process_and_predict.py

import pandas as pd
import pickle
import torch
import torchani
import torchani_mod
import qcelemental as qcel
import numpy as np
from tqdm import tqdm
from rdkit import Chem
from biopandas.pdb import PandasPdb
import os
from utils import GraphDataset
from torch_geometric.loader import DataLoader
from helpers import model_dict
import argparse
import time


def elements_to_atomicnums(elements):
    atomicnums = np.zeros(len(elements), dtype=int)

    for idx, e in enumerate(elements):
        atomicnums[idx] = qcel.periodictable.to_Z(e)

    return atomicnums


def LoadMolasDF(mol):
    m = mol

    atoms = []

    for atom in m.GetAtoms():
        if atom.GetSymbol() != "H": # Include only non-hydrogen atoms
            entry = [int(atom.GetIdx())]
            entry.append(str(atom.GetSymbol()))
            pos = m.GetConformer().GetAtomPosition(atom.GetIdx())
            entry.append(float("{0:.4f}".format(pos.x)))
            entry.append(float("{0:.4f}".format(pos.y)))
            entry.append(float("{0:.4f}".format(pos.z)))
            atoms.append(entry)

    df = pd.DataFrame(atoms)
    df.columns = ["ATOM_INDEX","ATOM_TYPE","X","Y","Z"]
    
    return df


def LoadPDBasDF_old(PDB, atom_keys):
    prot_atoms = []
    
    f = open(PDB)
    for i in f:
        if i[:4] == "ATOM":
            # Include only non-hydrogen atoms
            if (len(i[12:16].replace(" ","")) < 4 and i[12:16].replace(" ","")[0] != "H") or (len(i[12:16].replace(" ","")) == 4 and i[12:16].replace(" ","")[1] != "H" and i[12:16].replace(" ","")[0] != "H"):
                prot_atoms.append([int(i[6:11]),
                         i[17:20]+"-"+i[12:16].replace(" ",""),
                         float(i[30:38]),
                         float(i[38:46]),
                         float(i[46:54])
                        ])
                
    f.close()
    
    df = pd.DataFrame(prot_atoms, columns=["ATOM_INDEX","PDB_ATOM","X","Y","Z"])
    df = df.merge(atom_keys, left_on='PDB_ATOM', right_on='PDB_ATOM')[["ATOM_INDEX", "ATOM_TYPE", "X", "Y", "Z"]].sort_values(by="ATOM_INDEX").reset_index(drop=True)
    return df


def LoadPDBasDF(pdb_path, atom_keys):
    allowed_residues = atom_keys["RESIDUE"].unique()
    ppdb = PandasPdb().read_pdb(pdb_path)
    protein = ppdb.df['ATOM']
    protein = protein[~protein["atom_name"].str.startswith("H")]
    protein = protein[~protein["atom_name"].str.startswith(tuple(map(str, range(10))))]

    disgard = protein[~protein["residue_name"].isin(allowed_residues)]
    if len(disgard) > 0:
        print("WARNING: Protein contains unsupported residues.", pdb_path)
        print("Ignoring following residues:")
        print(disgard["residue_name"].unique())

    protein = protein[protein["residue_name"].isin(allowed_residues)]
    protein["PDB_ATOM"] = protein["residue_name"] + "-" + protein["atom_name"]
    protein = protein[['atom_number','PDB_ATOM','x_coord','y_coord','z_coord']].rename(columns={"atom_number":"ATOM_INDEX", "x_coord":"X", "y_coord":"Y", "z_coord":"Z"})
    protein = protein.merge(atom_keys, how='left', on='PDB_ATOM').sort_values(by="ATOM_INDEX").reset_index(drop=True)

    if list(protein["ATOM_TYPE"].isna()).count(True) > 0:
        print("WARNING: Protein contains unsupported atom types.", pdb_path)
        print("Ignoring following atom types:")
        print(protein[protein["ATOM_TYPE"].isna()]["PDB_ATOM"].unique())
    return protein


def GetMolAEVs_extended(protein_path, mol, atom_keys, radial_coefs, atom_map):
    # Protein and ligand structure are loaded as pandas DataFrame
    Target = LoadPDBasDF_old(protein_path, atom_keys)
    Ligand = LoadMolasDF(mol)
    
