It works.
On Sun, Aug 8, 2010 at 6:40 PM, Philip Bays <[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]>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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>
> J. Philip Bays
>
> Professor of Chemistry
>
> Science Hall 172
>
> 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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