Hello,
I am trying to use Matminer to generate some features on MOF structures for a machine learning project. When I run the code below (with mof in the first line referencing a local .cif file):
structure=CifParser(mof).get_structures(primitive=False)[0]
featurizer=MultipleFeaturizer([mfs.bonding.GlobalInstabilityIndex(),
mfs.bonding.StructuralHeterogeneity(),
mfs.composite.JarvisCFID(),
mfs.misc.EwaldEnergy(),
mfs.misc.StructureComposition(),
mfs.order.StructuralComplexity,
mfs.rdf.ElectronicRadialDistributionFunction(),
mfs.symmetry.GlobalSymmetryFeatures()
])
f = pd.DataFrame(featurizer.featurize(structure))
I am getting the following error:
AttributeError: Element has no attribute oxi_state!
From what I can tell, anytime site.species.elements[0].oxi_state is used in /matminer/featurizers/structure/bonding.py it references back to Line 449 in Pymatgen/core/composition.py, which is the elements attribute of the Composition class. The elements attribute is defined as:
def elements(self) → list[Element | Species | DummySpecies]
According to the pymatgen documentation the oxi_state attribute is only present in the Species class, not Element.
I tried updating my local version of bonding.py to:
site.species.elements[1].oxi_state
but then I got this error:
line 885, in calc_gii_iucr
site_val = site.species.elements[1].oxi_state
~~~~~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range
So now I’m pretty confused. Thank you for your help!