def test_get_fingerprint_distance(self):
"""Tests to check getting fingerprint distance."""
finger_1 = [0, 0, 0, 1]
finger_2 = [1, 0, 0, 0]
dist = get_fingerprint_distance(finger_1, finger_2)
self.assertAlmostEqual(dist, 1.4142135623730951)
# test automatic conversion from structure to fingerprint
dist = get_fingerprint_distance(self.fe, self.fe)
self.assertAlmostEqual(dist, 0.)
# test one structure one fingerprint
finger_1 = get_structure_fingerprint(self.fe)
dist = get_fingerprint_distance(self.fe, finger_1)
self.assertAlmostEqual(dist, 0.)
def _set_distance_matrix(self, structure: IStructure):
"""Utility func to calculate distance between structure and minerals.
First checks to see if the distances have already been calculated for
the structure. If not, the distances are stored in a class variable
for use by other class methods.
Args:
structure: A structure.
"""
if self._structure == structure and self._mineral_db is not None:
return
data = self.mineral_db.copy()
fingerprint = get_structure_fingerprint(structure)
if np.linalg.norm(fingerprint) < 0.4:
# fingerprint is too small for a reasonable match, indicates very
# little bonding or small order parameter matches
fingerprint = get_structure_fingerprint(structure,
prototype_match=False)
data["distance"] = data["fingerprint"].apply(
lambda x: get_fingerprint_distance(x, fingerprint))
self._mineral_db = data.sort_values(by="distance")
self._structure = structure