# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""mmCIF parsers."""

import warnings

import numpy as np

from Bio.File import as_handle
from Bio.PDB.MMCIF2Dict import MMCIF2Dict
from Bio.PDB.PDBExceptions import PDBConstructionException
from Bio.PDB.PDBExceptions import PDBConstructionWarning
from Bio.PDB.StructureBuilder import StructureBuilder


class MMCIFParser:
    """Parse a mmCIF file and return a Structure object."""

    def __init__(
        self,
        structure_builder=None,
        auth_chains=True,
        auth_residues=True,
        QUIET=False,
        PERMISSIVE=False,
    ):
        """Create a PDBParser object.

        The mmCIF parser calls a number of standard methods in an aggregated
        StructureBuilder object. Normally this object is instantiated by the
        MMCIParser object itself, but if the user provides his/her own
        StructureBuilder object, the latter is used instead.

        Arguments:
         - structure_builder - an optional user implemented StructureBuilder class.
         - auth_chains - True by default. If true, use the author chain IDs.
           If false, use the re-assigned mmCIF chain IDs.
         - auth_residues - True by default. If true, use the author residue numbering.
           If false, use the mmCIF "label" residue numbering, which has no insertion
           codes, and strictly increments residue numbers.
           NOTE: Non-polymers such as water don't have a "label" residue number,
           and will be skipped.
         - PERMISSIVE - Evaluated as a Boolean. If false (DEFAULT), exceptions in
           constructing the SMCRA data structure are fatal. If true,
           the exceptions are caught, but some residues or atoms will be missing.
           THESE EXCEPTIONS ARE DUE TO PROBLEMS IN THE PDB FILE!.

         - QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
           the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
           These warnings might be indicative of problems in the mmCIF file!

        """
        if structure_builder is not None:
            self._structure_builder = structure_builder
        else:
            self._structure_builder = StructureBuilder()
        self.header = None
        # self.trailer = None
        self.line_counter = 0
        self.build_structure = None
        self.auth_chains = bool(auth_chains)
        self.auth_residues = bool(auth_residues)
        self.QUIET = bool(QUIET)
        self.PERMISSIVE = bool(PERMISSIVE)

    # Public methods

    def get_structure(self, structure_id, filename):
        """Return the structure.

        Arguments:
         - structure_id - string, the id that will be used for the structure
         - filename - name of mmCIF file, OR an open text mode file handle

        """
        with warnings.catch_warnings():
            if self.QUIET:
                warnings.filterwarnings("ignore", category=PDBConstructionWarning)
            self._mmcif_dict = MMCIF2Dict(filename)
            self._build_structure(structure_id)
            self._structure_builder.set_header(self._get_header())

        return self._structure_builder.get_structure()

    # Private methods

    def _mmcif_get(self, key, dict, deflt):
        if key in dict:
            rslt = dict[key][0]
            if "?" != rslt:
                return rslt
        return deflt

    def _update_header_entry(self, target_key, keys):
        md = self._mmcif_dict
        for key in keys:
            val = md.get(key)
            try:
                item = val[0]
            except (TypeError, IndexError):
                continue
            if item != "?" and item != ".":
                self.header[target_key] = item
                break

    def _get_header(self):
        self.header = {
            "name": "",
            "head": "",
            "idcode": "",
            "deposition_date": "",
            "structure_method": "",
            "resolution": None,
        }

        self._update_header_entry(
            "idcode", ["_entry_id", "_exptl.entry_id", "_struct.entry_id"]
        )
        self._update_header_entry("name", ["_struct.title"])
        self._update_header_entry(
            "head", ["_struct_keywords.pdbx_keywords", "_struct_keywords.text"]
        )
        self._update_header_entry(
            "deposition_date", ["_pdbx_database_status.recvd_initial_deposition_date"]
        )
        self._update_header_entry("structure_method", ["_exptl.method"])
        self._update_header_entry(
            "resolution",
            [
                "_refine.ls_d_res_high",
                "_refine_hist.d_res_high",
                "_em_3d_reconstruction.resolution",
            ],
        )
        if self.header["resolution"] is not None:
            try:
                self.header["resolution"] = float(self.header["resolution"])
            except ValueError:
                self.header["resolution"] = None

        return self.header

    def _build_structure(self, structure_id):
        # two special chars as placeholders in the mmCIF format
        # for item values that cannot be explicitly assigned
        # see: pdbx/mmcif syntax web page
        _unassigned = {".", "?"}

