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4.10. Extended PDB topology parser

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4.12. PQR topology parser

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4.11. PDBQT topology parser

Use a PDBQT file to build a minimum internal structure representation (list of atoms), including AutoDock atom types (stored as Atom.type) and partial charges (Atom.charge).

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

This does not support multi-model PDBQT files (yet!)

Warning

Only cares for atoms and their names; connectivity is not deduced. Masses are guessed and set to 0 if unknown.

exception MDAnalysis.topology.PDBQTParser.PDBQTParseError[source]

Signifies an error during parsing a PDBQT file.

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

MDAnalysis.topology.PDBQTParser.parse(filename)[source]

Parse atom information from PDBQT 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.PDBQT.PDBQTReader.