Atom Utilities

Atom Utilities

This module contains utility functions for working with PDB atoms and elements.

hbat.utilities.atom_utils.get_element_from_pdb_atom(atom_name: str) → str

Map PDB atom name to chemical element using regex patterns.

This function uses regular expressions to identify the element type from PDB atom naming conventions, handling complex cases like: - Greek letter remoteness indicators (CA, CB, CG, CD, CE, CZ, CH) - Numbered variants (C1’, H2’’, OP1, etc.) - Ion charges (CA2+, MG2+, etc.) - IUPAC hydrogen naming conventions

Parameters:

atom_name (str) – PDB atom name (e.g., ‘CA’, ‘OP1’, ‘H2’’, ‘CA2+’)

Returns:

Chemical element symbol (e.g., ‘C’, ‘O’, ‘H’, ‘CA’)

Return type:

str

Examples

>>> get_element_from_pdb_atom('CA')
'C'
>>> get_element_from_pdb_atom('OP1')
'O'
>>> get_element_from_pdb_atom('CA2+')
'CA'
>>> get_element_from_pdb_atom('H2'')
'H'

hbat.utilities.atom_utils.pdb_atom_to_element(atom_name: str) → str

High-performance mapping of PDB atom name to chemical element.

Uses a pre-computed dictionary for common atoms and falls back to regex-based pattern matching for less common cases.

Parameters:

atom_name (str) – PDB atom name

Returns:

Chemical element symbol

Return type:

str