# Source code for MDAnalysis.topology.GSDParser

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    """GSD topology parser
    =========================

    .. versionadded:: 0.17.0

    The :class:`GSDParser` generates a topology from HOOMD_ GSD topology/trajectory
    files. The GSD file stores information on both the topology and the trajectory
    in the same file, and allows for varying atom numbers/identities and topologies
    during the course of the simulation. At the moment MDAnalysis can deal only
    with the case in which there is no variation. The trajectory data are read with
    the :class:`~MDAnalysis.coordinates.GSD.GSDReader` class.

    .. _HOOMD: http://codeblue.umich.edu/hoomd-blue/index.html
    .. _HOOMD GSD: https://github.com/glotzerlab/gsd

    To load a GSD HOOMD file::

       import MDAnalysis as mda
       u = mda.Universe("example.gsd")

    Classes
    -------

    .. autoclass:: GSDParser
       :members:
       :inherited-members:

    """
    import os
    import numpy as np

    from .base import TopologyReaderBase
    from ..core.topology import Topology
    from ..core.topologyattrs import (
        Atomtypes,
        Atomnames,
        Atomids,
        Angles,
        Bonds,
        Charges,
        Dihedrals,
        Impropers,
        Masses,
        Radii,
        Resids,
        Resnums,
        Resnames,
        Segids,
    )

    try:
        import gsd.hoomd
    except ImportError:
        HAS_GSD = False
    else:
        HAS_GSD = True

    class GSDParser(TopologyReaderBase):
        """Parses a Hoomd GSD file to create a Topology

        Reads the following Attributes:
         - Atomtypes
         - Bonds
         - Angles
         - Dihedrals
         - Impropers
         - Radii
         - Masses

        The GSD file also stores a `body` property in the particles, and the parser
        uses this information to set the residue names and indices.

        NOTE: if the `body` index of any particle is negative, the parser will add
        an integer number (the absolute value of the minimum of all the body
        indices) to all the body indices. This is because MDAnalysis cannot handle
        negative residue indices. This means that in that case the residue index in
        the MDAnalysis.Universe will not correspond to the body index stored in the
        GSD file.

        """

        format = "GSD"

        def __init__(self, filename):

            if not HAS_GSD:
                errmsg = (
                    "GSDParser: To read a Topology from a Hoomd GSD "
                    "file, please install gsd"
                )
                raise ImportError(errmsg)
            super(GSDParser, self).__init__(filename)

        def parse(self, **kwargs):
            """Parse Hoomd GSD file

            .. versionadded:: 0.17.0
            """
            attrs = {}

            with gsd.hoomd.open(self.filename, mode="r") as t:
                # Here it is assumed that the particle data does not change in the
                # trajectory.
                snap = t[0]

                natoms = snap.particles.N

                ptypes = snap.particles.types
                atypes = [ptypes[idx] for idx in snap.particles.typeid]
                if len(atypes) != natoms:
                    raise IOError("Number of types does not equal natoms.")
                attrs["types"] = Atomtypes(np.array(atypes, dtype=object))

                # set radii, masses, charges
                p = snap.particles
                attrs["diameter"] = Radii(
                    np.array(p.diameter / 2.0, dtype=np.float32)
                )
                attrs["mass"] = Masses(np.array(p.mass, dtype=np.float64))
                attrs["charge"] = Charges(np.array(p.charge, dtype=np.float32))

                # set bonds, angles, dihedrals, impropers
                for (
                    attrname,
                    attr,
                ) in (
                    ("bonds", Bonds),
                    ("angles", Angles),
                    ("dihedrals", Dihedrals),
                    ("impropers", Impropers),
                ):
                    try:
                        val = getattr(snap, attrname)
                        vals = [tuple(b_instance) for b_instance in val.group]
                    except:
                        vals = []
                    attrs[attrname] = attr(vals)

                # get body ids to set residue number and ids
                blist = snap.particles.body.astype(np.int64)
                bodies = np.unique(blist).astype(np.int32)
                # this fixes the fact that the Topology constructor gets stuck in an
                # infinite loop if any resid is negative.
                if (blist < 0).any():
                    m = blist.min()
                    blist += abs(m)
                bodies = np.unique(blist).astype(np.int32)
                nbodies = bodies.size

            attrs = list(attrs.values())
            attrs.append(Atomnames(np.array(atypes, dtype=object)))
            attrs.append(Atomids(np.arange(natoms) + 1))
            attrs.append(Resids(bodies))
            attrs.append(Resnums(bodies))
            attrs.append(Resnames(bodies))
            attrs.append(Segids(np.array(["SYSTEM"], dtype=object)))

            top = Topology(natoms, nbodies, 1, attrs=attrs, atom_resindex=blist)

            return top