5.15. PDB Topology Parser

This topology parser uses a standard PDB file to build a minimum internal structure representation (list of atoms).

The topology reader reads a PDB file line by line and ignores atom numbers but only reads residue numbers up to 9,999 correctly. If you have systems containing at least 10,000 residues then you need to use a different file format (e.g. the “extended” PDB, XPDB format, see ExtendedPDBParser) that can handle residue numbers up to 99,999.

Note

The parser processes atoms and their names. Masses are guessed and set to 0 if unknown. Partial charges are not set. Elements are parsed if they are valid. If partially missing or incorrect, empty records are assigned.

5.15.1. Classes

class MDAnalysis.topology.PDBParser.PDBParser(filename)[source]

Parser that obtains a list of atoms from a standard PDB file.

Creates the following Attributes:

names
chainids
tempfactors
occupancies
record_types (ATOM/HETATM)
resids
resnames
segids
elements
bonds

Guesses the following Attributes:

masses