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Code Editor : complex_chemical_formulas.py
# # complex_chemical_formulas.py # # Example that expands on the basic chemical_formulas.py parser to # include grouped multiplication notation, such as "3(C₆H₅OH)₂". # # Copyright (c) 2024, Paul McGuire # from collections import Counter import pyparsing as pp ppc = pp.common # fmt: off table_of_elements: dict[str, float] = { "H": 1.007, "He": 4.002, "Li": 6.941, "Be": 9.012, "B": 10.811, "C": 12.011, "N": 14.007, "O": 15.999, "F": 18.998, "Ne": 20.18, "Na": 22.99, "Mg": 24.305, "Al": 26.982, "Si": 28.086, "P": 30.974, "S": 32.065, "Cl": 35.453, "Ar": 39.948, "K": 39.098, "Ca": 40.078, "Sc": 44.956, "Ti": 47.867, "V": 50.942, "Cr": 51.996, "Mn": 54.938, "Fe": 55.845, "Co": 58.933, "Ni": 58.693, "Cu": 63.546, "Zn": 65.38, "Ga": 69.723, "Ge": 72.64, "As": 74.922, "Se": 78.96, "Br": 79.904, "Kr": 83.798, "Rb": 85.468, "Sr": 87.62, "Y": 88.906, "Zr": 91.224, "Nb": 92.906, "Mo": 95.96, "Tc": 98.0, "Ru": 101.07, "Rh": 102.906, "Pd": 106.42, "Ag": 107.868, "Cd": 112.411, "In": 114.818, "Sn": 118.71, "Sb": 121.76, "Te": 127.6, "I": 126.904, "Xe": 131.293, "Cs": 132.905, "Ba": 137.327, "La": 138.905, "Ce": 140.116, "Pr": 140.908, "Nd": 144.242, "Pm": 145.0, "Sm": 150.36, "Eu": 151.964, "Gd": 157.25, "Tb": 158.925, "Dy": 162.5, "Ho": 164.93, "Er": 167.259, "Tm": 168.934, "Yb": 173.054, "Lu": 174.967, "Hf": 178.49, "Ta": 180.948, "W": 183.84, "Re": 186.207, "Os": 190.23, "Ir": 192.217, "Pt": 195.084, "Au": 196.967, "Hg": 200.59, "Tl": 204.383, "Pb": 207.2, "Bi": 208.98, "Po": 210.0, "At": 210.0, "Rn": 222.0, "Fr": 223.0, "Ra": 226.0, "Ac": 227.0, "Th": 232.038, "Pa": 231.036, "U": 238.029, "Np": 237.0, "Pu": 244.0, "Am": 243.0, "Cm": 247.0, "Bk": 247.0, "Cf": 251.0, "Es": 252.0, "Fm": 257.0, "Md": 258.0, "No": 259.0, "Lr": 262.0, "Rf": 261.0, "Db": 262.0, "Sg": 266.0, "Bh": 264.0, "Hs": 267.0, "Mt": 268.0, "Ds": 271.0, "Rg": 272.0, "Cn": 285.0, "Nh": 284.0, "Fl": 289.0, "Mc": 288.0, "Lv": 292.0, "Ts": 295.0, "Og": 294.0, } # fmt: on # basic parser elements # - element - a chemical symbol, corresponding to one of the entries # in table_of_elements # - subcript_int - an integer made up of subscript digits # (a normal integer definition uses the one defined in pyparsing.common) # # element = pp.one_of(table_of_elements).set_name("element") element = pp.Regex(pp.util.make_compressed_re(table_of_elements)).set_name("element") element.add_parse_action(lambda t: Counter([t[0]])) subscript_digits = "₀₁₂₃₄₅₆₇₈₉" subscript_int = pp.Word(subscript_digits).set_name("subscript") # define mapping of the int value of each subscript digit subscript_int_map = {digit: value for value, digit in enumerate(subscript_digits)} @subscript_int.add_parse_action def convert_subscript_int(s: pp.ParseResults) -> int: ret = 0 for c in s[0]: ret = ret * 10 + subscript_int_map[c] return ret # # parse actions used internally by the infix_notation expression # def lmult(s, l, t): """ Multiply <element><subscript_integer> """ *terms, qty = t[0] return sum(qty * terms, Counter()) def rmult(s, l, t): """ Multiply <integer><element> """ qty, *terms = t[0] return sum(qty * terms, Counter()) def element_ref_sum(s, l, t): """ Add multiple consecutive element references """ return sum(t[0], Counter()) # optional separator in some chemical formulas optional_separator = pp.Optional(pp.one_of("= ·").suppress()) # define infix expression, where multipliers and subscripts # are treated like operators, so that grouping in ()'s gets # properly handled, even when they are nested element_ref = pp.infix_notation( element, [ (subscript_int, 1, pp.OpAssoc.LEFT, lmult), (ppc.integer, 1, pp.OpAssoc.RIGHT, rmult), (optional_separator, 2, pp.OpAssoc.LEFT, element_ref_sum), ], ) # define the overall parser for a chemical formula, made up # of one or more element_ref's formula = element_ref[1, ...].set_name("chemical_formula") # set names on unnamed expressions for better diagram output pp.autoname_elements() def molecular_weight(c: Counter) -> float: """ Compute overall molecular weight of a chemical formula, whose elements have been parsed into a Counter containing chemical symbols and counts of each element, using the table_of_elements dict to map chemical symbols to each element's atomic weight. """ return sum(table_of_elements[k] * v for k, v in c.items()) if __name__ == '__main__': import contextlib # create railroad diagram for this parser with contextlib.suppress(Exception): formula.create_diagram( "complex_chemical_formulas_diagram.html", vertical=2, show_groups=True ) formula.run_tests( """\ NaCl HOH H₂O H₂O₂ C₆H₅OH C₁₀H₂₁OH (C₆H₅OH)₂ 3(C₆H₅OH)₂ C(OH)₆ CH₃(CH₂)₂OH (CH₃)₃CH CH₃(CH₂)₅CH₃ Ba(BrO₃)₂·H₂O Ba(BrO₃)₂·2(H₂O) """, full_dump=False, post_parse=( lambda _, tokens: f"Molecular counts/weight: {dict(tokens[0])}" f", {molecular_weight(tokens[0]):.3f}" ), ) print()
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