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 Rothenberger
> 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]> 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
>>>
>>>
>>>
>>>
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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
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