Source code for ase.formula

import re
import sys
from typing import Dict, Tuple, List, Union

from ase.utils import gcd
from ase.data import chemical_symbols

if sys.version_info >= (3, 6):
    ordereddict = dict
else:
    from collections import OrderedDict as ordereddict


Tree = Union[str, Tuple['Tree', int], List['Tree']]


[docs]class Formula: def __init__(self, formula: str = '', _tree: Tree = None, _count: Dict[str, int] = None): """Chemical formula object. Parameters ---------- formula: str Text string representation of formula. Examples: ``'6CO2'``, ``'30Cu+2CO'``, ``'Pt(CO)6'``. Examples -------- >>> from ase.formula import Formula >>> w = Formula('H2O') >>> w.count() {'H': 2, 'O': 1} >>> 'H' in w True >>> w == 'HOH' True >>> f'{w:latex}' 'H$_{2}$O' >>> w.format('latex') 'H$_{2}$O' >>> divmod(6 * w + 'Cu', w) (6, Formula('Cu')) Raises ------ ValueError on malformed formula """ self._formula = formula self._tree = _tree or parse(formula) self._count = _count or count_tree(self._tree)
[docs] def count(self) -> Dict[str, int]: """Return dictionary mapping chemical symbol to number of atoms. Example ------- >>> Formula('H2O').count() {'H': 2, 'O': 1} """ return self._count.copy()
[docs] def reduce(self) -> Tuple['Formula', int]: """Reduce formula. Returns ------- formula: Formula Reduced formula. n: int Number of reduced formula units. Example ------- >>> Formula('2H2O').reduce() (Formula('H2O'), 2) """ dct, N = self._reduce() return self.from_dict(dct), N
[docs] def stoichiometry(self) -> Tuple['Formula', 'Formula', int]: """Reduce to unique stoichiomerty using "chemical symbols" A, B, C, ... Examples -------- >>> Formula('CO2').stoichiometry() (Formula('AB2'), Formula('CO2'), 1) >>> Formula('(H2O)4').stoichiometry() (Formula('AB2'), Formula('OH2'), 4) """ count1, N = self._reduce() c = ord('A') count2 = ordereddict() count3 = ordereddict() for n, symb in sorted((n, symb) for symb, n in count1.items()): count2[chr(c)] = n count3[symb] = n c += 1 return self.from_dict(count2), self.from_dict(count3), N
[docs] def format(self, fmt: str = '') -> str: """Format formula as string. Formats: * ``'hill'``: alphabetically ordered with C and H first * ``'metal'``: alphabetically ordered with metals first * ``'abc'``: count ordered first then alphabetically ordered * ``'latex'``: LaTeX representation * ``'html'``: HTML representation * ``'rest'``: reStructuredText representation Example ------- >>> Formula('H2O').format('html') 'H<sub>2</sub>O' """ return format(self, fmt)
[docs] def __format__(self, fmt: str) -> str: """Format Formula as str. Possible formats: ``'hill'``, ``'metal'``, ``'abc'``, ``'latex'``, ``'html'``, ``'rest'``. Example ------- >>> f = Formula('OH2') >>> '{f}, {f:hill}, {f:latex}'.format(f=f) 'OH2, H2O, OH$_{2}$' """ if fmt == 'hill': count = self.count() count2 = ordereddict() for symb in 'CH': if symb in count: count2[symb] = count.pop(symb) for symb, n in sorted(count.items()): count2[symb] = n return dict2str(count2) if fmt == 'metal': count = self.count() result2 = [(s, count.pop(s)) for s in non_metals if s in count] result = [(s, count[s]) for s in sorted(count)] result += sorted(result2) return dict2str(ordereddict(result)) if fmt == 'abc': _, f, N = self.stoichiometry() return dict2str({symb: n * N for symb, n in f._count.items()}) if fmt == 'latex': return self._tostr('$_{', '}$') if fmt == 'html': return self._tostr('<sub>', '</sub>') if fmt == 'rest': return self._tostr(r'\ :sub`', r'`\ ') if fmt == '': return self._formula raise ValueError('Invalid format specifier')
[docs] @staticmethod def from_dict(dct: Dict[str, int]) -> 'Formula': """Convert dict to Formula.""" return Formula(dict2str(dct), _tree=[([(symb, n) for symb, n in dct.items()], 1)], _count=dict(dct))
[docs] def from_list(symbols): # (List[str]) -> Formula """Convert list of chemical symbols to Formula.""" return Formula(''.join(symbols), _tree=[(symbols[:], 1)])
[docs] def __len__(self) -> int: """Number of atoms.""" return sum(self._count.values())
[docs] def __getitem__(self, symb: str) -> int: """Number of atoms with chemical symbol *symb*.""" return self._count.get(symb, 0)
[docs] def __contains__(self, f: Union[str, 'Formula']) -> bool: """Check if formula contains chemical symbols in *f*. Type of *f* must be str or Formula. Example ------- >>> 'OH' in Formula('H2O') True """ if isinstance(f, str): f = Formula(f) for symb, n in f._count.items(): if self[symb] < n: return False return True
[docs] def __eq__(self, other) -> bool: """Equality check. Note that order is not important. Example ------- >>> Formula('CO') == Formula('OC') True """ if isinstance(other, str): other = Formula(other) elif not isinstance(other, Formula): return False return self._count == other._count
