Revision: 21616
http://sourceforge.net/p/jmol/code/21616
Author: hansonr
Date: 2017-05-27 16:06:21 +0000 (Sat, 27 May 2017)
Log Message:
-----------
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: 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 full 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.
*
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-27 16:05:13 UTC
(rev 21615)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-27 16:06:21 UTC
(rev 21616)
@@ -32,7 +32,7 @@
*
* - only two Java classes; roughly 1000 lines
*
- * - efficient, one-pass process for each center using a single finite
digrapnh for all auxiliary descriptors
+ * - 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)
*
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-27 16:05:13 UTC
(rev 21615)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-27 16:06:21 UTC
(rev 21616)
@@ -84,7 +84,7 @@
*
* - only two Java classes; roughly 1000 lines
*
- * - efficient, one-pass process for each center using a single finite
digrapnh for all auxiliary descriptors
+ * - 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)
*
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