Support for specifying dataset in training script

bin/train.py

@@ -109,6 +109,7 @@ def plot_kl_divergence(train_dset, plots_folder: Path) -> None:
 
 
 def get_train_valid_test_sets(
+    dataset_key:str = "cath",
     angles_definitions: ANGLES_DEFINITIONS = "canonical-full-angles",
     max_seq_len: int = 512,
     min_seq_len: int = 0,
@@ -144,6 +145,7 @@ def get_train_valid_test_sets(
     logging.info(f"Creating data splits: {splits}")
     clean_dsets = [
         clean_dset_class(
+            pdbs=dataset_key,
             split=s,
             pad=max_seq_len,
             min_length=min_seq_len,
@@ -286,6 +288,7 @@ def train(
     # Controls output
     results_dir: str = "./results",
     # Controls data loading and noising process
+    dataset_key: str = "cath",  # cath, alhpafold, or a directory containing pdb files
     angles_definitions: ANGLES_DEFINITIONS = "canonical-full-angles",
     max_seq_len: int = 512,
     min_seq_len: int = 0,  # 0 means no filtering based on min sequence length
@@ -340,6 +343,7 @@ def train(
 
     # Get datasets and wrap them in dataloaders
     dsets = get_train_valid_test_sets(
+        dataset_key=dataset_key,
         angles_definitions=angles_definitions,
         max_seq_len=max_seq_len,
         min_seq_len=min_seq_len,

foldingdiff/datasets.py

@@ -246,7 +246,7 @@ class CathCanonicalAnglesDataset(Dataset):
                 fnames = glob.glob(os.path.join(CATH_DIR, "dompdb", "*"))
                 assert fnames, f"No files found in {CATH_DIR}/dompdb"
             elif pdbs == "alphafold":
-                pdbs = glob.glob(os.path.join(ALPHAFOLD_DIR, "*.pdb.gz"))
+                fnames = glob.glob(os.path.join(ALPHAFOLD_DIR, "*.pdb.gz"))
                 assert fnames, f"No files found in {ALPHAFOLD_DIR}"
             else:
                 raise ValueError(f"Unknown pdb set: {pdbs}")