benzodioxole is not reported as potentially ambiguous

Issue #35 resolved
Anonymous created an issue

But mysteriously, dioxole is reported as potentially ambigous. This might also be a good issue to track that the warning message should contain the original name/surface "dioxol" rather than some internal state "oxoxol".

Comments (1)

  1. Daniel Lowe repo owner

    By analogy to dioxolane (1,3 by default), dioxole is now 1,3 by default, hence benzodioxole is now interpreted as 1,3-benzodioxole, and neither case is considered ambiguous.

    OPSIN's internal state intentionally does not retain the precise relationship between the original input and the abstract parse tree that it works upon so as to allow parse tree rewriting without the added complexity of tracking the relationship between the modified parse tree and the original input. Generally if there are multiple ways of expressing a concept, OPSIN will convert of these ways into one of these ways and then only have code to handle that way of specifying the concept. For Hantzsch-Widman rings multiplied heteroatoms are treated as separate objects, and indeed oxoxol and dioxol are treated the same. This procedure of multiplying out features is applied to all other non-detachable features primarily as it simplifies locant assignment as there is now a distinct token that can have the locant associated with it.

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