Datasets:
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from torch.utils.data import Dataset
import os
import glob
from pathlib import Path
from sklearn.model_selection import train_test_split
from tools.subgraph_sampler import ProteinSubgraphSampler
from .pdb_processor import PDBProcessor
from .cache_manager import CacheManager
import random
import threading
from collections import OrderedDict
class ProteinDataset(Dataset):
def __init__(self, train=True, data_path=None, pdb_path=None, cache_path=None, transform=None, **kwargs):
self.train = train
self.data_path = data_path
self.pdb_path = pdb_path or "dataset/rcsb/human" # Default PDB path
self.cache_path = cache_path or "dataset/protein_cache" # Default cache path
self.transform = transform
# New parameters for on-the-fly processing
self.enable_pdb_processing = kwargs.get('enable_pdb_processing', True)
self.force_pdb_processing = kwargs.get('force_pdb_processing', False) # Force PDB processing even if .pt files exist
# Subgraph sampling parameters
self.min_nodes = kwargs.get('min_nodes', 10)
self.max_nodes = kwargs.get('max_nodes', 100)
# Initialize components
self.subgraph_sampler = ProteinSubgraphSampler(
min_nodes=self.min_nodes,
max_nodes=self.max_nodes
)
# Initialize PDB processor and cache manager
self.pdb_processor = None # Lazy initialization
self.cache_manager = CacheManager(self.cache_path)
# Determine data source and index files
self._determine_data_source()
self.file_paths = self._get_file_paths()
self.protein_ids = self._generate_protein_ids()
# Split the dataset
self.seed = kwargs.get('seed', 42)
self._create_data_splits()
# Improved memory management for multiprocessing
self.cache_size = kwargs.get('cache_size', 512) # Reduced default for multiprocessing
self.enable_cache = kwargs.get('enable_cache', True)
self.preload_cache = kwargs.get('preload_cache', False)
# Thread-safe cache using OrderedDict (LRU)
self._cache_lock = threading.Lock()
self._cache = OrderedDict()
# Worker-specific settings
self._worker_id = None
self._is_main_process = True
# Statistics
self._pdb_processed_count = 0
self._cache_hit_count = 0
self._pt_file_count = 0
self._failed_files = set() # Track files that failed to process
self._valid_files = None # Cache of validated files
# Error handling options
self.skip_invalid_files = kwargs.get('skip_invalid_files', True)
self.validate_on_init = kwargs.get('validate_on_init', False) # Pre-validate files during init
self.max_retry_attempts = kwargs.get('max_retry_attempts', 1)
# ESM-C configuration
self.esm_use_cpu = kwargs.get('esm_use_cpu', False)
if self.esm_use_cpu:
os.environ['ESM_USE_CPU'] = 'true'
print("Dataset: Configured ESM-C to use CPU only")
# Pre-validate files if requested
if self.validate_on_init and self.use_pdb_files:
self._validate_pdb_files()
def __getstate__(self):
"""Custom pickling - exclude locks and worker-specific state."""
state = self.__dict__.copy()
# Remove unpickleable entries
del state['_cache_lock']
# Reset worker-specific state for new process
state['_worker_id'] = None
state['_is_main_process'] = False # Workers are not main process
return state
def __setstate__(self, state):
"""Custom unpickling - restore state and create new lock."""
self.__dict__.update(state)
# Create new lock in worker process
self._cache_lock = threading.Lock()
# Worker will determine its own ID later
def _determine_data_source(self):
"""Determine whether to use preprocessed .pt files or PDB files."""
