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| import os | |
| import time | |
| import pickle | |
| import random | |
| from tqdm import tqdm | |
| import argparse | |
| import torch | |
| from torch_geometric.loader import DataLoader | |
| import torch.utils.data | |
| from rdkit import RDLogger | |
| torch.set_num_threads(5) | |
| RDLogger.DisableLog('rdApp.*') | |
| from utils import * | |
| from models import Generator | |
| from new_dataloader import DruggenDataset | |
| from loss import generator_loss | |
| from training_data import load_molecules | |
| class Inference(object): | |
| """Inference class for DrugGEN.""" | |
| def __init__(self, config): | |
| if config.set_seed: | |
| np.random.seed(config.seed) | |
| random.seed(config.seed) | |
| torch.manual_seed(config.seed) | |
| torch.cuda.manual_seed_all(config.seed) | |
| torch.backends.cudnn.deterministic = True | |
| torch.backends.cudnn.benchmark = False | |
| os.environ["PYTHONHASHSEED"] = str(config.seed) | |
| print(f'Using seed {config.seed}') | |
| self.device = torch.device("cuda" if torch.cuda.is_available() else 'cpu') | |
| # Initialize configurations | |
| self.submodel = config.submodel | |
| self.inference_model = config.inference_model | |
| self.sample_num = config.sample_num | |
| # Data loader. | |
| self.inf_raw_file = config.inf_raw_file # SMILES containing text file for first dataset. | |
| # Write the full path to file. | |
| self.inf_dataset_file = config.inf_dataset_file # Dataset file name for the first GAN. | |
| # Contains large number of molecules. | |
| self.inf_batch_size = config.inf_batch_size | |
| self.mol_data_dir = config.mol_data_dir # Directory where the dataset files are stored. | |
| self.dataset_name = self.inf_dataset_file.split(".")[0] | |
| self.max_atom = config.max_atom # Model is based on one-shot generation. | |
| # Max atom number for molecules must be specified. | |
| self.features = config.features # Small model uses atom types as node features. (Boolean, False uses atom types only.) | |
| # Additional node features can be added. Please check new_dataloarder.py Line 102. | |
| self.inf_dataset = DruggenDataset(self.mol_data_dir, | |
| self.inf_dataset_file, | |
| self.inf_raw_file, | |
| self.max_atom, | |
| self.features) # Dataset for the first GAN. Custom dataset class from PyG parent class. | |
| # Can create any molecular graph dataset given smiles string. | |
| # Nonisomeric SMILES are suggested but not necessary. | |
| # Uses sparse matrix representation for graphs, | |
| # For computational and speed efficiency. | |
| self.inf_loader = DataLoader(self.inf_dataset, | |
| shuffle=True, | |
| batch_size=self.inf_batch_size, | |
| drop_last=True) # PyG dataloader for the first GAN. | |
| # Atom and bond type dimensions for the construction of the model. | |
| self.atom_decoders = self.decoder_load("atom") # Atom type decoders for first GAN. | |
| # eg. 0:0, 1:6 (C), 2:7 (N), 3:8 (O), 4:9 (F) | |
| self.bond_decoders = self.decoder_load("bond") # Bond type decoders for first GAN. | |
| # eg. 0: (no-bond), 1: (single), 2: (double), 3: (triple), 4: (aromatic) | |
| self.m_dim = len(self.atom_decoders) if not self.features else int(self.inf_loader.dataset[0].x.shape[1]) # Atom type dimension. | |
| self.b_dim = len(self.bond_decoders) # Bond type dimension. | |
| self.vertexes = int(self.inf_loader.dataset[0].x.shape[0]) # Number of nodes in the graph. | |
| # Transformer and Convolution configurations. | |
| self.act = config.act | |
| self.dim = config.dim | |
| self.depth = config.depth | |
| self.heads = config.heads | |
| self.mlp_ratio = config.mlp_ratio | |
