import os import pandas as pd import torch from torch.nn import functional as F from transformers import AutoTokenizer from util.utils import * from rdkit import Chem 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_biomarker = 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) #--biomarker Model ##-- hyper param config file Load --## config = load_hparams('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_biomarker.type == 'cuda': model = torch.nn.DataParallel(model) def get_marker(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 marker_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_list = get_marker(a_inputs, d_inputs) return output_list except Exception as e: print(e) return {'Error_message': e} def smiles_aas_test(smile_acc,smile_don): mola = Chem.MolFromSmiles(smile_acc) smile_acc = Chem.MolToSmiles(mola, canonical=True) mold = Chem.MolFromSmiles(smile_don) smile_don = Chem.MolToSmiles(mold, canonical=True) batch_size = 1 datas = [] marker_list = [] marker_datas = [] marker_datas.append([smile_acc,smile_don]) if len(marker_datas) == batch_size: marker_list.append(list(marker_datas)) marker_datas.clear() if len(marker_datas) != 0: marker_list.append(list(marker_datas)) marker_datas.clear() for marker_datas in tqdm(marker_list, total=len(marker_list)): smiles_d , smiles_a = zip(*marker_datas) output_pred = marker_prediction(list(smiles_d), list(smiles_a) ) if len(datas) == 0: datas = output_pred else: datas = datas + output_pred # ## -- Export result data to csv -- ## # df = pd.DataFrame(datas) # df.to_csv('./results/predictData_nontonon_bindingdb_test.csv', index=None) # print(df) return datas if __name__ == '__main__': a = smiles_aas_test('CCCCCCCCCCCC1=C(/C=C2\C(=O)C3=C(C=C(F)C(F)=C3)C2=C(C#N)C#N)SC2=C1SC1=C2N(CC(CC)CCCC)C2=C1C1=NSN=C1C1=C2N(CC(CC)CCCC)C2=C1SC1=C2SC(/C=C2\C(=O)C3=C(C=C(F)C(F)=C3)C2=C(C#N)C#N)=C1CCCCCCCCCCC','CCCCCCC(CCCC)CC1=C(C)SC(C2=CC3=C(S2)C2=C(C=C(C4=CC(CC(CCCC)CCCCCC)=C(C5=CC6=C(C7=CC=C(CC(CC)CCCC)S7)C7=C(C=C(C)S7)C(C7=CC=C(CC(CC)CCCC)S7)=C6S5)S4)S2)C2=NSN=C23)=C1')