"""
Managing components/composition
"""
from typing import List, Dict, Union
import periodictable as pt
from periodictable.formulas import Formula
custom_components: List[str] = ['LOI', 'Ash']
# Kudos: pyrolite
DEFAULT_CHARGES: Dict = dict(
H=1,
Li=1,
Be=1,
B=3,
C=4,
O=-2,
F=-1,
Na=1,
Mg=2,
Al=3,
Si=4,
P=3,
Cl=-1,
K=1,
Ca=2,
Sc=3,
Ti=4,
V=3,
Cr=3,
Mn=2,
Fe=2,
Co=2,
Ni=2,
Cu=2,
Zn=2,
Br=-1,
Rb=1,
Sr=2,
Y=3,
Zr=4,
Nb=5,
Sn=4,
I=-1,
Cs=1,
Ba=2,
La=3,
Ce=3,
Pr=3,
Nd=3,
Sm=3,
Eu=3,
Gd=3,
Tb=3,
Dy=3,
Ho=3,
Er=3,
Tm=3,
Yb=3,
Lu=3,
Hf=4,
Pb=2,
Th=4,
U=4,
)
[docs]
def elements() -> List[str]:
res: List[str] = [el.symbol for el in pt.elements]
return res
[docs]
def is_element(candidates: List[str], strict: bool = True) -> Union[List[str], Dict[str, str]]:
if strict:
matches: list = list(set(candidates).intersection(elements()))
else:
e_map: Dict[str, str] = {e.symbol.lower(): e.symbol for e in pt.elements}
matches: Dict[str, str] = {c: e_map[c.lower()] for c in candidates if c.lower() in e_map.keys()}
return matches
[docs]
def oxides() -> List[Formula]:
# cats = {e for e in [el for el in pt.elements if str(el) in DEFAULT_CHARGES.keys()] if DEFAULT_CHARGES[str(e)] > 0}
cats = {el for el in pt.elements if (str(el) in DEFAULT_CHARGES.keys()) and (DEFAULT_CHARGES[str(el)] > 0)}
res: List[Formula] = []
for c in cats:
charge = DEFAULT_CHARGES[str(c)]
if charge % 2 == 0:
res.append(pt.formula(str(c) + str(1) + 'O' + str(charge // 2)))
else:
res.append(pt.formula(str(c) + str(2) + 'O' + str(charge)))
return res
[docs]
def is_oxide(candidates: List[str], strict: bool = True) -> Union[List[str], Dict[str, str]]:
if strict:
oxs = {str(o) for o in oxides()}
matches: list = list(set(candidates).intersection(oxs))
else:
o_map: Dict[str, str] = {str(o).lower(): str(o) for o in oxides()}
matches: Dict[str, str] = {c: o_map[c.lower()] for c in candidates if c.lower() in o_map.keys()}
return matches
[docs]
def is_compositional(candidates: List[str], strict: bool = True) -> Union[List[str], Dict[str, str]]:
"""
Check if a list of candidates are compositional components (elements or oxides)
Args:
candidates: list of string candidates
strict: If True, the candidates must be in the list of known compositional components (elements or oxides)
as chemical symbols.
Returns:
If strict, a list of compositional components, otherwise a dict of the original candidates (keys) and
their compositional component symbols (values)
"""
if strict:
comps = {str(o) for o in oxides()}.union(set(elements())).union(set(custom_components))
matches: list = list(set(candidates).intersection(comps))
else:
comp_map: Dict[str, str] = {**{str(o).lower(): str(o) for o in oxides()},
**{a.lower(): a for a in elements()},
**{c.lower(): c for c in custom_components}}
matches: Dict[str, str] = {c: comp_map[c.lower()] for c in candidates if c.lower() in comp_map.keys()}
return matches
[docs]
def get_components(candidates: List[str], strict: bool = True) -> list[str]:
return list(is_compositional(candidates, strict=strict).keys())