Writing a Topology Reader

Introduction

The topology data defines the structure of the MDAnalysis Universe, and is the first structure generated on initialising the Universe. The generation of this structure is done by a TopologyReader object, which generally reads this information from a file. The first argument in Universe init is the topology file.

Rules

A topology reader subclasses the class TopologyReader, and then must define the method parse. The parse method must return a dictionary of fields, as defined in Topology Data Structures

Examples

Class MyParser(TopologyParser)
    def parse(self):
        struc = dict()
        # required:
        struc['atoms'] = self._parse_atoms()  # required
        # optionally:
        struc['bonds'] = self._parse_bonds()

    def _parse_atoms(self):
        # atoms need to be a list of Atom instances
        a = Atom()

        return (A,)

    def _parse_bonds(self):
        # bonds will be a tuple of 2 length tuples
        return ((0, 1))

For an example of a very minimalistic TopologyReader, see the XYZParser

For an example of a TopologyReader populating many fields, see the PSFParser