        mmcif_dict = self._mmcif_dict

        atom_serial_list = mmcif_dict["_atom_site.id"]
        atom_id_list = mmcif_dict["_atom_site.label_atom_id"]
        residue_id_list = mmcif_dict["_atom_site.label_comp_id"]
        try:
            element_list = mmcif_dict["_atom_site.type_symbol"]
        except KeyError:
            element_list = None
        if self.auth_chains:
            chain_id_list = mmcif_dict["_atom_site.auth_asym_id"]
        else:
            chain_id_list = mmcif_dict["_atom_site.label_asym_id"]
        x_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_x"]]
        y_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_y"]]
        z_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_z"]]
        alt_list = mmcif_dict["_atom_site.label_alt_id"]
        icode_list = mmcif_dict["_atom_site.pdbx_PDB_ins_code"]
        b_factor_list = mmcif_dict["_atom_site.B_iso_or_equiv"]
        occupancy_list = mmcif_dict["_atom_site.occupancy"]
        fieldname_list = mmcif_dict["_atom_site.group_PDB"]
        try:
            serial_list = [int(n) for n in mmcif_dict["_atom_site.pdbx_PDB_model_num"]]
        except KeyError:
            # No model number column
            serial_list = None
        except ValueError:
            # Invalid model number (malformed file)
            raise PDBConstructionException("Invalid model number") from None
        try:
            aniso_u11 = mmcif_dict["_atom_site_anisotrop.U[1][1]"]
            aniso_u12 = mmcif_dict["_atom_site_anisotrop.U[1][2]"]
            aniso_u13 = mmcif_dict["_atom_site_anisotrop.U[1][3]"]
            aniso_u22 = mmcif_dict["_atom_site_anisotrop.U[2][2]"]
            aniso_u23 = mmcif_dict["_atom_site_anisotrop.U[2][3]"]
            aniso_u33 = mmcif_dict["_atom_site_anisotrop.U[3][3]"]
            aniso_flag = 1
        except KeyError:
            # no anisotropic B factors
            aniso_flag = 0

        if self.auth_residues:
            # if auth_seq_id is present, we use this.
            # Otherwise label_seq_id is used.
            if "_atom_site.auth_seq_id" in mmcif_dict:
                seq_id_list = mmcif_dict["_atom_site.auth_seq_id"]
            else:
                seq_id_list = mmcif_dict["_atom_site.label_seq_id"]
        else:
            seq_id_list = mmcif_dict["_atom_site.label_seq_id"]
            icode_list = ["."] * len(icode_list)

        # Now loop over atoms and build the structure
        current_chain_id = None
        current_residue_id = None
        current_resname = None
        structure_builder = self._structure_builder
        structure_builder.init_structure(structure_id)
        structure_builder.init_seg(" ")
        # Historically, Biopython PDB parser uses model_id to mean array index
        # so serial_id means the Model ID specified in the file
        current_model_id = -1
        current_serial_id = -1
        for i in range(len(atom_id_list)):
            # set the line_counter for 'ATOM' lines only and not
            # as a global line counter found in the PDBParser()
            structure_builder.set_line_counter(i)

            # Try coercing serial to int, for compatibility with PDBParser
            # But do not quit if it fails. mmCIF format specs allow strings.
            try:
                serial = int(atom_serial_list[i])
            except ValueError:
                serial = atom_serial_list[i]
                warnings.warn(
                    "PDBConstructionWarning: Some atom serial numbers are not numerical",
                    PDBConstructionWarning,
                )

            x = x_list[i]
            y = y_list[i]
            z = z_list[i]
            resname = residue_id_list[i]
            chainid = chain_id_list[i]
            altloc = alt_list[i]
            if altloc in _unassigned:
                altloc = " "
            resseq = seq_id_list[i]
            if resseq == ".":
                # Non-existing residue ID
                try:
                    msg_resseq = mmcif_dict["_atom_site.auth_seq_id"][i]
                    msg = f"Non-existing residue ID in chain '{chainid}', residue '{msg_resseq}'"
                except (KeyError, IndexError):
                    msg = f"Non-existing residue ID in chain '{chainid}'"
                warnings.warn(
                    "PDBConstructionWarning: " + msg,
                    PDBConstructionWarning,
                )
                continue
            int_resseq = int(resseq)
            icode = icode_list[i]
            if icode in _unassigned:
                icode = " "
            name = atom_id_list[i]
            # occupancy & B factor
            try:
                tempfactor = float(b_factor_list[i])
            except ValueError:
                raise PDBConstructionException("Invalid or missing B factor") from None
            try:
                occupancy = float(occupancy_list[i])
            except ValueError:
                raise PDBConstructionException("Invalid or missing occupancy") from None
            fieldname = fieldname_list[i]
            if fieldname == "HETATM":
                if resname == "HOH" or resname == "WAT":
                    hetatm_flag = "W"
                else:
                    hetatm_flag = "H"
            else:
                hetatm_flag = " "

