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_undercoordinated_n():
mofchecker = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files", "VUGYED_clean.cif"))
)
assert mofchecker.has_undercoordinated_n == False
mofchecker = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files", "mil-53-al-nh2.cif"))
)
assert mofchecker.has_undercoordinated_n == True
mofchecker = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files", "ABAXUZ.cif"))
)
assert mofchecker.has_undercoordinated_n == False
mofchecker = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files", "1246903.cif"))
)
assert mofchecker.has_undercoordinated_n == False
mofchecker = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "1246903_missing_H.cif")
)
)
assert mofchecker.has_undercoordinated_n == True
def test_has_oms(get_cn4_structure, get_cn5_paddlewheel_structure):
"""Test two specific structures"""
omsdetector = MOFChecker(get_cn4_structure)
assert omsdetector.has_oms
omsdetector = MOFChecker(get_cn5_paddlewheel_structure)
assert not omsdetector.has_oms
def test_has_oms(get_cn4_structre, get_cn5_paddlewheel_structure):
omsdetector = MOFChecker(get_cn4_structre)
assert omsdetector.has_oms == True
omsdetector = MOFChecker(get_cn5_paddlewheel_structure)
assert omsdetector.has_oms == False
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 test_lone_atom():
mofchecker = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files", "ABAVIJ_clean.cif"))
)
assert mofchecker.has_lone_atom == False
mofchecker = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files", "HKUST_floating.cif"))
)
assert mofchecker.has_lone_atom == True
def test_undercoordinated_c():
mofchecker = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files", "ABAVIJ_clean.cif"))
)
assert mofchecker.has_undercoordinated_c == False
mofchecker = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files", "AHOKIR_clean.cif"))
)
assert mofchecker.has_undercoordinated_c == True
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 test_lone_molecule_past_issue():
atoms = read(os.path.join(THIS_DIR, "test_files", "floating_check.cif"))
mofchecker = MOFChecker.from_ase(atoms)
assert len(mofchecker.lone_molecule_indices) == 1
assert len(mofchecker.lone_molecule_indices[0]) == 5
species = []
for ind in mofchecker.lone_molecule_indices[0]:
species.append(str(mofchecker.structure[ind].specie))
assert set(species) == set(["H", "H", "H", "H", "C"])
assert mofchecker.has_lone_molecule == True
mofchecker = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "OTOXIF_clean.cif")))
assert mofchecker.has_lone_molecule == False
def test_undercoordinated_n_past_issue():
mofchecker = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files",
"axipee.cif")))
assert mofchecker.has_undercoordinated_n == False
mofchecker = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "ABOVOF_FSR.cif")))
assert mofchecker.has_undercoordinated_n == False
mofchecker = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files",
"abiqae.cif")))
assert mofchecker.has_undercoordinated_n == False
def test_graph_hash_false_negatives():
"""Test the hash on past issues of false negatives.
Cases of structures that should match but the graph hash did not.
"""
# issue 107: Mn-MOF-74: ASR ORIWET and COKNUN… give different hash
oriwet = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files",
"ORIWET.cif")))
coknun = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files",
"COKNUN.cif")))
assert oriwet.graph_hash == coknun.graph_hash
assert oriwet.scaffold_hash == coknun.scaffold_hash
def test_lone_molecule():
mofchecker = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "ABAVIJ_clean.cif")))
assert mofchecker.has_lone_molecule == False
mofchecker = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "HKUST_floating.cif")))
assert mofchecker.has_lone_molecule == True
assert mofchecker.lone_molecule_indices == [[144]]
atoms = read(os.path.join(THIS_DIR, "test_files", "overvalent_h.cif"))
mofchecker = MOFChecker.from_ase(atoms, primitive=False)
assert len(mofchecker.lone_molecule_indices) == 3
def test_undercoordinated_c():
mofchecker = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "ABAVIJ_clean.cif")))
assert mofchecker.has_undercoordinated_c == False
mofchecker = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "AHOKIR_clean.cif")))
assert mofchecker.has_undercoordinated_c == True
mofchecker = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "missing_h_on_c.cif")))
assert mofchecker.has_undercoordinated_c == True
assert len(mofchecker.undercoordinated_c_indices) == 2
assert len(mofchecker.undercoordinated_c_candidate_positions) == 2
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_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_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 check_structure(self, _=None):
if self.structure is None:
self.text.value = ""
else:
self.text.value = ""
