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import biotite.structure.io.pdbx as pdbx
import numpy as np
from Bio.PDB import PDBParser
from biotite.structure import annotate_sse
from biotite.structure.io.pdb import PDBFile


def cacl_secondary_structure(path, binder_chain=None):
    """
    Calculate the ratio of secondary structures in a PDB or CIF file.

    Args:
        path (str): Path to the PDB (.pdb) or CIF (.cif) file.
        binder_chain (str, optional): The chain ID to filter the structure.
            If provided, only atoms from this chain will be considered. Defaults to None.

    Returns:
        tuple: The ratio of secondary structures (alpha, beta, loop)
    """
    # Check the file extension and read the file accordingly
    if path.endswith(".cif"):
        pdb_name = pdbx.PDBxFile.read(path)
        atom_array = pdbx.get_structure(pdb_name, model=1)
    elif path.endswith(".pdb"):
        pdb_name = PDBFile.read(path)
        atom_array = pdb_name.get_structure()[0]
    else:
        raise ValueError("File must be either a .pdb or .cif file")

    if binder_chain is not None:
        chain_mask = atom_array.chain_id == binder_chain
        atom_array = atom_array[chain_mask]
    sse_array = annotate_sse(atom_array)

    count_a = np.sum(sse_array == "a")
    count_b = np.sum(sse_array == "b")
    count_c = np.sum(sse_array == "c")
    total = len(sse_array)
    return (
        round(count_a / total, 3),
        round(count_b / total, 3),
        round(count_c / total, 3),
    )


def cacl_ref_rg(num_res):
    """
    reference radius of gyration value.
    Ref: Bindcraft repo (https://github.com/martinpacesa/BindCraft/blob/05702c435e2172a99c2b3faf87487badb6e54727/functions/colabdesign_utils.py#L369)
    """
    return 2.38 * num_res**0.365


def get_chain_rg(pdb_file, chain_id, atom_name="CA"):
    """
    Calculate the radius of gyration of a specific chain in a PDB file.

    Args:
        pdb_file (str): Path to the PDB file.
        chain_id (str): The chain ID to calculate the radius of gyration for.
        atom_name (str, optional): The name of the atom to use for calculation. Defaults to "CA".

    Returns:
        tuple: The radius of gyration and the normalized radius of gyration.
    """
    parser = PDBParser(QUIET=True)
    structure = parser.get_structure("struct", pdb_file)
    coords = []
    for model in structure:
        for chain in model:
            if chain.id == chain_id:
                for res in chain:
                    if atom_name in res:
                        atom = res[atom_name]
                        coords.append(atom.coord)
    coords = np.array(coords)
    if coords.size == 0:
        raise ValueError("No atoms found!")
    center = coords.mean(axis=0)
    num_res = len(coords)
    rg = np.sqrt(((coords - center) ** 2).sum(axis=1).mean())
    return round(rg, 2), round(rg / cacl_ref_rg(num_res), 4)