self.use_pdb_files = False
self.data_source_type = "unknown"
# Check if we should force PDB processing
if self.force_pdb_processing:
if os.path.exists(self.pdb_path):
self.use_pdb_files = True
self.data_source_type = "pdb_forced"
print(f"Dataset: Forced PDB processing from {self.pdb_path}")
else:
raise ValueError(f"PDB path not found: {self.pdb_path}")
# Check for preprocessed .pt files first (backward compatibility)
elif self.data_path and os.path.exists(self.data_path):
pt_files = glob.glob(os.path.join(self.data_path, "*.pt"))
if pt_files:
self.use_pdb_files = False
self.data_source_type = "preprocessed"
print(f"Dataset: Using preprocessed .pt files from {self.data_path}")
return
# Fall back to PDB files if enabled
if self.enable_pdb_processing and os.path.exists(self.pdb_path):
pdb_files = glob.glob(os.path.join(self.pdb_path, "*.pdb"))
if pdb_files:
self.use_pdb_files = True
self.data_source_type = "pdb_fallback"
print(f"Dataset: Using PDB files from {self.pdb_path} (no preprocessed files found)")
else:
raise ValueError(f"No PDB files found in {self.pdb_path}")
else:
if not self.enable_pdb_processing:
raise ValueError(f"No preprocessed files found in {self.data_path} and PDB processing is disabled")
else:
raise ValueError(f"No data files found in {self.data_path} or {self.pdb_path}")
def _get_file_paths(self):
"""Get all protein file paths based on determined data source."""
file_paths = []
if self.use_pdb_files:
# Use PDB files
if os.path.exists(self.pdb_path):
pattern = '*.pdb'
file_paths.extend(glob.glob(os.path.join(self.pdb_path, pattern)))
else:
# Use preprocessed .pt files
if self.data_path and os.path.exists(self.data_path):
pattern = '*.pt'
file_paths.extend(glob.glob(os.path.join(self.data_path, pattern)))
# Sort for consistent ordering
file_paths.sort()
print(f"Dataset: Found {len(file_paths)} files ({self.data_source_type})")
return file_paths
def _generate_protein_ids(self):
"""Generate protein IDs from file names"""
protein_ids = []
for file_path in self.file_paths:
filename = Path(file_path).stem # Get filename without extension
# Handle different filename patterns
if self.use_pdb_files:
# For PDB files, use the filename directly
protein_ids.append(filename)
else:
# For .pt files, remove 'pytorch_graph_' prefix if present
if filename.startswith('pytorch_graph_'):
protein_id = filename[len('pytorch_graph_'):]
else:
protein_id = filename
protein_ids.append(protein_id)
return protein_ids
def _create_data_splits(self):
"""Create train/test splits and select files based on self.train"""
if not hasattr(self, 'file_paths') or not self.file_paths:
raise ValueError("File paths are not initialized. Please check data_path.")
# Split the dataset into train and test sets
train_files, test_files = train_test_split(
self.file_paths, test_size=0.1, random_state=self.seed)
# if self.train:
# self.file_paths = train_files
# else:
# self.file_paths = test_files
# Regenerate protein IDs after split
self.protein_ids = self._generate_protein_ids()
def _validate_pdb_files(self):
"""Pre-validate PDB files to identify problematic ones."""
if not self.use_pdb_files:
return
print(f"Dataset: Pre-validating {len(self.file_paths)} PDB files...")
valid_files = []
failed_files = []
for i, file_path in enumerate(self.file_paths):
if i % 50 == 0:
print(f"Dataset: Validation progress: {i}/{len(self.file_paths)}")
try:
if self._is_pdb_file_valid(file_path):
valid_files.append(file_path)
else:
failed_files.append(file_path)
self._failed_files.add(file_path)
except Exception as e:
print(f"Dataset: Validation failed for {file_path}: {e}")
failed_files.append(file_path)
self._failed_files.add(file_path)
print(f"Dataset: Validation complete - Valid: {len(valid_files)}, Failed: {len(failed_files)}")
if failed_files:
print(f"Dataset: Failed files: {[Path(f).name for f in failed_files[:10]]}" +
(f" (and {len(failed_files)-10} more)" if len(failed_files) > 10 else ""))
# Update file paths to only include valid files
if self.skip_invalid_files:
self.file_paths = valid_files
self.protein_ids = self._generate_protein_ids()
print(f"Dataset: Using {len(self.file_paths)} valid files after filtering")
def _is_pdb_file_valid(self, pdb_file_path):
"""Quick validation check for PDB file without full processing."""