self.mfchk = MOFChecker.from_ase(self.structure, primitive=False)
issue_found = False
for (check_name, check) in self.mfchk.checks.items():
if check_name in ENABLED_CHECKS:
if not check.is_ok:
issue_found = True
self.text.value += "\u2705 OK: " if check.is_ok else "\u274C Fail: "
self.text.value += f"{check.description} </br>"
self.check_button.button_style = "danger" if issue_found else "success"
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 check_structure(self, _=None):
if self.structure is None:
return
self.mfchk = MOFChecker.from_ase(self.structure, primitive=False)
self.checks = []
if self.structure:
self.checks = [
check for (check_name, check) in self.mfchk.checks.items()
if check_name in ENABLED_CHECKS
]
issue_found = False
with self._output:
clear_output()
for check in self.checks:
if not check.is_ok:
issue_found = True
try:
selection = list(
chain.from_iterable(check.flagged_indices))
except TypeError:
selection = check.flagged_indices
button = ipw.Button(description="Select",
layout={"width": "initial"})
button.on_click(
fct.partial(self._select_atoms, selection=selection))
text = ipw.HTML("Found " + check.name.lower())
display(ipw.HBox([text, button]))
if (self.mfchk.undercoordinated_c_candidate_positions +
self.mfchk.undercoordinated_n_candidate_positions):
self.missing_h_button.disabled = False
self.missing_h_button.on_click(self.add_missing_hydrogens)
display(
ipw.HBox([
ipw.HTML("Missing hydrogens found"),
self.missing_h_button
]))
if not issue_found:
display(ipw.HTML("No issues found \u2705"))
def test_overvalent_c_past_issue():
# based on issue https://github.com/kjappelbaum/mofchecker/issues/63
mofchecker = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "AGARUW_clean.cif")))
assert mofchecker.has_overvalent_c == False
def _run_check(structure):
mofcheckerinstance = MOFChecker(structure)
result = mofcheckerinstance.get_mof_descriptors()
return mofcheckerinstance, result
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_is_porous(get_cn5_paddlewheel_structure):
mc = MOFChecker(get_cn5_paddlewheel_structure)
assert mc.is_porous == True
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_chargecheck():
mofchecker = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "AMUFIZ_clean.cif")))
assert mofchecker.has_high_charges == False
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_partial_occupancy():
with pytest.raises(NotImplementedError):
MOFChecker.from_cif(os.path.join(THIS_DIR, "test_files", "ABUBIK.cif"))
def slow_check_undercoordinated_c_past_issue():
mofchecker = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "DALVIY_clean.cif")))
assert mofchecker.has_undercoordinated_c == False
def test_graph_hash_robustness(): # pylint: disable=too-many-locals
"""Check that duplicating or rotating the structure produces the same hash."""
structure = Structure.from_file(
os.path.join(THIS_DIR, "test_files", "ABAXUZ.cif"))
original_hash = MOFChecker(structure).graph_hash
# rotate structure
rotation_transformer = RotationTransformation([1, 0, 0], 10)
rotated_structure = rotation_transformer.apply_transformation(structure)
assert MOFChecker(rotated_structure).graph_hash == original_hash
# create supercell
structure.make_supercell([1, 2, 1])
assert MOFChecker(structure).graph_hash == original_hash
# check the MOF-74 structures
mohgoi_checker = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files",
"MOHGOI.cif")))
todyuj_checker = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files",
"TODYUJ.cif")))
vogtiv_checker = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files",
"VOGTIV.cif")))
# There water on TODYUJ
assert mohgoi_checker.graph_hash != todyuj_checker.graph_hash
# one is the supercell of the other
assert mohgoi_checker.graph_hash == vogtiv_checker.graph_hash
# MOF-74-Zr.cif
mof_74_zr = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "MOF-74-Zr.cif")))
assert mof_74_zr.graph_hash != todyuj_checker.graph_hash
assert mof_74_zr.graph_hash != vogtiv_checker.graph_hash
# # MOF-74-Zn.cif
mof_74_zn = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "MOF-74-Zn.cif")))
assert mof_74_zr.scaffold_hash == mof_74_zn.scaffold_hash
assert mof_74_zr.graph_hash != mof_74_zn.graph_hash
# # MOF-5 is not ZIF-8
mof_5 = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "mof-5_cellopt.cif")))
zif_8 = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "ZIF-8-RASPA.cif")))
assert mof_5.graph_hash != zif_8.graph_hash
# # Mn-MOF-74 and UiO-67
coknun = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "coknun01.cif")))
wizmac = MOFChecker(
Structure.from_file(
os.path.join(THIS_DIR, "test_files", "WIZMAV02_auto.cif")))
assert coknun.graph_hash != wizmac.graph_hash
def test_graph_hash():
"""Basic check that the function call works"""
mofchecker = MOFChecker(
Structure.from_file(os.path.join(THIS_DIR, "test_files",
"ABAXUZ.cif")))
assert isinstance(mofchecker.graph_hash, str)