    # Define AEV coeficients
    # Radial coefficients
    RcR = radial_coefs[0]
    EtaR = radial_coefs[1]
    RsR = radial_coefs[2]
    
    # Angular coefficients (Ga)
    RcA = 2.0
    Zeta = torch.tensor([1.0])
    TsA = torch.tensor([1.0]) # Angular shift in GA
    EtaA = torch.tensor([1.0])
    RsA = torch.tensor([1.0])  # Radial shift in GA
    
    # Reduce size of Target df to what we need based on radial cutoff RcR
    distance_cutoff = RcR + 0.1
    
    for i in ["X","Y","Z"]:
        Target = Target[Target[i] < float(Ligand[i].max())+distance_cutoff]
        Target = Target[Target[i] > float(Ligand[i].min())-distance_cutoff]
    
    Target = Target.merge(atom_map, on='ATOM_TYPE', how='left')
    
    # Create tensors of atomic numbers and coordinates of molecule atoms and 
    # protein atoms combined. Encode molecule atoms as hydrogen
    mol_len = torch.tensor(len(Ligand))
    atomicnums = np.append(np.ones(mol_len)*6, Target["ATOM_NR"])
    atomicnums = torch.tensor(atomicnums, dtype=torch.int64)
    atomicnums = atomicnums.unsqueeze(0)
    
    coordinates = pd.concat([Ligand[['X','Y','Z']], Target[['X','Y','Z']]])
    coordinates = torch.tensor(coordinates.values)
    coordinates = coordinates.unsqueeze(0)
    
    # Use torchani_mod to calculate AEVs
    atom_symbols = []
    for i in range(1, 23):
        atom_symbols.append(qcel.periodictable.to_symbol(i))
        
    AEVC = torchani_mod.AEVComputer(RcR, RcA, EtaR, RsR, 
                                EtaA, Zeta, RsA, TsA, len(atom_symbols))
    
    SC = torchani.SpeciesConverter(atom_symbols)
    sc = SC((atomicnums, coordinates))
    
    aev = AEVC.forward((sc.species, sc.coordinates), mol_len)
    
    # find indices of columns to keep
    # keep all radial terms
    n = len(atom_symbols)
    n_rad_sub = len(EtaR)*len(RsR)
    indices = list(np.arange(n*n_rad_sub))
    
    return Ligand, aev.aevs.squeeze(0)[:mol_len,indices]


def one_of_k_encoding(x, allowable_set):
    if x not in allowable_set:
        raise Exception("input {0} not in allowable set{1}:".format(x, allowable_set))
    return list(map(lambda s: x == s, allowable_set))


def atom_features(atom, features=["atom_symbol",
                                  "num_heavy_atoms", 
                                  "total_num_Hs", 
                                  "explicit_valence", 
                                  "is_aromatic", 
                                  "is_in_ring"]):
    # Computes the ligand atom features for graph node construction
    # The standard features are the following:
    # atom_symbol = one hot encoding of atom symbol
    # num_heavy_atoms = # of heavy atom neighbors
    # total_num_Hs = # number of hydrogen atom neighbors
    # explicit_valence = explicit valence of the atom
    # is_aromatic = boolean 1 - aromatic, 0 - not aromatic
    # is_in_ring = boolean 1 - is in ring, 0 - is not in ring

    feature_list = []
    if "atom_symbol" in features:
        feature_list.extend(one_of_k_encoding(atom.GetSymbol(),['F', 'N', 'Cl', 'O', 'Br', 'C', 'B', 'P', 'I', 'S']))
    if "num_heavy_atoms" in features:
        feature_list.append(len([x.GetSymbol() for x in atom.GetNeighbors() if x.GetSymbol() != "H"]))
    if "total_num_Hs" in features:
        feature_list.append(len([x.GetSymbol() for x in atom.GetNeighbors() if x.GetSymbol() == "H"]))
    if "explicit_valence" in features: #-NEW ADDITION FOR PLIG
        feature_list.append(atom.GetExplicitValence())
    if "is_aromatic" in features:
        
        if atom.GetIsAromatic():
            feature_list.append(1)
        else:
            feature_list.append(0)
    if "is_in_ring" in features:
        if atom.IsInRing():
            feature_list.append(1)
        else:
            feature_list.append(0)
    
