def test_formulas(x):
f = Formula(x)
y = str(f)
assert y == x
print(f.count(), '{:latex}'.format(f))
a, b = divmod(f, 'H2O')
assert a * Formula('H2O') + b == f
assert f != 117 # check that formula can be compared to non-formula object
def from_formula(self, formula: Formula) -> BagType:
formula_dict = formula.count()
bag = [0] * self.symbol_table.count()
for symbol, value in formula_dict.items():
bag[self.symbol_table.get_index(symbol)] = value
return tuple(bag)
def parse_selection(selection, **kwargs):
if selection is None or selection == '':
expressions = []
elif isinstance(selection, int):
expressions = [('id', '=', selection)]
elif isinstance(selection, list):
expressions = selection
else:
expressions = [w.strip() for w in selection.split(',')]
keys = []
comparisons = []
for expression in expressions:
if isinstance(expression, (list, tuple)):
comparisons.append(expression)
continue
if expression.count('<') == 2:
value, expression = expression.split('<', 1)
if expression[0] == '=':
op = '>='
expression = expression[1:]
else:
op = '>'
key = expression.split('<', 1)[0]
comparisons.append((key, op, value))
for op in ['!=', '<=', '>=', '<', '>', '=']:
if op in expression:
break
else:
if expression in atomic_numbers:
comparisons.append((expression, '>', 0))
else:
try:
count = Formula(expression).count()
except ValueError:
keys.append(expression)
else:
comparisons.extend(
(symbol, '>', n - 1) for symbol, n in count.items())
continue
key, value = expression.split(op)
comparisons.append((key, op, value))
cmps = []
for key, value in kwargs.items():
comparisons.append((key, '=', value))
for key, op, value in comparisons:
if key == 'age':
key = 'ctime'
op = invop[op]
value = now() - time_string_to_float(value)
elif key == 'formula':
if op != '=':
raise ValueError('Use fomula=...')
f = Formula(value)
count = f.count()
cmps.extend((atomic_numbers[symbol], '=', n)
for symbol, n in count.items())
key = 'natoms'
value = len(f)
elif key in atomic_numbers:
key = atomic_numbers[key]
value = int(value)
elif isinstance(value, str):
value = convert_str_to_int_float_or_str(value)
if key in numeric_keys and not isinstance(value, (int, float)):
msg = 'Wrong type for "{}{}{}" - must be a number'
raise ValueError(msg.format(key, op, value))
cmps.append((key, op, value))
return keys, cmps
assert Atoms('MoS2').get_chemical_formula() == 'MoS2'
assert Atoms('SnO2').get_chemical_formula(mode='metal') == 'SnO2'
if sys.version_info >= (3, 6):
assert Formula('A3B2C2D').format('abc') == 'DB2C2A3'
for sym in ['', 'Pu', 'Pu2', 'U2Pu2', 'U2((Pu2)2H)']:
for mode in ['all', 'reduce', 'hill', 'metal']:
for empirical in [False, True]:
if empirical and mode in ['all', 'reduce']:
continue
atoms = Atoms(sym)
formula = atoms.get_chemical_formula(mode=mode,
empirical=empirical)
atoms2 = Atoms(formula)
print(repr(sym), '->', repr(formula))
n1 = np.sort(atoms.numbers)
n2 = np.sort(atoms2.numbers)
if empirical and len(atoms) > 0:
reduction = len(n1) // len(n2)
n2 = np.repeat(n2, reduction)
assert (n1 == n2).all()
for x in ['H2O', '10H2O', '2(CuO2(H2O)2)10', 'Cu20+H2', 'H' * 15, 'AuBC2', '']:
f = Formula(x)
y = str(f)
assert y == x
print(f.count(), '{:latex}'.format(f))
a, b = divmod(f, 'H2O')
assert a * Formula('H2O') + b == f
assert f != 117
