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4.3. MDAnalysis topology tables

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4.5. AMBER PRMTOP topology parser

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4.4. PSF topology parser

Reads a CHARMM/NAMD/XPLOR PSF file to build the system. Currently uses the list of atoms (including atom types, which can be either integers or strings, masses and partial charges) and the bond connectivity.

It reads both standard and extended (“EXT”) PSF formats and can also parse NAMD space-separated “PSF” file variants.

exception MDAnalysis.topology.PSFParser.PSFParseError

Signifies an error during parsing of a CHARMM PSF file.

MDAnalysis.topology.PSFParser.parse(filename)

Parse CHARMM/NAMD/XPLOR PSF file filename.

Returns :MDAnalysis internal structure dict as defined here.