Bob,
That's great, but see my note sent a few minutes ago. I don't think the
issue in my note creates a problem for your new compare function. It's
comparing internal Jmol SMILES. I think, however, I've encountered a
problem related to stereo SMILES via Jmol vs "absolute" SMILES.
Otis
Otis Rothenberger
chemagic.com
On 8/9/2010 12:30 AM, Robert Hanson wrote:
It works.
On Sun, Aug 8, 2010 at 6:40 PM, Philip Bays <[email protected]
<mailto:[email protected]>> wrote:
Bob:
If this works it is really great. In my stereochemistry
tutorials, I have models randomly chosen and then have a data set
so I know what the relationship is between the two structures
chosen. Your compare function would obviate all of the data and
do it automatically. Cool!! I know that one comparison in my
data file is wrong, but I don't know which it is. This is the
easy way to avoid trying to figure that out!!
Phil
On Aug 8, 2010, at 6:48 PM, Robert Hanson wrote:
I've got the following:
*x =compare({atomset1}, {atomset2}, "ISOMER")* Carries out a
comparisons of atoms in the two atom sets and returns one of the
following strings (Jmol 12.2):
CONSTITUTIONAL ISOMERS having the same molecular formula but not
the same connectivity
ENANTIOMERS configurationally enantiomeric (mirror images)
DIASTERIOMERS differing in one or more stereocenters (including
double bonds)
CONFORMATIONAL ISOMERS (x.xxxx) having the same constitution and
configuration, but differing significantly in conformation
(having root-mean-square deviations greater than 0.1; RMSD
reported in parentheses
IDENTICAL the same, constitutionally, configurationally, and
conformationally
NONE no relationship
Conformational/Identical is tricky, because it's going to have to
be based on some RMSD cut-off. I think we'll have to see how that
works. Right now I have it reporting the RMSD with the result.
But also I'm trying to fix that square planar geometry report. I
know when I produced that bug -- just have to figure out how to
remove it.
On Sun, Aug 8, 2010 at 2:28 PM, Otis Rothenberger
<[email protected] <mailto:[email protected]>> wrote:
Bob,
The constitutional part sounds tricky, but interesting. From
a model kit application perspective, I think incorporating
the command in Jmol is a good idea.
Your script suggestions broke configurational into
enantiomeric and diastereomeric. Will that be part of the
command? If not, the return from the suggested compare
command can be used to fish these types out as needed. I
know the term geometric isomer is dated, but I like the term.
From the logic of your script breakdown, I don't see a way to
catch geometric isomers. If you have any ideas on this, I'd
love to hear them.
Otis
Otis Rothenberger
chemagic.com <http://chemagic.com/>
On 8/8/2010 12:40 PM, Bob Hanson wrote:
Otis, I'm integrating this into Jmol today. Should be able to
distinguish constitutional, configurational, and conformational isomers.
Command will be:
X=compare({1.1},{2.1},"ISOMER")
Bob
On Aug 8, 2010, at 2:00 AM, Otis Rothenberger<[email protected]>
<mailto:[email protected]> wrote:
Bob,
I tacked your compare suggestions on to the end of our two model (same
frame) identity check. After a 1 second delay, your isomer type
comparison is displayed. In case users interested in this type of thing
missed your code in my previous verbose email chain re SMILES problems,
I'll post it in this separate note. All I can say is great and useful
toy. I've been playing with variations (2R,3R)-2-bromo-3-chlorobutane
and others way past bed time.
Otis
Bob Hanson Wrote:
The way I was thinking to categorize two models is this:
var m1 = {molecule=1} # or whatever
var m2 = {molecule=2} # or whatever
# check molecular formulas
var sameMF = (m1.find("MF") == m2.find("MF"))
# get SMILES string for molecule 1
var smiles = m1.find("SMILES")
var smiles_enantiomer =
sm.replace("@@","!@").replace("@","@@").replace("!@@","@")
var smiles_nostereo = smiles.replace("@","")
# note: we can't just compare SMILES strings like we can molecular
formulas
# because SMILES strings here are not "cannonical" - but that is no
problem at all
# instead, we "find" the SMILES string for one model in the other. Using
"SMILES"
# here instead of "SMARTS" guarantees an exact search and not a
substructure search
var identical = sameMF&& (m2.find("SMILES",smiles)> 0)
var configurationalIsomers = sameMF&& !identical&&
(m2.find("SMILES",sm_nostereo)> 0)
var enantiomers = configurationalIsomers&&
(m2.find("SMILES",smiles_enantiomer)> 0)
var diastereomers = configurationalIsomers&& !enantiomers
var constitutionalIsomers = sameMF&& !identical&&
!configurationalIsomers
--
Otis Rothenberger
chemagic.com <http://chemagic.com/>
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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
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J. Philip Bays
Professor of Chemistry
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Saint Mary's College
Notre Dame IN 46556
(574) 284-4663
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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
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