# Copyright 2019-2022 by Robert T. Miller.  All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.

"""Convert XYZ Structure to internal coordinates and back, test result."""

import re
import numpy as np

from itertools import zip_longest

try:
    import numpy
except ImportError:
    from Bio import MissingPythonDependencyError

    raise MissingPythonDependencyError(
        "Install NumPy to build proteins from internal coordinates."
    )

from Bio.PDB.PDBExceptions import PDBException
from io import StringIO
from Bio.File import as_handle
from Bio.PDB.PDBIO import PDBIO

from Bio.PDB.Structure import Structure
from Bio.PDB.internal_coords import IC_Residue
from Bio.PDB.PICIO import write_PIC, read_PIC, enumerate_atoms, pdb_date

# for typing
from typing import Dict, Union, Any, Tuple
from Bio.PDB.Atom import Atom
from Bio.PDB.Residue import Residue, DisorderedResidue
from Bio.PDB.Model import Model
from Bio.PDB.Chain import Chain


def structure_rebuild_test(entity, verbose: bool = False, quick: bool = False) -> Dict:
    """Test rebuild PDB structure from internal coordinates.

    Generates internal coordinates for entity and writes to a .pic file in
    memory, then generates XYZ coordinates from the .pic file and compares the
    resulting entity against the original.

    See :data:`IC_Residue.pic_accuracy` to vary numeric accuracy of the
    intermediate .pic file if the only issue is small differences in coordinates.

    Note that with default settings, deuterated initial structures will fail
    the comparison, as will structures loaded with alternate `IC_Residue.accept_atoms`
    settings.  Use `quick=True` and/or variations on `AtomKey.d2h` and
    `IC_Residue.accept_atoms` settings.

    :param Entity entity: Biopython Structure, Model or Chain.
        Structure to test
    :param bool verbose: default False.
        print extra messages
    :param bool quick: default False.
        only check the internal coords atomArrays are identical
    :returns: dict
        comparison dict from :func:`.compare_residues`
    """
    sp = StringIO()
    entity.atom_to_internal_coordinates(verbose)
    write_PIC(entity, sp)
    sp.seek(0)
    pdb2 = read_PIC(sp, verbose=verbose, quick=quick)
    if isinstance(entity, Chain):
        pdb2 = next(pdb2.get_chains())  # there's only one, get first
    if verbose:
        report_IC(pdb2, verbose=True)

    pdb2.internal_to_atom_coordinates(verbose)
    r = compare_residues(entity, pdb2, verbose=verbose, quick=quick)
    return r


def report_IC(
    entity: Union[Structure, Model, Chain, Residue],
    reportDict: Dict[str, Any] = None,
    verbose: bool = False,
) -> Dict[str, Any]:
    """Generate dict with counts of ic data elements for each entity level.

    reportDict entries are:
        - idcode : PDB ID
        - hdr : PDB header lines
        - mdl : models
        - chn : chains
        - res : residue objects
        - res_e : residues with dihedra and/or hedra
        - dih : dihedra
        - hed : hedra

    :param Entity entity: Biopython PDB Entity object: S, M, C or R
    :raises PDBException: if entity level not S, M, C, or R
    :raises Exception: if entity does not have .level attribute
    :returns: dict with counts of IC data elements
    """
    if reportDict is None:
        reportDict = {
            "idcode": None,
            "hdr": 0,
            "mdl": 0,
            "chn": 0,
            "chn_ids": [],
            "res": 0,
            "res_e": 0,
            "dih": 0,
            "hed": 0,
        }
    try:
        if "A" == entity.level:
            raise PDBException("No IC output at Atom level")
        elif isinstance(entity, Residue) or isinstance(
            entity, DisorderedResidue
        ):  # "R" == entity.level:
            if entity.internal_coord:
                reportDict["res"] += 1
                dlen = len(entity.internal_coord.dihedra)
                hlen = len(entity.internal_coord.hedra)
                if 0 < dlen or 0 < hlen:
                    reportDict["res_e"] += 1
                    reportDict["dih"] += dlen
                    reportDict["hed"] += hlen

        elif isinstance(entity, Chain):  # "C" == entity.level:
            reportDict["chn"] += 1
            reportDict["chn_ids"].append(entity.id)
            for res in entity:
                reportDict = report_IC(res, reportDict)

        elif isinstance(entity, Model):  # "M" == entity.level:
            reportDict["mdl"] += 1
            for chn in entity:
                reportDict = report_IC(chn, reportDict)

        elif isinstance(entity, Structure):  # "S" == entity.level:
            if hasattr(entity, "header"):
                if reportDict["idcode"] is None:
                    reportDict["idcode"] = entity.header.get("idcode", None)

