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4.7. GRO topology parser

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4.9. Primitive PDB topology parser

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4.8. PDB topology parser

Use a PDB file to build a minimum internal structure representation.

Warning

Only cares for atoms and their names; neither connectivity nor (partial) charges are deduced. Masses are guessed and set to 0 if unknown.

exception MDAnalysis.topology.PDBParser.PDBParseError[source]

Signifies an error while reading a PDB file.

x.__init__(...) initializes x; see help(type(x)) for signature

MDAnalysis.topology.PDBParser.parse(pdbfile)[source]

Parse atom information from PDB file pdbfile.

Only reads the list of atoms.

This functions uses the Bio.PDB.PDBParser as used by MDAnalysis.coordinates.pdb.extensions.get_structure().

Returns:MDAnalysis internal structure dict

See also

The structure dict is defined in MDAnalysis.topology.PSFParser.parse().