            resseq = (hetatm_flag, int_resseq, icode)

            if serial_list is not None:
                # model column exists; use it
                serial_id = serial_list[i]
                if current_serial_id != serial_id:
                    # if serial changes, update it and start new model
                    current_serial_id = serial_id
                    current_model_id += 1
                    structure_builder.init_model(current_model_id, current_serial_id)
                    current_chain_id = None
                    current_residue_id = None
                    current_resname = None
            else:
                # no explicit model column; initialize single model
                structure_builder.init_model(current_model_id)

            if current_chain_id != chainid:
                current_chain_id = chainid
                structure_builder.init_chain(current_chain_id)
                current_residue_id = None
                current_resname = None

            if current_residue_id != resseq or current_resname != resname:
                current_residue_id = resseq
                current_resname = resname
                structure_builder.init_residue(resname, hetatm_flag, int_resseq, icode)

            coord = np.array((x, y, z), "f")
            element = element_list[i].upper() if element_list else None
            try:
                structure_builder.init_atom(
                    name,
                    coord,
                    tempfactor,
                    occupancy,
                    altloc,
                    name,
                    serial_number=serial,
                    element=element,
                )
            except PDBConstructionException as message:
                self._handle_PDB_exception(message)

            if aniso_flag == 1 and i < len(aniso_u11):
                u = (
                    aniso_u11[i],
                    aniso_u12[i],
                    aniso_u13[i],
                    aniso_u22[i],
                    aniso_u23[i],
                    aniso_u33[i],
                )
                mapped_anisou = [float(_) for _ in u]
                anisou_array = np.array(mapped_anisou, "f")
                structure_builder.set_anisou(anisou_array)
        # Now try to set the cell
        try:
            a = float(mmcif_dict["_cell.length_a"][0])
            b = float(mmcif_dict["_cell.length_b"][0])
            c = float(mmcif_dict["_cell.length_c"][0])
            alpha = float(mmcif_dict["_cell.angle_alpha"][0])
            beta = float(mmcif_dict["_cell.angle_beta"][0])
            gamma = float(mmcif_dict["_cell.angle_gamma"][0])
            cell = np.array((a, b, c, alpha, beta, gamma), "f")
            spacegroup = mmcif_dict["_symmetry.space_group_name_H-M"][0]
            spacegroup = spacegroup[1:-1]  # get rid of quotes!!
            if spacegroup is None:
                raise Exception
            structure_builder.set_symmetry(spacegroup, cell)
        except Exception:
            pass  # no cell found, so just ignore

    def _handle_PDB_exception(self, message):
        """Handle exception (PRIVATE).

        This method catches an exception that occurs in the StructureBuilder
        object (if PERMISSIVE), or raises it again.
        """
        message = "%s" % (message)
        if self.PERMISSIVE:
            # just print a warning - some residues/atoms may be missing
            warnings.warn(
                "PDBConstructionException: %s\n"
                "Exception ignored.\n"
                "Some atoms or residues may be missing in the data structure."
                % message,
                PDBConstructionWarning,
            )
        else:
            # exceptions are fatal - raise again with new message
            raise PDBConstructionException(message) from None


class FastMMCIFParser:
    """Parse an MMCIF file and return a Structure object."""

    def __init__(
        self, structure_builder=None, auth_chains=True, auth_residues=True, QUIET=False
    ):
        """Create a FastMMCIFParser object.

        The mmCIF parser calls a number of standard methods in an aggregated
        StructureBuilder object. Normally this object is instantiated by the
        parser object itself, but if the user provides his/her own
        StructureBuilder object, the latter is used instead.

        The main difference between this class and the regular MMCIFParser is
        that only 'ATOM' and 'HETATM' lines are parsed here. Use if you are
        interested only in coordinate information.

