# 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.

"""Output of PDB files."""

import os
import warnings

from Bio import BiopythonWarning
from Bio.Data.IUPACData import atom_weights
from Bio.PDB.PDBExceptions import PDBIOException
from Bio.PDB.StructureBuilder import StructureBuilder

_ATOM_FORMAT_STRING = (
    "%s%5i %-4s%c%3s %c%4i%c   %8.3f%8.3f%8.3f%s%6.2f      %4s%2s%2s\n"
)
_PQR_ATOM_FORMAT_STRING = (
    "%s%5i %-4s%c%3s %c%4i%c   %8.3f%8.3f%8.3f %7s  %6s      %2s\n"
)

_TER_FORMAT_STRING = (
    "TER   %5i      %3s %c%4i%c                                                      \n"
)


class Select:
    """Select everything for PDB output (for use as a base class).

    Default selection (everything) during writing - can be used as base class
    to implement selective output. This selects which entities will be written out.
    """

    def __repr__(self):
        """Represent the output as a string for debugging."""
        return "<Select all>"

    def accept_model(self, model):
        """Overload this to reject models for output."""
        return 1

    def accept_chain(self, chain):
        """Overload this to reject chains for output."""
        return 1

    def accept_residue(self, residue):
        """Overload this to reject residues for output."""
        return 1

    def accept_atom(self, atom):
        """Overload this to reject atoms for output."""
        return 1


_select = Select()


class StructureIO:
    """Base class to derive structure file format writers from."""

    def __init__(self):
        """Initialise."""

    def set_structure(self, pdb_object):
        """Check what the user is providing and build a structure."""
        # The idea here is to build missing upstream components of
        # the SMCRA object representation. E.g., if the user provides
        # a Residue, build Structure/Model/Chain.

        if pdb_object.level == "S":
            structure = pdb_object
        else:  # Not a Structure
            sb = StructureBuilder()
            sb.init_structure("pdb")
            sb.init_seg(" ")

            if pdb_object.level == "M":
                sb.structure.add(pdb_object.copy())
                self.structure = sb.structure
            else:  # Not a Model
                sb.init_model(0)

                if pdb_object.level == "C":
                    sb.structure[0].add(pdb_object.copy())
                else:  # Not a Chain
                    chain_id = "A"  # default
                    sb.init_chain(chain_id)

                    if pdb_object.level == "R":  # Residue
                        # Residue extracted from a larger structure?
                        if pdb_object.parent is not None:
                            og_chain_id = pdb_object.parent.id
                            sb.structure[0][chain_id].id = og_chain_id
                            chain_id = og_chain_id

                        sb.structure[0][chain_id].add(pdb_object.copy())

                    else:  # Atom
                        sb.init_residue("DUM", " ", 1, " ")  # Dummy residue
                        sb.structure[0][chain_id].child_list[0].add(pdb_object.copy())

                        # Fix chain identifier if Atom has grandparents.
                        try:
                            og_chain_id = pdb_object.parent.parent.id
                        except AttributeError:  # pdb_object.parent == None
                            pass
                        else:
                            sb.structure[0][chain_id].id = og_chain_id

            # Return structure
            structure = sb.structure
        self.structure = structure


class PDBIO(StructureIO):
    """Write a Structure object (or a subset of a Structure object) as a PDB or PQR file.

    Examples
    --------
    >>> from Bio.PDB import PDBParser
    >>> from Bio.PDB.PDBIO import PDBIO
    >>> parser = PDBParser()
    >>> structure = parser.get_structure("1a8o", "PDB/1A8O.pdb")
    >>> io=PDBIO()
    >>> io.set_structure(structure)
    >>> io.save("bio-pdb-pdbio-out.pdb")
    >>> import os
    >>> os.remove("bio-pdb-pdbio-out.pdb")  # tidy up


    """

    def __init__(self, use_model_flag=0, is_pqr=False):
        """Create the PDBIO object.

