Hi all, Just patched a related bug and spotted this curiosity and would do with some opinions. The test specifies that when using the SMARTS pattern [R2] one should find 6 matches in the molecule quinine. This is one of the examples from the tutorial and Daylight's DepictMatch can highlight these for you. However, the answer of course depends on how you define a ring. Now, before you read on, how many would you count? In Daylight's case it looks as though they are using the non-unique SSSR. As the set is non-unique there are certain patterns match only some of the time and will usually depend on atom order (see example below). Currently the CDK uses the essential rings (unique subset of SSSR) so this random behaviour is not seen but in this case it would say there are only 2 atoms (on the naphthalene) belonging to two rings. In my mind the correct answer is 8 which we could easily reach using a different unique ring set. However, if the Daylight implementation uses the SSSR, perhaps it is what the CDK should use (as it did previously). It would not be intuitive in some cases but it would match the official SMARTS usage. Thoughts? For the random matches, try these on Depict Match: C1NC(CC2)CCC12 order1 C1CC2CCC1NC2 order2 pattern: N([R2])[R2] quinine C123C5C(O)C=CC2C(N(C)CC1)Cc(ccc4O)c3c4O5 |
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