        Arguments:
         - structure_builder - an optional user implemented StructureBuilder class.
         - auth_chains - True by default. If true, use the author chain IDs.
           If false, use the re-assigned mmCIF chain IDs.
         - auth_residues - True by default. If true, use the author residue numbering.
           If false, use the mmCIF "label" residue numbering, which has no insertion
           codes, and strictly increments residue numbers.
           NOTE: Non-polymers such as water don't have a "label" residue number,
           and will be skipped.

         - QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
           the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
           These warnings might be indicative of problems in the mmCIF file!

        """
        if structure_builder is not None:
            self._structure_builder = structure_builder
        else:
            self._structure_builder = StructureBuilder()

        self.line_counter = 0
        self.build_structure = None
        self.auth_chains = bool(auth_chains)
        self.auth_residues = bool(auth_residues)
        self.QUIET = bool(QUIET)

    # Public methods

    def get_structure(self, structure_id, filename):
        """Return the structure.

        Arguments:
         - structure_id - string, the id that will be used for the structure
         - filename - name of the mmCIF file OR an open filehandle

        """
        with warnings.catch_warnings():
            if self.QUIET:
                warnings.filterwarnings("ignore", category=PDBConstructionWarning)
            with as_handle(filename) as handle:
                self._build_structure(structure_id, handle)

        return self._structure_builder.get_structure()

    # Private methods

    def _build_structure(self, structure_id, filehandle):
        # two special chars as placeholders in the mmCIF format
        # for item values that cannot be explicitly assigned
        # see: pdbx/mmcif syntax web page
        _unassigned = {".", "?"}

        # Read only _atom_site. and atom_site_anisotrop entries
        read_atom, read_aniso = False, False
        _fields, _records = [], []
        _anisof, _anisors = [], []
        for line in filehandle:
            if line.startswith("_atom_site."):
                read_atom = True
                _fields.append(line.strip())
            elif line.startswith("_atom_site_anisotrop."):
                read_aniso = True
                _anisof.append(line.strip())
            elif read_atom and line.startswith("#"):
                read_atom = False
            elif read_aniso and line.startswith("#"):
                read_aniso = False
            elif read_atom:
                _records.append(line.strip())
            elif read_aniso:
                _anisors.append(line.strip())

        # Dumping the shlex module here since this particular
        # category should be rather straightforward.
        # Quite a performance boost..
        _record_tbl = zip(*map(str.split, _records))
        _anisob_tbl = zip(*map(str.split, _anisors))

        mmcif_dict = dict(zip(_fields, _record_tbl))
        mmcif_dict.update(dict(zip(_anisof, _anisob_tbl)))

        # Build structure object
        atom_serial_list = mmcif_dict["_atom_site.id"]
        atom_id_list = mmcif_dict["_atom_site.label_atom_id"]
        residue_id_list = mmcif_dict["_atom_site.label_comp_id"]

        try:
            element_list = mmcif_dict["_atom_site.type_symbol"]
        except KeyError:
            element_list = None

        if self.auth_chains:
            chain_id_list = mmcif_dict["_atom_site.auth_asym_id"]
        else:
            chain_id_list = mmcif_dict["_atom_site.label_asym_id"]

        x_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_x"]]
        y_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_y"]]
        z_list = [float(x) for x in mmcif_dict["_atom_site.Cartn_z"]]
        alt_list = mmcif_dict["_atom_site.label_alt_id"]
        icode_list = mmcif_dict["_atom_site.pdbx_PDB_ins_code"]
        b_factor_list = mmcif_dict["_atom_site.B_iso_or_equiv"]
        occupancy_list = mmcif_dict["_atom_site.occupancy"]
        fieldname_list = mmcif_dict["_atom_site.group_PDB"]

        try:
            serial_list = [int(n) for n in mmcif_dict["_atom_site.pdbx_PDB_model_num"]]
        except KeyError:
            # No model number column
            serial_list = None
        except ValueError:
            # Invalid model number (malformed file)
            raise PDBConstructionException("Invalid model number") from None

        try:
            aniso_u11 = mmcif_dict["_atom_site_anisotrop.U[1][1]"]
            aniso_u12 = mmcif_dict["_atom_site_anisotrop.U[1][2]"]
            aniso_u13 = mmcif_dict["_atom_site_anisotrop.U[1][3]"]
            aniso_u22 = mmcif_dict["_atom_site_anisotrop.U[2][2]"]
            aniso_u23 = mmcif_dict["_atom_site_anisotrop.U[2][3]"]
            aniso_u33 = mmcif_dict["_atom_site_anisotrop.U[3][3]"]
            aniso_flag = 1
        except KeyError:
            # no anisotropic B factors
            aniso_flag = 0

