python_pdb.parsers module

Functions for parsing PDB files into python objects and vice versa.

python_pdb.parsers.parse_pdb(contents: str, silent: bool = False) → Structure

Create structure object from PDB file.

This function is a wrapper around the Structure.from_pdb(…) classmethod that provides additional functionality of suppressing warnings.

Parameters:

• contents – contents of a PDB file in string format.

• silent – suppress any warnings while building the structure (Default: False)

Returns:

Structure object parsed from the PDB file.

python_pdb.parsers.parse_pdb_to_pandas(contents: str) → DataFrame

Create pandas dataframe from the contents of a pdb file.

Parameters:

contents – the contents of a pdb file.

Returns:

• record_type

  • atom_number

  • atom_name

  • alt_loc

  • residue_name

  • chain_id

  • residue_seq_id

  • residue_insert_code

  • pos_x

  • pos_y

  • pos_z

  • occupancy

  • b_factor

  • element

  • charge

and optionally model_index if there are multiple models.

Return type:

dataframe with the following columns representing a structure

python_pdb.parsers.stringify_structure(structure: Structure) → str

Format structure as pdb atom records.