    return np.array(feature_list)


def mol_to_graph(mol, mol_df, aevs, extra_features=["atom_symbol",
                                                    "num_heavy_atoms", 
                                                    "total_num_Hs", 
                                                    "explicit_valence",
                                                    "is_aromatic",
                                                    "is_in_ring"]):

    features = []
    heavy_atom_index = []
    idx_to_idx = {}
    counter = 0
    
    # Generate nodes
    for atom in mol.GetAtoms():
        if atom.GetSymbol() != "H": # Include only non-hydrogen atoms
            idx_to_idx[atom.GetIdx()] = counter
            aev_idx = mol_df[mol_df['ATOM_INDEX'] == atom.GetIdx()].index
            heavy_atom_index.append(atom.GetIdx())
            feature = np.append(atom_features(atom), aevs[aev_idx,:])
            features.append(feature)
            counter += 1
    
    #Generate edges
    edges = []
    for bond in mol.GetBonds():
        idx1 = bond.GetBeginAtomIdx()
        idx2 = bond.GetEndAtomIdx()
        if idx1 in heavy_atom_index and idx2 in heavy_atom_index:
            bond_type = one_of_k_encoding(bond.GetBondType(),[1,12,2,3])
            bond_type = [float(b) for b in bond_type]
            edge1 = [idx_to_idx[idx1], idx_to_idx[idx2]]
            edge1.extend(bond_type)
            edge2 = [idx_to_idx[idx2], idx_to_idx[idx1]]
            edge2.extend(bond_type)
            edges.append(edge1)
            edges.append(edge2)
    
    df = pd.DataFrame(edges, columns=['atom1', 'atom2', 'single', 'aromatic', 'double', 'triple'])
    df = df.sort_values(by=['atom1','atom2'])
    
    edge_index = df[['atom1','atom2']].to_numpy().tolist()
    edge_attr = df[['single','aromatic','double','triple']].to_numpy().tolist()
    
    
    return len(mol_df), features, edge_index, edge_attr


def predict(model, device, loader, y_scaler=None):
    model.eval()
    total_preds = torch.Tensor()
    total_labels = torch.Tensor()
    print('Make prediction for {} samples...'.format(len(loader.dataset)))
    with torch.no_grad():
        for data in loader:
            data = data.to(device)
            output = model(data)
            total_preds = torch.cat((total_preds, output.cpu()), 0)
            total_labels = torch.cat((total_labels, data.y.view(-1, 1).cpu()), 0)

    return y_scaler.inverse_transform(total_labels.numpy().flatten().reshape(-1,1)).flatten(), y_scaler.inverse_transform(total_preds.detach().numpy().flatten().reshape(-1,1)).flatten()


def process_data(config):

    """
    Load data
    """

    df = pd.read_csv(config.dataset_csv)

    """
    Check what molecules are readible by RDKit, and which contain rare atoms
    """
    print("Checking what molecules are readible by RDKit, and which contain rare atoms\n")
    allowed_elements = set(['F', 'N', 'Cl', 'O', 'Br', 'C', 'B', 'P', 'I', 'S'])
    non_readable = []
    rare_atoms_ids = []
    for index, row in tqdm(df.iterrows()):
        suppl = Chem.SDMolSupplier(row["sdf_file"], removeHs=False)
        assert(len(suppl) == 1)
        lig = suppl[0]
        if lig is None:
            non_readable.append(row["unique_id"])
        else:
            mol_df = LoadMolasDF(lig)
            if not set(mol_df["ATOM_TYPE"].values).issubset(allowed_elements):
                rare_atoms_ids.append(row["unique_id"])

    print("Number of sdf files not read by RDkit:",len(non_readable))
    print("Number of sdf files with rare elements:",len(rare_atoms_ids))
    df = df[~df["unique_id"].isin(rare_atoms_ids)].reset_index(drop=True)
    df = df[~df["unique_id"].isin(non_readable)].reset_index(drop=True)
    print("\n")

