%11[C@H]5[C@H]4[C@H]3[C@@H]%112.[C@H]6%12[C@H]%10[C@H ]9[C@H]8[C@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. Bob I'm playing around with two octahedral models and > > var x = compare({selected}, {not selected}, @j, 'stddev') > > where @j is the selected SMILES. > > Matches look good. What model characteristics would lead to a correct > non-match of a say 0.2ish vs NaN - same stoichiometric formula. I'm not > seeing a pattern. > > NaN means there was not a basic nonstereochemical SMILES match in the first place, I think. > I do see the auto SMILES update. This time I just used the link commands > that I have set up for model kit mode. It also auto updates on an sp3 invert > click. Neat. > > The "database" that we are setting up was simply a .js JSON structure. The > size got way out of hand, so I moved it to the server side and write JSON > from it as needed. I can see that I have some SMILES to change in the > database in light of some of the things you've been doing. > > Otis > > Otis Rothenbergerchemagic.com > > > On 11/14/2010 11:32 PM, Robert Hanson wrote: > > One correction. I had Jmol generating octahedral stereochemistry only if > two or more trans pairs are identical. While those cases don't need @ or @@, > one more case is like that as well -- when three of the four groups that are > not listed first or last are identical. Also, I was forgetting that even if > we don't need @ or @@, we still need to get the first and last groups to be > axially related. > > Hurray for the SMILES "." convention!!! (Which makes this all possible.) > > This should be fixed now: > > http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip > > -- > 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 > > > ------------------------------------------------------------------------------ > Centralized Desktop Delivery: Dell and VMware Reference Architecture > Simplifying enterprise desktop deployment and management using > Dell EqualLogic storage and VMware View: A highly scalable, end-to-end > client virtualization framework. Read more! > http://p.sf.net/sfu/dell-eql-dev2dev > > > _______________________________________________ > Jmol-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > ------------------------------------------------------------------------------ > Centralized Desktop Delivery: Dell and VMware Reference Architecture > Simplifying enterprise desktop deployment and management using > Dell EqualLogic storage and VMware View: A highly scalable, end-to-end > client virtualization framework. Read more! > http://p.sf.net/sfu/dell-eql-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- 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 |