Added a module for working with RMG reaction families #754
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Module: Main
Module: Mapping
Module: rmgdb
Module: Scheduler
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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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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It is obsolete now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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Now we can identify for each ARC reaction all possible pathways between the reactants and products according to reaction families supported by RMG.
Also added dummy ARC families (w/o kinetics) to assist in identifying reaction templates.
Tests added.