more fixes

run_pretrained_openfold.py

@@ -237,14 +237,13 @@ def load_models_from_command_line(args, config):
         for path in args.openfold_checkpoint_path.split(","):
             model = AlphaFold(config)
             model = model.eval()
-            checkpoint_basename = None
-            if os.path.isdir(path):
-                # A DeepSpeed checkpoint
             checkpoint_basename = os.path.splitext(
                 os.path.basename(
                     os.path.normpath(path)
                 )
             )[0]
+            if os.path.isdir(path):
+                # A DeepSpeed checkpoint
                 ckpt_path = os.path.join(
                     args.output_dir,
                     checkpoint_basename + ".pt",
@@ -313,7 +312,7 @@ def main(args):
 
     for fasta_file in os.listdir(args.fasta_dir):
 
-        batch, tag, feature_dict = generate_batch(
+        batch_data = generate_batch(
             fasta_file,
             args.fasta_dir,
             alignment_dir,
@@ -321,6 +320,12 @@ def main(args):
             feature_processor,
             prediction_dir)
 
+        if batch_data is None:
+            # this file has already been processed
+            continue
+
+        batch, tag, feature_dict = batch_data
+
         for model, model_version in load_models_from_command_line(args, config):
 
             working_batch = deepcopy(batch)