    """
    Check what protein structures are readible by Biopandas
    """
    print("Checking what protein structures are readible by Biopandas\n")
    atom_keys = pd.read_csv("data/PDB_Atom_Keys.csv", sep=",")
    atom_keys["RESIDUE"] = atom_keys["PDB_ATOM"].apply(lambda x: x.split("-")[0])
    non_readable = []
    for index, row in tqdm(df.iterrows()):
        try:
            LoadPDBasDF(row["pdb_file"], atom_keys)
        except:
            non_readable.append(row["unique_id"])

    print("Number of pdb files not read by Biopandas:",len(non_readable))
    df = df[~df["unique_id"].isin(non_readable)].reset_index(drop=True)
    print("\n")

    """
    Analyse atom features
    """
    print("Analyse atom features\n")
    features = []
    for index, row in tqdm(df.iterrows()):
        suppl = Chem.SDMolSupplier(row["sdf_file"], removeHs=False)
        lig = suppl[0]
        for atom in lig.GetAtoms():
            if atom.GetSymbol() != "H":
                feature = []
                feature.append(atom.GetSymbol())
                feature.append(len([x.GetSymbol() for x in atom.GetNeighbors() if x.GetSymbol() != "H"]))
                feature.append(len([x.GetSymbol() for x in atom.GetNeighbors() if x.GetSymbol() == "H"]))
                feature.append(atom.GetExplicitValence())                
                if atom.GetIsAromatic():
                    feature.append(1)
                else:
                    feature.append(0)
                if atom.IsInRing():
                    feature.append(1)
                else:
                    feature.append(0)
            
            features.append(feature)

    features = pd.DataFrame(features, columns=["atom_symbol",
                                                "num_heavy_atoms",
                                                "total_num_Hs",
                                                "explicit_valence",
                                                "is_aromatic",
                                                "is_in_ring"])

    print(features["atom_symbol"].value_counts())
    print(features["num_heavy_atoms"].value_counts())
    print(features["total_num_Hs"].value_counts())
    print(features["explicit_valence"].value_counts())
    print(features["is_aromatic"].value_counts())
    print(features["is_in_ring"].value_counts())
    print("\n")

    """
    Edge analysis
    """
    print("Edge analysis\n")
    bond_types = []
    unspecified_bond_mol = []
    for index, row in tqdm(df.iterrows()):
        suppl = Chem.SDMolSupplier(row["sdf_file"], removeHs=False)
        lig = suppl[0]

        heavy_atom_index = []
        idx_to_idx = {}
        counter = 0
        for atom in lig.GetAtoms():
            if atom.GetSymbol() != "H": # Include only non-hydrogen atoms
                idx_to_idx[atom.GetIdx()] = counter
                heavy_atom_index.append(atom.GetIdx())
                counter += 1
        
        conf = lig.GetConformer()
        for bond in lig.GetBonds():
            idx1 = bond.GetBeginAtomIdx()
            idx2 = bond.GetEndAtomIdx()
            if idx1 in heavy_atom_index and idx2 in heavy_atom_index:
                bond_types.append(bond.GetBondType())
                if bond.GetBondType() == 0:
                    unspecified_bond_mol.append(row["unique_id"])

    features = pd.DataFrame(data={"bond_type":bond_types})
    print(features["bond_type"].value_counts())

    print("Number of molecules with unspecified bond types:",len(unspecified_bond_mol))
    df = df[~df["unique_id"].isin(unspecified_bond_mol)].reset_index(drop=True)
    print("\n")

    # save the processed dataset
    new_dataset_csv = config.dataset_csv.split(".")[0] + "_processed.csv"
    print("Saving processed dataset as {}\n".format(new_dataset_csv))
    df.to_csv(new_dataset_csv, index=False)
    print("\n")

def generate_graphs(config):

    """
    Generate for all complexes: ANI-2x with 22 atom types. Only 2-atom interactions.
    """
    new_dataset_csv = config.dataset_csv.split(".")[0] + "_processed.csv"
    df = pd.read_csv(new_dataset_csv)
    atom_keys = pd.read_csv("data/PDB_Atom_Keys.csv", sep=",")

    print("Generating graphs\n")

    t = time.time()

    atom_map = pd.DataFrame(pd.unique(atom_keys["ATOM_TYPE"]))
    atom_map[1] = list(np.arange(len(atom_map)) + 1)
    atom_map = atom_map.rename(columns={0:"ATOM_TYPE", 1:"ATOM_NR"})

