import os import pandas as pd import torch from torch.nn import functional as F from transformers import AutoTokenizer from rdkit import Chem from .util.utils import * from tqdm import tqdm from .train import markerModel os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID" os.environ["CUDA_VISIBLE_DEVICES"] = '0 ' device_count = torch.cuda.device_count() device_biberta= torch.device('cuda' if torch.cuda.is_available() else "cpu") device = torch.device('cpu') a_model_name = 'DeepChem/ChemBERTa-10M-MLM' d_model_name = 'DeepChem/ChemBERTa-10M-MTR' tokenizer = AutoTokenizer.from_pretrained(a_model_name) d_tokenizer = AutoTokenizer.from_pretrained(d_model_name) #--bibertaModel ##-- hyper param config file Load --## config = load_hparams('tool/dap/config/predict.json') config = DictX(config) model = markerModel(config.d_model_name, config.p_model_name, config.lr, config.dropout, config.layer_features, config.loss_fn, config.layer_limit, config.pretrained['chem'], config.pretrained['prot']) model = markerModel.load_from_checkpoint(config.load_checkpoint,strict=False) model.eval() model.freeze() if device_biberta.type == 'cuda': model = torch.nn.DataParallel(model) def get_biberta(drug_inputs, prot_inputs): output_preds = model(drug_inputs, prot_inputs) predict = torch.squeeze( (output_preds)).tolist() # output_preds = torch.relu(output_preds) # predict = torch.tanh(output_preds) # predict = predict.squeeze(dim=1).tolist() return predict def biberta_prediction(smiles, aas): try: aas_input = [] for ass_data in aas: aas_input.append(' '.join(list(ass_data))) a_inputs = tokenizer(smiles, padding='max_length', max_length=510, truncation=True, return_tensors="pt") # d_inputs = tokenizer(smiles, truncation=True, return_tensors="pt") a_input_ids = a_inputs['input_ids'].to(device) a_attention_mask = a_inputs['attention_mask'].to(device) a_inputs = {'input_ids': a_input_ids, 'attention_mask': a_attention_mask} d_inputs = d_tokenizer(aas_input, padding='max_length', max_length=510, truncation=True, return_tensors="pt") # p_inputs = prot_tokenizer(aas_input, truncation=True, return_tensors="pt") d_input_ids = d_inputs['input_ids'].to(device) d_attention_mask = d_inputs['attention_mask'].to(device) d_inputs = {'input_ids': d_input_ids, 'attention_mask': d_attention_mask} output_predict = get_biberta(a_inputs, d_inputs) output_list = [{'acceptor': smiles[i], 'donor': aas[i], 'predict': output_predict[i]} for i in range(0,len(aas))] return output_list except Exception as e: print(e) return {'Error_message': e} def smiles_aas_test(file): batch_se = 80 try: datas = [] biberta_list = [] biberta_datas = [] smiles_aas = pd.read_csv(file) smiles_d , smiles_a = (smiles_aas['donor'],smiles_aas['acceptor']) donor,acceptor =[],[] for i in smiles_d: s = Chem.MolToSmiles(Chem.MolFromSmiles(i)) donor.append(s) for i in smiles_a: s = Chem.MolToSmiles(Chem.MolFromSmiles(i)) acceptor.append(s) output_pred = biberta_prediction(list(acceptor), list(donor) ) if len(datas) == 0: datas = output_pred else: datas = datas + output_pred # ## -- Export result data to csv -- ## df = pd.DataFrame(datas) # print(df) return datas except Exception as e: print(e) return {'Error_message': e}