Bob, I've been using the new JmolSmilesApplet with excellent results. I just encountered a curious failure to distinguish between a non-stereo smiles string and a stereo string. Using your Universal SMILES String comparator, if you draw cis-1,3-dichlorocyclohexane in the "Correct Answer"display and a simple line formula in the "Student Answer" display the latter is correctly identified as different. However, if the trans-isomer is drawn as the reference, the simple formula is said to be a match. Diastereomeric formulas and enantiomeric formulas are correctly identified as different.
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