Source code for tcmu.data.atom

import pathlib as pl


# read data
data_dir = pl.Path(__file__).parents[0] / "_atom_data_info"

with open(data_dir / "name.txt") as data:
    lines = data.readlines()
_element_order = [line.split(",")[1].strip() for line in lines]

with open(data_dir / "symbol.txt") as data:
    lines = data.readlines()
_symbol_order = [line.split(",")[1].strip() for line in lines]

with open(data_dir / "radius.txt") as data:
    lines = data.readlines()
_radii = {int(line.split(",")[0]): float(line.split(",")[1].strip()) for line in lines}

with open(data_dir / "ionic_radius.txt") as data:
    lines = data.readlines()
_ionic_radii = {(int(line.split(",")[0]), line.split(",")[1], int(line.split(",")[2])): float(line.split(",")[3].strip()) for line in lines}

with open(data_dir / "color.txt") as data:
    lines = data.readlines()
_colors = {int(line.split(",")[0]): [int(x.strip()) for x in line.split(",")[1:]] for line in lines}



[docs]
def parse_element(val):
    """
    Parse a str or int to an atom number.

    Args:
        val: Element name, symbol or atom number.

    Returns:
        Atom number corresponding to val.

    Examples:

        .. code-block:: python

            parse_element('Hydrogen') == 1
            parse_element('C') == 6
            parse_element(23) == 23
    """
    # we will assume an integer value is an atom number already
    if isinstance(val, int):
        return val
    # if it is not an int it should be a string
    if val.lower() in _element_order:
        # first try to get it in the element name list
        return _element_order.index(val.lower())
    if val in _symbol_order:
        # alternatively try to get it in the symbol list
        return _symbol_order.index(val)
    raise KeyError(f'Element "{val}" not parsable.')




[docs]
def radius(element):
    """
    Args:
        element: the symbol, name or atom number of the element. See :func:`parse_element`.
    Return:
        The empirical covalent radius of an element in angstroms, up to element 96.
    Source:
        https://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page)
    """
    num = parse_element(element)
    return _radii.get(num)




[docs]
def ionic_radius(element, charge=0, spin_state=None):
    """
    Args:
        element: the symbol, name or atom number of the element. See :func:`parse_element`.
        charge: the charge of the ion.
        spin_state: some elements are classified as `high` or `low` spin. Other elements have spin-state `none`.
    Return:
        The empirical covalent radius of an element in angstroms, up to element 96.
    Source:
        https://en.wikipedia.org/wiki/Ionic_radius
    """
    num = parse_element(element)
    spin_state = str(spin_state)
    return _ionic_radii.get((num, spin_state, charge))




[docs]
def color(element, mode: str = "rgb"):
    """
    Args:
        element: the symbol, name or atom number of the element. See :func:`parse_element`.
        mode: the type of color to return. Can be `rgb` or `hex`.

    Return:
        The standard CPK colors of the elements, up to element 109.
        If the mode is `rgb` returns a tuple of RGB values between `0` and `255`.
    Source:
        https://en.wikipedia.org/wiki/CPK_coloring
    """
    num = parse_element(element)
    c = _colors[num]
    if mode == "rgb":
        return c
    if mode == "hex":
        return "#%02x%02x%02x" % tuple(c)




[docs]
def atom_number(element):
    return parse_element(element)




[docs]
def symbol(element):
    num = parse_element(element)
    return _symbol_order[num]




[docs]
def element(element):
    num = parse_element(element)
    return _element_order[num]



if __name__ == "__main__":
    print(symbol(0))
    print(ionic_radius(1, -1))
Table of Contents

Source code for tcmu.data.atom
