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4.13. DESRES Molecular Structure file format topology parser

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4.12. PQR topology parser

Read atoms with charges from a PQR file (as written by PDB2PQR). No connectivity is deduced.

See also

The file format is described in MDAnalysis.coordinates.PQR.

class MDAnalysis.topology.PQRParser.PQRParser(filename, guess_bonds_mode=False, **kwargs)[source]

Parse atom information from PQR file filename.

Only reads the list of atoms. Reads the charges and radii from the PQR file and populates the MDAnalysis.core.AtomGroup.Atom.charge and MDAnalysis.core.AtomGroup.Atom.radius attribute.

Returns :MDAnalysis internal structure dict

See also

The structure dict is defined in MDAnalysis.topology and PQRReader is used to read the PQR file.

Changed in version 0.9.0: Read chainID from a PQR file and use it as segid (before we always used ‘SYSTEM’ as the new segid).

parse()[source]

Parse atom information from PQR file filename.

Returns :MDAnalysis internal structure dict