try:
from Bio.PDB import PDBParser
import numpy as np
parser = PDBParser(QUIET=True)
structure = parser.get_structure("test", pdb_file_path)
# Check if we have any valid chains with coordinates
valid_residues = 0
for model in structure:
for chain in model:
for residue in chain:
if residue.has_id("CA"):
ca_atom = residue["CA"]
coords = ca_atom.get_coord()
# Check for NaN or infinite coordinates
if np.any(np.isnan(coords)) or np.any(np.isinf(coords)):
print(f"Dataset: Invalid coordinates in {pdb_file_path}: {coords}")
return False
valid_residues += 1
# Early exit if we have enough valid residues
if valid_residues >= self.min_nodes:
return True
if valid_residues < self.min_nodes:
print(f"Dataset: Too few valid residues in {pdb_file_path}: {valid_residues} < {self.min_nodes}")
return False
return True
except Exception as e:
print(f"Dataset: Validation error for {pdb_file_path}: {e}")
return False
def _get_worker_info(self):
"""Get current worker information for multiprocessing awareness"""
try:
import torch.utils.data as data
worker_info = data.get_worker_info()
if worker_info is not None:
self._worker_id = worker_info.id
self._is_main_process = False
# Adjust cache size per worker
self.cache_size = max(32, self.cache_size // worker_info.num_workers)
return worker_info
except:
return None
def _get_pdb_processor(self):
"""Get PDB processor with lazy initialization."""
if self.pdb_processor is None:
self.pdb_processor = PDBProcessor()
return self.pdb_processor
def _load_single_graph(self, file_path):
"""Load a single protein graph with improved thread-safe caching"""
if not self.enable_cache:
return self._load_from_disk(file_path)
# Get worker info on first access
if self._worker_id is None:
self._get_worker_info()
# Thread-safe cache access
with self._cache_lock:
# Check cache first
if file_path in self._cache:
# Move to end (most recently used)
graph_data = self._cache.pop(file_path)
self._cache[file_path] = graph_data
return graph_data
# Load from disk if not in cache
graph_data = self._load_from_disk(file_path)
if graph_data is not None and self.enable_cache:
self._add_to_cache(file_path, graph_data)
return graph_data
def _load_from_disk(self, file_path):
"""Load graph data from disk or process PDB file on-demand."""
try:
if self.use_pdb_files:
return self._load_from_pdb(file_path)
else:
return self._load_from_pt_file(file_path)
except Exception as e:
print(f"Error loading {file_path}: {e}")
return None
def _load_from_pt_file(self, file_path):
"""Load graph data from preprocessed .pt file."""
try:
graph_data = torch.load(file_path, map_location='cpu')
self._pt_file_count += 1
return graph_data
except Exception as e:
print(f"Error loading .pt file {file_path}: {e}")
return None
def _load_from_pdb(self, pdb_file_path):
"""Load graph data from PDB file with persistent caching."""