| self.dropout = config.dropout | |
| self.build_model() | |
| def build_model(self): | |
| """Create generators and discriminators.""" | |
| self.G = Generator(self.act, | |
| self.vertexes, | |
| self.b_dim, | |
| self.m_dim, | |
| self.dropout, | |
| dim=self.dim, | |
| depth=self.depth, | |
| heads=self.heads, | |
| mlp_ratio=self.mlp_ratio, | |
| submodel = self.submodel) | |
| self.print_network(self.G, 'G') | |
| self.G.to(self.device) | |
| def decoder_load(self, dictionary_name): | |
| ''' Loading the atom and bond decoders''' | |
| with open("data/decoders/" + dictionary_name + "_" + self.dataset_name + '.pkl', 'rb') as f: | |
| return pickle.load(f) | |
| def print_network(self, model, name): | |
| """Print out the network information.""" | |
| num_params = 0 | |
| for p in model.parameters(): | |
| num_params += p.numel() | |
| print(model) | |
| print(name) | |
| print("The number of parameters: {}".format(num_params)) | |
| def restore_model(self, submodel, model_directory): | |
| """Restore the trained generator and discriminator.""" | |
| print('Loading the model...') | |
| G_path = os.path.join(model_directory, '{}-G.ckpt'.format(submodel)) | |
| self.G.load_state_dict(torch.load(G_path, map_location=lambda storage, loc: storage)) | |
| def inference(self): | |
| # Load the trained generator. | |
| self.restore_model(self.submodel, self.inference_model) | |
| # smiles data for metrics calculation. | |
| chembl_smiles = [line for line in open("data/chembl_train.smi", 'r').read().splitlines()] | |
| chembl_test = [line for line in open("data/chembl_test.smi", 'r').read().splitlines()] | |
| drug_smiles = [line for line in open("data/akt_inhibitors.smi", 'r').read().splitlines()] | |
| drug_mols = [Chem.MolFromSmiles(smi) for smi in drug_smiles] | |
| drug_vecs = [AllChem.GetMorganFingerprintAsBitVect(x, 2, nBits=1024) for x in drug_mols if x is not None] | |
| # Make directories if not exist. | |
| if not os.path.exists("experiments/inference/{}".format(self.submodel)): | |
| os.makedirs("experiments/inference/{}".format(self.submodel)) | |
| self.G.eval() | |
| start_time = time.time() | |
| metric_calc_dr = [] | |
| uniqueness_calc = [] | |
| real_smiles_snn = [] | |
| nodes_sample = torch.Tensor(size=[1,45,1]).to(self.device) | |
| val_counter = 0 | |
| none_counter = 0 | |
| # Inference mode | |
| with torch.inference_mode(): | |
| pbar = tqdm(range(self.sample_num)) | |
| pbar.set_description('Inference mode for {} model started'.format(self.submodel)) | |
| for i, data in enumerate(self.inf_loader): | |
| val_counter += 1 | |
| # Preprocess dataset | |
| _, a_tensor, x_tensor = load_molecules( | |
| data=data, | |
| batch_size=self.inf_batch_size, | |
| device=self.device, | |
| b_dim=self.b_dim, | |
| m_dim=self.m_dim, | |
| ) | |
| _, _, node_sample, edge_sample = self.G(a_tensor, x_tensor) | |
| g_edges_hat_sample = torch.max(edge_sample, -1)[1] | |
| g_nodes_hat_sample = torch.max(node_sample, -1)[1] | |
| fake_mol_g = [self.inf_dataset.matrices2mol_drugs(n_.data.cpu().numpy(), e_.data.cpu().numpy(), strict=True, file_name=self.dataset_name) | |
| for e_, n_ in zip(g_edges_hat_sample, g_nodes_hat_sample)] | |
| a_tensor_sample = torch.max(a_tensor, -1)[1] | |
| x_tensor_sample = torch.max(x_tensor, -1)[1] | |
| real_mols = [self.inf_dataset.matrices2mol_drugs(n_.data.cpu().numpy(), e_.data.cpu().numpy(), strict=True, file_name=self.dataset_name) | |
| for e_, n_ in zip(a_tensor_sample, x_tensor_sample)] | |
| inference_drugs = [None if line is None else Chem.MolToSmiles(line) for line in fake_mol_g] | |
| inference_drugs = [None if x is None else max(x.split('.'), key=len) for x in inference_drugs] | |
