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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