The way you would do this is to check the structure using different SMARTS
codes with different "directives".
On Mon, May 16, 2016 at 5:34 AM, Mike Casey <mike.ca...@ucd.ie> wrote:
> Hi Bob,
>
>
> From one of your earlier postings I assumed that your algorithm for
> detecting 'strict' aromaticity must be checking the supplied structure
> against a set of criteria (cyclic, uninterrupted pi system, planar, 4n + 2
> electrons), so that it might be possible for the algorithm (optionally) to
> return 'flags' (meets, or does not meet, each criterion) that could then be
> used to generate the appropriate feedback to the learner. I have now read
> your pdf on how the Jmol SMILES aromaticity algorithm works and, broadly
> speaking, it does seem to function in that manner. So, following the steps
> listed in your pdf document, and thinking particularly about the STRICT
> directive, would it be possible to create an option for the function to
> return a set of diagnostics, as follows?
>
> 1. Criterion 1: Does the structure contain at least one ring?
>
if ({*}.search("[R]")) {.....} // a ring exists
if ({*}.search("[r5,r6]")) {.....} // a 5- or 6-membered ring exists
> 2.a., 2.c. (and 4.?) Criterion 2: Does the structure contain a ring(set)
> in which all the ring atoms are involved in the pi system? (I'm not sure
> what kinds of structures the algorithm is seeking to exclude in Step 4, but
> I think it relates to Criterion 2.)
>
That one I don't have a direct test for. As long as you can restrict this
to 5- and 6-membered rings, perhaps just making sure all ring bonds have
only two or three connections would suffice:
if ({*}.search("[r5;d2,d3]1[$4([r5;d2,d3])]1 ||
[r6;d2,d3]1[$5([r6;d2,d3])]1")) {...} // 5- or 6-membered ring all with 2
or 3 substituents
> 2.b. & 3. Criterion 3: Does the structure contain a ring(set) that meets
> Criterion 2, and is planar?
>
>
> 2.c. & 3. Criterion 4: Does the structure contain a ring(set) that meets
> Criteria 2 & 3, and involves 4n+2 electrons, or 4n electrons?
>
>
if ({*}.search("a")) {...} // an aromatic atom in a planar ring that
satisfies the Hueckel 4n+2 rule
or
if ({*}.search("/open/a")) {...} // an aromatic atom in a planar ring
satisfying a more relaxed Hueckel 4n+2 rule that includes, for example,
unsaturated lactones and lactams such as pyran-2-one and 1H-pyridin-2-one
If you want to find large-ring aromatic compounds with 18 or more
electrons, you need to use the /open/ directive as above, and look for a
ring at least as large as the ring you want.
Bob
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