Merge remote-tracking branch 'refs/remotes/jnwei/pl_upgrades' into pl_upgrades

openfold/utils/superimposition.py

@@ -35,10 +35,10 @@ def _superimpose_np(reference, coords):
 
 
 def _superimpose_single(reference, coords):
-    reference_np = reference.detach().to(torch.float).cpu().numpy()    
-    coords_np = coords.detach().to(torch.float).cpu().numpy()
-    superimposed, rmsd = _superimpose_np(reference_np, coords_np)
-    return coords.new_tensor(superimposed), coords.new_tensor(rmsd)
+	reference_np = reference.detach().to(torch.float).cpu().numpy()  
+	coords_np = coords.detach().to(torch.float).cpu().numpy()
+	superimposed, rmsd = _superimpose_np(reference_np, coords_np)
+	return coords.new_tensor(superimposed), coords.new_tensor(rmsd)
 
 
 def superimpose(reference, coords, mask):

train_openfold.py

@@ -682,9 +682,9 @@ if __name__ == "__main__":
     trainer_group.add_argument(
         "--reload_dataloaders_every_n_epochs", type=int, default=1,
     )
-
-    trainer_group.add_argument("--accumulate_grad_batches", type=int, default=1,
-                               help="Accumulate gradients over k batches before next optimizer step.")
+    trainer_group.add_argument(
+        "--accumulate_grad_batches", type=int, default=1,
+        help="Accumulate gradients over k batches before next optimizer step.")
 
     args = parser.parse_args()
 
@@ -700,5 +700,4 @@ if __name__ == "__main__":
         raise ValueError(
             "Choose between loading pretrained Jax-weights and a checkpoint-path")
 
-
     main(args)