def __str__(self):
output = self.symbol
if self._oxi_state >= 0:
output += formula_double_format(self._oxi_state) + "+"
else:
output += formula_double_format(-self._oxi_state) + "-"
return output
def __str__(self):
output = self.symbol
if self._oxi_state >= 0:
output += formula_double_format(self._oxi_state) + "+"
else:
output += formula_double_format(-self._oxi_state) + "-"
return output
def __str__(self):
output = self.symbol
if self._oxi_state >= 0:
output += formula_double_format(self._oxi_state) + "+"
else:
output += formula_double_format(-self._oxi_state) + "-"
for p, v in self._properties.items():
output += "%s=%s" % (p, v)
return output
def __str__(self):
output = self.symbol
if self._oxi_state >= 0:
output += formula_double_format(self._oxi_state) + "+"
else:
output += formula_double_format(-self._oxi_state) + "-"
for p, v in self._properties.items():
output += "%s=%s" % (p, v)
return output
def alphabetical_formula(self):
"""
Returns a reduced formula string with appended charge
"""
alph_formula = self._composition.alphabetical_formula
chg_str = ""
if self._charge > 0:
chg_str = " +" + formula_double_format(self._charge, False)
elif self._charge < 0:
chg_str = " " + formula_double_format(self._charge, False)
return alph_formula + chg_str
def alphabetical_formula(self):
"""
Returns a reduced formula string with appended charge
"""
alph_formula = self._composition.alphabetical_formula
chg_str = ""
if self._charge > 0:
chg_str = " +" + formula_double_format(self._charge, False)
elif self._charge < 0:
chg_str = " " + formula_double_format(self._charge, False)
return alph_formula + chg_str
def formula(self):
"""
Returns a formula string, with elements sorted by electronegativity,
e.g., Li4 Fe4 P4 O16.
"""
formula = self._composition.formula
chg_str = ""
if self._charge > 0:
chg_str = " +" + formula_double_format(self._charge, False)
elif self._charge < 0:
chg_str = " " + formula_double_format(self._charge, False)
return formula + chg_str
def formula(self):
"""
Returns a formula string, with elements sorted by electronegativity,
e.g., Li4 Fe4 P4 O16.
"""
formula = self._composition.formula
chg_str = ""
if self._charge > 0:
chg_str = " +" + formula_double_format(self._charge, False)
elif self._charge < 0:
chg_str = " " + formula_double_format(self._charge, False)
return formula + chg_str
def formula(self):
"""
Returns a formula string, with elements sorted by electronegativity,
e.g., Li4 Fe4 P4 O16.
"""
sym_amt = self.get_el_amt_dict()
syms = sorted(sym_amt.keys(), key=lambda sym: get_el_sp(sym).X)
formula = [s + formula_double_format(sym_amt[s], False) for s in syms]
return " ".join(formula)
def formula(self):
"""
Returns a formula string, with elements sorted by electronegativity,
e.g., Li4 Fe4 P4 O16.
"""
sym_amt = self.get_el_amt_dict()
syms = sorted(sym_amt.keys(), key=lambda sym: get_el_sp(sym).X)
formula = [s + formula_double_format(sym_amt[s], False) for s in syms]
return " ".join(formula)
def alphabetical_formula(self):
"""
Returns a formula string, with elements sorted by alphabetically
e.g., Fe4 Li4 O16 P4.
"""
sym_amt = self.get_el_amt_dict()
syms = sorted(sym_amt.keys())
formula = [s + formula_double_format(sym_amt[s], False) for s in syms]
return " ".join(formula)
def alphabetical_formula(self):
"""
Returns a formula string, with elements sorted by alphabetically
e.g., Fe4 Li4 O16 P4.
"""
sym_amt = self.get_el_amt_dict()
syms = sorted(sym_amt.keys())
formula = [s + formula_double_format(sym_amt[s], False) for s in syms]
return " ".join(formula)
def reduced_formula(self):
"""
Returns a reduced formula string with appended charge.