try:
# Check persistent cache first
if self.cache_manager.exists(pdb_file_path):
graph_data = self.cache_manager.load(pdb_file_path)
if graph_data is not None:
self._cache_hit_count += 1
return graph_data
# Process PDB file on-the-fly
print(f"Processing PDB file on-the-fly: {pdb_file_path}")
processor = self._get_pdb_processor()
graph_data = processor.process_pdb_file(pdb_file_path)
if graph_data is not None:
# Save to persistent cache
self.cache_manager.save(pdb_file_path, graph_data)
self._pdb_processed_count += 1
return graph_data
else:
print(f"Failed to process PDB file: {pdb_file_path}")
return None
except Exception as e:
print(f"Error processing PDB file {pdb_file_path}: {e}")
return None
def _add_to_cache(self, file_path, graph_data):
"""Add graph to cache with thread-safe LRU eviction"""
if self.cache_size <= 0:
# Cache is disabled
return
with self._cache_lock:
# Remove oldest items if cache is full
while len(self._cache) >= self.cache_size:
if self._cache: # Check if cache is not empty before popitem
self._cache.popitem(last=False) # Remove oldest (FIFO)
else:
break # Exit if cache becomes empty
# Add new item (will be most recent)
self._cache[file_path] = graph_data
def clear_cache(self):
"""Clear the cache to free memory"""
with self._cache_lock:
self._cache.clear()
def get_cache_info(self):
"""Get cache statistics"""
with self._cache_lock:
basic_info = {
'cache_size': len(self._cache),
'max_cache_size': self.cache_size,
'worker_id': self._worker_id,
'is_main_process': self._is_main_process,
'cache_enabled': self.enable_cache,
'data_source_type': self.data_source_type,
'use_pdb_files': self.use_pdb_files,
'pdb_processed_count': self._pdb_processed_count,
'cache_hit_count': self._cache_hit_count,
'pt_file_count': self._pt_file_count
}
# Add persistent cache info if using PDB files
if self.use_pdb_files:
persistent_cache_info = self.cache_manager.get_cache_stats()
basic_info.update({
'persistent_cache': persistent_cache_info
})
return basic_info
def get_processing_stats(self):
"""Get detailed processing statistics."""
return {
'data_source': self.data_source_type,
'total_files': len(self.file_paths),
'failed_files_count': len(self._failed_files),
'failed_files': [Path(f).name for f in list(self._failed_files)[:10]], # Show first 10
'pdb_processed_on_fly': self._pdb_processed_count,
'persistent_cache_hits': self._cache_hit_count,
'pt_files_loaded': self._pt_file_count,
'success_rate': (len(self.file_paths) - len(self._failed_files)) / len(self.file_paths) if len(self.file_paths) > 0 else 0,
'cache_manager_stats': self.cache_manager.get_cache_stats() if self.use_pdb_files else None
}
def get_failed_files(self):
"""Get list of files that failed to process."""
return list(self._failed_files)
def clear_failed_files(self):
"""Clear the list of failed files (useful for retrying)."""
self._failed_files.clear()
print("Dataset: Cleared failed files list")
def warm_cache(self, num_samples=None):
"""Pre-load a subset of the dataset into cache"""
if not self.enable_cache or not self._is_main_process:
return
num_samples = num_samples or min(self.cache_size, len(self.file_paths))
print(f"Warming cache with {num_samples} samples...")
# Load a random subset for better distribution
indices = random.sample(range(len(self.file_paths)), num_samples)
for i, idx in enumerate(indices):
file_path = self.file_paths[idx]
self._load_single_graph(file_path)
if (i + 1) % 50 == 0:
print(f"Cache warming progress: {i + 1}/{num_samples}")
print(f"Cache warmed. Current cache info: {self.get_cache_info()}")
def __len__(self):
# Return dataset size
return len(self.file_paths)
def _data_to_dict(self, data_obj):
"""Convert PyTorch Geometric Data object to dictionary format for subgraph sampler."""
from torch_geometric.data import Data
if isinstance(data_obj, Data):
return {
'node_features': data_obj.x,
'edge_index': data_obj.edge_index,
'edge_attr': data_obj.edge_attr,
'node_pos': data_obj.pos,
'num_nodes': data_obj.x.shape[0] if data_obj.x is not None else 0
}
else:
# Already dictionary format
return data_obj
def _dict_to_data(self, dict_obj):
"""Convert dictionary format back to PyTorch Geometric Data object."""
from torch_geometric.data import Data
if isinstance(dict_obj, dict):
return Data(
x=dict_obj['node_features'],
edge_index=dict_obj['edge_index'],
edge_attr=dict_obj['edge_attr'],
pos=dict_obj['node_pos']
)
else:
# Already Data object
return dict_obj
def _get_num_nodes(self, graph_obj):
"""Get number of nodes from either Data object or dictionary."""
