see http://sourceforge.net/projects/jmol/files/
version=12.1.22
# new feature: P2N reader -- see http://q4md-forcefieldtools.org/
# -- adds "altName" auxiliary data
# -- allows FILTER "altName"
# -- allows label %{altName}
#
# new feature: label %{dataName}
# -- allows reading values from a DATA array.
# -- case-sensitive
# -- data are read sequentially as string data, one per data line.
# -- if data of that name are not found, looks for data in auxiliaryInfo
for that name.
# and bases the index as atom index relative to the model.
#
# new feature: Edit...Preferences...Clear History
# -- resets window positions and clear all history.
# -- thank you, Tami Caraballo!
# bug fix: zap 1.1 when models have cartoons or other bioshapes crashes Jmol
# 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)
#
# Using [n] or [nH] explicitly avoids this issue entirely.
# bug fix: Ramachandran approximation of P straightness off by a few percent
--
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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