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4.8. PDB topology parser

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4.10. Extended PDB topology parser

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4.9. Primitive 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. Bond connectivity can be guessed if the bonds=True keyword is set for Universe.

class MDAnalysis.topology.PrimitivePDBParser.PrimitivePDBParser(filename, **kwargs)[source]

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

New in version 0.8.

parse()[source]

Parse atom information from PDB file filename.

Returns:MDAnalysis internal structure dict

See also

The structure dict is defined in MDAnalysis.topology and the file is read with MDAnalysis.coordinates.PDB.PrimitivePDBReader.