Hydrolysis families and tests #770
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LeenFahoum
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CodeQL found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.
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I added some minor initial comments, I think that the commits should first be organized in terms of function definitions (there's a missing """ to one of the docstrings, making other functions hard to read)
arc/job/adapters/ts/heuristics.py
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| spc (ARCSpecies): The species to check. | ||
| Returns: | ||
| bool: Whether the species is water. |
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I think that the issue is that there's no closing """ for the docstring
arc/job/adapters/ts/heuristics.py
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| return O_counter == 1 and H_counter == 2 | ||
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| def get_neighbors_by_electronegativity(spc: ARCSpecies, |
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this commit deletes the def of another functions
alongd
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Thanks, Leen!
Please see the comments I added
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Hi Alon, |
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Thank you @LeenFahoum for this contribution!
Please see me comments below
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Looks great. I only added two small comments
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carbonyl based, nitrile, and ether hydrolysis
carbonyl- based, nitrile, and ether hydrolysis
Adds the following:
1.Reaction setup and family filtering
-hydrolysis(reaction): Main entry to generate TS guesses for hydrolysis reactions
-get_products_and_check_families(): Retrieves hydrolysis product data and checks for carbonyl-based and ether hydrolysis families
-load_hydrolysis_parameters(): Loads family-specific parameters from hydrolysis_families_parameters.yml
2.Reactant and atom index mapping
-extract_reactant_and_indices(): Identifies reactants and key atomic indices (a, b, e, d, o, h1)
-process_hydrolysis_reaction(): Extracts water and main reactant from reactants
-get_neighbors_by_electronegativity(): Ranks neighbors by effective electronegativity, returns the top-ranked and remaining neighbors, excluding a specified atom.
3.Z-matrix setup and geometric manipulation
-setup_zmat_indices(): Converts XYZ indices to Z-matrix indices
-process_chosen_d_indices(): Applies bond stretching and generates TS variants with or without dihedral adjustment
-stretch_ab_bond(): Stretches the a–b bond based on family parameters
-get_matching_dihedrals(): Identifies dihedral angles in the Z-matrix that involve a specified set of atom indices.
-Add nitrile fallback second-pass with controlled dihedral adjustment
- First pass attempts nitrile TSG without forcing dihedral changes
- If nitrile hydrolysis is present but no nitrile TSG is formed, run an additional pass that forces dihedral adjustments
- Stop immediately once at least one nitrile TSG is found OR if all possible dihedral indices were exhausted without producing a valid TSG
-Use fixed factors; try original angle first, flip only if needed
- Use a fixed defined list of dihedral adjustment factors (instead of previous scattered handling)
- Apply these factors to modify the original angle first
- Only attempt the 180° flipped angle if no TS guesses are generated from the original angle variants
- Improve normalization and docstrings for clarity
4.TS generation and validation
-process_family_specific_adjustments(): Applies family-specific internal coordinates and generates TS guesses
-generate_hydrolysis_ts_guess(): Builds TS geometry, validates bonds, collisions, and uniqueness
-check_ts_bonds(): Validates water bond geometry in TS guess
-check_dao_angle(): Rejects guesses with near-linear angels for DAO angel
- added is_water method into ARCSpecies as a class method
carbonyl-based, nitrile, and ether hydrolysis
-Allow setting multiple optimization methods via opt_methods -Default to ['SLSQP', 'Nelder-Mead', 'BFGS'] if not specified -Handle None values in BEST_GUESSES to prevent errors -Add function to get sorted distances from a given atom in a molecule
-test_add_atoms_using_internal_coords() -test_sorted_distances_of_atom() -Update formatting of tests and add tests
Raise a ValueError when only one of solvation_method or solvent is defined. Both must be provided together or both must be None.
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new hydrolysis families and tests