Getting Atom Names in Bio.PDB

Question

I am trying to run a code using BioPython that will allow me to iterate through the atoms of multiple proteins and remove all hydrogen atoms from them. To identify which atoms correspond to hydrogen I wrote the following code:

atom = residues[0].get_atoms()

atoms = list(atom)

atoms

[<Atom N>,
 <Atom CA>,
 <Atom C>,
 <Atom O>,
 <Atom CB>,
 <Atom OG1>,
 <Atom CG2>,
 <Atom H1>,
 <Atom H2>,
 <Atom H3>,
 <Atom HA>,
 <Atom HB>,
 <Atom HG1>,
 <Atom HG21>,
 <Atom HG22>,
 <Atom HG23>]

How can I make it so that BioPython will return the name of the actual element of these atoms, such as "Carbon" or "Hydrogen"?

Note, I tried to use the following functions from the Bio.PDB.Atom module:

"get_name()",

"get_id"

"get_full_id"

They did not return the desired element name.

Answer 1

You may need to translate the elements yourself. You can use the periodictable package.

Note that biopython uses upper-case e.g. FE for element names and periodictable uses title-case e.g. Fe.

I created two methods below: one that takes a symbol i.e. symbol_to_english, and another that takes the atom i.e. atom_to_english and passes its name to symbol_to_english.

import periodictable as pt
from Bio.PDB.Atom import Atom

def symbol_to_english(symbol: str) -> str:
    """This function converts a symbol to its English name.

    Args:
        symbol (str): The symbol of the element.

    Returns:
        str: The English name of the element.
    """
    try:
        return pt.elements.isotope(symbol.title()).name.title()
    except Exception as exc:
        raise ValueError(f"Could not convert symbol {symbol} to English.") from exc

def atom_to_english(atom: Atom) -> str:
    """This function converts an atom's element to its English name.

    Args:
        atom (Atom): The atom to convert.

    Returns:
        str: The English name of the atom's element.
    """
    return symbol_to_english(atom.element)

if __name__ == "__main__":
    atoms = [Atom("FE", (1, 2, 3), 1.0, 1.0, "", "FE", 1, "FE")]
    names = [atom_to_english(atom) for atom in atoms]

    print(names)  # ['Iron']

Answer 2

Atom's element is stored in:

atom.element

It's a string with periodic table element abbreviation: C and H rather than Carbon and Hydrogen.