Add mmCIF cache generation script, remove verbose warnings

openfold/data/data_modules.py

@@ -80,7 +80,7 @@ class OpenFoldSingleDataset(torch.utils.data.Dataset):
         if(template_release_dates_cache_path is None):
             logging.warning(
                 "Template release dates cache does not exist. Remember to run "
-                "scripts/generate_mmcif_caches.py before running OpenFold"
+                "scripts/generate_mmcif_cache.py before running OpenFold"
             )
 
         template_featurizer = templates.TemplateHitFeaturizer(
@@ -358,6 +358,8 @@ class OpenFoldDataModule(pl.LightningDataModule):
                     max_template_hits=self.config.eval.max_template_hits,
                     mode="eval",
                 )
+            else:
+                self.val_dataset = None
         else:           
             self.predict_dataset = dataset_gen(
                 data_dir=self.predict_data_dir,
@@ -387,6 +389,7 @@ class OpenFoldDataModule(pl.LightningDataModule):
         )
 
     def val_dataloader(self):
+        if(self.val_dataset is not None):
             return torch.utils.data.DataLoader(
                 self.val_dataset,
                 batch_size=self.config.data_module.data_loaders.batch_size,
@@ -394,6 +397,8 @@ class OpenFoldDataModule(pl.LightningDataModule):
                 collate_fn=self._gen_batch_collator("eval")
             )
 
+        return None
+
     def predict_dataloader(self):
         return torch.utils.data.DataLoader(
             self.predict_dataset,

openfold/data/mmcif_parsing.py

@@ -345,7 +345,7 @@ def _get_header(parsed_info: MmCIFDict) -> PdbHeader:
                 raw_resolution = parsed_info[res_key][0]
                 header["resolution"] = float(raw_resolution)
             except ValueError:
-                logging.warning(
+                logging.info(
                     "Invalid resolution format: %s", parsed_info[res_key]
                 )
 
@@ -475,27 +475,3 @@ def get_atom_coords(
         all_atom_mask[res_index] = mask
 
     return all_atom_positions, all_atom_mask
-
-
-def generate_mmcif_cache(mmcif_dir: str, out_path: str):
-    data = {}
-    for f in os.listdir(mmcif_dir):
-        if f.endswith(".cif"):
-            with open(os.path.join(mmcif_dir, f), "r") as fp:
-                mmcif_string = fp.read()
-            file_id = os.path.splitext(f)[0]
-            mmcif = parse(file_id=file_id, mmcif_string=mmcif_string)
-            if mmcif.mmcif_object is None:
-                logging.warning(f"Could not parse {f}. Skipping...")
-                continue
-            else:
-                mmcif = mmcif.mmcif_object
-
-            local_data = {}
-            local_data["release_date"] = mmcif.header["release_date"]
-            local_data["no_chains"] = len(list(mmcif.structure.get_chains()))
-
-            data[file_id] = local_data
-
-    with open(out_path, "w") as fp:
-        fp.write(json.dumps(data))

scripts/generate_mmcif_cache.py

+import argparse
+from functools import partial
+import logging
+from multiprocessing import Pool
+import os
+import sys
+sys.path.append(".") # an innocent hack to get this to run from the top level
+
+from tqdm import tqdm
+
+from openfold.data.mmcif_parsing import parse 
+
+
+def parse_file(f, args):
+    with open(os.path.join(args.mmcif_dir, f), "r") as fp:
+        mmcif_string = fp.read()
+    file_id = os.path.splitext(f)[0]
+    mmcif = parse(file_id=file_id, mmcif_string=mmcif_string)
+    if mmcif.mmcif_object is None:
+        logging.info(f"Could not parse {f}. Skipping...")
+        return {}
+    else:
+        mmcif = mmcif.mmcif_object
+
+    local_data = {}
+    local_data["release_date"] = mmcif.header["release_date"]
+    local_data["no_chains"] = len(list(mmcif.structure.get_chains()))
+
+    return {file_id: local_data}
+
+
+def main(args):
+    files = [f for f in os.listdir(args.mmcif_dir) if ".cif" in f]
+    fn = partial(parse_file, args=args)
+    data = {}
+    with Pool(processes=args.no_workers) as p:
+        with tqdm(total=len(files)) as pbar:
+            for d in p.imap_unordered(fn, files, chunksize=args.chunksize):
+                data.update(d)
+                pbar.update()
+
+    with open(args.output_path, "w") as fp:
+        fp.write(json.dumps(data))
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "mmcif_dir", type=str, help="Directory containing mmCIF files"
+    )
+    parser.add_argument(
+        "output_path", type=str, help="Path for .json output"
+    )
+    parser.add_argument(
+        "--no_workers", type=int, default=4,
+        help="Number of workers to use for parsing"
+    )
+    parser.add_argument(
+        "--chunksize", type=int, default=10,
+        help="How many files should be distributed to each worker at a time"
+    )
+
+    args = parser.parse_args()
+
+    main(args)

train_openfold.py

@@ -43,15 +43,24 @@ class OpenFoldWrapper(pl.LightningModule):
         # Compute loss
         loss = self.loss(outputs, batch)
 
-        return {"loss": loss, "pred": outputs["sm"]["positions"][-1].detach()}
+        return {"loss": loss}
 
-    def training_epoch_end(self, outs):
-        out = outs[-1]["pred"].cpu()
-        with open("prediction/preds_" + str(time.strftime("%H:%M:%S")) + ".pickle", "wb") as f:
-            pickle.dump(out, f, protocol=pickle.HIGHEST_PROTOCOL)
+    def validation_step(self, batch, batch_idx):
+        # At the start of validation, load the EMA weights
+        if(self.cached_weights is None):
+            self.cached_weights = model.state_dict()
+            self.model.load_state_dict(self.ema.state_dict()["params"])
         
-    #def validation_step(self, batch, batch_idx):
-    #    outputs = self(batch)
+        # Calculate validation loss
+        outputs = self(batch)
+        batch = tensor_tree_map(lambda t: t[..., -1], batch)
+        loss = self.loss(outputs, batch)
+        return {"val_loss": loss}
+
+    def validation_epoch_end(self, _):
+        # Restore the model weights to normal
+        self.model.load_state_dict(self.cached_weights)
+        self.cached_weights = None
 
     def configure_optimizers(self, 
         learning_rate: float = 1e-3,
@@ -140,7 +149,8 @@ if __name__ == "__main__":
     )
     parser.add_argument(
         "--template_release_dates_cache_path", type=str, default=None,
-        help="Output of templates.generate_mmcif_cache"
+        help="""Output of scripts/generate_mmcif_cache.py run on template mmCIF
+                files."""
     )
     parser.add_argument(
         "--use_small_bfd", type=bool, default=False,