def test_get_symmetry_hash():
"""Test the symmetry hashes"""
zif3 = MOFChecker.from_cif(
os.path.join(THIS_DIR, "test_files", "ZIF-3.cif"))
print(type(zif3.structure))
hash_a = get_symmetry_hash(zif3.structure, tight=True)
assert len(hash_a) == 275
hash_b = get_symmetry_hash(zif3.structure)
assert len(hash_b) == 47
assert hash_a[-3:] == hash_b[-3:]
zif4 = MOFChecker.from_cif(
os.path.join(THIS_DIR, "test_files", "ZIF-4.cif"))
hash_zif4_a = get_symmetry_hash(zif4.structure, tight=True)
hash_zif4_b = get_symmetry_hash(zif4.structure)
assert hash_zif4_a != hash_a
assert hash_zif4_b != hash_b
assert zif4.symmetry_hash == hash_zif4_b
structure = Structure.from_file(
os.path.join(THIS_DIR, "test_files", "ABAXUZ.cif"))
original_hash = get_symmetry_hash(MOFChecker(structure).structure)
# rotate structure
rotation_transformer = RotationTransformation([1, 0, 0], 10)
rotated_structure = rotation_transformer.apply_transformation(structure)
assert get_symmetry_hash(
MOFChecker(rotated_structure).structure) == original_hash
# create supercell
structure.make_supercell([1, 2, 1])
print(type(structure))
assert get_symmetry_hash(MOFChecker(structure).structure) == original_hash
def test_overvalent_h():
mofchecker = MOFChecker.from_cif(
os.path.join(THIS_DIR, "test_files", "overvalent_h.cif"))
assert mofchecker.has_overvalent_h
assert len(mofchecker.overvalent_h_indices) == 3
mofchecker = MOFChecker.from_cif(
os.path.join(THIS_DIR, "test_files", "XIGFOJ_manual.cif"))
assert not mofchecker.has_overvalent_h
def get_feat_one_structure(cif):
"""Run the MOFCheck on one structure"""
try:
mofchecker = MOFChecker.from_cif(cif)
descriptors = mofchecker.get_mof_descriptors()
return descriptors
except NoMetal:
print("{} has no metal".format(cif))
return None
def test_unknown_elements():
"""Parsing structure with unknown element raises warning for covalent radius."""
# with pytest.warns(UserWarning) as record:
# mofchecker = MOFCheƒ√cker.from_cif(
# os.path.join(THIS_DIR, "test_files", "GUPQOA.cif")
# )
# mofchecker.get_mof_descriptors()
# assert len(record) >= 1
with pytest.raises(NotImplementedError):
mofchecker = MOFChecker.from_cif(
os.path.join(THIS_DIR, "test_files", "GUPQOA.cif"))
mofchecker.get_mof_descriptors()
def test_graph_hash_false_positives():
"""Test the hash on past issues of false positives.
Cases where different structures gave the same hash.
"""
# issue 130
cof_18141N2 = MOFChecker.from_cif( # pylint: disable=invalid-name
os.path.join(THIS_DIR, "test_files", "18141N2.cif"))
cof_20211N2 = MOFChecker.from_cif( # pylint: disable=invalid-name
os.path.join(THIS_DIR, "test_files", "20211N2.cif"))
assert cof_18141N2.graph_hash != cof_20211N2.graph_hash
# # Daniele's report
mmpf7 = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files",
"943643.cif")))
mmpf8 = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files",
"943644.cif")))
assert mmpf7.graph_hash != mmpf8.graph_hash
assert mmpf7.scaffold_hash != mmpf8.scaffold_hash
def test_overvalent_c(get_overvalent_c_structures):
for structure in get_overvalent_c_structures:
mofchecker = MOFChecker(structure)
assert mofchecker.has_overvalent_c == True
mofchecker = MOFChecker.from_cif(
os.path.join(THIS_DIR, "test_files", "XIGFOJ_manual.cif"))
assert mofchecker.has_overvalent_c == False
# alkine ligand
mofchecker = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "RUDQUD_clean.cif")))
assert mofchecker.has_overvalent_c == False
def run(primitive, descriptors, cif_files):
"""
Check provided structures and print list of JSON objects with descriptors.
"""
# Note: we want to see output as things progress,
# thus this clumsy way of creating a JSON list
print("[")
for index, structure_file in enumerate(cif_files):
mofchecker = MOFChecker.from_cif(structure_file, primitive=primitive)
descriptors = mofchecker.get_mof_descriptors(descriptors=descriptors)
string = json.dumps(descriptors, indent=2)
if index != len(cif_files) - 1:
string += ","
print(string)
print("]")
def test_overlaps():
mofchecker = MOFChecker.from_cif(
os.path.join(THIS_DIR, "test_files", "overvalent_h.cif"))
assert not mofchecker.has_atomic_overlaps
def test_name():
s = os.path.join(THIS_DIR, "test_files", "ABAVIJ_clean.cif")
mofchecker = MOFChecker.from_cif(s)
assert mofchecker.name == "ABAVIJ_clean"
def test_partial_occupancy():
with pytest.raises(NotImplementedError):
MOFChecker.from_cif(os.path.join(THIS_DIR, "test_files", "ABUBIK.cif"))
def test_has_oms_multiple(get_testdict):
"""Test on a bunch of different structures"""
for key, value in get_testdict.items():
omsdetector = MOFChecker.from_cif(key)
assert omsdetector.has_oms == value
def test_has_oms_multiple(get_testdict):
for k, v in get_testdict.items():
print(k)
omsdetector = MOFChecker.from_cif(k)
assert omsdetector.has_oms == v