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# MDAnalysis --- https://www.mdanalysis.org
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# (see the file AUTHORS for the full list of names)
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# Please cite your use of MDAnalysis in published work:
#
# 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
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# 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
#

"""
CRD topology parser
===================

Read a list of atoms from a CHARMM CARD coordinate file (CRD_)
to build a basic topology.  Reads atom ids (ATOMNO), atom names (TYPES),
resids (RESID), residue numbers (RESNO), residue names (RESNames), segment ids
(SEGID) and tempfactor (Weighting).

Residues are detected through a change is either resid or resname
while segments are detected according to changes in segid.

.. note::

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

.. _CRD: https://www.charmmtutorial.org/index.php/CHARMM:The_Basics


Classes
-------

.. autoclass:: CRDParser
   :members:
   :inherited-members:

"""
import numpy as np

from ..lib.util import openany, FORTRANReader
from .base import TopologyReaderBase, change_squash
from ..core.topology import Topology
from ..core.topologyattrs import (
    Atomids,
    Atomnames,
    Resids,
    Resnames,
    Resnums,
    Segids,
    Tempfactors,
)


class CRDParser(TopologyReaderBase):
    """Parse a CHARMM CARD coordinate file for topology information.

    Reads the following Attributes:
     - Atomids
     - Atomnames
     - Tempfactors
     - Resids
     - Resnames
     - Resnums
     - Segids


    .. note::

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

    .. versionchanged:: 2.8.0
       Type and mass are not longer guessed here. Until 3.0 these will still be
       set by default through through universe.guess_TopologyAttrs() API.
    """

    format = "CRD"

    def parse(self, **kwargs):
        """Create the Topology object

        Returns
        -------
        MDAnalysis Topology object

        Todo
        ----
        Could use the resnum and temp factor better
        """
        extformat = FORTRANReader(
            "2I10,2X,A8,2X,A8,3F20.10,2X,A8,2X,A8,F20.10"
        )
        stdformat = FORTRANReader("2I5,1X,A4,1X,A4,3F10.5,1X,A4,1X,A4,F10.5")

        atomids = []
        atomnames = []
        tempfactors = []
        resids = []
        resnames = []
        resnums = []
        segids = []

        with openany(self.filename) as crd:
            for linenum, line in enumerate(crd):
                # reading header
                if line.split()[0] == "*":
                    continue
                elif line.split()[-1] == "EXT" and int(line.split()[0]):
                    r = extformat
                    continue
                elif (
                    line.split()[0] == line.split()[-1]
                    and line.split()[0] != "*"
                ):
                    r = stdformat
                    continue
                # anything else should be an atom
                try:
                    (
                        serial,
                        resnum,
                        resName,
                        name,
                        x,
                        y,
                        z,
                        segid,
                        resid,
                        tempFactor,
                    ) = r.read(line)
                except Exception:
                    errmsg = (
                        f"Check CRD format at line {linenum + 1}: "
                        f"{line.rstrip()}"
                    )
                    raise ValueError(errmsg) from None

                atomids.append(serial)
                atomnames.append(name)
                tempfactors.append(tempFactor)
                resids.append(resid)
                resnames.append(resName)
                resnums.append(resnum)
                segids.append(segid)

        # Convert to np arrays
        atomids = np.array(atomids, dtype=np.int32)
        atomnames = np.array(atomnames, dtype=object)
        tempfactors = np.array(tempfactors, dtype=np.float32)
        resids = np.array(resids, dtype=np.int32)
        resnames = np.array(resnames, dtype=object)
        resnums = np.array(resnums, dtype=np.int32)
        segids = np.array(segids, dtype=object)

        atom_residx, (res_resids, res_resnames, res_resnums, res_segids) = (
            change_squash(
                (resids, resnames), (resids, resnames, resnums, segids)
            )
        )
        res_segidx, (seg_segids,) = change_squash((res_segids,), (res_segids,))

        top = Topology(
            len(atomids),
            len(res_resids),
            len(seg_segids),
            attrs=[
                Atomids(atomids),
                Atomnames(atomnames),
                Tempfactors(tempfactors),
                Resids(res_resids),
                Resnames(res_resnames),
                Resnums(res_resnums),
                Segids(seg_segids),
            ],
            atom_resindex=atom_residx,
            residue_segindex=res_segidx,
        )

        return top