        :param use_model_flag: if 1, force use of the MODEL record in output.
        :type use_model_flag: int
        :param is_pqr: if True, build PQR file. Otherwise build PDB file.
        :type is_pqr: Boolean
        """
        self.use_model_flag = use_model_flag
        self.is_pqr = is_pqr

    # private methods

    def _get_atom_line(
        self,
        atom,
        hetfield,
        segid,
        atom_number,
        resname,
        resseq,
        icode,
        chain_id,
        charge="  ",
    ):
        """Return an ATOM PDB string (PRIVATE)."""
        if hetfield != " ":
            record_type = "HETATM"
        else:
            record_type = "ATOM  "

        # Atom properties

        # Check if the atom serial number is an integer
        # Not always the case for structures built from
        # mmCIF files.
        try:
            atom_number = int(atom_number)
        except ValueError:
            raise ValueError(
                f"{atom_number!r} is not a number."
                "Atom serial numbers must be numerical"
                " If you are converting from an mmCIF"
                " structure, try using"
                " preserve_atom_numbering=False"
            )

        if atom_number > 99999:
            raise ValueError(
                f"Atom serial number ('{atom_number}') exceeds PDB format limit."
            )

        # Check if the element is valid, unknown (X), or blank
        if atom.element:
            element = atom.element.strip().upper()
            if element.capitalize() not in atom_weights and element != "X":
                raise ValueError(f"Unrecognised element {atom.element}")
            element = element.rjust(2)
        else:
            element = "  "

        # Format atom name
        # Pad if:
        #     - smaller than 4 characters
        # AND - is not C, N, O, S, H, F, P, ..., one letter elements
        # AND - first character is NOT numeric (funky hydrogen naming rules)
        name = atom.fullname.strip()
        if len(name) < 4 and name[:1].isalpha() and len(element.strip()) < 2:
            name = " " + name

        altloc = atom.altloc
        x, y, z = atom.coord

        # Write PDB format line
        if not self.is_pqr:
            bfactor = atom.bfactor
            try:
                occupancy = f"{atom.occupancy:6.2f}"
            except (TypeError, ValueError):
                if atom.occupancy is None:
                    occupancy = " " * 6
                    warnings.warn(
                        f"Missing occupancy in atom {atom.full_id!r} written as blank",
                        BiopythonWarning,
                    )
                else:
                    raise ValueError(
                        f"Invalid occupancy value: {atom.occupancy!r}"
                    ) from None

            args = (
                record_type,
                atom_number,
                name,
                altloc,
                resname,
                chain_id,
                resseq,
                icode,
                x,
                y,
                z,
                occupancy,
                bfactor,
                segid,
                element,
                charge,
            )
            return _ATOM_FORMAT_STRING % args

        # Write PQR format line
        else:
            try:
                pqr_charge = f"{atom.pqr_charge:7.4f}"
            except (TypeError, ValueError):
                if atom.pqr_charge is None:
                    pqr_charge = " " * 7
                    warnings.warn(
                        f"Missing PQR charge in atom {atom.full_id} written as blank",
                        BiopythonWarning,
                    )
                else:
                    raise ValueError(
                        f"Invalid PQR charge value: {atom.pqr_charge!r}"
                    ) from None

            try:
                radius = f"{atom.radius:6.4f}"
            except (TypeError, ValueError):
                if atom.radius is None:
                    radius = " " * 6
                    warnings.warn(
                        f"Missing radius in atom {atom.full_id} written as blank",
                        BiopythonWarning,
                    )
                else:
                    raise ValueError(f"Invalid radius value: {atom.radius}") from None

            args = (
                record_type,
                atom_number,
                name,
                altloc,
                resname,
                chain_id,
                resseq,
                icode,
                x,
                y,
                z,
                pqr_charge,
                radius,
                element,
            )

            return _PQR_ATOM_FORMAT_STRING % args

    @staticmethod
    def _revert_write(handle, truncate_to=None, delete_file=False):
        """Revert data written to file by removing the file or truncating it.

