import numpy as np
import os.path
import subprocess
import torch

from Bio.PDB import PDBParser
from src import const
from src.visualizer import save_xyz_file
from src.utils import FoundNaNException
from src.datasets import get_one_hot


def generate_linkers(ddpm, data, sample_fn, name, with_pocket=False, offset_idx=0):
    chain = node_mask = None
    for i in range(5):
        try:
            chain, node_mask = ddpm.sample_chain(data, sample_fn=sample_fn, keep_frames=1)
            break
        except FoundNaNException:
            continue

    print('Generated linker')
    x = chain[0][:, :, :ddpm.n_dims]
    h = chain[0][:, :, ddpm.n_dims:]

    # Put the molecule back to the initial orientation
    if with_pocket:
        com_mask = data['fragment_only_mask'] if ddpm.center_of_mass == 'fragments' else data['anchors']
    else:
        com_mask = data['fragment_mask'] if ddpm.center_of_mass == 'fragments' else data['anchors']

    pos_masked = data['positions'] * com_mask
    N = com_mask.sum(1, keepdims=True)
    mean = torch.sum(pos_masked, dim=1, keepdim=True) / N
    x = x + mean * node_mask

    if with_pocket:
        node_mask[torch.where(data['pocket_mask'])] = 0

    batch_size = len(data['positions'])
    names = [f'output_{offset_idx + i + 1}_{name}' for i in range(batch_size)]
    save_xyz_file('results', h, x, node_mask, names=names, is_geom=True, suffix='')
    print('Saved XYZ files')


def try_to_convert_to_sdf(name, num_samples):
    out_files = []
    for i in range(num_samples):
        out_xyz = f'results/output_{i + 1}_{name}_.xyz'
        out_sdf = f'results/output_{i + 1}_{name}_.sdf'
        subprocess.run(f'obabel {out_xyz} -O {out_sdf}', shell=True)
        if os.path.exists(out_sdf):
            out_files.append(out_sdf)
        else:
            out_files.append(out_xyz)

    return out_files


def get_pocket(mol, pdb_path):
    struct = PDBParser().get_structure('', pdb_path)
    residue_ids = []
    atom_coords = []

    for residue in struct.get_residues():
        resid = residue.get_id()[1]
        for atom in residue.get_atoms():
            atom_coords.append(atom.get_coord())
            residue_ids.append(resid)

    residue_ids = np.array(residue_ids)
    atom_coords = np.array(atom_coords)
    mol_atom_coords = mol.GetConformer().GetPositions()

    distances = np.linalg.norm(atom_coords[:, None, :] - mol_atom_coords[None, :, :], axis=-1)
    contact_residues = np.unique(residue_ids[np.where(distances.min(1) <= 6)[0]])

    pocket_coords_full = []
    pocket_types_full = []

    pocket_coords_bb = []
    pocket_types_bb = []

    for residue in struct.get_residues():
        resid = residue.get_id()[1]
        if resid not in contact_residues:
            continue

        for atom in residue.get_atoms():
            atom_name = atom.get_name()
            atom_type = atom.element.upper()
            atom_coord = atom.get_coord()

            pocket_coords_full.append(atom_coord.tolist())
            pocket_types_full.append(atom_type)

            if atom_name in {'N', 'CA', 'C', 'O'}:
                pocket_coords_bb.append(atom_coord.tolist())
                pocket_types_bb.append(atom_type)

    pocket_pos = []
    pocket_one_hot = []
    pocket_charges = []
    for coord, atom_type in zip(pocket_coords_full, pocket_types_full):
        if atom_type not in const.GEOM_ATOM2IDX.keys():
            continue

        pocket_pos.append(coord)
        pocket_one_hot.append(get_one_hot(atom_type, const.GEOM_ATOM2IDX))
        pocket_charges.append(const.GEOM_CHARGES[atom_type])

    pocket_pos = np.array(pocket_pos)
    pocket_one_hot = np.array(pocket_one_hot)
    pocket_charges = np.array(pocket_charges)

    return pocket_pos, pocket_one_hot, pocket_charges