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]>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 Rothenbergerchemagic.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]>
> <[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 Rothenbergerchemagic.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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