[Jmol-users] Jmol 14.17.1

[Robert H. <ha...@st...>]

*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
 *
 * 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).
 *
 * 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), 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


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