                hdr = entity.header.get("head", None)
                if hdr:
                    reportDict["hdr"] += 1
                nam = entity.header.get("name", None)
                if nam:
                    reportDict["hdr"] += 1
            for mdl in entity:
                reportDict = report_IC(mdl, reportDict)
        else:
            raise PDBException("Cannot identify level: " + str(entity.level))
    except KeyError:
        raise Exception(
            "write_PIC: argument is not a Biopython PDB Entity " + str(entity)
        )

    if verbose:
        print(
            "{} : {} models {} chains {} {} residue objects "
            "{} residues with {} dihedra {} hedra".format(
                reportDict["idcode"],
                reportDict["mdl"],
                reportDict["chn"],
                reportDict["chn_ids"],
                reportDict["res"],
                reportDict["res_e"],
                reportDict["dih"],
                reportDict["hed"],
            )
        )

    return reportDict


def IC_duplicate(entity) -> Structure:
    """Duplicate structure entity with IC data, no atom coordinates.

    Employs :func:`.write_PIC`, :func:`.read_PIC` with StringIO buffer.
    Calls :meth:`.Chain.atom_to_internal_coordinates` if needed.

    :param Entity entity: Biopython PDB Entity (will fail for Atom)
    :returns: Biopython PDBStructure, no Atom objects except initial coords
    """
    sp = StringIO()
    hasInternalCoords = False
    for res in entity.get_residues():
        if res.internal_coord:
            if len(res.internal_coord.hedra) > 0:
                hasInternalCoords = True
                break
    if not hasInternalCoords:
        if isinstance(entity, Residue):  # "R" == entity.level:
            # works better at chain level but leave option here
            res = entity
            if not res.internal_coord:
                res.internal_coord = IC_Residue(entity)
            res.internal_coord.atom_to_internal_coordinates()
        else:
            entity.atom_to_internal_coordinates()

    write_PIC(entity, sp)
    sp.seek(0)
    return read_PIC(sp)


def _atmfid_d2h(atm: Atom) -> Tuple:
    afid = list(atm.get_full_id())
    afid4 = list(afid[4])
    afid40 = re.sub("D", "H", afid4[0], count=1)
    new_afid = (afid[0], afid[1], afid[2], afid[3], (afid40, afid4[1]))
    return tuple(new_afid)


def _cmp_atm(
    r0: Residue,
    r1: Residue,
    a0: Atom,
    a1: Atom,
    verbose: bool,
    cmpdict: Dict,
    rtol: float = None,
    atol: float = None,
) -> None:
    cmpdict["aCount"] += 1
    if a0 is None:
        if verbose:
            print(
                r1.get_full_id(),
                "None !=",
                a1.get_full_id(),
                a1.parent.resname,
            )
    elif a1 is None:
        if verbose:
            print(
                r0.get_full_id(),
                a0.get_full_id(),
                a0.parent.resname,
                "!= None",
            )
    else:
        if a0.get_full_id() == a1.get_full_id() or _atmfid_d2h(a0) == a1.get_full_id():
            cmpdict["aFullIdMatchCount"] += 1
        elif verbose:
            print(
                r0.get_full_id(),
                a0.get_full_id(),
                a0.parent.resname,
                "!=",
                a1.get_full_id(),
            )
        ac_rslt = False
        if rtol is None and atol is None:
            a0c = numpy.round(a0.get_coord(), 3)
            a1c = numpy.round(a1.get_coord(), 3)
            ac_rslt = numpy.array_equal(a0c, a1c)
        else:
            a0c = a0.get_coord()
            a1c = a1.get_coord()
            ac_rslt = numpy.allclose(a0c, a1c, rtol=rtol, atol=atol)

        if ac_rslt:
            cmpdict["aCoordMatchCount"] += 1
        elif verbose:
            print(
                "atom coords disagree:",
                r0.get_full_id(),
                a0.get_full_id(),
                a1.get_full_id(),
                a0c,
                "!=",
                a1c,
            )


def _cmp_res(
    r0: Residue,
    r1: Residue,
    verbose: bool,
    cmpdict: Dict,
    rtol: float = None,
    atol: float = None,
) -> None:
    r0id, r0fid, r1fid = r0.id, r0.full_id, r1.full_id
    chn = r0.parent.id
    if chn not in cmpdict["chains"]:
        cmpdict["chains"].append(chn)
    cmpdict["rCount"] += 1
    if r0fid == r1fid:
        cmpdict["rMatchCount"] += 1
    elif verbose:
        print(r0fid, "!=", r1fid)

