Added a Linear TS search job adapter
#695
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Additional details and impacted files@@ Coverage Diff @@
## main #695 +/- ##
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+ Coverage 73.80% 73.97% +0.17%
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Files 99 101 +2
Lines 27352 27596 +244
Branches 5718 5746 +28
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+ Hits 20187 20415 +228
- Misses 5738 5745 +7
- Partials 1427 1436 +9
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| from arc.plotter import save_geo | ||
| from arc.species.converter import order_xyz_by_atom_map, zmat_to_xyz | ||
| from arc.species.species import ARCSpecies, TSGuess, colliding_atoms | ||
| from arc.species.zmat import check_ordered_zmats, get_atom_order, update_zmat_by_xyz, xyz_to_zmat |
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Unused import Note
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AI 7 months ago
To fix the problem, we need to remove the unused import statement for get_atom_order from the file arc/job/adapters/ts/linear.py. This will clean up the code and remove unnecessary dependencies, making the code easier to read and maintain.
| @@ -18,3 +18,3 @@ | ||
| from arc.species.species import ARCSpecies, TSGuess, colliding_atoms | ||
| from arc.species.zmat import check_ordered_zmats, get_atom_order, update_zmat_by_xyz, xyz_to_zmat | ||
| from arc.species.zmat import check_ordered_zmats, update_zmat_by_xyz, xyz_to_zmat | ||
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| H -0.53390611 -2.06386676 -0.83047533 | ||
| H -0.42088759 -4.06846526 -2.17670487 | ||
| H 1.36205133 -3.75009763 -2.57288841""")]) | ||
| cls.rxn_1.determine_family(rmg_database=cls.rmgdb) |
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Wrong name for an argument in a call Error
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AI 7 months ago
To fix the problem, we need to ensure that the keyword argument used in the method call matches the parameter name expected by the determine_family method. We should check the method definition of determine_family in the ARCReaction class to find the correct parameter name and update the method call accordingly.
The best way to fix the problem without changing existing functionality is to replace the incorrect keyword argument rmg_database with the correct parameter name. This change should be made in the file arc/job/adapters/ts/linear_test.py on line 77 and line 101.
| @@ -76,3 +76,3 @@ | ||
| H 1.36205133 -3.75009763 -2.57288841""")]) | ||
| cls.rxn_1.determine_family(rmg_database=cls.rmgdb) | ||
| cls.rxn_1.determine_family(rmgdb=cls.rmgdb) | ||
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| @@ -100,3 +100,3 @@ | ||
| H 0.27058353 -0.73979548 1.43184405""")]) | ||
| cls.rxn_2.determine_family(rmg_database=cls.rmgdb) | ||
| cls.rxn_2.determine_family(rmgdb=cls.rmgdb) | ||
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|
| H -1.41423043 0.87863077 0.42354512 | ||
| H 1.02430791 0.21530309 0.12674144 | ||
| H 0.27058353 -0.73979548 1.43184405""")]) | ||
| cls.rxn_2.determine_family(rmg_database=cls.rmgdb) |
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Wrong name for an argument in a call Error
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AI 7 months ago
To fix the problem, we need to ensure that the correct parameter name is used when calling the determine_family method. This involves checking the method definition of determine_family in the ARCReaction class to find the correct parameter name and updating the call accordingly.
- First, identify the correct parameter name expected by the
determine_familymethod. - Update the call to
determine_familyon line 101 to use the correct parameter name.
| @@ -100,3 +100,3 @@ | ||
| H 0.27058353 -0.73979548 1.43184405""")]) | ||
| cls.rxn_2.determine_family(rmg_database=cls.rmgdb) | ||
| cls.rxn_2.determine_family(rmgdb=cls.rmgdb) | ||
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Also fixed the is_isomerization() method
Also testing the atom_order arg
| Returns: | ||
| float: The reaction weight. | ||
| """ | ||
| reactants, products = rxn.get_reactants_and_products(arc=True, return_copies=False) |
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The best fix is to remove the unsupported keyword argument arc=True from the call to rxn.get_reactants_and_products on line 407 in arc/job/adapters/ts/linear.py. The parameter return_copies=False should remain if it is valid. No imports or new method definitions are needed. The change should be made only to line 407, leaving the rest of the functionality and file untouched.
| @@ -404,7 +404,7 @@ | ||
| Returns: | ||
| float: The reaction weight. | ||
| """ | ||
| reactants, products = rxn.get_reactants_and_products(arc=True, return_copies=False) | ||
| reactants, products = rxn.get_reactants_and_products(return_copies=False) | ||
| r_e0 = [r.e0 for r in reactants] | ||
| p_e0 = [p.e0 for p in products] | ||
| ts_e0 = rxn.ts_species.e0 |
1 participant
Added a method for generating TS structures from atom mapped reactants and products.
The method works for unimolecular reactions, and at present is only implemented for isomerization reactions.