add lanthanide and actinide support to xyz2mol_tmc#2
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corinwagen merged 3 commits intomasterfrom Mar 10, 2026
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Mar 6, 2026
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- Extend TRANSITION_METALS/TRANSITION_METALS_NUM to include Ce-Yb (58-70) and Ac-Lr (89-103); add missing Lu to ALLOWED_OXIDATION_STATES
- Add oxidation states for all new f-block elements
- Add atomic_valence_electrons for all metals in both xyz2mol_tmc.py and xyz2mol_local.py (required to avoid KeyError in charge assignment)
- Extend ATOM_LIST in xyz2mol_local.py with Am-Lr (was missing, causing ValueError for any actinide heavier than Pu)
- Rebuild MetalNon_Hg and fix_NO2 SMARTS programmatically from TRANSITION_METALS_NUM so future additions are automatic
- Route Ln/An through get_tmc_mol in steamroll.py (previously fell back to geometry-only xyz2ac_obabel); empty _SKIP_XYZ2MOL
- Add tests: lookup completeness, SMARTS validity, Ce 18-crown-6 end-to-end, [UCl6]2- actinide end-to-end, ferrocene regression
- Extend TRANSITION_METALS/TRANSITION_METALS_NUM to include Ce-Yb (58-70) and Ac-Lr (89-103); add missing Lu to ALLOWED_OXIDATION_STATES - Add oxidation states for all new f-block elements - Add atomic_valence_electrons for all metals in both xyz2mol_tmc.py and xyz2mol_local.py (required to avoid KeyError in charge assignment) - Extend __ATOM_LIST__ in xyz2mol_local.py with Am-Lr (was missing, causing ValueError for any actinide heavier than Pu) - Rebuild MetalNon_Hg and fix_NO2 SMARTS programmatically from TRANSITION_METALS_NUM so future additions are automatic - Route Ln/An through get_tmc_mol in steamroll.py (previously fell back to geometry-only xyz2ac_obabel); empty _SKIP_XYZ2MOL - Add tests: lookup completeness, SMARTS validity, Ce 18-crown-6 end-to-end, [UCl6]2- actinide end-to-end, ferrocene regression Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
jevandezande
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Mar 6, 2026
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LGTM, with soft request to clean up prior code.
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| # Lanthanides — 4f electrons treated as core-like; dominant +3 chemistry. | ||
| # Note: only used in get_proposed_ligand_charge() which runs on metal-free fragments. | ||
| atomic_valence_electrons[58] = 3 # Ce |
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Can we rewrite this section so that the whole dictionary gets built at once?
| atomic_valence_electrons[53] = 7 | ||
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| # d-block TMs — match values in xyz2mol_tmc.py | ||
| atomic_valence_electrons[21] = 3 # Sc |
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Can we rewrite this section so that the whole dictionary gets built at once?
corinwagen
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jevandezande
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Mar 9, 2026
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| **{z: [20] for z in range(21, 31)}, # Sc–Zn | ||
| **{z: [20] for z in range(39, 49)}, # Y–Cd | ||
| **{z: [20] for z in range(57, 81)}, # La–Hg | ||
| **{z: [20] for z in range(89, 104)}, # Ac–Lr |
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yeah, it's much clearer this way
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