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 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_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 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"))