From: Robert H. <ha...@st...> - 2010-11-12 12:50:13
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Ah, HA! Found it. It was in the SMILES reader translating indicated stereochemistry to actual 3D positions when a new component mark "." was followed by a stereochemistry indicator with H, "[C@H]", which was followed immediately with the SECOND ring bond connection number. Wow. That's obscure. One little line in the code.... Amazing. Good test, Otis! version=12.1.22_dev # bug fix: SMILES matching string with ".[C@H]1" reads stereochemistry incorrectly http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip On Thu, Nov 11, 2010 at 10:27 PM, Robert Hanson <ha...@st...> wrote: > > > On Thu, Nov 11, 2010 at 7:37 PM, Otis Rothenberger <osr...@ch...>wrote: > >> Bob is the master of Jmol SMILES, so I'll direct the second question to >> him. >> >> The SMILES on these compounds present another problem in Jmol. By way of >> example, if we construct an unconnected ferrocene in SPARTAN and then >> edit the molfile connection table so that the cyclopentadienyl anion >> carbons are assigned "aromatic" and the coordinate bonds to iron are >> assigned as type 8 ("any", evidently interpreted by Jmol as partial ), >> then we get the following SMILES from Jmol: >> >> [C@H]12[Fe]3456789%10[C@H]%11[C@@H]%10[C@@H]9[C@@H]8[C@H]%117.[C@H]16[C@ >> @H]5[C@@H]4[C@H]23 >> >> > looks like ferrocene to me.... ;) > > > >> The NIH Resolver reads this and returns evidence that it understands the >> bond connections - correctly connected 2D molfile and correctly >> connected GIF image. This appears to be a correct SMILES for the >> ferrocene that we constructed. It appears that the SMILES is very >> confused about the geometry of the cylopentadienyl anion hydrogens, but >> the connections are correct. >> >> > > > > -- > 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 > -- 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 |