Lambda notation bug?

Issue #10 resolved
Anonymous created an issue

Hi Dan,

I noticed that OPSIN fails to parse the following name:


however, both of the following are parsed fine:

1lambda6,4lambda3-thiomorpholine-1,1-dione (different name for the same compound) 1lambda6,2-benzothiazole-1,1-dione

So it looks like there isn't a problem with the 1,4 thiomorpholine numbering, and neither is it always necessry to specify lambda values for all locants. Is this a bug, or have I missed something?

Fantastic piece of software, by the way....

Comments (5)

  1. Daniel Lowe repo owner

    I don't think it's a bug. The nitrogen in morpholine is in its standard valency so you correctly don't need to employ the lambda convention. But this means the name can be written simply as: 1lambda6-thiomorpholine-1,1-dione

    The different from the 1lambda6,2-benzothiazole-1,1-dione case is that benzothiazole contains a Hantzsch-Widman ring which should have the position of its heteroatoms given e.g. 1lambda6,2-benzothiazole-1,1-dione is different from 1lambda6,3-benzothiazole-1,1-dione. thiomorpholine on the other hand is a trivial name and always has the sulfur at position 1/ nitrogen at position 4. (you could argue it's semi-systematic and is a modification of the trivial name morpholine)

    I will report this bug to ChemAxon ;-)

  2. pmortenson

    Thanks, Dan, that sounds pretty clear cut. As you correctly surmised, we use ChemAxon to generate names, and then round trip them with OPSIN as a check. When the round trip doesn't work, I have to try to assign blame....

    The 1,3 isomer is correctly named as a thiazinane, which OPSIN happily parses. So I'll kick this one over to Hungary!

    All the best, Paul

  3. Daniel Bonniot

    Paul, Daniel,

    I can confirm this was a bug in ChemAxon Structure-to-Name. The second locant (4) was printed by mistake as an unanticipated consequence of printing the lambda locant.

    I fixed this in our trunk, so this will be released in our 6.2 version. The generated name is now as expected: 1λ⁶-thiomorpholine-1,1-dione

    In my tests this improves the generated name in roughly 0.2% of the compounds in a large diverse set, which is nothing to sneeze at :) Thanks for discovering and reporting this issue.

    Daniel Bonniot, ChemAxon

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