"""
reduced_formula = self._composition.reduced_formula
charge = self._charge / float(self._composition.
get_reduced_composition_and_factor()[1])
if charge > 0:
if abs(charge) == 1:
chg_str = "[+]"
else:
chg_str = "[" + formula_double_format(charge, False) + "+]"
elif charge < 0:
if abs(charge) == 1:
chg_str = "[-]"
else:
chg_str = "[{}-]".format(formula_double_format(abs(charge),
False))
else:
chg_str = "(aq)"
return reduced_formula + chg_str
def reduced_formula(self):
"""
Returns a reduced formula string with appended charge.
"""
reduced_formula = self._composition.reduced_formula
charge = self._charge / float(
self._composition.get_reduced_composition_and_factor()[1])
if charge > 0:
if abs(charge) == 1:
chg_str = "[+]"
else:
chg_str = "[" + formula_double_format(charge, False) + "+]"
elif charge < 0:
if abs(charge) == 1:
chg_str = "[-]"
else:
chg_str = "[{}-]".format(
formula_double_format(abs(charge), False))
else:
chg_str = "(aq)"
return reduced_formula + chg_str
def formula(self):
"""
Returns a formula string, with elements sorted by electronegativity,
e.g., Li4 Fe4 P4 O16.
"""
sym_amt = self.get_el_amt_dict()
syms = sorted(sym_amt.keys(),
key=lambda s: smart_element_or_specie(s).X)
formula = []
for s in syms:
if sym_amt[s] != 0:
formula.append(s + formula_double_format(sym_amt[s], False))
return " ".join(formula)
def formula(self):
"""
Returns a formula string, with elements sorted by electronegativity,
e.g., Li4 Fe4 P4 O16.
"""
sym_amt = self.get_el_amt_dict()
syms = sorted(sym_amt.keys(),
key=lambda s: smart_element_or_specie(s).X)
formula = []
for s in syms:
if sym_amt[s] != 0:
formula.append(s + formula_double_format(sym_amt[s], False))
return " ".join(formula)
def reduce_formula(sym_amt):
"""
Helper method to reduce a sym_amt dict to a reduced formula and factor.
Args:
sym_amt (dict): {symbol: amount}.
Returns:
(reduced_formula, factor).
"""
syms = sorted(sym_amt.keys(), key=lambda s: get_el_sp(s).X)
syms = list(
filter(lambda s: abs(sym_amt[s]) > Composition.amount_tolerance, syms))
num_el = len(syms)
contains_polyanion = (
num_el >= 3 and
get_el_sp(syms[num_el - 1]).X - get_el_sp(syms[num_el - 2]).X < 1.65)
factor = 1
# Enforce integers for doing gcd.
if all((int(i) == i for i in sym_amt.values())):
factor = abs(gcd(*(int(i) for i in sym_amt.values())))
reduced_form = []
n = num_el - 2 if contains_polyanion else num_el
for i in range(0, n):
s = syms[i]
normamt = sym_amt[s] * 1.0 / factor
reduced_form.append(s)
reduced_form.append(formula_double_format(normamt))
if contains_polyanion:
poly_sym_amt = {
syms[i]: sym_amt[syms[i]] / factor
for i in range(n, num_el)
}
(poly_form, poly_factor) = reduce_formula(poly_sym_amt)
if poly_factor != 1:
reduced_form.append("({}){}".format(poly_form, int(poly_factor)))
else:
reduced_form.append(poly_form)
reduced_form = "".join(reduced_form)
return reduced_form, factor
def reduce_formula(sym_amt):
"""
Helper method to reduce a sym_amt dict to a reduced formula and factor.
Args:
sym_amt (dict): {symbol: amount}.
Returns:
(reduced_formula, factor).
