import random import pandas as pd import pytorch_lightning as pl from torch_geometric.data import Data, Dataset from torch_geometric.loader import DataLoader, DataListLoader from .dataset import CombinedDataset, prepare_data_composite, protein_graph_path from sklearn.model_selection import train_test_split, KFold from torch_geometric.utils import degree import torch from tqdm import tqdm class DInterface(pl.LightningDataModule): def __init__(self, num_workers=8, dataset='', **kwargs): super().__init__() pl.seed_everything(kwargs.get('seed'), workers=True) self.num_workers = num_workers self.kwargs = kwargs self.batch_size = kwargs.get('batch_size', 8) self.incl_columns = kwargs.get('incl_columns', []) self.test_size = kwargs.get('test_size', 0.5) self.seed = kwargs.get('seed') self.k_folds = kwargs.get('k_folds', None) # None means no K-Fold, just train/val/test split self.current_fold = kwargs.get('fold_num', 0) # Default to first fold self.benchmark = kwargs.get('benchmark', 'posex_self_docking') # Prepare dataset differently based on AS criteria if isinstance(self.benchmark, list): for b in self.benchmark: ds, num_classes = prepare_data_composite(self.incl_columns, b) if hasattr(self, 'dataset'): self.dataset = pd.concat([self.dataset, ds], ignore_index=True) else: self.dataset = ds self.num_classes = num_classes elif isinstance(self.benchmark, str): self.dataset, self.num_classes = prepare_data_composite(self.incl_columns, self.benchmark) else: raise ValueError("benchmark must be a string or a list of strings") self.load_data_module() def setup(self, stage=None): if self.k_folds is not None: print("K-Fold enabled") self.kf = KFold(n_splits=self.k_folds, shuffle=True, random_state=self.seed) self.folds = list(self.kf.split(self.dataset)) train_idx, test_idx = self.folds[self.current_fold] self.trainset, self.valset = train_test_split(self.dataset.iloc[train_idx], test_size=0.1, random_state=self.seed) self.testset = self.dataset.iloc[test_idx] else: print("K-Fold disabled") if self.test_size == 1 or self.test_size == 0: self.trainset, self.valset = train_test_split(self.dataset, test_size=0.1, random_state=self.seed) self.testset = self.dataset else: train_val, self.testset = train_test_split(self.dataset, test_size=self.test_size, random_state=self.seed) self.trainset, self.valset = train_test_split(train_val, test_size=self.test_size, random_state=self.seed) def train_dataloader(self): # Combining the protein and ligand graphs into the dataset trainset_combined = CombinedDataset(self.trainset) return DataLoader(trainset_combined, batch_size=self.batch_size, shuffle=True, num_workers=self.num_workers, persistent_workers=False, drop_last=False) def val_dataloader(self): valset_combined = CombinedDataset(self.valset) return DataLoader(valset_combined, batch_size=self.batch_size, shuffle=False, num_workers=self.num_workers, persistent_workers=False, drop_last=False) def test_dataloader(self): testset_combined = CombinedDataset(self.testset) return DataLoader(testset_combined, batch_size=self.batch_size, shuffle=False, num_workers=self.num_workers, persistent_workers=False) def get_train_deg(self): deg_hist = torch.zeros(256, dtype=torch.long) return deg_hist graph_ds = self.trainset # or self.graph_dataset if that’s what you saved for idx in range(len(graph_ds)): # Load just the graph part directly protein_name = graph_ds.iloc[idx]['protein'] ligand_name = graph_ds.iloc[idx]['ligand'] graph_path = f'{protein_graph_path}/pyg_graph_{protein_name}_{ligand_name}_protein.pt' graph = torch.load(graph_path, weights_only=False) d = degree(graph.edge_index[1], num_nodes=graph.x.size(0), dtype=torch.long) deg_hist.index_add_(0, d, torch.ones_like(d)) return deg_hist # These are from the template, but not used in our implementation. def load_data_module(self): pass def instancialize(self, **other_args): pass