    if hasattr(r0, "internal_coord") and r0.internal_coord is not None:
        ric0 = r0.internal_coord
        ric1 = r1.internal_coord
        r0prev = sorted(ric.rbase for ric in ric0.rprev)
        r1prev = sorted(ric.rbase for ric in ric1.rprev)
        r0next = sorted(ric.rbase for ric in ric0.rnext)
        r1next = sorted(ric.rbase for ric in ric1.rnext)

        if r0prev != r1prev:
            if verbose:
                print(r0, "rprev error:", r0prev, "!=", r1prev)
            cmpdict["rpnMismatchCount"] += 1
        if r0next != r1next:
            if verbose:
                print(r0, "rnext error", r0next, "!=", r1next)
            cmpdict["rpnMismatchCount"] += 1

    if " " == r0id[0] and not (" " == r0.resname[0] or 2 == len(r0.resname)):
        # skip water, DNA (' ' == [0] for pdb, 2 == len() for mmcif)
        cmpdict["residues"] += 1
        longer = r0 if len(r0.child_dict) >= len(r1.child_dict) else r1
        for ak in longer.child_dict:
            a0 = r0.child_dict.get(ak, None)
            if a0 is None:
                aknd = re.sub("D", "H", ak, count=1)
                a0 = r0.child_dict.get(aknd, None)
            a1 = r1.child_dict.get(ak, None)
            if a1 is None:
                aknd = re.sub("D", "H", ak, count=1)
                a1 = r1.child_dict.get(aknd, None)
            if (
                a0 is None
                or a1 is None
                or 0 == a0.is_disordered() == a1.is_disordered()
            ):
                _cmp_atm(r0, r1, a0, a1, verbose, cmpdict, rtol=rtol, atol=atol)
            elif 2 == a0.is_disordered() == a1.is_disordered():
                cmpdict["disAtmCount"] += 1
                for da0k in a0.child_dict:
                    _cmp_atm(
                        r0,
                        r1,
                        a0.child_dict.get(da0k, None),
                        a1.child_dict.get(da0k, None),
                        verbose,
                        cmpdict,
                        rtol=rtol,
                        atol=atol,
                    )
            else:
                if verbose:
                    print("disorder disagreement:", r0.get_full_id(), ak)
                cmpdict["aCount"] += 1


def compare_residues(
    e0: Union[Structure, Model, Chain],
    e1: Union[Structure, Model, Chain],
    verbose: bool = False,
    quick: bool = False,
    rtol: float = None,
    atol: float = None,
) -> Dict[str, Any]:
    """Compare full IDs and atom coordinates for 2 Biopython PDB entities.

    Skip DNA and HETATMs.

    :param Entity e0,e1: Biopython PDB Entity objects (S, M or C).
        Structures, Models or Chains to be compared
    :param bool verbose:
        Whether to print mismatch info, default False
    :param bool quick: default False.
        Only check atomArrays are identical, aCoordMatchCount=0 if different
    :param float rtol, atol: default 1e-03, 1e-03 or round to 3 places.
        Numpy allclose parameters; default is to round atom coordinates to 3
        places and test equal.  For 'quick' will use defaults above for
        comparing atomArrays
    :returns dict:
        Result counts for Residues, Full ID match Residues, Atoms,
        Full ID match atoms, and Coordinate match atoms; report string;
        error status (bool)
    """
    cmpdict: Dict[str, Any] = {}
    cmpdict["chains"] = []  # list of chain IDs (union over both structures)
    cmpdict["residues"] = 0  # count of not HETATM residues in longest chain
    cmpdict["rCount"] = 0  # Biopython Residues (includes HETATMs, waters)
    cmpdict["rMatchCount"] = 0  # full ID match Biopython Residues e0, e1
    cmpdict["rpnMismatchCount"] = 0  # res prev, next links not matched
    cmpdict["aCount"] = 0  # Atoms including disordered in longest e0 or e1
    cmpdict["disAtmCount"] = 0  # disordered atoms in longest e0 or e1
    cmpdict["aCoordMatchCount"] = 0  # atoms with coordinates match e0, e1
    cmpdict["aFullIdMatchCount"] = 0  # atoms with full ID match e0, e1
    cmpdict["id0"] = e0.get_full_id()
    cmpdict["id1"] = e1.get_full_id()
    cmpdict["pass"] = None
    cmpdict["report"] = None