"""
syms = sorted(sym_amt.keys(),
key=lambda s: get_el_sp(s).X)
syms = list(filter(lambda s: abs(sym_amt[s]) >
Composition.amount_tolerance, syms))
num_el = len(syms)
contains_polyanion = (num_el >= 3 and
get_el_sp(syms[num_el - 1]).X
- get_el_sp(syms[num_el - 2]).X < 1.65)
factor = 1
# Enforce integers for doing gcd.
if all((int(i) == i for i in sym_amt.values())):
factor = abs(gcd(*(int(i) for i in sym_amt.values())))
reduced_form = []
n = num_el - 2 if contains_polyanion else num_el
for i in range(0, n):
s = syms[i]
normamt = sym_amt[s] * 1.0 / factor
reduced_form.append(s)
reduced_form.append(formula_double_format(normamt))
if contains_polyanion:
poly_sym_amt = {syms[i]: sym_amt[syms[i]] / factor
for i in range(n, num_el)}
(poly_form, poly_factor) = reduce_formula(poly_sym_amt)
if poly_factor != 1:
reduced_form.append("({}){}".format(poly_form, int(poly_factor)))
else:
reduced_form.append(poly_form)
reduced_form = "".join(reduced_form)
return reduced_form, factor
def reduce_formula(sym_amt):
"""
Help method to reduce a sym_amt dict to a reduced formula and factor.
Args:
Dict of the form {symbol: amount}.
Returns:
(reduced_formula, factor).
"""
syms = sorted(sym_amt.keys(), key=lambda s: smart_element_or_specie(s).X)
syms = filter(lambda s: sym_amt[s] > Composition.amount_tolerance, syms)
num_el = len(syms)
contains_polyanion = (num_el >= 3
and smart_element_or_specie(syms[num_el - 1]).X -
smart_element_or_specie(syms[num_el - 2]).X < 1.65)
factor = reduce(gcd, sym_amt.values())
reduced_form = []
n = num_el - 2 if contains_polyanion else num_el
for i in range(0, n):
s = syms[i]
normamt = sym_amt[s] * 1.0 / factor
reduced_form.append(s)
reduced_form.append(formula_double_format(normamt))
if contains_polyanion:
poly_sym_amt = {
syms[i]: sym_amt[syms[i]] / factor
for i in range(n, num_el)
}
(poly_form, poly_factor) = reduce_formula(poly_sym_amt)
if poly_factor != 1:
reduced_form.append("({}){}".format(poly_form, int(poly_factor)))
else:
reduced_form.append(poly_form)
reduced_form = "".join(reduced_form)
return reduced_form, factor
def reduce_formula(sym_amt):
"""
Help method to reduce a sym_amt dict to a reduced formula and factor.
Args:
Dict of the form {symbol: amount}.
Returns:
(reduced_formula, factor).
"""
syms = sorted(sym_amt.keys(),
key=lambda s: smart_element_or_specie(s).X)
syms = filter(lambda s: sym_amt[s] > Composition.amount_tolerance,
syms)
num_el = len(syms)
contains_polyanion = (num_el >= 3 and
smart_element_or_specie(syms[num_el - 1]).X
- smart_element_or_specie(syms[num_el - 2]).X < 1.65)
factor = reduce(gcd, sym_amt.values())
reduced_form = []
n = num_el - 2 if contains_polyanion else num_el
for i in range(0, n):
s = syms[i]
normamt = sym_amt[s] * 1.0 / factor
reduced_form.append(s)
reduced_form.append(formula_double_format(normamt))
if contains_polyanion:
poly_sym_amt = {syms[i]: sym_amt[syms[i]] / factor
for i in range(n, num_el)}
(poly_form, poly_factor) = reduce_formula(poly_sym_amt)
if poly_factor != 1:
reduced_form.append("({}){}".format(poly_form, int(poly_factor)))
else:
reduced_form.append(poly_form)
reduced_form = "".join(reduced_form)
return reduced_form, factor
def __str__(self):
return " ".join([
"{}{}".format(k, formula_double_format(v, ignore_ones=False))
for k, v in self.to_dict.items()
])
def test_formula_double_format(self):
self.assertEqual(formula_double_format(1.00), "")
self.assertEqual(formula_double_format(2.00), "2")
self.assertEqual(formula_double_format(2.10), "2.1")
def __str__(self):
return " ".join([
"{}{}".format(k, formula_double_format(v, ignore_ones=False))
for k, v in self.as_dict().items()])
def test_formula_double_format(self):
self.assertEqual(formula_double_format(1.00), "")
self.assertEqual(formula_double_format(2.00), "2")
self.assertEqual(formula_double_format(2.10), "2.1")
