# Source code for MDAnalysis.topology.PDBParser

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    """
    PDB Topology Parser
    =========================================================================

    This topology parser uses a standard PDB file to build a minimum
    internal structure representation (list of atoms).

    The topology reader reads a PDB file line by line and ignores atom
    numbers but only reads residue numbers up to 9,999 correctly. If you
    have systems containing at least 10,000 residues then you need to use
    a different file format (e.g. the "extended" PDB, *XPDB* format, see
    :mod:`~MDAnalysis.topology.ExtendedPDBParser`) that can handle residue
    numbers up to 99,999.

    .. note::

        Atomtypes will be created from elements if they are present and valid.
        Otherwise, they will be guessed on Universe creation.
        By default, masses will also be guessed on Universe creation.
        This may change in release 3.0.
        See :ref:`Guessers` for more information.

    .. Note::

       The parser processes atoms and their names.
       Partial charges are not set. Elements are parsed if they are
       valid. If partially missing or incorrect, empty records are assigned.

    See Also
    --------
    * :mod:`MDAnalysis.topology.ExtendedPDBParser`
    * :class:`MDAnalysis.coordinates.PDB.PDBReader`
    * :class:`MDAnalysis.core.universe.Universe`

    Classes
    -------

    .. autoclass:: PDBParser
       :members:
       :inherited-members:

    """
    import numpy as np
    import warnings
    import logging

    from ..guesser.tables import SYMB2Z
    from ..lib import util
    from .base import TopologyReaderBase, change_squash
    from ..core.topology import Topology
    from ..core.topologyattrs import (
        Atomnames,
        Atomids,
        AltLocs,
        Bonds,
        ChainIDs,
        Atomtypes,
        Elements,
        ICodes,
        Occupancies,
        RecordTypes,
        Resids,
        Resnames,
        Resnums,
        Segids,
        Tempfactors,
        FormalCharges,
    )

    # Set up a logger for the PDBParser
    logger = logging.getLogger("MDAnalysis.topology.PDBParser")

    def float_or_default(val, default):
        try:
            return float(val)
        except ValueError:
            return default

    DIGITS_UPPER = "0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ"
    DIGITS_LOWER = DIGITS_UPPER.lower()
    DIGITS_UPPER_VALUES = dict([pair for pair in zip(DIGITS_UPPER, range(36))])
    DIGITS_LOWER_VALUES = dict([pair for pair in zip(DIGITS_LOWER, range(36))])

    def decode_pure(digits_values, s):
        """Decodes the string s using the digit, value associations for each
        character.

        Parameters
        ----------
        digits_values: dict
            A dictionary containing the base-10 numbers that each hexadecimal
            number corresponds to.
        s: str
            The contents of the pdb index columns.

        Returns
        -------
        The integer in base-10 corresponding to traditional base-36.
        """
        result = 0
        n = len(digits_values)
        for c in s:
            result *= n
            result += digits_values[c]
        return result

    def hy36decode(width, s):
        """
        Decodes base-10/upper-case base-36/lower-case base-36 hybrid.

        Parameters
        ----------
        width: int
            The number of columns in the pdb file store atom index.
        s: str
            The contents of the pdb index columns.

        Returns
        -------
        int
            Base-10 integer corresponding to hybrid36.
        """
        if (len(s) == width):
            f = s[0]
            if (f == "-" or f == " " or f.isdigit()):
                return int(s)
            elif (f in DIGITS_UPPER_VALUES):
                return decode_pure(digits_values=DIGITS_UPPER_VALUES,
                                   s=s) - 10 * 36 ** (width - 1) + 10 ** width
            elif (f in DIGITS_LOWER_VALUES):
                return decode_pure(digits_values=DIGITS_LOWER_VALUES,
                                   s=s) + 16 * 36 ** (width - 1) + 10 ** width
        raise ValueError("invalid number literal.")

    class PDBParser(TopologyReaderBase):
        """Parser that obtains a list of atoms from a standard PDB file.

        Creates the following Attributes (if present):
         - names
         - chainids
         - tempfactors
         - occupancies
         - record_types (ATOM/HETATM)
         - resids
         - resnames
         - segids
         - elements
         - bonds
         - formalcharges

        Note that `PDBParser` accepts an optional keyword argument
        ``force_chainids_to_segids``. If set to ``True``, the chain IDs (even if
        empty values are in the chain ID column in the file) will forcibly be used
        instead of the segment IDs for creating segments.

