# 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 parser"""

from __future__ import print_function

from string import ascii_letters

import numpy
import warnings

from Bio._py3k import range

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


class MMCIFParser(object):
    """Parse a PDB file and return a Structure object."""

    def __init__(self, structure_builder=None, QUIET=False):
        """Create a PDBParser object.
        The PDB parser call a number of standard methods in an aggregated
        StructureBuilder object. Normally this object is instanciated 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.
         - 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 PDB 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.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)
        self._mmcif_dict = MMCIF2Dict(filename)
        self._build_structure(structure_id)
        return self._structure_builder.get_structure()

    # Private methods

    def _build_structure(self, structure_id):
        mmcif_dict = self._mmcif_dict
        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
        seq_id_list = mmcif_dict["_atom_site.label_seq_id"]
        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")
        try:
            aniso_u11 = mmcif_dict["_atom_site.aniso_U[1][1]"]
            aniso_u12 = mmcif_dict["_atom_site.aniso_U[1][2]"]
            aniso_u13 = mmcif_dict["_atom_site.aniso_U[1][3]"]
            aniso_u22 = mmcif_dict["_atom_site.aniso_U[2][2]"]
            aniso_u23 = mmcif_dict["_atom_site.aniso_U[2][3]"]
            aniso_u33 = mmcif_dict["_atom_site.aniso_U[3][3]"]
            aniso_flag = 1
        except KeyError:
            # no anisotropic B factors
            aniso_flag = 0
        # 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"]
        # Now loop over atoms and build the structure
        current_chain_id = None
        current_residue_id = 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 = 0
        for i in range(0, len(atom_id_list)):

            # set the line_counter for 'ATOM' lines only and not
            # as a global line counter found in the PDBParser()
            # this number should match the '_atom_site.id' index in the MMCIF
            structure_builder.set_line_counter(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 == ".":
                altloc = " "
            resseq = seq_id_list[i]
            icode = icode_list[i]
            if icode == "?":
                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")
            try:
                occupancy = float(occupancy_list[i])
            except ValueError:
                raise PDBConstructionException("Invalid or missing occupancy")
            fieldname = fieldname_list[i]
            if fieldname == "HETATM":
                hetatm_flag = "H"
            else:
                hetatm_flag = " "
            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
            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)

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

            coord = numpy.array((x, y, z), 'f')
            element = element_list[i] if element_list else None
            structure_builder.init_atom(name, coord, tempfactor, occupancy, altloc,
                name, element=element)
            if aniso_flag == 1:
                u = (aniso_u11[i], aniso_u12[i], aniso_u13[i],
                    aniso_u22[i], aniso_u23[i], aniso_u33[i])
                mapped_anisou = [float(x) for x in u]
                anisou_array = numpy.array(mapped_anisou, 'f')
                structure_builder.set_anisou(anisou_array)
        # Now try to set the cell
        try:
            a = float(mmcif_dict["_cell.length_a"])
            b = float(mmcif_dict["_cell.length_b"])
            c = float(mmcif_dict["_cell.length_c"])
            alpha = float(mmcif_dict["_cell.angle_alpha"])
            beta = float(mmcif_dict["_cell.angle_beta"])
            gamma = float(mmcif_dict["_cell.angle_gamma"])
            cell = numpy.array((a, b, c, alpha, beta, gamma), 'f')
            spacegroup = mmcif_dict["_symmetry.space_group_name_H-M"]
            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


if __name__ == "__main__":
    import sys

    if len(sys.argv) != 2:
        print("Usage: python MMCIFparser.py filename")
        raise SystemExit
    filename = sys.argv[1]

    p = MMCIFParser()

    structure = p.get_structure("test", filename)

    for model in structure.get_list():
        print(model)
        for chain in model.get_list():
            print(chain)
            print("Found %d residues." % len(chain.get_list()))
