PDBPython

The scope of this module is downloading or reading PDB-Files and subsequently parsing them.

Disclaimer

This project is only intended for my personal use and may change significantly over time. You are free to use this code at own risk.

Classes

PDBFile

The class PDBFile is initialized with pdb_id (str, an identifier for the file) and pdb_content (str, the content of a PDB-file). In default check_lines (bool) is set to True, which will raise an AssertionError if the reconstructed line for an atom differs from the original line (alignment of atom label is allowed to differ). After reviewing differences you can suppress the error with setting check_lines to False.
The CONNECT info in PDB-files is often referencing atoms not present in the file. When setting allow_connect_errors to False these errors are ignored.

Constructing a PDBFile object from online database or file.

The class PDBFile can also be constructed from a file:

pdbfile_obj = PDBFile.from_file("./path/to/file.pdb", "PDB_ID_of_File")

Or directly from PDBe

pdbfile_obj = PDBFile.from_online("PDB_ID")

PDBStructure

Most PDB files contain only one protein model, however there are PDB files which contain multiple protein conformations (mainly NMR-resolved structures). Models are herein called PDBStructure and can be accessed via the PDBFIle object:

pdbfile_obj = PDBFile.from_online("PDB_ID")
model_0 = pdbfile_obj.model[0]

On this note: My naming conventions with model and structure may be not very consistent. This is a #TODO for future refactorings.

PDBResidue

Each PDBStructure consists of residudes represented by PDBResidue-objects. Which themselves consist of PDBAtom- objects.
Residues can be accessed via:

pdbfile_obj = PDBFile.from_online("PDB_ID")
model_0 = pdbfile_obj.model[0]
residue = model_0.residues

Residues specified by chain and residue-ID can also be accessed via a dictionary:

chain = "A"
res_id = 1
residue_A_1 = model_0.residue_dict[(chain, res_id)]

For some atoms in a residue alternative positions are given. When specific atom positions are required other locations can be removed via:

residue.remove_alternate_positions(keep="A")

keep specifies the alternative position to keep. The default value is "A".
To apply this to all residues of a PDBStructure, call:

model_0.remove_alternate_positions(keep="A")