        See Also
        --------
        :class:`MDAnalysis.coordinates.PDB.PDBReader`

        .. versionadded:: 0.8
        .. versionchanged:: 0.18.0
           Added parsing of Record types
        .. versionchanged:: 1.0.0
           Added parsing of valid Elements
        .. versionchanged:: 2.0.0
           Bonds attribute is not added if no bonds are present in PDB file.
           If elements are invalid or partially missing, empty elements records
           are now assigned (Issue #2422).
           Aliased ``bfactors`` topologyattribute to ``tempfactors``.
           ``bfactors`` is deprecated and will be removed in 3.0 (Issue #1901)
        .. versionchanged:: 2.3.0
           Formal charges are now read from PDB files if present. No formalcharge
           attribute is created if no formal charges are present in the PDB file.
           Any formal charges not set are assumed to have a value of 0.
           Raise `UserWarning` instead `RuntimeError`
           when CONECT records are corrupt.
        .. versionchanged:: 2.5.0
           Formal charges will not be populated if an unknown entry is encountered,
           instead a UserWarning is emitted.
        .. versionchanged:: 2.8.0
            Removed type and mass guessing (attributes guessing takes place now
            through universe.guess_TopologyAttrs() API).
        .. versionchanged:: 2.10.0
            segID is read from 73-76 instead of 67-76 and added the
            `force_chainids_to_segids` keyword argument. Some infos in logger will
            be generated if the segids is not present or if the chainids are not
            completely equal to segids.
        """
        format = ['PDB', 'ENT']

        def parse(self, **kwargs):
            """Parse atom information from PDB file

            Returns
            -------
            MDAnalysis Topology object
            """
            top = self._parseatoms(**kwargs)

            try:
                bonds = self._parsebonds(top.ids.values)
            except AttributeError:
                warnings.warn("Invalid atom serials were present, "
                              "bonds will not be parsed")
            except RuntimeError:
                warnings.warn("CONECT records was corrupt, "
                              "bonds will not be parsed")
            else:
                # Issue 2832: don't append Bonds if there are no bonds
                if bonds:
                    top.add_TopologyAttr(bonds)

            return top

        def _parseatoms(self, **kwargs):
            """Create the initial Topology object"""
            resid_prev = 0  # resid looping hack

            record_types = []
            serials = []
            names = []
            altlocs = []
            chainids = []
            icodes = []
            tempfactors = []
            occupancies = []
            resids = []
            resnames = []
            segids = []
            elements = []
            formalcharges = []

            self._wrapped_serials = False  # did serials go over 100k?
            last_wrapped_serial = 100000  # if serials wrap, start from here
            with util.openany(self.filename) as f:
                for line in f:
                    line = line.strip()  # Remove extra spaces
                    if not line:  # Skip line if empty
                        continue
                    if line.startswith('END'):
                        break
                    if not line.startswith(('ATOM', 'HETATM')):
                        continue

                    record_types.append(line[:6].strip())
                    try:
                        serial = int(line[6:11])
                    except:
                        try:
                            serial = hy36decode(5, line[6:11])
                        except ValueError:
                            # serial can become '***' when they get too high
                            self._wrapped_serials = True
                            serial = last_wrapped_serial
                            last_wrapped_serial += 1
                    finally:
                        serials.append(serial)

                    names.append(line[12:16].strip())
                    altlocs.append(line[16:17].strip())
                    resnames.append(line[17:21].strip())
                    chainids.append(line[21:22].strip())
                    elements.append(line[76:78].strip())
                    formalcharges.append(line[78:80].strip())

                    # Resids are optional
                    try:
                        if self.format == "XPDB":  # fugly but keeps code DRY
                            # extended non-standard format used by VMD
                            resid = int(line[22:27])
                        else:
                            resid = int(line[22:26])
                            # Wrapping
                            while resid - resid_prev < -5000:
                                resid += 10000
                            resid_prev = resid
                    except ValueError:
                        warnings.warn("PDB file is missing resid information.  "
                                      "Defaulted to '1'")
                        resid = 1
                    finally:
                        resids.append(resid)
                        icodes.append(line[26:27].strip())

                    occupancies.append(float_or_default(line[54:60], 0.0))
                    tempfactors.append(float_or_default(line[60:66], 1.0))  # AKA bfactor

                    segids.append(line[72:76].strip())

            # Warn about wrapped serials
            if self._wrapped_serials:
                warnings.warn("Serial numbers went over 100,000.  "
                              "Higher serials have been guessed")

            # If segids is not equal to chainids, warn the user
            if any([a != b for a, b in zip(segids, chainids)]):
                logger.debug("Segment IDs and Chain IDs are not completely equal.")

            # If segids not present, try to use chainids
            if not any(segids):
                logger.info("Setting segids from chainIDs because no segids "
                            "found in the PDB file.")
                segids = chainids

            # If force_chainids_to_segids is set, use chainids as segids
            if kwargs.get("force_chainids_to_segids", False):
                logger.info("force_chainids_to_segids is set. "
                            "Using chain IDs as segment IDs.")
                segids = chainids

            n_atoms = len(serials)

            attrs = []
            # Make Atom TopologyAttrs
            for vals, Attr, dtype in (
                    (names, Atomnames, object),
                    (altlocs, AltLocs, object),
                    (chainids, ChainIDs, object),
                    (record_types, RecordTypes, object),
                    (serials, Atomids, np.int32),
                    (tempfactors, Tempfactors, np.float32),
                    (occupancies, Occupancies, np.float32),
            ):
                attrs.append(Attr(np.array(vals, dtype=dtype)))
            # OPT: We do this check twice, maybe could refactor to avoid this
            if any(elements):
                # Feed atomtypes as raw element column, but validate elements
                atomtypes = elements
                attrs.append(Atomtypes(np.array(elements, dtype=object)))