        if self.auth_residues:
            # if auth_seq_id is present, we use this.
            # Otherwise label_seq_id is used.
            if "_atom_site.auth_seq_id" in mmcif_dict:
                seq_id_list = mmcif_dict["_atom_site.auth_seq_id"]
            else:
                seq_id_list = mmcif_dict["_atom_site.label_seq_id"]
        else:
            seq_id_list = mmcif_dict["_atom_site.label_seq_id"]
            icode_list = ["."] * len(icode_list)

        # Now loop over atoms and build the structure
        current_chain_id = None
        current_residue_id = None
        current_resname = None
        structure_builder = self._structure_builder
        structure_builder.init_structure(structure_id)
        structure_builder.init_seg(" ")

        # Historically, Biopython PDB parser uses model_id to mean array index
        # so serial_id means the Model ID specified in the file
        current_model_id = -1
        current_serial_id = -1
        for i in range(len(atom_id_list)):
            # set the line_counter for 'ATOM' lines only and not
            # as a global line counter found in the PDBParser()
            structure_builder.set_line_counter(i)

            serial = atom_serial_list[i]

            x = x_list[i]
            y = y_list[i]
            z = z_list[i]
            resname = residue_id_list[i]
            chainid = chain_id_list[i]
            altloc = alt_list[i]
            if altloc in _unassigned:
                altloc = " "
            resseq = seq_id_list[i]
            if resseq == ".":
                # Non-existing residue ID
                try:
                    msg_resseq = mmcif_dict["_atom_site.auth_seq_id"][i]
                    msg = f"Non-existing residue ID in chain '{chainid}', residue '{msg_resseq}'"
                except (KeyError, IndexError):
                    msg = f"Non-existing residue ID in chain '{chainid}'"
                warnings.warn(
                    "PDBConstructionWarning: " + msg,
                    PDBConstructionWarning,
                )
                continue
            int_resseq = int(resseq)
            icode = icode_list[i]
            if icode in _unassigned:
                icode = " "
            # Remove occasional " from quoted atom names (e.g. xNA)
            name = atom_id_list[i].strip('"')

            # occupancy & B factor
            try:
                tempfactor = float(b_factor_list[i])
            except ValueError:
                raise PDBConstructionException("Invalid or missing B factor") from None

            try:
                occupancy = float(occupancy_list[i])
            except ValueError:
                raise PDBConstructionException("Invalid or missing occupancy") from None

            fieldname = fieldname_list[i]
            if fieldname == "HETATM":
                hetatm_flag = "H"
            else:
                hetatm_flag = " "

            resseq = (hetatm_flag, int_resseq, icode)

            if serial_list is not None:
                # model column exists; use it
                serial_id = serial_list[i]
                if current_serial_id != serial_id:
                    # if serial changes, update it and start new model
                    current_serial_id = serial_id
                    current_model_id += 1
                    structure_builder.init_model(current_model_id, current_serial_id)
                    current_chain_id = None
                    current_residue_id = None
                    current_resname = None
            else:
                # no explicit model column; initialize single model
                structure_builder.init_model(current_model_id)

            if current_chain_id != chainid:
                current_chain_id = chainid
                structure_builder.init_chain(current_chain_id)
                current_residue_id = None
                current_resname = None

            if current_residue_id != resseq or current_resname != resname:
                current_residue_id = resseq
                current_resname = resname
                structure_builder.init_residue(resname, hetatm_flag, int_resseq, icode)

            coord = np.array((x, y, z), "f")
            element = element_list[i] if element_list else None
            structure_builder.init_atom(
                name,
                coord,
                tempfactor,
                occupancy,
                altloc,
                name,
                serial_number=serial,
                element=element,
            )
            if aniso_flag == 1 and i < len(aniso_u11):
                u = (
                    aniso_u11[i],
                    aniso_u12[i],
                    aniso_u13[i],
                    aniso_u22[i],
                    aniso_u23[i],
                    aniso_u33[i],
                )
                mapped_anisou = [float(_) for _ in u]
                anisou_array = np.array(mapped_anisou, "f")
                structure_builder.set_anisou(anisou_array)
