Breaking: Update AseAtomsAdaptor to handle Structure.properties/Molecule.properties
#3270
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Andrew-S-Rosen
changed the title
Structure.properties and Molecule.properties do not get lost with ASE Atoms interconversionAseAtomsAdaptor to handle Structure.properties/Molecule.properties
janosh
added
enhancement
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I see you @shyuep! 👀😅 I plan to finish this PR later today. |
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@janosh: When you're back on GitHub, would you mind helping me out with the |
Andrew-S-Rosen
changed the title
AseAtomsAdaptor to handle Structure.properties/Molecule.propertiesAseAtomsAdaptor to handle Structure.properties/Molecule.properties
Andrew-S-Rosen
changed the title
AseAtomsAdaptor to handle Structure.properties/Molecule.propertiesAseAtomsAdaptor to handle Structure.properties/Molecule.properties
| @@ -292,10 +297,14 @@ def test_back_forth(self): | |||
| # Molecule --> Atoms --> Molecule --> Atoms | |||
| molecule = Molecule.from_file(TEST_FILES_DIR / "acetylene.xyz") | |||
| molecule.set_charge_and_spin(-2, spin_multiplicity=3) | |||
| molecule.info = {"test": "hi"} | |||
| molecule.properties = {"test": "hi"} | |||
| atoms = aio.AseAtomsAdaptor.get_atoms(molecule) | |||
| molecule_back = aio.AseAtomsAdaptor.get_molecule(atoms) | |||
| atoms_back = aio.AseAtomsAdaptor.get_atoms(molecule_back) | |||
| for k, v in atoms.todict().items(): | |||
| assert str(atoms_back.todict()[k]) == str(v) | |||
| assert molecule_back == molecule | |||
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This doesn't check that the properties were restored since Molecule.__eq__ doesn't currently look at properties. I think that'll be unexpected behavior for must users so we should change IMolecule.__eq__ and IStructure.__eq__ even though it's strictly speaking a breaking change.
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I agree that that's worthwhile to change!
janosh
changed the title
AseAtomsAdaptor to handle Structure.properties/Molecule.propertiesAseAtomsAdaptor to handle Structure.properties/Molecule.properties
| @@ -216,12 +217,19 @@ def get_structure(atoms: Atoms, cls: type[Structure] = Structure, **cls_kwargs) | |||
| else: | |||
| sel_dyn = None | |||
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| # Atoms.info <---> Structure.properties (excluding properties["calc"]) | |||
| properties = jsanitize(getattr(atoms, "info", {})) | |||
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@janosh: Just wanted to point out one subtlety to you. Currently, we have the mapping: Atoms.info <--> Structure.properties, since they serve the same purpose between ASE and Pymtatgen, respectively. However, I jsanitize-d the atoms.info before assigning it to .properties to ensure the Structure/Molecule object can be (de)serialized since this is often an implicit assumption of Structure/Molecule objects but is not necessarily one for ASE Atoms objects. In practice, this means that there could be some scenarios where a user interconverts between ASE Atoms and Pymatgen Structure/Molecule with some loss of information; namely, if the atoms.info is modified by jsanitize() then it can't be restored in its original form. There might be a better solution than this, but I implemented it because oftentimes ASE will dump un-serializable class objects (namely, a Spacegroup class) into atoms.info, such as when reading in a CIF with symmetry flags.
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Thanks for highlighting! Seems like a good way to go about this for now. I'll keep this in mind if we run into any issues.
Ensure
Structure.propertiesandMolecule.propertiesdo not get lost with ASEAtomsinterconversion.Recent PR that added
properties: #3264Breaking because
IMolecule.__eq__andIStructure.__eq__were changed to checkself.properties == other.properties. See #3270 (comment).