Guide to new Topology format

Richard Gowers edited this page Dec 8, 2015 · 1 revision

The new (as of Dec 2015) topology format requires that topology parsers return a single Topology object, where previously they returned a list of Atom instances.

Below is an annotated version of the parse for GRO files.

The Topology object contains many tables of data, called Attributes, which *Groups later refer to. For example, Atomnames is an Attribute. Attributes facilitate access to arrays of data. For an AtomGroup accessing the names, this simply applies AtomGroup.indices as a mask to the array, but it also handles the ResidueGroup and SegmentGroup cases.

import numpy as np

from ..lib.util import openany
from ..core.topologyattrs import (
    Resids,
    Resnames,
    Atomids,
    Atomnames,
)
from ..core.topology import Topology
from .base import TopologyReader, squash_by

All Parsers must still inherit from mda.topology.base.TopologyReader and define a parse method

class GROParser(TopologyReader)
    def parse(self):
        """Return the *Topology* object for this file"""
        # Gro has the following columns
        # resid, resname, name, index, (x,y,z)
        with openany(self.filename, 'r') as inf:
            inf.readline()
            n_atoms = int(inf.readline())

            # Allocate arrays
            # This isn't necessary, appending to lists is also
            # possible where the number of atoms isn't known beforehand.
            # But ultimately all data must be stored in np.arrays
            resids = np.zeros(n_atoms, dtype=np.int32)
            # String data must use dtype=object so that any size string
            # can be stored.
            resnames = np.zeros(n_atoms, dtype=object)
            names = np.zeros(n_atoms, dtype=object)
            indices = np.zeros(n_atoms, dtype=np.int32)

            for i in xrange(n_atoms):
                line = inf.readline()
                resids[i] = int(line[:5])
                resnames[i] = line[5:10].strip()
                names[i] = line[10:15].strip()
                indices[i] = int(line[15:20])

Whereas previously each Atom kept a record of its resname, all Residue properties are now stored on a per-Residue basis, meaning that only one record of Residue name is ever kept.

Considering a trivial case of 4 atoms:

  • Atom 1, Resid 3, Resname 'A'
  • Atom 2, Resid 3, Resname 'A'
  • Atom 3, Resid 4, Resname 'B'
  • Atom 4, Resid 4, Resname 'B'

The squash_by function reduces this information to the following:

  • Atom 1, Resindex 0
  • Atom 2, Resindex 0
  • Atom 3, Resindex 1
  • Atom 4, Resindex 1

Represented in the array residx

And then a separate record of information per-Residue

  • Resindex 0, Resid 3, Resname 'A'
  • Resindex 1, Resid 4, Resname 'B'

Represented in the arrays new_resids and new_resnames

        residx, new_resids, (new_resnames,) = squash_by(resids, resnames)

        # new_resids is len(residues)
        # so resindex 0 has resid new_resids[0]
        atomnames = Atomnames(names)
        atomids = Atomids(indices)
        residueids = Resids(new_resids)
        residuenames = Resnames(new_resnames)

Finally, the Topology is created by declaring its size in n_atoms, n_residues and n_segments, passing a list of the Attributes, and the relationship between atom indices and residue indices, and residue indices and segment indices.

        top = Topology(n_atoms, len(new_resids), 0,
                       attrs=[atomnames, atomids, residueids, residuenames],
                       atom_resindex=residx,
                       residue_segindex=None)

        return top

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