From: Robert H. <ha...@st...> - 2010-11-12 15:40:05
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On Fri, Nov 12, 2010 at 9:22 AM, Otis Rothenberger <osr...@ch...>wrote: > Bob, > > Thanks for the quick repair job! > > Follow-up question: By my testing, the SPn SMILES notation allows > complete FIND/compare ability for simple square planar complexes. Does > the order of the ligands in the octahedral SMILES carry the same punch? > I've had success with simple tests, but there's a lot more to test here, > so I though I'd go directly to the SMILES master. > > There are two kinds of finds: A) {structure}.find("SMILES", smilesString) B) smilesString1.find("SMILES", smilesString2) for (A), all stereochemical notation is implemented -- allenyl, tetrahedral, square planar, trigonal bipyramidal, and octahedral. for (B), allenyl, tetrahedral, and square planar are fully implemented. Trigonal bipyramidal requires that the two axial ligands be listed first and last; in the case of octahedral, we require that the two designated "axial" groups be listed first and last. No reason for this other that I did not finish the job and have no access to the unpublished supposed additional @OHn and @TBn designations. I think I could easily enough implement octahedral checking as long as any two diametrically opposed groups are given first and last. Not 100% sure I can get Jmol to produce accurate SMILES for *any* octahedral or trigonal bipyramidal compound. Bob > Markus (Resolver) wrote several weeks ago indicating that the Resolver > SMILES are only internally unique. He mentioned that Daylight never > released their algorithm. I'm carrying them in our data base with the > hope that in our mini-internal system I can use them to pick up isomer > types in coordination complexes. This would not be a general algorithm, > but it would allow detecting isomer types in our database for problem > exercises. > > Otis > > Otis Rothenberger > chemagic.com > > > On 11/12/2010 7:50 AM, Robert Hanson wrote: > > 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 > > > > > > > > > > > ------------------------------------------------------------------------------ > 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 |