from torch_geometric.data import Data
if isinstance(graph_obj, Data):
return graph_obj.x.shape[0] if graph_obj.x is not None else 0
else:
return graph_obj.get('num_nodes', graph_obj['node_features'].shape[0])
def __getitem__(self, idx):
"""Load protein graph on-demand and generate two contrastive views with robust error handling."""
max_attempts = len(self.file_paths) # Maximum attempts to find a valid sample
attempt = 0
while attempt < max_attempts:
try:
# Get current file (with wraparound if we've tried many times)
current_idx = (idx + attempt) % len(self.file_paths)
file_path = self.file_paths[current_idx]
protein_id = self.protein_ids[current_idx]
# Skip files that we know have failed before
if self.skip_invalid_files and file_path in self._failed_files:
attempt += 1
continue
# Check graph file existence, skip to debug
pt_file_path = '/'.join(file_path.split('/')[:-2]) + '/graph_cache/protein_pdb_files/' + 'pytorch_graph_' + protein_id + '.pt'
if os.path.exists(pt_file_path) and not self.force_pdb_processing:
return {
'load_error': False
}
# Load graph data
protein_graph = self._load_single_graph(file_path)
if protein_graph is None:
# Mark this file as failed and try next
self._failed_files.add(file_path)
print(f"Dataset: Marking {Path(file_path).name} as failed, trying next file...")
attempt += 1
continue
# Validate graph data
if not self._validate_graph_data(protein_graph):
self._failed_files.add(file_path)
print(f"Dataset: Graph validation failed for {Path(file_path).name}, trying next file...")
attempt += 1
continue
# Check if graph is large enough for subgraph sampling
num_nodes = self._get_num_nodes(protein_graph)
if num_nodes < self.min_nodes:
self._failed_files.add(file_path)
print(f"Dataset: Graph too small for {Path(file_path).name} ({num_nodes} < {self.min_nodes}), trying next file...")
attempt += 1
continue
# Generate two contrastive views
view1, view2, sampling_strategy, noise_applied = self._generate_contrastive_views(protein_graph)
# Validate views
if view1 is None or view2 is None:
print(f"Dataset: Failed to generate views for {Path(file_path).name}, trying next file...")
attempt += 1
continue
# Successfully created a valid sample
return {
'protein_graph': protein_graph,
'protein_id': protein_id,
'idx': current_idx,
'file_path': file_path,
'load_error': False,
'view1': view1,
'view2': view2,
'sampling_strategy': sampling_strategy,
'noise_applied': noise_applied,
'attempts_needed': attempt + 1
}
except Exception as e:
print(f"Dataset: Unexpected error processing {self.file_paths[(idx + attempt) % len(self.file_paths)]}: {e}")
attempt += 1
continue
# If we get here, we couldn't find any valid sample after many attempts
print(f"Dataset: Could not find valid sample after {max_attempts} attempts starting from idx {idx}")
# Return a dummy sample to prevent DataLoader from crashing
return self._create_dummy_sample(idx)
def _validate_graph_data(self, graph_data):
"""Validate that graph data is complete and has no NaN/infinite values."""
try:
if graph_data is None:
return False
# Check for NaN or infinite values
import torch
# Check node features
if torch.any(torch.isnan(graph_data.x)) or torch.any(torch.isinf(graph_data.x)):
print("Dataset: NaN/Inf found in node_features")
return False
# Check node positions
if torch.any(torch.isnan(graph_data.pos)) or torch.any(torch.isinf(graph_data.pos)):
print("Dataset: NaN/Inf found in node_pos")
return False
# Check edge attributes if present
if graph_data.edge_attr is not None:
if torch.any(torch.isnan(graph_data.edge_attr)) or torch.any(torch.isinf(graph_data.edge_attr)):
print("Dataset: NaN/Inf found in edge_attr")
return False
# Check tensor shapes are consistent
num_nodes = graph_data.x.shape[0]
if graph_data.pos.shape[0] != num_nodes:
print(f"Dataset: Inconsistent shapes - features: {graph_data.x.shape}, pos: {graph_data.pos.shape}")
return False
return True
except Exception as e:
print(f"Dataset: Error validating graph data: {e}")
return False
def _generate_contrastive_views(self, protein_graph):
"""Generate two contrastive views with error handling."""
