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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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All important tests are in the legacy CI, some extra tests marked as `@pytest.mark.slow` will run through this routine instead of slowing down each new PR
Also fixed the is_isomerization() method
Also testing the atom_order arg
And updated update_zmat_by_xyz()
added the linear adapter families
So that parallel execution of tests on CI won't run w/o job.execute()
When an ARCSpecies is constructed with both an adjlist (or SMILES) and xyz, mol_from_xyz re-perceives the molecule from the 3D geometry. Previously, perceive_molecule_from_xyz was called with n_radicals=None (the default) even when the existing mol carried radical information. For singlet biradicals this caused the perception to produce a closed-shell molecule with lone pairs instead of radical centers, which then replaced the original mol and broke downstream family detection (e.g., Intra_Disproportionation was not identified). Now, when self.mol already has radical electrons and the user did not explicitly set number_of_radicals, the radical count is derived from self.mol and forwarded to perceive_molecule_from_xyz and is_mol_valid.
To read additional types of RMG-database families
get_entries_label_with_parentheses, TestSplitEntries
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Adds a new Linear TS search adapter that builds TS guesses from atom-mapped reactants and products via Z-matrix chimera construction with Hammond-biased weighting. The adapter is incore-only, plugs into ARC's scheduler like heuristics/autotst_ts, and delegates heavy geometry work to a new linear_utils/ subpackage (5 modules). Currently implemented for isomerization/unimolecular reactions.
The PR also carries supporting additions to arc/species/zmat.py (anchors, smart-anchor detection, zmat re-indexing helpers), arc/species/converter.py (atom-map reordering), arc/reaction/reaction.py (is_unimolecular, refined is_isomerization), and a biradical-preservation fix in arc/species/species.py. CI was hardened: pinned action,
-n 4 --dist workstealfor stability, and obabel test made self-contained.