Chiral Smiles interpretation?

[Dale Cameron]

I don't see any stereochemical differentiation when searching or in depiction even if a chiral smiles is used.  It does correctly depict the "flat" version of the compound but when you take a miles from one enantiomer and do a substructure search, you get both back enantiomers, even with a chiral smiles search string.  Any chance this is something I'm doing wrong with LICCS or is this an underlying problem of handling stereochemistry?  I just put in an amino acid to test this out using the following smiles.

CC(N[C@H]([C@@H](C)C)C(NC)=O)=O CC(N[C@@H]([C@@H](C)C)C(NC)=O)=O Very nice tool!  I'm hoping this is something easy to deal with (or something I'm doing wrong) as chirality if very important to me and if a substructure search can't decipher enantiomers, that would be a problem. Best wishes, Dale

[Kevin Lawson]

Hi Dale

Thanks for your interest.  It's not something you are doing wrong.  LICSS uses the CDK java libraries to do substructure searching and, as far as I can see from posts to the CDK User group cdk-user, the Smiles Parser doesn't currently appear to support the building of chiral molecules from chiral smiles [and/or the Smarts matcher used for SSS doesn't distinguish chirality when matching].  I will post a question to cdk-user asking for more info (unless anyone on this group can throw any light on this situation) but, for the moment, I don't think this problem is going to be easy to surmount...

Sorry!

Best wishes

Kevin

[Dale Cameron]

Thanks Kevin,

Yes, the depictor also doesn't recognize the chirality as well.  I look forward to the possibility of a solution but I too have had difficulty finding more info when I went looking into the CDK blogs, etc.  I will continue to store chiral smiles in hopes of an eventual solution but regardless, it's still nice to see chemistry in Excel in this manner.  I'm still hoping I can use the tool as the basis of a rudimentary database but we'll have to see. :)  I'm having a depiction problem right now as well with branched things but I'll post that separately.

Cheers,

Dale