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4.8. PDB topology parser

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4.10. PDBQT topology parser

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4.9. Primitive PDB topology parser

Use a PDB file to build a minimum internal structure representation (list of atoms).

Reads a PDB file line by line and is not fuzzy about numbering.

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.PrimitivePDBParser.PDBParseError

Signifies an error during parsing a PDB file.

MDAnalysis.topology.PrimitivePDBParser.parse(filename)

Parse atom information from PDB file filename.

Returns :MDAnalysis internal structure dict

See also

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