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PDB Format

Read and write Protein Data Bank structure files as ATOM/HETATM records.

Overview​

PropertyValue
Format idpdb
ClassPDBIterable
Extensions.pdb
ReadYes
WriteYes
Extranone (stdlib)
Maturitystable

Record shape​

{
    "record_type": "ATOM",
    "serial": 1,
    "name": "CA",
    "resName": "ALA",
    "chainID": "A",
    "resSeq": 1,
    "x": 1.0,
    "y": 2.0,
    "z": 3.0,
    "element": "C",
    "model": 1,
}

Only ATOM/HETATM lines are yielded. Write emits fixed-width ATOM/HETATM lines.

Parameters​

ParameterDescription
modelOptional filter to the N-th MODEL in multi-model files

Usage​

from iterable import open_iterable

with open_iterable("protein.pdb") as source:
    for atom in source:
        print(atom["name"], atom["resName"], atom["x"], atom["y"], atom["z"])

with open_iterable("protein.pdb", iterableargs={"model": 1}) as source:
    for atom in source:
        print(atom["model"], atom["serial"])

Error Handling​

  • Missing dependency: optional libraries raise ImportError with an install hint (pip install 'iterabledata[<extra>]' when an extra exists).
  • Write mode: read-only formats raise WriteNotSupportedError or ValueError when opened with mode="w".
  • Bad or unsupported input: may raise ValueError, OSError, or library-specific errors.
  • See Troubleshooting for decoding, detection, and engine issues.

See also​