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def setUp(self):
self.t = utils.PeriodicTable()
def testcorrect(self):
"""Is coreelectrons equal to what it should be?"""
pt = PeriodicTable()
ans = []
for x in self.data.atomnos:
ans.append(self.coredict[pt.element[x]])
ans = numpy.array(ans, "i")
numpy.testing.assert_array_equal(self.data.coreelectrons, ans)
def setUp(self):
self.pt = cclib.parser.utils.PeriodicTable()
def after_parsing(self):
"""NWChem-specific routines for after parsing a file.
Currently, expands self.shells() into self.aonames.
"""
# setup a few necessary things, including a regular expression
# for matching the shells
table = utils.PeriodicTable()
elements = [table.element[x] for x in self.atomnos]
pattern = re.compile("(\ds)+(\dp)*(\dd)*(\df)*(\dg)*")
labels = {}
labels['s'] = ["%iS"]
labels['p'] = ["%iPX", "%iPY", "%iPZ"]
if self.shells['type'] == 'spherical':
labels['d'] = ['%iD-2', '%iD-1', '%iD0', '%iD1', '%iD2']
labels['f'] = ['%iF-3', '%iF-2', '%iF-1', '%iF0',
'%iF1', '%iF2', '%iF3']
labels['g'] = ['%iG-4', '%iG-3', '%iG-2', '%iG-1', '%iG0',
'%iG1', '%iG2', '%iG3', '%iG4']
elif self.shells['type'] == 'cartesian':
labels['d'] = ['%iDXX', '%iDXY', '%iDXZ',
'%iDYY', '%iDYZ',
'%iDZZ']
def symbol2int(symbol):
t = utils.PeriodicTable()
return t.number[symbol]
def before_parsing(self):
self.geoopt = False # Is this a GeoOpt? Needed for SCF targets/values.
self.periodic_table = utils.PeriodicTable()
def stoichiometry(self):
"""Return the stoichemistry of the object according to the Hill system"""
cclib_pt = PeriodicTable()
elements = [cclib_pt.element[ano] for ano in self.data.atomnos]
counts = {el: elements.count(el) for el in set(elements)}
formula = ""
elcount = lambda el, c: "%s%i" % (el, c) if c > 1 else el
if 'C' in elements:
formula += elcount('C', counts['C'])
counts.pop('C')
if 'H' in elements:
formula += elcount('H', counts['H'])
counts.pop('H')
for el, c in sorted(counts.items()):
formula += elcount(el, c)
if getattr(self.data, 'charge', 0):
magnitude = abs(self.data.charge)