What it does:
Removes atoms with missing coordinates from a structure file
When to use:
When there are missing atoms marked with a specific coordinate placeholder value
Python code
from Bio.PDB import PDBParser
import numpy as np
def remove_missing_atoms(pdb_fn: str, missing_coord_placeholder: float):
"""
Removes atoms with missing coordinates from a PDB structure.
Parameters:
-----------
pdb_fn : str
Path to the PDB file
missing_coord_placeholder : float
Value used as a placeholder for missing coordinates
Returns:
--------
structure : Bio.PDB.Structure.Structure
Structure object with missing atoms removed
"""
parser = PDBParser(QUIET=True)
structure = parser.get_structure('X', pdb_fn)
for model in list(structure):
for chain in list(model):
for residue in list(chain):
for atom in list(residue):
if np.any(atom.coord == missing_coord_placeholder):
chain.detach_child(residue.id)
if len(residue) == 0:
chain.detach_child(residue.id)
if len(chain) == 0:
model.detach_child(chain.id)
if len(model) == 0:
structure.detach_child(model.id)
return structure
Python
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Example usage
pdb_fn = "1ABC.pdb"
missing_coord_placeholder = 99.999 # Common placeholder value
structure = remove_missing_atoms(pdb_fn, missing_coord_placeholder)
Python
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Tips and Tricks
β’
Always iterate over each child with for {ChildInstance} in list({ParentInstance}): .
If you iterate each child with for {ChildInstance} in {ParentInstance}: while performing {ParentInstance}.detach_child({ChildInstance}.id), the size of the collection (ParentInstance) changes, which can lead to runtime errors if you donβt use list({ParentInstance}). This is because for {ChildInstance} in {ParentInstance}: is essentially iterating over a Python Iterator.
β’
The function removes atoms with the specified placeholder value and then cleans up any empty residues, chains, or models that might result from removing those atoms.
β’
Common placeholder values in PDB files include 99.999, 0.0, or NaN, depending on the source of the file.