    if quick:
        if isinstance(e0, Chain):
            if (
                e0.internal_coord.atomArray is not None
                and np.shape(e0.internal_coord.atomArray)
                == np.shape(e1.internal_coord.atomArray)
                and numpy.allclose(
                    e0.internal_coord.atomArray,
                    e1.internal_coord.atomArray,
                    rtol=1e-03 if rtol is None else rtol,
                    atol=1e-03 if atol is None else atol,
                )
            ):
                cmpdict["aCount"] = numpy.size(e0.internal_coord.atomArray, 0)
                cmpdict["aCoordMatchCount"] = numpy.size(e0.internal_coord.atomArray, 0)
                if cmpdict["aCoordMatchCount"] > 0:
                    cmpdict["pass"] = True
                else:
                    cmpdict["pass"] = False
            else:
                cmpdict["aCount"] = (
                    0
                    if e0.internal_coord.atomArray is None
                    else numpy.size(e0.internal_coord.atomArray, 0)
                )
                cmpdict["pass"] = False
        else:
            cmpdict["pass"] = True
            for c0, c1 in zip_longest(e0.get_chains(), e1.get_chains()):
                if c0.internal_coord.atomArray is not None:
                    if numpy.allclose(
                        c0.internal_coord.atomArray,
                        c1.internal_coord.atomArray,
                        rtol=1e-03 if rtol is None else rtol,
                        atol=1e-03 if atol is None else atol,
                    ):
                        cmpdict["aCoordMatchCount"] += numpy.size(
                            c0.internal_coord.atomArray, 0
                        )
                    else:
                        cmpdict["pass"] = False
                    cmpdict["aCount"] += numpy.size(c0.internal_coord.atomArray, 0)
            if cmpdict["aCoordMatchCount"] < cmpdict["aCount"]:
                cmpdict["pass"] = False

    else:
        for r0, r1 in zip_longest(e0.get_residues(), e1.get_residues()):
            if 2 == r0.is_disordered() == r1.is_disordered():
                for dr0, dr1 in zip_longest(
                    r0.child_dict.values(), r1.child_dict.values()
                ):
                    _cmp_res(dr0, dr1, verbose, cmpdict, rtol=rtol, atol=atol)
            else:
                _cmp_res(r0, r1, verbose, cmpdict, rtol=rtol, atol=atol)

        if (
            cmpdict["rMatchCount"] == cmpdict["rCount"]
            and cmpdict["aCoordMatchCount"] == cmpdict["aCount"]
            and cmpdict["aFullIdMatchCount"] == cmpdict["aCount"]
            and cmpdict["rpnMismatchCount"] == 0
        ):
            cmpdict["pass"] = True
        else:
            cmpdict["pass"] = False

    rstr = (
        "{}:{} {} -- {} of {} residue IDs match; {} residues {} atom coords, "
        "{} full IDs of {} atoms ({} disordered) match : {}".format(
            cmpdict["id0"],
            cmpdict["id1"],
            cmpdict["chains"],
            cmpdict["rMatchCount"],
            cmpdict["rCount"],
            cmpdict["residues"],
            cmpdict["aCoordMatchCount"],
            cmpdict["aFullIdMatchCount"],
            cmpdict["aCount"],
            cmpdict["disAtmCount"],
            "ERROR" if not cmpdict["pass"] else "ALL OK",
        )
    )
    if not cmpdict["pass"]:
        if cmpdict["rMatchCount"] != cmpdict["rCount"]:
            rstr += " -RESIDUE IDS-"
        if cmpdict["aCoordMatchCount"] != cmpdict["aFullIdMatchCount"]:
            rstr += " -COORDINATES-"
        if cmpdict["aFullIdMatchCount"] != cmpdict["aCount"]:
            rstr += " -ATOM IDS-"
    cmpdict["report"] = rstr

    return cmpdict


def write_PDB(
    entity: Structure, file: str, pdbid: str = None, chainid: str = None
) -> None:
    """Write PDB file with HEADER and TITLE if available."""
    enumerate_atoms(entity)
    with as_handle(file, "w") as fp:
        try:
            if hasattr(entity, "header"):
                if not pdbid:
                    pdbid = entity.header.get("idcode", None)
                hdr = entity.header.get("head", None)
                dd = pdb_date(entity.header.get("deposition_date", None))

                if hdr:
                    fp.write(
                        ("HEADER    {:40}{:8}   {:4}\n").format(
                            hdr.upper(), (dd or ""), (pdbid or "")
                        )
                    )
                nam = entity.header.get("name", None)
                if nam:
                    fp.write("TITLE     " + nam.upper() + "\n")
            io = PDBIO()
            io.set_structure(entity)
            io.save(fp, preserve_atom_numbering=True)
        except KeyError:
            raise Exception(
                "write_PDB: argument is not a Biopython PDB Entity " + str(entity)
            )