File size: 2,537 Bytes
4d12519 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 | import json
from pytorch_lightning import LightningDataModule
from torch.utils.data import DataLoader, ConcatDataset, Dataset
from data_provider.stage1_dm import SwissProtDataset, OntoProteinDataset
import pandas as pd
class BindingDB(Dataset):
def __init__(self, data_path, prompt='', return_prompt=False):
super(BindingDB, self).__init__()
self.data_path = data_path
self.user_prompt = prompt
self.return_prompt = return_prompt
self.data_list = self._load_and_preprocess(self.data_path)
self.text2id = self._build_text_vocab()
def _load_and_preprocess(self, data_path):
data_list = []
df = pd.read_csv(data_path)
for _, row in df.iterrows():
try:
ligand_smiles = str(row['ligand']).strip()
prot_seq = str(row['protein']).strip()
result = str(row['ic50']).strip()
text_seq = f"<answer>{result}</answer>\n"
prompt = f"""
【Protein sequence (1-letter amino acid codes)】；{ligand_smiles}【Ligand structure (SMILES)】
Task: Evaluate the inhibitory effect of the ligand on the given protein.
Note: IC50 (half maximal inhibitory concentration) is the concentration of a substance required to inhibit 50% of the protein's activity. Lower IC50 values indicate stronger inhibition.
Based on the provided protein and ligand, predict the inhibitory strength by classifying the IC50 level:
"""
if self.user_prompt:
prompt += self.user_prompt
# extra可以返回原始feather字符串，也可以返回feather_vals
# 或 feather_raw
data_list.append((prot_seq, text_seq, prompt))
except Exception as e:
print(f"警告: 跳过有问题的行: {row}，原因: {e}")
return data_list
def _build_text_vocab(self):
text2id = {}
for _, text_seq, _ in self.data_list:
if text_seq not in text2id:
text2id[text_seq] = len(text2id)
return text2id
def shuffle(self):
random.shuffle(self.data_list)
return self
def __len__(self):
return len(self.data_list)
def __getitem__(self, index):
prot_seq, text_seq, prompt = self.data_list[index]
if self.return_prompt:
return prot_seq, prompt, text_seq,index
return prot_seq, text_seq, index |