pymolecule-parser: A parser for a molecule formula that supports nested brackets

Installation

pip install pymolecule-parser

Usage

• pymolecule_parser.parse returns a dictionary of atoms and their numbers. (type: dict[str, int])

from pymolecule_parser import parse

dict_1 = parse("H2O") # {'H': 2, 'O': 1}
dict_2 = parse("3H2O") # {'H': 6, 'O': 3}
dict_3 = parse("H2O2(OH)2") # {'H': 4, 'O': 4}
dict_4 = parse("[Co(NH3)6]Cl3") # {'Co': 1, 'N': 6, 'H': 18, 'Cl': 3}

Options

• strict_mode
  • If strict_mode is True, the parser expects all atoms in the argument to be from hydrogen (H) to oganeson (Og), otherwise raises an exception
  • If strict_mode is False, the parser parses arguments even if they are not existing atoms if they satisfy the rules for writing atoms (first letter is uppercase, subsequent letters are lowercase)
  • Default: False (non-strict mode)

If you want to use strict mode, please use the following code.

from pymolecule_parser import parse

dict_1 = parse("H2O", strict_mode=True) # {'H': 2, 'O': 1}

Limitations

The following notations are not supported.

• Ion notations
  • For example, [Cu(NH3)4]2+ is not supported. Use Cu(NH3)4 instead.
• middle dot ·
  • For example, CuSO4·5H2O is not supported. Use CuSO4(H2O)5 instead.

License

Apache License 2.0

Author

Kohei Noda