fix some problems and add save .pkl

fastfold/model/fastnn/kernel/softmax.py

@@ -4,7 +4,7 @@ import logging
 
 import torch
 
-_triton_available = True
+_triton_available = False
 if _triton_available:
     try:
         from .triton.softmax import softmax_triton_kernel_wrapper

fastfold/model/hub/alphafold.py

@@ -399,7 +399,6 @@ class AlphaFold(nn.Module):
             outputs["single"] = s
 
         # Predict 3D structure
-        z = [z]
         outputs_sm = self.structure_module(
             s,
             z,

fastfold/model/nn/structure_module.py

@@ -787,7 +787,6 @@ class StructureModule(nn.Module):
         for i in range(self.no_blocks):
             # [*, N, C_s]
             s = s + self.ipa(s, z, rigids, mask)
-            del z
             s = self.ipa_dropout(s)
             torch.cuda.empty_cache()
             s = self.layer_norm_ipa(s)

inference.py

@@ -21,6 +21,7 @@ import time
 from datetime import date
 import tempfile
 import contextlib
+import logging
 
 import numpy as np
 import torch
@@ -43,6 +44,10 @@ from fastfold.data.parsers import parse_fasta
 from fastfold.utils.import_weights import import_jax_weights_
 from fastfold.utils.tensor_utils import tensor_tree_map
 
+logging.basicConfig()
+logger = logging.getLogger(__file__)
+logger.setLevel(level=logging.INFO)
+
 if int(torch.__version__.split(".")[0]) >= 1 and int(torch.__version__.split(".")[1]) > 11:
     torch.backends.cuda.matmul.allow_tf32 = True
 
@@ -450,6 +455,15 @@ def inference_monomer_model(args):
     # with open(relaxed_output_path, 'w') as f:
     #     f.write(relaxed_pdb_str)
     
+    if(args.save_outputs):
+            output_dict_path = os.path.join(
+                args.output_dir, f'{tag}_{args.model_name}_output_dict.pkl'
+            )
+            with open(output_dict_path, "wb") as fp:
+                pickle.dump(out, fp, protocol=pickle.HIGHEST_PROTOCOL)
+
+            logger.info(f"Model output written to {output_dict_path}...")
+
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
@@ -483,6 +497,10 @@ if __name__ == "__main__":
                         help="""Path to model parameters. If None, parameters are selected
              automatically according to the model name from 
              ./data/params""")
+    parser.add_argument(
+        "--save_outputs", action="store_true", default=False,
+        help="Whether to save all model outputs, including embeddings, etc."
+    )
     parser.add_argument("--cpus",
                         type=int,
                         default=12,