Robert Hanson
2017-05-27 17:29:06 UTC
Jmol.___JmolVersion="14.17.1" // 2017.05.27
*Jmol-14.17.1-binary.zip (69.8 MB)
<https://sourceforge.net/projects/jmol/files/latest/download?source=files>*
* 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
*
ready for testing. For example:
https://chemapps.stolaf.edu/jmol/jsmol/cip.htm?model=morphine
* 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
*Jmol-14.17.1-binary.zip (69.8 MB)
<https://sourceforge.net/projects/jmol/files/latest/download?source=files>*
* 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
*
ready for testing. For example:
https://chemapps.stolaf.edu/jmol/jsmol/cip.htm?model=morphine
* 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