import torch
import torch.nn as nn
import rdkit.Chem as Chem
import torch.nn.functional as F
from .nnutils import index_select_ND
from .chemutils import get_mol

ELEM_LIST = [
    "C",
    "N",
    "O",
    "S",
    "F",
    "Si",
    "P",
    "Cl",
    "Br",
    "Mg",
    "Na",
    "Ca",
    "Fe",
    "Al",
    "I",
    "B",
    "K",
    "Se",
    "Zn",
    "H",
    "Cu",
    "Mn",
    "unknown",
]

ATOM_FDIM = len(ELEM_LIST) + 6 + 5 + 4 + 1
BOND_FDIM = 5 + 6
MAX_NB = 6


def onek_encoding_unk(x, allowable_set):
    if x not in allowable_set:
        x = allowable_set[-1]
    return [x == s for s in allowable_set]


def atom_features(atom):
    return torch.Tensor(
        onek_encoding_unk(atom.GetSymbol(), ELEM_LIST)
        + onek_encoding_unk(atom.GetDegree(), [0, 1, 2, 3, 4, 5])
        + onek_encoding_unk(atom.GetFormalCharge(), [-1, -2, 1, 2, 0])
        + onek_encoding_unk(int(atom.GetChiralTag()), [0, 1, 2, 3])
        + [atom.GetIsAromatic()]
    )


def bond_features(bond):
    bt = bond.GetBondType()
    stereo = int(bond.GetStereo())
    fbond = [
        bt == Chem.rdchem.BondType.SINGLE,
        bt == Chem.rdchem.BondType.DOUBLE,
        bt == Chem.rdchem.BondType.TRIPLE,
        bt == Chem.rdchem.BondType.AROMATIC,
        bond.IsInRing(),
    ]
    fstereo = onek_encoding_unk(stereo, [0, 1, 2, 3, 4, 5])
    return torch.Tensor(fbond + fstereo)


class MPN(nn.Module):
    def __init__(self, hidden_size, depth):
        super(MPN, self).__init__()
        self.hidden_size = hidden_size
        self.depth = depth

        self.W_i = nn.Linear(ATOM_FDIM + BOND_FDIM, hidden_size, bias=False)
        self.W_h = nn.Linear(hidden_size, hidden_size, bias=False)
        self.W_o = nn.Linear(ATOM_FDIM + hidden_size, hidden_size)

    def forward(self, fatoms, fbonds, agraph, bgraph, scope):
        fatoms = torch.as_tensor(fatoms, device=self.W_i.weight.device)
        fbonds = torch.as_tensor(fbonds, device=self.W_i.weight.device)
        agraph = torch.as_tensor(agraph, device=self.W_i.weight.device)
        bgraph = torch.as_tensor(bgraph, device=self.W_i.weight.device)

        binput = self.W_i(fbonds)
        message = F.relu(binput)

        for i in range(self.depth - 1):
            nei_message = index_select_ND(message, 0, bgraph)
            nei_message = nei_message.sum(dim=1)
            nei_message = self.W_h(nei_message)
            message = F.relu(binput + nei_message)

        nei_message = index_select_ND(message, 0, agraph)
        nei_message = nei_message.sum(dim=1)
        ainput = torch.cat([fatoms, nei_message], dim=1)
        atom_hiddens = F.relu(self.W_o(ainput))

        max_len = max([x for _, x in scope])
        batch_vecs = []
        for st, le in scope:
            cur_vecs = atom_hiddens[st : st + le].mean(dim=0)
            batch_vecs.append(cur_vecs)

        mol_vecs = torch.stack(batch_vecs, dim=0)
        return mol_vecs

    @staticmethod
    def tensorize(mol_batch):
        padding = torch.zeros(ATOM_FDIM + BOND_FDIM)
        fatoms, fbonds = [], [padding]  # Ensure bond is 1-indexed
        in_bonds, all_bonds = [], [(-1, -1)]  # Ensure bond is 1-indexed
        scope = []
        total_atoms = 0

        for smiles in mol_batch:
            mol = get_mol(smiles)
            # mol = Chem.MolFromSmiles(smiles)
            n_atoms = mol.GetNumAtoms()
            for atom in mol.GetAtoms():
                fatoms.append(atom_features(atom))
                in_bonds.append([])

            for bond in mol.GetBonds():
                a1 = bond.GetBeginAtom()
                a2 = bond.GetEndAtom()
                x = a1.GetIdx() + total_atoms
                y = a2.GetIdx() + total_atoms

                b = len(all_bonds)
                all_bonds.append((x, y))
                fbonds.append(torch.cat([fatoms[x], bond_features(bond)], 0))
                in_bonds[y].append(b)

                b = len(all_bonds)
                all_bonds.append((y, x))
                fbonds.append(torch.cat([fatoms[y], bond_features(bond)], 0))
                in_bonds[x].append(b)

            scope.append((total_atoms, n_atoms))
            total_atoms += n_atoms

        total_bonds = len(all_bonds)
        fatoms = torch.stack(fatoms, 0)
        fbonds = torch.stack(fbonds, 0)
        agraph = torch.zeros(total_atoms, MAX_NB).long()
        bgraph = torch.zeros(total_bonds, MAX_NB).long()

        for a in range(total_atoms):
            for i, b in enumerate(in_bonds[a]):
                agraph[a, i] = b

        for b1 in range(1, total_bonds):
            x, y = all_bonds[b1]
            for i, b2 in enumerate(in_bonds[x]):
                if all_bonds[b2][0] != y:
                    bgraph[b1, i] = b2

        return (fatoms, fbonds, agraph, bgraph, scope)

