got it! This was a nifty little bug in SMILES processing, not properly
accounting for the H atoms on aromatic atoms. Had implications for aromatic
amines and the generation of unambiguous SMILES strings and molecular
formulas for compounds such as imidazole as well; this is now fixed. See
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip.
Note below that Jmol does not determine Huckel bonding patterns for aromatic
rings, so it is best to use [nH] and [n] in SMARTS strings to be sure of a
match.
Bob
version=12.1.22_dev
# 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)
On Tue, Nov 9, 2010 at 8:18 PM, Robert Hanson <[email protected]> wrote:
>
>
> On Tue, Nov 9, 2010 at 11:03 AM, Otis Rothenberger
> <[email protected]>wrote:
>
>> One more question, probably naive: With the FIND that worked above, I
>> was surprised by the result:
>>
>> {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15}
>>
>>
> Jmol is missing three H atoms; I will check that out.
>
>>
>>
>>
>> ------------------------------------------------------------------------------
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>
>
>
> --
> 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
>
--
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
------------------------------------------------------------------------------
The Next 800 Companies to Lead America's Growth: New Video Whitepaper
David G. Thomson, author of the best-selling book "Blueprint to a
Billion" shares his insights and actions to help propel your
business during the next growth cycle. Listen Now!
http://p.sf.net/sfu/SAP-dev2dev
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