Dev branch - #10
Draft
csnbritt wants to merge 14 commits into
Draft
Conversation
…mit, refactored rdchiralRun to call new rdchiralStep for single-step execution, added chemistry problem detection in handle_outcomes, modified combine_enantiomers_into_racemic to return replacement mapping dictionary, updated rdchiralReaction initialization to wrap multi-reactant SMARTS in parentheses for pseudo-intramolecular treatment, added extract_from_reaction_smiles convenience function, removed __future__ print_function imports, updated tests
…ed split_reaction_smarts to decompose multi-reactant templates by atom map connectivity, added fix_return_mapped_dict_enantiomers helper to correctly update mapped outcome dictionaries when enantiomers are combined into racemics, implemented invert_chirality_around_unmapped_ring_closure to fix chiral tags around ring closures in SMARTS, refactored get_frag_around_tetrahedral_center to preserve chirality from initial fragment SMILES
…, Sb, Te, Bi at degree 3), implemented double bond stereochemistry tracking in template extraction via get_stereogenic_double_bonds and ensure_complete_stereo_double_bonds, added has_local_stereo_changed to detect actual tetrahedral inversion using atom-map-canonicalized neighbor ordering, moved validate_tetra_not_destroyed after fix_double_bond_stereochemistry in handle_outcomes, improved regex pattern in invert_chirality_around
…parate functions (rdchiralStep and rdchiralStep_return_mapped), removed return_mapped parameter from rdchiralStep/return_non_stereo_outcome_early/handle_outcomes, changed handle_outcomes to always compute mapped outcomes and atoms_changed, updated rdchiralRun/rdchiralRunText return type annotations from Any to Union types, added TypeVar _ChangesT for fix_return_mapped_dict_enantiomers type safety, and simplified early-return logic
…iral_step_return_mapped, refactored get_fragments_for_changed_atoms to use atom_chirality_matches for direct stereochemistry validation instead of iterative flipping with substructure matching, removed random.seed and clear_isotope function, changed atoms_are_different default check_local_stereo to True, added check_local_stereo=True to get_changed_atoms call, moved mols_changed append after fragment generation, and updated README
…clarified mypyc performance characteristics, added roundtrip check scripts to gitignore whitelist, expanded consistency.md with deterministic template extraction and new feature descriptions, updated benchmarks.md environment naming from pure_python/mypyc to rdchiral_plus/rdchiral_plus_mypyc, and added new consistency tables for rdchiralRun_return_mapped and rdchiralRun_return_mapped_keep_mapnums
…statement and roundtrip consistency description
…cstrings for template extraction functions with comprehensive Args/Returns/Note sections following project guidelines, reordered consistency.md feature list to group related items, updated README consistency section to clarify roundtrip methodology, and updated analyze_consistency.py reference to include new CSV suffixes
…ms when False instead of replacing enantiomers, updated docstrings to clarify combine_enantiomers semantics across rdchiralRunText/rdchiral_step/rdchiral_step_return_mapped/rdchiralRun, simplified fix_return_mapped_dict_enantiomers to handle both keep_mapnums paths by deriving achiral mapped SMILES from chiral keys, added canonicalize_tautomers parameter to mols_from_smiles_list and extract_from_reaction with TautomerEnumerator support
…port from template extraction and molecule conversion functions, deleted _enumerate_tautomers helper and TAUTOMER_ENUMERATOR global instances
… get_strict_smarts_for_atom to prevent unintended stereochemistry constraints in extracted templates
…wheels only, commented out chemistry problem detection warning in handle_outcomes, updated README roundtrip consistency metrics to 99.94% success rate, and added three new integration test cases for stereochemistry preservation and multi-fragment products
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.