Let the Linear TS adapter generate guesses for requested atom maps - #1044
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Let the Linear TS adapter generate guesses for requested atom maps#1044kfir4444 wants to merge 2 commits into
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
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Coverage 65.55% 65.56%
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| if uni_is_product: | ||
| try: | ||
| atom_map = cached_map_rxn(rxn=rxn, product_dict_index=i, map_cache=map_cache) | ||
| atom_map = cached_map_rxn(rxn=rxn, product_dict_index=i, map_cache=map_cache, |
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the requested atom map can still be ignored in some cases. when a molecule splits into fragments, parts of the code still choose their own atom correspondence. so you ask for map a, and you may instead receive another map, reported as successful
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Summary
LinearAdapterderives an atom map per reaction path viamap_rxnand never reads a map set on the reaction, so pre-setting one changed nothing and was not reported. This addsLinearAdapter(atom_map=...), taking one map or several: each requested map replaces the derived one for a full pass over the weight grid, so a TS guess can be requested for a specific reactants-to-products correspondence. Requested maps are validated (permutation, atom count, element-preserving) and unusable ones are reported rather than silently dropped. A pre-setrxn.atom_mapstill does not take part in the derivation - other adapters populate it as a side effect of reading it - but the adapter now warns that it is unused and points at the new argument, and the docstrings say guesses are generated per product dictionary.Closes #1042