Thank you, Nico, for releasing Jmol 12.0.22. One major bug fix, several
minor ones, and several having to do with SMILES:
version=12.0.22
major:
# bug fix: zap 1.1 when models have cartoons or other bioshapes crashes Jmol
(broken in 12.0.RC8)
minor:
# bug fix: Linux file name completion from LOAD "[tab press] improperly
lowers the case of file names
# bug fix: IDTF exporter can create incomplete rendering of bonds
# bug fix: Ramachandran approximation of P straightness off by a few percent
SMILES:
# bug fix: Jmol SMILES generation does not include stereohemistry
# for octahedral and trigonal bipyramidal
# bug fix: SMILES matching string with "....@h]" reads stereochemistry
incorrectly
# bug fix: load SMILES with %nn fails
# bug fix: Jmol creating possibly ambiguous aromatic amine SMILES
# 1-H-4-methylimidazole was: n1cnc(C)c1; now: [nH]1c[n]c(C)c1
# bug fix: {*}.find("SMILES",smilesString) does not include aromatic H
# bug fix: Smiles MF calculation for aromatic atoms N and C in error.
# NOTE: Jmol may undercount the number of hydrogen atoms
# for aromatic amines where the ring bonding to N is
# not explicit. Each "n" will be assigned a bonding count
# of two unless explicitly indicated as -n-.
# Thus, we take the position that "n" is the
# N of pyridine unless otherwise indicated.
#
# For example:
# $ print "c1ncccc1C".find("SMILES","MF")
# H 7 C 5 N 1 (correct)
# $ print "c1nc-n-c1C".find("SMILES","MF")
# H 6 C 4 N 2 (correct)
# but
# $ print "c1ncnc1C".find("SMILES","MF")
# H 5 C 4 N 2 (incorrect)
--
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
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