        This method is used when the writer throws an exception, to avoid
        writing incomplete files that might confuse users or workflows.
        """
        if delete_file:
            try:
                handle.close()
                os.remove(handle.name)
            except OSError as err:
                # Windows can be finnicky with closing
                # file and deleting them, raising PermissionError
                pass
        elif truncate_to is not None:
            # If the user gave a file handle, seek back to the
            # starting position and truncate the file from there
            # on. Note that the truncation depends on how we
            # opened the file, but we assume the file was opened
            # for writing/appending anyway.
            handle.seek(truncate_to)
            handle.truncate()
        else:
            raise Exception("One of 'truncate_to' or 'delete_file' must be provided")

    # Public methods
    def save(self, file, select=_select, write_end=True, preserve_atom_numbering=False):
        """Save structure to a file.

        :param file: output file
        :type file: string or filehandle

        :param select: selects which entities will be written.
        :type select: object

        Typically select is a subclass of L{Select}, it should
        have the following methods:

         - accept_model(model)
         - accept_chain(chain)
         - accept_residue(residue)
         - accept_atom(atom)

        These methods should return 1 if the entity is to be
        written out, 0 otherwise.

        Typically select is a subclass of L{Select}.
        """
        if isinstance(file, str):
            fhandle = open(file, "w")
        else:
            # filehandle, I hope :-)
            fd_position = file.tell()
            fhandle = file

        get_atom_line = self._get_atom_line

        # multiple models?
        if len(self.structure) > 1 or self.use_model_flag:
            model_flag = 1
        else:
            model_flag = 0

        for model in self.structure.get_list():
            if not select.accept_model(model):
                continue
            # necessary for ENDMDL
            # do not write ENDMDL if no residues were written
            # for this model
            model_residues_written = 0
            if not preserve_atom_numbering:
                atom_number = 1
            if model_flag:
                fhandle.write(f"MODEL      {model.serial_num}\n")

            for chain in model.get_list():
                if not select.accept_chain(chain):
                    continue
                chain_id = chain.id
                if len(chain_id) > 1:
                    if isinstance(file, str):
                        self._revert_write(fhandle, delete_file=True)
                    else:
                        self._revert_write(fhandle, truncate_to=fd_position)
                    raise PDBIOException(
                        f"Chain id ('{chain_id}') exceeds PDB format limit."
                    )

                # necessary for TER
                # do not write TER if no residues were written
                # for this chain
                chain_residues_written = 0

                for residue in chain.get_unpacked_list():
                    if not select.accept_residue(residue):
                        continue
                    hetfield, resseq, icode = residue.id
                    resname = residue.resname
                    segid = residue.segid
                    resid = residue.id[1]
                    if resid > 9999:
                        if isinstance(file, str):
                            self._revert_write(fhandle, delete_file=True)
                        else:
                            self._revert_write(fhandle, truncate_to=fd_position)

                        raise PDBIOException(
                            f"Residue number ('{resid}') exceeds PDB format limit."
                        )

                    for atom in residue.get_unpacked_list():
                        if not select.accept_atom(atom):
                            continue
                        chain_residues_written = 1
                        model_residues_written = 1
                        if preserve_atom_numbering:
                            atom_number = atom.serial_number

                        try:
                            s = get_atom_line(
                                atom,
                                hetfield,
                                segid,
                                atom_number,
                                resname,
                                resseq,
                                icode,
                                chain_id,
                            )
                        except Exception as err:
                            if isinstance(file, str):
                                self._revert_write(fhandle, delete_file=True)
                            else:
                                self._revert_write(fhandle, truncate_to=fd_position)

                            # catch and re-raise with more information
                            raise PDBIOException(
                                f"Error when writing atom {atom.full_id}: {err}"
                            ) from err
                        else:
                            fhandle.write(s)
                            # inconsequential if preserve_atom_numbering is True
                            atom_number += 1

                if chain_residues_written:
                    fhandle.write(
                        _TER_FORMAT_STRING
                        % (atom_number, resname, chain_id, resseq, icode)
                    )

            if model_flag and model_residues_written:
                fhandle.write("ENDMDL\n")
        if write_end:
            fhandle.write("END   \n")

        if isinstance(file, str):
            fhandle.close()
