Hydrolysis families and tests #770
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were used to report the git branch and commit of the repos
ARC reaction families are families for which only a template/recipe is given without kinetic data. They can be used by ARC to atom-map a reaction and search for a transition state just like RMG families. They have the same format as the `group.py` file in RMG reaction families, only here the files are named by the family label. ARC families should be located under ARC/data/families/ to be discovered by ARC. Also added ARC_FAMILIES_PATH to settings
It is obsolete now
Currently the rmgdb module is only used by processor which will be dealt with in a different PR
It is no longer an object, no need to call family.label No need to call determine_family() since family is now a property of reaction
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| from arc.mapping.engine import (assign_labels_to_products, | ||
| are_adj_elements_in_agreement, | ||
| create_qc_mol, | ||
| flip_map, | ||
| fingerprint, | ||
| get_atom_indices_of_labeled_atoms_in_an_rmg_reaction, | ||
| get_rmg_reactions_from_arc_reaction, | ||
| get_atom_indices_of_labeled_atoms_in_a_reaction, |
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Module-level cyclic import Error
| find_all_bdes, | ||
| cut_species_based_on_atom_indices, | ||
| update_xyz, | ||
| RESERVED_FINGERPRINT_KEYS,) | ||
| RESERVED_FINGERPRINT_KEYS, |
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Module-level cyclic import Error
| from arc.common import convert_list_index_0_to_1, extremum_list, generate_resonance_structures, logger, key_by_val | ||
| from arc.exceptions import SpeciesError | ||
| from arc.reaction.family import ReactionFamily, get_reaction_family_products |
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Module-level cyclic import Error
| from arc.common import convert_list_index_0_to_1, extremum_list, generate_resonance_structures, logger, key_by_val | ||
| from arc.exceptions import SpeciesError | ||
| from arc.reaction.family import ReactionFamily, get_reaction_family_products |
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| """ | ||
| label_dict = get_label_dict(rxn) | ||
| if not is_reactants: | ||
| product_pairs = pair_reaction_products(reaction=rxn, products=products) if products is not None else None |
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Unused local variable Note
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| if TYPE_CHECKING: | ||
| from arc.species import ARCSpecies | ||
| from arc.reaction.reaction import ARCReaction |
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| # def get_all_reactions_paths(rxn: 'ARCReaction') -> List['ARCReaction']: | ||
| # """ | ||
| # Get all possible reaction paths with labeled atoms for a given ARC reaction. | ||
| # | ||
| # Args: | ||
| # rxn ('ARCReaction'): The ARC reaction object. | ||
| # | ||
| # Returns: | ||
| # List['ARCReaction']: A list of reactions, each represents a possible reaction path. | ||
| # """ | ||
| # reaction_paths = list() | ||
| # for reactant in rxn.get_reactants_and_products(arc=True, return_copies=True)[0]: | ||
| # all_reactions.extend(reactant.generate_reactions()) | ||
| # return all_reactions |
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Commented-out code Note
| from arc.common import get_logger | ||
| from arc.exceptions import ReactionError, InputError | ||
| from arc.reaction.family import ReactionFamily, get_reaction_family_products |
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| from arc.common import get_logger | ||
| from arc.exceptions import ReactionError, InputError | ||
| from arc.reaction.family import ReactionFamily, get_reaction_family_products |
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| @@ -0,0 +1,117 @@ | |||
| import unittest | |||
| from rmgpy.molecule import Molecule | |||
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Unused import Note test
new hydrolysis families and tests