[docs] def __add__(self, other: Union[str, 'Formula']) -> 'Formula': """Add two formulas.""" if not isinstance(other, str): other = other._formula return Formula(self._formula + '+' + other)
def __radd__(self, other: str): # -> Formula return Formula(other) + self
[docs] def __mul__(self, N: int) -> 'Formula': """Repeat formula `N` times.""" if N == 0: return Formula('') return self.from_dict({symb: n * N for symb, n in self._count.items()})
def __rmul__(self, N: int): # -> Formula return self * N
[docs] def __divmod__(self, other: Union['Formula', str]) -> Tuple[int, 'Formula']: """Return the tuple (self // other, self % other). Invariant:: div, mod = divmod(self, other) div * other + mod == self Example ------- >>> divmod(Formula('H2O'), 'H') (2, Formula('O')) """ if isinstance(other, str): other = Formula(other) N = min(self[symb] // n for symb, n in other._count.items()) dct = self.count() if N: for symb, n in other._count.items(): dct[symb] -= n * N if dct[symb] == 0: del dct[symb] return N, self.from_dict(dct)
def __rdivmod__(self, other): return divmod(Formula(other), self) def __mod__(self, other): return divmod(self, other)[1] def __rmod__(self, other): return Formula(other) % self def __floordiv__(self, other): return divmod(self, other)[0] def __rfloordiv__(self, other): return Formula(other) // self def __iter__(self, tree=None): if tree is None: tree = self._tree if isinstance(tree, str): yield tree elif isinstance(tree, tuple): tree, N = tree for _ in range(N): yield from self.__iter__(tree) else: for tree in tree: yield from self.__iter__(tree) def __str__(self): return self._formula def __repr__(self): return 'Formula({!r})'.format(self._formula) def _reduce(self): N = 0 for n in self._count.values(): if N == 0: N = n else: N = gcd(n, N) dct = {symb: n // N for symb, n in self._count.items()} return dct, N def _tostr(self, sub1, sub2): parts = [] for tree, n in self._tree: s = tree2str(tree, sub1, sub2) if s[0] == '(' and s[-1] == ')': s = s[1:-1] if n > 1: s = str(n) + s parts.append(s) return '+'.join(parts)
def dict2str(dct): return ''.join(symb + (str(n) if n > 1 else '') for symb, n in dct.items()) def parse(f: str): # -> Tree if not f: return [] parts = f.split('+') result = [] for part in parts: n, f = strip_number(part) result.append((parse2(f), n)) return result def parse2(f: str) -> Tree: units = [] while f: if f[0] == '(': level = 0 for i, c in enumerate(f[1:], 1): if c == '(': level += 1 elif c == ')': if level == 0: break level -= 1 else: raise ValueError f2 = f[1:i] n, f = strip_number(f[i + 1:]) unit = (parse2(f2), n) else: m = re.match('([A-Z][a-z]?)([0-9]*)', f) if m is None: raise ValueError symb = m.group(1) number = m.group(2) if number: unit = (symb, int(number)) else: unit = symb f = f[m.end():] units.append(unit) if len(units) == 1: return unit return units def strip_number(s: str) -> Tuple[int, str]: m = re.match('[0-9]*', s) assert m is not None return int(m.group() or 1), s[m.end():] def tree2str(tree: Tree, sub1: str, sub2: str) -> str: if isinstance(tree, str): return tree if isinstance(tree, tuple): tree, N = tree s = tree2str(tree, sub1, sub2) if N == 1: if s[0] == '(' and s[-1] == ')': return s[1:-1] return s return s + sub1 + str(N) + sub2 return '(' + ''.join(tree2str(tree, sub1, sub2) for tree in tree) + ')' def count_tree(tree: Tree) -> Dict[str, int]: if isinstance(tree, str): return {tree: 1} if isinstance(tree, tuple): tree, N = tree return {symb: n * N for symb, n in count_tree(tree).items()} dct = {} # type: Dict[str, int] for tree in tree: for symb, n in count_tree(tree).items(): m = dct.get(symb, 0) dct[symb] = m + n return dct # non metals, half-metals/metalloid, halogen, noble gas: non_metals = ['H', 'He', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Si', 'P', 'S', 'Cl', 'Ar', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Sb', 'Te', 'I', 'Xe', 'Po', 'At', 'Rn'] # Backwards compatibility:
[docs]def formula_hill(numbers, empirical=False): """Convert list of atomic numbers to a chemical formula as a string. Elements are alphabetically ordered with C and H first. If argument `empirical`, element counts will be divided by greatest common divisor to yield an empirical formula""" symbols = [chemical_symbols[Z] for Z in numbers] f = Formula('', [(symbols, 1)]) if empirical: f, _ = f.reduce() return f.format('hill')
# Backwards compatibility:
[docs]def formula_metal(numbers, empirical=False): """Convert list of atomic numbers to a chemical formula as a string. Elements are alphabetically ordered with metals first. If argument `empirical`, element counts will be divided by greatest common divisor to yield an empirical formula""" symbols = [chemical_symbols[Z] for Z in numbers] f = Formula('', [(symbols, 1)]) if empirical: f, _ = f.reduce() return f.format('metal')