Source code for ase.symbols

import warnings

import numpy as np

from ase.data import atomic_numbers, chemical_symbols
from ase.formula import Formula


def string2symbols(s):
    """Convert string to list of chemical symbols."""
    return list(Formula(s))


def symbols2numbers(symbols):
    if isinstance(symbols, str):
        symbols = string2symbols(symbols)
    numbers = []
    for s in symbols:
        if isinstance(s, str):
            numbers.append(atomic_numbers[s])
        else:
            numbers.append(int(s))
    return numbers


[docs]class Symbols: """A sequence of chemical symbols. ``atoms.symbols`` is a :class:`ase.symbols.Symbols` object. This object works like an editable view of ``atoms.numbers``, except its elements are manipulated as strings. Examples: >>> from ase.build import molecule >>> atoms = molecule('CH3CH2OH') >>> atoms.symbols Symbols('C2OH6') >>> atoms.symbols[:3] Symbols('C2O') >>> atoms.symbols == 'H' array([False, False, False, True, True, True, True, True, True], dtype=bool) >>> atoms.symbols[-3:] = 'Pu' >>> atoms.symbols Symbols('C2OH3Pu3') >>> atoms.symbols[3:6] = 'Mo2U' >>> atoms.symbols Symbols('C2OMo2UPu3') >>> atoms.symbols.formula Formula('CCOMoMoUPuPuPu') The :class:`ase.formula.Formula` object is useful for extended formatting options and analysis. """ def __init__(self, numbers): self.numbers = numbers @classmethod def fromsymbols(cls, symbols): numbers = symbols2numbers(symbols) return cls(np.array(numbers)) @property def formula(self): """Formula object.""" return Formula.from_list([chemical_symbols[Z] for Z in self.numbers]) def __getitem__(self, key): num = self.numbers[key] if np.isscalar(num): return chemical_symbols[num] return Symbols(num) def __setitem__(self, key, value): numbers = symbols2numbers(value) if len(numbers) == 1: numbers = numbers[0] self.numbers[key] = numbers def __len__(self): return len(self.numbers) def __str__(self): return self.get_chemical_formula('reduce') def __repr__(self): return 'Symbols(\'{}\')'.format(self) def __eq__(self, obj): if not hasattr(obj, '__len__'): return False try: symbols = Symbols.fromsymbols(obj) except Exception: # Typically this would happen if obj cannot be converged to # atomic numbers. return False return self.numbers == symbols.numbers def get_chemical_formula(self, mode='hill', empirical=False): """Get chemical formula. See documentation of ase.atoms.Atoms.get_chemical_formula().""" if mode in ('reduce', 'all') and empirical: warnings.warn("Empirical chemical formula not available " "for mode '{}'".format(mode)) if len(self) == 0: return '' numbers = self.numbers if mode == 'reduce': n = len(numbers) changes = np.concatenate(([0], np.arange(1, n)[numbers[1:] != numbers[:-1]])) symbols = [chemical_symbols[e] for e in numbers[changes]] counts = np.append(changes[1:], n) - changes tokens = [] for s, c in zip(symbols, counts): tokens.append(s) if c > 1: tokens.append(str(c)) formula = ''.join(tokens) elif mode == 'all': formula = ''.join([chemical_symbols[n] for n in numbers]) else: symbols = [chemical_symbols[Z] for Z in numbers] f = Formula('', _tree=[(symbols, 1)]) if empirical: f, _ = f.reduce() if mode in {'hill', 'metal'}: formula = f.format(mode) else: raise ValueError( "Use mode = 'all', 'reduce', 'hill' or 'metal'.") return formula