def calculate_composition(composition):
# Replace symbol keys with integer
for key in list(composition.keys()):
if isinstance(key, str):
composition[ep.atomic_number(key)] = composition.pop(key)
# Replace wildcard
totalfraction = 0.0
countwildcard = 0
for z, fraction in composition.items():
if z <= 0 or z >= 99:
raise ValueError("Atomic number '%i' must be between [1, 99]" % z)
if fraction == '?':
countwildcard += 1
else:
totalfraction += float(fraction)
if countwildcard > 0:
if totalfraction <= 1.0:
wildcardfraction = (1.0 - totalfraction) / float(countwildcard)
else:
raise ValueError('Wild card(s) could not be replaced since total fraction is already 1.0')
for z, fraction in composition.items():
if fraction == '?':
fraction = wildcardfraction
composition[z] = float(fraction)
# Check total fraction
totalfraction = sum(composition.values())
if abs(totalfraction - 1.0) > 1e-6:
raise ValueError("The total weight fraction (%s) should be 1.0." % totalfraction)
return defaultdict(float, composition)
def composition_from_formula(formula):
# Parse chemical formula
formulaData = CHEMICAL_FORMULA_PARSER.parseString(formula)
zs = []
atomicfractions = []
for symbol, atomicfraction in formulaData:
zs.append(ep.atomic_number(symbol=symbol))
atomicfractions.append(float(atomicfraction))
# Calculate total atomic mass
totalatomicmass = 0.0
for z, atomicfraction in zip(zs, atomicfractions):
atomicmass = ep.atomic_mass_kg_mol(z)
totalatomicmass += atomicfraction * atomicmass
# Create composition
composition = defaultdict(float)
for z, atomicfraction in zip(zs, atomicfractions):
atomicmass = ep.atomic_mass_kg_mol(z)
weightfraction = atomicfraction * atomicmass / totalatomicmass
composition[z] += weightfraction
return composition
def from_string(s):
"""
Returns a :class:`Transition` or :class:`transitionset` from the given
string.
The first word must be the symbol of the element followed by either the
Siegbahn (e.g. ``Al Ka1``) or IUPAC (``Al K-L3``) notation of the
transition.
The second word can also represent transition family (e.g. ``Al K``) or
shell (``Al LIII``).
:arg s: string representing the transition
:return: transition or set of transitions
"""
words = s.split(" ")
if len(words) != 2:
raise ValueError("The transition string must have 2 words: " + \
"1. the symbol of the element and 2. the transition notation")
z = ep.atomic_number(symbol=words[0])
notation = words[1]
# Fix to be compatible with old transition, e.g. N5N6/N6N7
if '/' in notation: notation = notation[:notation.index('/')]
if notation == 'Le': notation = 'Ln'
notation = _siegbahn_ascii_to_unicode(notation)
if notation in _SIEGBAHNS: # Transition with Siegbahn notation
return Transition(z, siegbahn=notation)
elif notation in _TRANSITIONSETS: # transitionset from Family, group or shell
return _TRANSITIONSETS[notation](z)
elif '-' in notation: # Transition with IUPAC notation
dest, src = notation.split('-')
return Transition(z,
src=Subshell(z, iupac=src),
dest=Subshell(z, iupac=dest))
else:
raise ValueError("Cannot parse transition string: %s" % s)
def from_string(s):
"""
Returns a :class:`Transition` or :class:`transitionset` from the given
string.
The first word must be the symbol of the element followed by either the
Siegbahn (e.g. ``Al Ka1``) or IUPAC (``Al K-L3``) notation of the
transition.
The second word can also represent transition family (e.g. ``Al K``) or
shell (``Al LIII``).
:arg s: string representing the transition
:return: transition or set of transitions
"""
words = s.split(" ")
if len(words) != 2:
raise ValueError("The transition string must have 2 words: " + \
"1. the symbol of the element and 2. the transition notation")
z = ep.atomic_number(symbol=words[0])
notation = words[1]
# Fix to be compatible with old transition, e.g. N5N6/N6N7
if '/' in notation: notation = notation[:notation.index('/')]
if notation == 'Le': notation = 'Ln'
notation = _siegbahn_ascii_to_unicode(notation)
if notation in _SIEGBAHNS: # Transition with Siegbahn notation
return Transition(z, siegbahn=notation)
elif notation in _TRANSITIONSETS: # transitionset from Family, group or shell
return _TRANSITIONSETS[notation](z)
elif '-' in notation: # Transition with IUPAC notation
dest, src = notation.split('-')
return Transition(z, src=Subshell(z, iupac=src), dest=Subshell(z, iupac=dest))
else:
raise ValueError("Cannot parse transition string: %s" % s)
def setSelection(self, selection):
def _uncheckedAll():
for widget in self._group.buttons():
widget.setChecked(False)
if selection is None:
_uncheckedAll()
self.selectionChanged.emit()
return
if isinstance(selection, (int, six.string_types)):
selection = [selection]
if not self.isMultipleSelection() and len(selection) > 1:
raise ValueError('Multiple selection mode is off. Cannot select more than one element')
_uncheckedAll()
for z in selection:
if isinstance(z, six.string_types):
z = ep.atomic_number(z.strip())
self._group.button(z).setChecked(True)
self.selectionChanged.emit()
def testatomic_number(self):
self.assertEqual(13, ep.atomic_number(symbol='Al'))
self.assertEqual(13, ep.atomic_number(name='Aluminium'))
def testatomic_number(self):
self.assertEqual(1, ep.atomic_number(symbol='H'))
self.assertEqual(1, ep.atomic_number(name='Hydrogen'))
self.assertEqual(118, ep.atomic_number(symbol='Uuo'))
self.assertEqual(118, ep.atomic_number(name='Ununoctium'))
def testatomic_number(self):
self.assertEqual(13, ep.atomic_number(symbol='Al'))
self.assertEqual(13, ep.atomic_number(name='Aluminium'))
def testatomic_number(self):
self.assertEqual(1, ep.atomic_number(symbol='H'))
self.assertEqual(1, ep.atomic_number(name='Hydrogen'))
self.assertEqual(118, ep.atomic_number(symbol='Uuo'))
self.assertEqual(118, ep.atomic_number(name='Ununoctium'))
