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# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
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# doi: 10.25080/majora-629e541a-00e
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# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#

"""
DESRES Molecular Structure file format topology parser
======================================================

Classes to read a topology from a DESRES_ Molecular Structure file
format (DMS_) coordinate files (as used by the Desmond_ MD package).

.. _DESRES: http://www.deshawresearch.com
.. _Desmond: http://www.deshawresearch.com/resources_desmond.html
.. _DMS: http://www.deshawresearch.com/Desmond_Users_Guide-0.7.pdf

Classes
-------

.. autoclass:: DMSParser
   :members:
   :inherited-members:

"""
import numpy as np
import sqlite3
import os

from .base import TopologyReaderBase, change_squash
from ..core.topology import Topology
from ..core.topologyattrs import (
    Atomids,
    Atomnames,
    Bonds,
    Charges,
    ChainIDs,
    Masses,
    Resids,
    Resnums,
    Resnames,
    Segids,
    AtomAttr,  # for custom Attributes
)


class Atomnums(AtomAttr):
    """The number for each Atom"""

    attrname = "atomnums"
    singular = "atomnum"


class DMSParser(TopologyReaderBase):
    """Read a topology from a DESRES_ Molecular Structure file.

    Format (DMS_) coordinate files (as used by the Desmond_ MD package).

    Reads the following attributes:
      Atom:
        - Atomids
        - Atomnums
        - Atomnames
        - Masses
        - Charges
        - Chainids
      Residue:
        - Resnames
        - Resids
      Segment:
        - Segids

    .. note::

        By default, atomtypes will be guessed on Universe creation.
        This may change in release 3.0.
        See :ref:`Guessers` for more information.

    .. _DESRES: http://www.deshawresearch.com
    .. _Desmond: http://www.deshawresearch.com/resources_desmond.html
    .. _DMS: http://www.deshawresearch.com/Desmond_Users_Guide-0.7.pdf
    .. versionchanged:: 2.8.0
        Removed type guessing (attributes guessing takes place now
        through universe.guess_TopologyAttrs() API).

    """

    format = "DMS"

    def parse(self, **kwargs):
        """Parse DMS file *filename* and return the Topology object"""
        # Fix by SB: Needed because sqlite3.connect does not raise anything
        # if file is not there
        if not os.path.isfile(self.filename):
            raise IOError("No such file: {0}".format(self.filename))

        def dict_factory(cursor, row):
            """
            Fetch SQL records as dictionaries, rather than the default tuples.
            """
            d = {}
            for idx, col in enumerate(cursor.description):
                d[col[0]] = row[idx]
            return d

        attrs = {}

        # Row factories for different data types
        facs = {
            np.int32: lambda c, r: r[0],
            np.float32: lambda c, r: r[0],
            object: lambda c, r: str(r[0].strip()),
        }

        with sqlite3.connect(self.filename) as con:
            # Selecting single column, so just strip tuple
            for attrname, dt in [
                ("id", np.int32),
                ("anum", np.int32),
                ("mass", np.float32),
                ("charge", np.float32),
                ("name", object),
                ("resname", object),
                ("resid", np.int32),
                ("chain", object),
                ("segid", object),
            ]:
                try:
                    cur = con.cursor()
                    cur.row_factory = facs[dt]
                    cur.execute("SELECT {} FROM particle" "".format(attrname))
                    vals = cur.fetchall()
                except sqlite3.DatabaseError:
                    errmsg = "Failed reading the atoms from DMS Database"
                    raise IOError(errmsg) from None
                else:
                    attrs[attrname] = np.array(vals, dtype=dt)

            try:
                cur.row_factory = dict_factory
                cur.execute("SELECT * FROM bond")
                bonds = cur.fetchall()
            except sqlite3.DatabaseError:
                errmsg = "Failed reading the bonds from DMS Database"
                raise IOError(errmsg) from None
            else:
                bondlist = []
                bondorder = {}
                for b in bonds:
                    desc = tuple(sorted([b["p0"], b["p1"]]))
                    bondlist.append(desc)
                    bondorder[desc] = b["order"]
                attrs["bond"] = bondlist
                attrs["bondorder"] = bondorder

        topattrs = []
        # Bundle in Atom level objects
        for attr, cls in [
            ("id", Atomids),
            ("anum", Atomnums),
            ("mass", Masses),
            ("charge", Charges),
            ("name", Atomnames),
            ("chain", ChainIDs),
        ]:
            topattrs.append(cls(attrs[attr]))

        # Residues
        atom_residx, (res_resids, res_resnums, res_resnames, res_segids) = (
            change_squash(
                (attrs["resid"], attrs["resname"], attrs["segid"]),
                (
                    attrs["resid"],
                    attrs["resid"].copy(),
                    attrs["resname"],
                    attrs["segid"],
                ),
            )
        )

        n_residues = len(res_resids)
        topattrs.append(Resids(res_resids))
        topattrs.append(Resnums(res_resnums))
        topattrs.append(Resnames(res_resnames))

        if any(res_segids) and not any(val is None for val in res_segids):
            res_segidx, (res_segids,) = change_squash(
                (res_segids,), (res_segids,)
            )

            uniq_seg = np.unique(res_segids)
            idx2seg = {idx: res_segids[idx] for idx in res_segidx}
            res_segids = uniq_seg
            nidx = {segid: nidx for nidx, segid in enumerate(uniq_seg)}

            res_segidx = np.array([nidx[idx2seg[idx]] for idx in res_segidx])

            n_segments = len(res_segids)
            topattrs.append(Segids(res_segids))
        else:
            n_segments = 1
            topattrs.append(Segids(np.array(["SYSTEM"], dtype=object)))
            res_segidx = None

        topattrs.append(Bonds(attrs["bond"]))

        top = Topology(
            len(attrs["id"]),
            n_residues,
            n_segments,
            attrs=topattrs,
            atom_resindex=atom_residx,
            residue_segindex=res_segidx,
        )

        return top