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* Speed up tautomer canonicalization by deferring on SSSR calc * Lazy kekulization for tautomer enumeration Defer kekulization of tautomers until they are actually needed for transform matching. This avoids creating kekulized copies for: 1. The initial tautomer (until first iteration) 2. New tautomers that may never be processed (if enumeration ends early) The Tautomer class now supports lazy initialization of the kekulized form via getKekulized() method. Performance improvement: ~7% additional speedup (total ~22-24% from baseline) * Use count-only substructure matching in tautomer scoring * Add SubstructMatchCount regression test * MolStandardize: reduce enumerate overhead * MolStandardize: avoid per-tautomer ring recomputation * Atom: cache PeriodicTable pointer in valence calcs * Atom: reuse PeriodicTable in getEffectiveAtomicNum * PeriodicTable: add atomic fast path for getTable * GraphMol: reduce ROMol copy reallocations * MolStandardize: use quickCopy for per-match product copies Use RWMol(*kmol, true) in tautomer enumeration to avoid copying properties/bookmarks/conformers for each candidate. This reduces deep-copy overhead without changing chemistry. * MolStandardize: pre-filter scoring patterns by element/connectivity For tautomer scoring, pre-compute which SubstructTerms are relevant for a given input molecule. Since tautomerization only moves H atoms and changes bond orders (never creates/destroys heavy-atom bonds), patterns requiring missing elements or connectivity can be skipped for all tautomers of that molecule. Two-stage filtering: 1. Element check: skip patterns requiring atoms not in the molecule 2. Connectivity check: skip patterns whose bond-order-agnostic structure doesn't match the input molecule's connectivity This reduces the number of VF2 substructure calls per tautomer from 12 to typically 3-5, depending on the molecule's composition. * MolStandardize: preserve molecule properties for canonical tautomer Copy molecule properties from the original input to the canonical tautomer result. Since quickCopy during enumeration skips d_props to avoid overhead, extended SMILES data like link nodes (LN) was lost. This restores them on the final result. * TautomerQuery: preserve molecule properties (e.g. link nodes) in tautomers TautomerQuery::fromMol() uses TautomerEnumerator::enumerate() which uses quickCopy for performance. This doesn't copy molecule properties like _molLinkNodes. Without this fix, XQMol output would lose link node extensions in the SMILES. Copy properties from the original query molecule to all enumerated tautomers before constructing the TautomerQuery. This preserves extended SMILES data without impacting enumeration performance. * MolStandardize: use parallel iteration and cache bond lookups Replace O(n) getAtomWithIdx/getBondWithIdx calls with parallel iteration over atom/bond ranges in canonicalizeInPlace and enumerate. Cache bond lookups in setTautomerStereoAndIsoHs to avoid repeated O(n) searches. * perf: add specialized matchers for simple tautomer scoring patterns Replace VF2 graph matching with O(n) loops for 6 simple patterns: - countDoubleOrAromaticBonds: C=O, N=O, P=O patterns - countMethyls: [CX4H3] methyl groups - countCarbonDoubleHetero: [C]=[/home/dcvuser/rdkit;Code/GraphMol/MolStandardize/Tautomer.h] aliphatic C=hetero - countAromaticCarbonExocyclicN: [c]=aromatic C=exocyclic N Complex patterns (benzoquinone, oxim, guanidine, aci-nitro) still use VF2. Combined with the pre-filtering optimization, this achieves ~3.7x speedup (~2500ms vs ~9300ms original) for tautomer canonicalization. * Fix tautomer canonicalize dropping conformers from quickCopy quickCopy (RWMol(*mol, true)) skips conformers, so tautomer enumeration products lose 2D/3D coordinates. This causes InChI generation to omit the /b (double bond E/Z stereo) layer, since E/Z is derived from atomic coordinates. Fix: copy conformers from the original molecule onto the canonical tautomer after pickCanonical in TautomerEnumerator::canonicalize(). Tests: SMILES-based E/Z check in testTautomer.cpp, molblock-based conformer preservation check in catch_tests.cpp. * add test on canonicalize losing stereo * add regression test for exocyclic C=C tautomer canonicalization The getTautomerStateKey() pre-filter (commit 2595ef748) can falsely deduplicate distinct tautomers when their atom-index-ordered state patterns happen to match, leading canonicalize() to pick the wrong canonical form for molecules with STEREOTRANS-pinned exocyclic C=C bonds after RemoveHs. Test verifies that O=C(CC1=CC2=CC=COC2)NC1=O canonicalizes to the exocyclic form O=C1CC(=CC2=CC=COC2)C(=O)N1, not the endocyclic form O=C1C=C(C=C2CC=COC2)C(=O)N1. Currently expected to FAIL until the state key dedup bug is fixed. * MolStandardize: expand tautomer connectivity SMARTS * MolStandardize: scope tautomer pattern enum * MolStandardize: trim tautomer pattern enum * MolStandardize: use symmetric ring scoring
11 KiB
11 KiB