Bob:
Spiro works fine. Thanks. I realize you are a fan of Gibbs. Gibbs lab has been
demolished. Neither of the 2 new residential colleges were named in his honor
but he is being “honored” by a walkway!
http://news.yale.edu/2017/02/23/celebrating-history-gibbs-lab-and-future-science-yale
Fred
****************************************
Professor Frederick E. Ziegler, Emeritus
Sterling Chemistry Laboratory
225 Prospect Street
Yale University
P.O. Box 208107
New Haven, Connecticut 06520-8107
E-mail: frederick.zieg...@yale.edu
Telephone: (203) 432-3959
****************************************
> On May 27, 2017, at 1:13 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> Jmol-14.17.1-binary.zip (69.8 MB)
> <https://sourceforge.net/projects/jmol/files/latest/download?source=files>
> Jmol.___JmolVersion="14.17.1" // 2017.05.27
>
> new feature: atom property x.cipRule
> -- CIP sequence rule deciding this center
> -- one of 1a, 1b, 2, 3, 4a, 4b, 4c, 5, or blank
>
> bug fix: polyhedra broken in Jmol 14.10.0
>
> bug fix: finalizing CIP algorithm
> -- adding spiro chirality from P-93.5.3
> -- completing root path for auxiliary descriptors
>
> bug fix: JSmol: JSME/JSmol 2D->3D fails when one H of a CH2 is explicitly
> wedge and the other H is implicit (not shown at all). (JSmolJME.js)
>
> code:
>
> /**
> * A fully validated relatively efficient implementation of Cahn-Ingold-Prelog
> * rules for assigning R/S, M/P, and E/Z stereochemical descriptors. Based on
> * IUPAC Blue Book rules of 2013.
> * https://iupac.org/projects/project-details/?project_nr=2001-043-1-800
> <https://iupac.org/projects/project-details/?project_nr=2001-043-1-800>
> *
> * Features include:
> *
> * - deeply validated
> *
> * - implemented in Java (Jmol) and JavaScript (JSmol)
> *
> * - only two Java classes; roughly 1000 lines
> *
> * - efficient, one-pass process for each center using a single finite
> digraph for all auxiliary descriptors
> *
> * - exhaustive processing of all 8 sequence rules (1a, 1b, 2, 3, 4a, 4b,
> 4c, 5)
> *
> * - includes R/S, r/s, M/P (axial, not planar), E/Z
> *
> * - covers any-length odd and even cumulenes
> *
> * - uses Jmol conformational SMARTS to detect atropisomers and helicenes
> *
> * - covers chiral phosphorus and sulfur, including trigonal pyramidal and
> tetrahedral
> *
> * - properly treats complex combinations of R/S, M/P, and seqCis/seqTrans
> centers (Rule 4b)
> *
> * - properly treats neutral-species resonance structures using fractional
> atomic mass and a modified Rule 1b
> *
> * - implements CIP spiro rule (BB P-93.5.3.1)
> *
> * - detects small rings (fewer than 8 members) and removes E/Z
> specifications for such
> *
> * - detects chiral bridgehead nitrogens
> *
> * - reports atom descriptor along with the rule that ultimately decided it
> *
> * Primary 236-compound Chapter-9 validation set (AY-236) provided by Andres
> * Yerin, ACD/Labs (Moscow).
> *
> * Mikko Vainio also supplied a 64-compound testing suite (MV-64), which is
> * available on SourceForge in the Jmol-datafiles directory.
> * (https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip
> <https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip>).
> *
> * Additional test structures provided by John Mayfield.
> *
> * Additional thanks to the IUPAC Blue Book Revision project, specifically
> * Karl-Heinz Hellwich for alerting me to the errata page for the 2013 IUPAC
> * specs (http://www.chem.qmul.ac.uk/iupac/bibliog/BBerrors.html
> <http://www.chem.qmul.ac.uk/iupac/bibliog/BBerrors.html>), Gerry Moss
> * for discussions, Andres Yerin for discussion and digraph checking.
> *
> * Many thanks to the members of the BlueObelisk-Discuss group, particularly
> * Mikko Vainio, John Mayfield (aka John May), Wolf Ihlenfeldt, and Egon
> Willighagen, for
> * encouragement, examples, serious skepticism, and extremely helpful advice.
> *
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr <http://www.stolaf.edu/people/hansonr>
>
>
> 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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