try:
num_nodes = protein_graph.x.shape[0]
can_sample_subgraph = num_nodes >= self.min_nodes
# Generate two contrastive views with sampling probabilities
a = getattr(self, 'complete_graph_percent', 0)
complete_prob = a / 100.0
seq_prob = (50 - 0.5 * a) / 100.0
dist_prob = seq_prob
rand_val = random.random()
# Convert Data object to dictionary for subgraph sampler compatibility
protein_graph_dict = self._data_to_dict(protein_graph)
if not can_sample_subgraph or rand_val < complete_prob:
# Use complete graph for both views
view1_dict = self.subgraph_sampler.apply_noise(protein_graph_dict, "identity")
view2_dict = self.subgraph_sampler.apply_noise(protein_graph_dict, "identity")
sampling_strategy = 'complete' if can_sample_subgraph else 'complete_forced'
elif rand_val < complete_prob + seq_prob:
# Sequential sampling for both views
view1_dict = self.subgraph_sampler.sample_sequential_subgraph(protein_graph_dict)
view2_dict = self.subgraph_sampler.sample_sequential_subgraph(protein_graph_dict)
sampling_strategy = 'sequential'
else:
# Distance-based sampling for both views
view1_dict = self.subgraph_sampler.sample_distance_subgraph(protein_graph_dict)
view2_dict = self.subgraph_sampler.sample_distance_subgraph(protein_graph_dict)
sampling_strategy = 'distance'
# Convert back to Data objects
view1 = self._dict_to_data(view1_dict)
view2 = self._dict_to_data(view2_dict) # Validate views before applying noise
if not self._validate_graph_data(view1) or not self._validate_graph_data(view2):
print("Dataset: Invalid views generated during subgraph sampling")
return None, None, sampling_strategy, 'none'
# Apply noise transformations
apply_masking = random.random() < 0.5
if apply_masking:
view1_dict = self._data_to_dict(view1)
view2_dict = self._data_to_dict(view2)
view1_dict = self.subgraph_sampler.apply_noise(view1_dict, "random_edge_masking", edge_mask_prob=0.15)
view2_dict = self.subgraph_sampler.apply_noise(view2_dict, "random_edge_masking", edge_mask_prob=0.15)
view1 = self._dict_to_data(view1_dict)
view2 = self._dict_to_data(view2_dict)
noise_applied = 'masking'
else:
view1_dict = self._data_to_dict(view1)
view2_dict = self._data_to_dict(view2)
view1_dict = self.subgraph_sampler.apply_noise(view1_dict, "identity")
view2_dict = self.subgraph_sampler.apply_noise(view2_dict, "identity")
view1 = self._dict_to_data(view1_dict)
view2 = self._dict_to_data(view2_dict)
noise_applied = 'identity'
# Final validation of views
if not self._validate_graph_data(view1) or not self._validate_graph_data(view2):
print("Dataset: Invalid views after noise application")
return None, None, sampling_strategy, noise_applied
return view1, view2, sampling_strategy, noise_applied
except Exception as e:
print(f"Dataset: Error generating contrastive views: {e}")
return None, None, 'error', 'none'
def _create_dummy_sample(self, idx):
"""Create a dummy sample when all else fails to prevent DataLoader crashes."""
return {
'protein_graph': None,
'protein_id': f'dummy_{idx}',
'idx': idx,
'file_path': 'dummy',
'load_error': True,
'view1': None,
'view2': None,
'sampling_strategy': 'dummy',
'noise_applied': 'none',
'attempts_needed': -1
} |