Chemical identity comparison for Molecules and Species #1329
Commits on May 17, 2019
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Refactor some class properties using @Property decorator
More pythonic and prevents extra getter/setter functions from cluttering the namespace.
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Refactor Molecule SMILES and InChI attributes
Allow instantiation using either SMILES or InChI Change SMILES and InChI to all lowercase for easier typing Make smiles and inchi read only properties that generate and save the respective identifiers to private attributes
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Add strict argument for isomorphism comparison
For strict=False, ignores electrons (i.e. bond order, radicals, lone pairs, etc.) Only implemented for Molecule isomorphism, exceptions raised in other cases For atoms, strict argument is added to the `equivalent` method For bonds, strict argument is handled within vf2
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Remove generate_res argument from Species.isIsomorphic
Because its functionality is replaced by the strict argument
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Rename isomorphic_species_lists to same_species_lists
Also add strict argument which is passed to isIsomorphic
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Refactor CERM.checkForExistingSpecies using strict=False isomorphism
Since this option allows us to compare resonance structures directly, we don't need to worry about nonreactive resonance structures or aromatic resonance structures. Also, the return value of checkForExistingSpecies is reduced to a single value, since returning whether or not the species was found is redundant with returning the species itself.
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Refactor product checking in __generateReactions
No need to ensure species - the reactions will always contain Molecules at this point, so either Molecule or Species objects are acceptable for the product list to compare with Aromatic resonance structure generation can be omitted by using the strict=False option, which neglects electrons during the isomorphism comparison
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Revise test for prod_resonance option for generating reactions
Remove checks that the product list is converted in place to Species objects, since that step was removed
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Add strict option to Graph.isMappingValid
Similar to strict option for isomorphism, setting strict=False ignores electrons and bond orders for the comparison, which is useful for comparing different resonance structures
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Add strict argument to isIdentical methods
Of Molecule, Species, and Reaction, which is passed to Graph.isMappingValid
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Do not generate resonance structures for degeneracy determination
Instead, use the strict=False option to ignore resonance issues Change ensure_species to not generate resonance structures by default Add call to ensure_independent_atom_ids in addReverseAttribute because the changes to resonance structure generation means that products may not necessarily have proper atom IDs
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Enable Species instantiation by SMILES or InChI argument
Add SMILES property and unit tests
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Fix reaction degeneracy bug with keep_isomorphic argument
In certain situations, we would call ensure_species with keep_isomorphic=False, which would ultimately result in wrong degeneracy values. This fixes that oversight and makes sure that keep_isomorphic=True when generating reactions. A unit test is also added.