    # Radial coefficients: ANI-2x
    RcR = 5.1 # Radial cutoff
    EtaR = torch.tensor([19.7]) # Radial decay
    RsR = torch.tensor([0.80, 1.07, 1.34, 1.61, 1.88, 2.14, 2.41, 2.68, 
                        2.95, 3.22, 3.49, 3.76, 4.03, 4.29, 4.56, 4.83]) # Radial shift
    radial_coefs = [RcR, EtaR, RsR]

    mol_graphs = {}
    for index, row in tqdm(df.iterrows()):
        suppl = Chem.SDMolSupplier(row["sdf_file"], removeHs=False)
        lig = suppl[0]

        protein_path = row["pdb_file"]

        mol_df, aevs = GetMolAEVs_extended(protein_path, lig, atom_keys, radial_coefs, atom_map)
        graph = mol_to_graph(lig, mol_df, aevs)
        mol_graphs[row["unique_id"]] = graph

    #save the graphs to use as input for the GNN models
    output_file_graphs = "data/" + config.data_name + "_graphs.pickle"
    with open(output_file_graphs, 'wb') as handle:
        pickle.dump(mol_graphs, handle, protocol=pickle.HIGHEST_PROTOCOL)


    t2 = time.time()
    print("Time to generate graphs:", t2-t)


def make_predictions(config):
    """
    Define model_name and load scaler
    """
    print("Make predictions\n")

    model_name = config.trained_model_name
    

    with open('output/trained_models/' + model_name + '.pickle','rb') as f:
        scaler = pickle.load(f)

    """
    Create .pt file from graphs
    """
    new_dataset_csv = config.dataset_csv.split(".")[0] + "_processed.csv"

    data = pd.read_csv(new_dataset_csv)

    with open("data/" + config.data_name + "_graphs.pickle", 'rb') as handle:
        graphs_dict = pickle.load(handle)

    test_ids = list(data["unique_id"])
    test_y = list(data["pK"])
    if os.path.exists("data/processed/" + config.data_name + ".pt"):
        os.remove("data/processed/" + config.data_name + ".pt")
    test_data = GraphDataset(root='data', dataset=config.data_name, ids=test_ids, y=test_y, graphs_dict=graphs_dict, y_scaler=scaler)

    """
    Make predictions
    """

    test_loader = DataLoader(test_data, batch_size=300, shuffle=False)

    modeling = model_dict['GATv2Net']
    model = modeling(node_feature_dim=test_data.num_node_features, edge_feature_dim=test_data.num_edge_features, config=config)

    for i in range(10):
        model_path = 'output/trained_models/' + config.trained_model_name + '_' + str(i) + '.model'
        model.load_state_dict(torch.load(model_path, map_location=torch.device('cpu')))

        G_test, P_test = predict(model, torch.device('cpu'), test_loader, test_data.y_scaler)

        if(i == 0):
            df_test = pd.DataFrame(data=G_test, index=range(len(G_test)), columns=['truth'])

        col = 'preds_' + str(i)
        df_test[col] = P_test

    df_test['preds'] = df_test.iloc[:,1:].mean(axis=1)

    df_test['unique_id'] = data['unique_id']

    data = data.merge(df_test, on='unique_id', how='left')

    assert(np.allclose(data['pK'], data['truth'], rtol=1e-03))

    """
    Save predictions
    """
    print("Saving predictions\n")
    data.to_csv("output/predictions/" + config.data_name + "_predictions.csv", index=False)


def parse_args():
    parser = argparse.ArgumentParser()
    parser.add_argument('--trained_model_name', type=str, default='20231116-181233_model_GATv2Net_pdbbind_core')
    parser.add_argument('--dataset_csv', type=str, default='data/example_dataset.csv')
    parser.add_argument('--data_name', type=str, default='example')
    parser.add_argument('--hidden_dim', type=int, default=256)
    parser.add_argument('--head', type=int, default=3)
    parser.add_argument('--activation_function', type=str, default='leaky_relu')
    args = parser.parse_args()
    return args


if __name__ == "__main__":    
    config = parse_args()
    
    process_data(config)
    t1 = time.time()
    generate_graphs(config)
    print("Time to generate graphs:", time.time()-t1)
    make_predictions(config)
    print("Total time to generate graphs and make predictions is %s seconds" % (time.time() - t1))