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src/split_dataset.py

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+import pandas as pd
+import shutil
+import os
+import glob
+
+# ============================================================
+# CONFIGURATION - Edit these paths as needed
+# ============================================================
+PDB_ROOT = "pdb"
+OUTPUT_ROOT = "pdb_2021aug02"
+
+TRAIN_CSV      = "train.csv"
+VALIDATION_CSV = "validation.csv"
+TEST_CSV       = "test.csv"
+
+SPLITS = {
+    "training":   TRAIN_CSV,
+    "validation": VALIDATION_CSV,
+    "test":       TEST_CSV
+}
+
+# ============================================================
+# HELPER FUNCTIONS
+# ============================================================
+
+def get_subfolder(name):
+    """
+    Extract subfolder from filename.
+    E.g., '1nb4_A' -> 'nb'  (characters at index 1 and 2)
+    """
+    # Strip extension if present
+    base = os.path.splitext(name)[0]
+    return base[1:3].lower()  # e.g., '1nb4_A' -> 'nb'
+
+
+
+def read_csv_entries(csv_file):
+    """
+    Read comma-separated entries from a single-line CSV.
+    E.g., 5naf_A,5naf_B,5naf_C,...
+    """
+    entries = []
+    with open(csv_file, 'r') as f:
+        for line in f:
+            entries.extend(line.strip().split(','))
+    return [e.strip() for e in entries if e.strip()]
+
+def find_pt_file(pdb_root, name):
+    """
+    Locate the .pt file given the entry name.
+    E.g., '1nb4_A' -> pdb_root/nb/1nb4_A.pt
+    """
+    subfolder = get_subfolder(name)
+    pt_path = os.path.join(pdb_root, subfolder, f"{name}.pt")
+    if os.path.exists(pt_path):
+        return pt_path, subfolder
+    return None, subfolder
+
+
+def copy_file(src, dst_dir, filename):
+    """
+    Copy file to destination directory, creating dirs if needed.
+    """
+    os.makedirs(dst_dir, exist_ok=True)
+    dst = os.path.join(dst_dir, filename)
+    shutil.copy2(src, dst)
+    return dst
+
+
+# ============================================================
+# MAIN
+# ============================================================
+
+def main():
+    stats = {}
+
+    for split_name, csv_file in SPLITS.items():
+        print(f"\n{'='*50}")
+        print(f"Processing: {split_name.upper()} <- {csv_file}")
+        print(f"{'='*50}")
+
+        if not os.path.exists(csv_file):
+            print(f"  [WARNING] CSV file not found: {csv_file}")
+            continue
+
+        entries = read_csv_entries(csv_file)
+        print(f"  Total entries found in CSV: {len(entries)}")
+
+        copied  = 0
+        missing = []
+
+        for name in entries:
+            src_path, subfolder = find_pt_file(PDB_ROOT, name)
+
+            if src_path:
+                # Destination: e.g., OUTPUT_ROOT/validation/nb/1nb4_A.pt
+                dst_dir = os.path.join(OUTPUT_ROOT, split_name, subfolder)
+                copy_file(src_path, dst_dir, f"{name}.pt")
+                copied += 1
+            else:
+                missing.append(name)
+
+        print(f"Copied  : {copied}")
+        print(f"Missing : {len(missing)}")
+
+        if missing:
+            missing_log = os.path.join(OUTPUT_ROOT, f"{split_name}_missing.txt")
+            with open(missing_log, "w") as f:
+                f.write("\n".join(missing))
+            print(f"Missing entries logged to: {missing_log}")
+
+        stats[split_name] = {"copied": copied, "missing": len(missing)}
+
+    # ---- Summary ----
+    print(f"\n{'='*50}")
+    print("SUMMARY")
+    print(f"{'='*50}")
+    for split, s in stats.items():
+        print(f"  {split:<12}: {s['copied']} copied, {s['missing']} missing")
+
+
+if __name__ == "__main__":
+    main()