| for molecules in inference_drugs: | |
| if molecules is None: | |
| none_counter += 1 | |
| with open("experiments/inference/{}/inference_drugs.txt".format(self.submodel), "a") as f: | |
| for molecules in inference_drugs: | |
| if molecules is not None: | |
| molecules = molecules.replace("*", "C") | |
| f.write(molecules) | |
| f.write("\n") | |
| uniqueness_calc.append(molecules) | |
| nodes_sample = torch.cat((nodes_sample, g_nodes_hat_sample.view(1,45,1)), 0) | |
| pbar.update(1) | |
| metric_calc_dr.append(molecules) | |
| generation_number = len([x for x in metric_calc_dr if x is not None]) | |
| if generation_number == self.sample_num or none_counter == self.sample_num: | |
| break | |
| real_smiles_snn.append(real_mols[0]) | |
| et = time.time() - start_time | |
| gen_vecs = [AllChem.GetMorganFingerprintAsBitVect(Chem.MolFromSmiles(x), 2, nBits=1024) for x in uniqueness_calc if Chem.MolFromSmiles(x) is not None] | |
| real_vecs = [AllChem.GetMorganFingerprintAsBitVect(x, 2, nBits=1024) for x in real_smiles_snn if x is not None] | |
| print("Inference mode is lasted for {:.2f} seconds".format(et)) | |
| print("Metrics calculation started using MOSES.") | |
| # post-process * to Carbon atom in valid molecules | |
| return{ | |
| "Runtime (seconds)": f"{et:.2f}", | |
| "Validity": f"{fraction_valid(metric_calc_dr):.2f}", | |
| "Uniqueness": f"{fraction_unique(uniqueness_calc):.2f}", | |
| "Novelty (Train)": f"{novelty(metric_calc_dr, chembl_smiles):.2f}", | |
| "Novelty (Inference)": f"{novelty(metric_calc_dr, chembl_test):.2f}", | |
| } | |
| if __name__=="__main__": | |
| parser = argparse.ArgumentParser() | |
| # Inference configuration. | |
| parser.add_argument('--submodel', type=str, default="DrugGEN", help="Chose model subtype: DrugGEN, NoTarget", choices=['DrugGEN', 'NoTarget']) | |
| parser.add_argument('--inference_model', type=str, help="Path to the model for inference") | |
| parser.add_argument('--sample_num', type=int, default=10000, help='inference samples') | |
| # Data configuration. | |
| parser.add_argument('--inf_dataset_file', type=str, default='chembl45_test.pt') | |
| parser.add_argument('--inf_raw_file', type=str, default='data/chembl_test.smi') | |
| parser.add_argument('--inf_batch_size', type=int, default=1, help='Batch size for inference') | |
| parser.add_argument('--mol_data_dir', type=str, default='data') | |
| parser.add_argument('--features', type=str2bool, default=False, help='features dimension for nodes') | |
| # Model configuration. | |
| parser.add_argument('--act', type=str, default="relu", help="Activation function for the model.", choices=['relu', 'tanh', 'leaky', 'sigmoid']) | |
| parser.add_argument('--max_atom', type=int, default=45, help='Max atom number for molecules must be specified.') | |
| parser.add_argument('--dim', type=int, default=128, help='Dimension of the Transformer Encoder model for the GAN.') | |
| parser.add_argument('--depth', type=int, default=1, help='Depth of the Transformer model from the GAN.') | |
| parser.add_argument('--heads', type=int, default=8, help='Number of heads for the MultiHeadAttention module from the GAN.') | |
| parser.add_argument('--mlp_ratio', type=int, default=3, help='MLP ratio for the Transformer.') | |
| parser.add_argument('--dropout', type=float, default=0., help='dropout rate') | |
| # Seed configuration. | |
| parser.add_argument('--set_seed', type=bool, default=False, help='set seed for reproducibility') | |
| parser.add_argument('--seed', type=int, default=1, help='seed for reproducibility') | |
| config = parser.parse_args() | |
| inference = Inference(config) | |
| inference.inference() | |