# Source code for MDAnalysis.topology.PDBQTParser

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    # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
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    """
    PDBQT topology parser
    =====================

    Use a PDBQT_ file to build a minimum internal structure representation (list of
    atoms), including AutoDock_ atom types (stored as :attr:`Atom.type`) and
    partial charges (:attr:`Atom.charge`).

    * Reads a PDBQT file line by line and does not require sequential atom numbering.
    * Multi-model PDBQT files are not supported.

    .. note::

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

    Notes
    -----
    Only reads atoms and their names; connectivity is not
    deduced.

    See Also
    --------
    :class:`MDAnalysis.coordinates.PDBQT`

    Classes
    -------
    .. autoclass:: PDBQTParser
       :members:
       :inherited-members:

    .. _PDBQT:
       https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf
    .. _AutoDock:
       http://autodock.scripps.edu/
    """
    import numpy as np

    from ..lib import util
    from .base import TopologyReaderBase, change_squash
    from ..core.topology import Topology
    from ..core.topologyattrs import (
        Atomids,
        Atomnames,
        AltLocs,
        Atomtypes,
        Charges,
        ICodes,
        Occupancies,
        RecordTypes,
        Resids,
        Resnums,
        Resnames,
        Segids,
        ChainIDs,
        Tempfactors,
    )

    class PDBQTParser(TopologyReaderBase):
        """Read topology from a PDBQT file.

        Creates the following Attributes:
         - atom ids (serial)
         - atom types
         - atom names
         - altLocs
         - resnames
         - chainIDs (assigned to segid as well)
         - resids
         - record_types (ATOM/HETATM)
         - icodes
         - occupancies
         - tempfactors
         - charges

        .. versionchanged:: 0.18.0
           Added parsing of Record types
        .. versionchanged:: 2.7.0
           Columns 67 - 70 in ATOM records, corresponding to the field *footnote*,
           are now ignored. See Autodock's `reference`_.
        .. versionchanged:: 2.8.0
            Removed mass guessing (attributes guessing takes place now
            through universe.guess_TopologyAttrs() API).

           .. _reference:
              https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf
        """

        format = "PDBQT"

        def parse(self, **kwargs):
            """Parse atom information from PDBQT file *filename*.

            Returns
            -------
            MDAnalysis Topology object
            """
            record_types = []
            serials = []
            names = []
            altlocs = []
            resnames = []
            chainids = []
            resids = []
            icodes = []
            occupancies = []
            tempfactors = []
            charges = []
            atomtypes = []

            with util.openany(self.filename) as f:
                for line in f:
                    line = line.strip()
                    if not line.startswith(("ATOM", "HETATM")):
                        continue
                    record_types.append(line[:6].strip())
                    serials.append(int(line[6:11]))
                    names.append(line[12:16].strip())
                    altlocs.append(line[16:17].strip())
                    resnames.append(line[17:21].strip())
                    chainids.append(line[21:22].strip())
                    resids.append(int(line[22:26]))
                    icodes.append(line[26:27].strip())
                    occupancies.append(float(line[54:60]))
                    tempfactors.append(float(line[60:66]))
                    charges.append(float(line[70:76]))
                    atomtypes.append(line[77:80].strip())

            n_atoms = len(serials)

            attrs = []
            for attrlist, Attr, dtype in (
                (record_types, RecordTypes, object),
                (serials, Atomids, np.int32),
                (names, Atomnames, object),
                (altlocs, AltLocs, object),
                (occupancies, Occupancies, np.float32),
                (tempfactors, Tempfactors, np.float32),
                (charges, Charges, np.float32),
                (atomtypes, Atomtypes, object),
            ):
                attrs.append(Attr(np.array(attrlist, dtype=dtype)))

            resids = np.array(resids, dtype=np.int32)
            icodes = np.array(icodes, dtype=object)
            resnames = np.array(resnames, dtype=object)
            chainids = np.array(chainids, dtype=object)

            attrs.append(ChainIDs(chainids))

            residx, (resids, icodes, resnames, chainids) = change_squash(
                (resids, icodes), (resids, icodes, resnames, chainids)
            )
            n_residues = len(resids)
            attrs.append(Resids(resids))
            attrs.append(Resnums(resids.copy()))
            attrs.append(ICodes(icodes))
            attrs.append(Resnames(resnames))

            segidx, (segids,) = change_squash((chainids,), (chainids,))
            n_segments = len(segids)
            attrs.append(Segids(segids))

            top = Topology(
                n_atoms,
                n_residues,
                n_segments,
                attrs=attrs,
                atom_resindex=residx,
                residue_segindex=segidx,
            )

            return top