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Some work on TautomerEnumerator (#3327)
* - Added a TautomerEnumerator constructor which allows passing CleanupParameters - Added three configurable parameters to CleanupParameters - Added a callback to TautomerEnumerator - Fixed a bug where the same tautomer could be mapped by both isomeric and non-isomeric SMILES - TautomerEnumerator::enumerate() now returns a TautomerEnumeratorResult and does not take dynamic_bitset pointers as optional parameters - Added a missing transform from the Sitzmann paper - General code cleanup and optimization * - TautomerEnumeratorResult is now iterable in both C++ and Python - further optimizations - implemented a TautomerEnumerator.PickCanonical() Python wrapper - added C++ and Python accessors to SMILES and SmilesTautomerMap * - make sure the number of tautomers reported by rdLogger is correct and definitive * make sure that if N maxTautomers are requested, N tautomers are returned if the theoretical number of tautomers is M>N * avoid that sulfonic acids hit the formamidinesulfinic acid tautomerisation rule * offer an option to allow the old API to still be used. * Changes in response to review and following discussion with Gareth and Greg * - made TautomerEnumeratorResult an enum class (was a plain C enum) - made TautomerEnumeratorResult::const_iterator a bidirectional_iterator - added tests to fully probe the TautomerEnumeratorResult::const_iterator functionality * - change the difference_type definition - added tests for the above * - cosmetic change to improve code readability Co-authored-by: greg landrum <greg.landrum@gmail.com>
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@@ -29,8 +29,8 @@ oxim/nitroso via phenol f [O!H0]-[N]=[C]-[C]=[C]-[C]=[OH0]
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oxim/nitroso via phenol r [O!H0]-[c]=[c]-[c]=[c]-[N]=[OH0]
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cyano/iso-cyanic acid f [O!H0]-[C]#[N] ==
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cyano/iso-cyanic acid r [N!H0]=[C]=[O] #-
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//formamidinesulfinic acid f [O,N;!H0]-[C]=[S,Se,Te]=[O] =-- // TODO: WAT!?
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//formamidinesulfinic acid r [O!H0]-[S,Se,Te]-[C]=[O,N] =--
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formamidinesulfinic acid f [O,N;!H0]-[C]=[S,Se,Te;v6]=[O] =--
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formamidinesulfinic acid r [O!H0]-[S,Se,Te;v4]-[C]=[O,N] ==-
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isocyanide f [C-0!H0]#[N+0] # -+
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isocyanide r [N+!H0]#[C-] # -+
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phosphonic acid f [OH]-[PH0] =
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