                validated_elements = []
                for elem in elements:
                    if elem.capitalize() in SYMB2Z:
                        validated_elements.append(elem.capitalize())
                    else:
                        wmsg = (f"Unknown element {elem} found for some atoms. "
                                f"These have been given an empty element record. "
                                f"If needed they can be guessed using "
                                f"universe.guess_TopologyAttrs(context='default',"
                                " to_guess=['elements']).")
                        warnings.warn(wmsg)
                        validated_elements.append('')
                attrs.append(Elements(np.array(validated_elements, dtype=object)))
            else:
                warnings.warn("Element information is missing, elements attribute "
                              "will not be populated. If needed these can be"
                              " guessed using universe.guess_TopologyAttrs("
                              "context='default', to_guess=['elements']).")

            if any(formalcharges):
                try:
                    for i, entry in enumerate(formalcharges):
                        if not entry == '':
                            if entry == '0':
                                # Technically a lack of charge shouldn't be in the
                                # PDB but MDA has a few files that specifically
                                # have 0 entries, indicating that some folks
                                # interpret 0 as an allowed entry
                                formalcharges[i] = 0
                            elif ('+' in entry) or ('-' in entry):
                                formalcharges[i] = int(entry[::-1])
                            else:
                                raise ValueError
                        else:
                            formalcharges[i] = 0
                except ValueError:
                    wmsg = (f"Unknown entry {entry} encountered in formal charge "
                            "field. This likely indicates that the PDB file is "
                            "not fully standard compliant. The formalcharges "
                            "attribute will not be populated.")
                    warnings.warn(wmsg)
                else:
                    attrs.append(FormalCharges(np.array(formalcharges, dtype=int)))

            # Residue level stuff from here
            resids = np.array(resids, dtype=np.int32)
            resnames = np.array(resnames, dtype=object)
            if self.format == 'XPDB':  # XPDB doesn't have icodes
                icodes = [''] * n_atoms
            icodes = np.array(icodes, dtype=object)
            resnums = resids.copy()
            segids = np.array(segids, dtype=object)

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

            if (
                kwargs.get("force_chainids_to_segids", False) or
                (any(segids) and not any(val is None for val in segids))
            ):
                segidx, (segids,) = change_squash((segids,), (segids,))
                n_segments = len(segids)
                attrs.append(Segids(segids))
            else:
                n_segments = 1
                attrs.append(Segids(np.array(['SYSTEM'], dtype=object)))
                segidx = None
                logger.info("Segment/chain ID is empty, "
                            "setting segids to default value 'SYSTEM'.")

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

            return top

        def _parsebonds(self, serials):
            # Could optimise this by saving lines in the main loop
            # then doing post processing after all Atoms have been read
            # ie do one pass through the file only
            # Problem is that in multiframe PDB, the CONECT is at end of file,
            # so the "break" call happens before bonds are reached.

            # If the serials wrapped, this won't work
            if self._wrapped_serials:
                warnings.warn("Invalid atom serials were present, bonds will not"
                              " be parsed")
                raise AttributeError  # gets caught in parse

            # Mapping between the atom array indicies a.index and atom ids
            # (serial) in the original PDB file
            mapping = dict((s, i) for i, s in enumerate(serials))

            bonds = set()
            with util.openany(self.filename) as f:
                lines = (line for line in f if line[:6] == "CONECT")
                for line in lines:
                    atom, atoms = _parse_conect(line.strip())
                    for a in atoms:
                        try:
                            bond = tuple([mapping[atom], mapping[a]])
                        except KeyError:
                            # Bonds to TER records have no mapping
                            # Ignore these as they are not real atoms
                            warnings.warn(
                                "PDB file contained CONECT record to TER entry. "
                                "These are not included in bonds.")
                        else:
                            bonds.add(bond)

            bonds = tuple(bonds)

            return Bonds(bonds)

    def _parse_conect(conect):
        """parse a CONECT record from pdbs

        Parameters
        ----------
        conect : str
            white space striped CONECT record

        Returns
        -------
        atom_id : int
            atom index of bond
        bonds : set
            atom ids of bonded atoms

        Raises
        ------
        RuntimeError
            Raised if ``conect`` is not a valid CONECT record
        """
        atom_id = int(conect[6:11])
        n_bond_atoms = len(conect[11:]) // 5

        try:
            if len(conect[11:]) % n_bond_atoms != 0:
                raise RuntimeError("Bond atoms aren't aligned proberly for CONECT "
                                   "record: {}".format(conect))
        except ZeroDivisionError:
            # Conect record with only one entry (CONECT A\n)
            warnings.warn("Found CONECT record with single entry, ignoring this")
            return atom_id, []  # return empty list to allow iteration over nothing

        bond_atoms = (int(conect[11 + i * 5: 16 + i * 5]) for i in
                      range(n_bond_atoms))
        return atom_id, bond_atoms