Hydrolysis families and tests #770
Open
+3,033
−246
Conversation
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
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
LeenFahoum
force-pushed
the
hydrolysis
branch
from
15076b7 to
e86ce34
Compare
There was a problem hiding this comment.
CodeQL found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.
LeenFahoum
force-pushed
the
hydrolysis
branch
from
49622d7 to
ef9d75c
Compare
LeenFahoum
force-pushed
the
hydrolysis
branch
from
28d0988 to
262761d
Compare
alongd
reviewed
Mar 2, 2025
arc/job/adapters/ts/heuristics.py
Outdated
| spc (ARCSpecies): The species to check. | ||
| Returns: | ||
| bool: Whether the species is water. |
There was a problem hiding this comment.
I think that the issue is that there's no closing """ for the docstring
arc/job/adapters/ts/heuristics.py
Outdated
| return O_counter == 1 and H_counter == 2 | ||
|
|
||
|
|
||
| def get_neighbors_by_electronegativity(spc: ARCSpecies, |
There was a problem hiding this comment.
this commit deletes the def of another functions
alongd
reviewed
May 7, 2025
|
Hi Alon, |
and typo fix
ester, nitrile, ether, and imine hydrolysis
ester, nitrile, ether,, and imine 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 ester 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, f, d, o, h1)
-process_hydrolysis_reaction(): Extracts water and main reactant from reactants
-is_water(): Recognizes water molecule
-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.
-generate_dihedral_variants(): Generates dihedral angle variants for near 0 and near 180 dihedrals
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
ester, nitrile, ether,, and imine 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
-test_add_atoms_using_internal_coords() -Update formatting of tests and add tests -test_add_atoms_to_xyz_using_internal_coords()
Raise a ValueError when only one of solvation_method or solvent is defined. Both must be provided together or both must be None.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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.
new hydrolysis families and tests