Drop alignments that are missing structure data in training

openfold/data/data_modules.py

@@ -24,6 +24,7 @@ from openfold.utils.tensor_utils import tensor_tree_map, dict_multimap
 class OpenFoldSingleDataset(torch.utils.data.Dataset):
     def __init__(self,
         data_dir: str,
+        chain_data_cache_path: str,
         alignment_dir: str, 
         template_mmcif_dir: str,
         max_template_date: str,
@@ -80,6 +81,11 @@ class OpenFoldSingleDataset(torch.utils.data.Dataset):
         """
         super(OpenFoldSingleDataset, self).__init__()
         self.data_dir = data_dir
+
+        with open(chain_data_cache_path, "r") as fp:
+            self.chain_data_cache = json.load(fp)
+        assert isinstance(self.chain_data_cache, dict)
+
         self.alignment_dir = alignment_dir
         self.config = config
         self.treat_pdb_as_distillation = treat_pdb_as_distillation
@@ -104,12 +110,35 @@ class OpenFoldSingleDataset(torch.utils.data.Dataset):
             self._chain_ids = list(alignment_index.keys())
         else:
             self._chain_ids = list(os.listdir(alignment_dir))
-        
+
         if(filter_path is not None):
             with open(filter_path, "r") as f:
                 chains_to_include = set([l.strip() for l in f.readlines()])
 
-            self._chain_ids = [c for c in self._chain_ids if c in chains_to_include]
+            self._chain_ids = [
+                c for c in self._chain_ids if c in chains_to_include
+            ]
+
+        # Filter to include only chains where we have structure data
+        # (i.e. entries in chain_data_cache)
+        original_chain_ids = self._chain_ids
+        self._chain_ids = [
+            c for c in self._chain_ids if c in self.chain_data_cache
+        ]
+        if len(self._chain_ids) < len(original_chain_ids):
+            missing = [
+                c for c in original_chain_ids if c not in self.chain_data_cache
+            ]
+            max_to_print = 10
+            missing_examples = ", ".join(missing[:max_to_print])
+            if len(missing) > max_to_print:
+                missing_examples += ", ..."
+            logging.warning(
+                "Ignoring %d alignment entries (%s) that have no corresponding "
+                "entries in chain_data_cache (%s).",
+                len(missing),
+                missing_examples,
+                chain_data_cache_path)
        
         self._chain_id_to_idx_dict = {
             chain: i for i, chain in enumerate(self._chain_ids)
@@ -234,7 +263,10 @@ class OpenFoldSingleDataset(torch.utils.data.Dataset):
             data, self.mode 
         )
 
-        feats["batch_idx"] = torch.tensor([idx for _ in range(feats["aatype"].shape[-1])], dtype=torch.int64, device=feats["aatype"].device)
+        feats["batch_idx"] = torch.tensor(
+            [idx for _ in range(feats["aatype"].shape[-1])],
+            dtype=torch.int64,
+            device=feats["aatype"].device)
 
         return feats
 
@@ -297,7 +329,6 @@ class OpenFoldDataset(torch.utils.data.Dataset):
         datasets: Sequence[OpenFoldSingleDataset],
         probabilities: Sequence[int],
         epoch_len: int,
-        chain_data_cache_paths: List[str],
         generator: torch.Generator = None,
         _roll_at_init: bool = True,
     ):
@@ -305,11 +336,6 @@ class OpenFoldDataset(torch.utils.data.Dataset):
         self.probabilities = probabilities
         self.epoch_len = epoch_len
         self.generator = generator
-        
-        self.chain_data_caches = []
-        for path in chain_data_cache_paths:
-            with open(path, "r") as fp:
-                self.chain_data_caches.append(json.load(fp))
 
         def looped_shuffled_dataset_idx(dataset_len):
             while True:
@@ -328,7 +354,7 @@ class OpenFoldDataset(torch.utils.data.Dataset):
             max_cache_len = int(epoch_len * probabilities[dataset_idx])
             dataset = self.datasets[dataset_idx]
             idx_iter = looped_shuffled_dataset_idx(len(dataset))
-            chain_data_cache = self.chain_data_caches[dataset_idx]
+            chain_data_cache = dataset.chain_data_cache
             while True:
                 weights = []
                 idx = []
@@ -591,6 +617,7 @@ class OpenFoldDataModule(pl.LightningDataModule):
         if(self.training_mode):
             train_dataset = dataset_gen(
                 data_dir=self.train_data_dir,
+                chain_data_cache_path=self.train_data_cache_path,
                 alignment_dir=self.train_alignment_dir,
                 filter_path=self.train_filter_path,
                 max_template_hits=self.config.train.max_template_hits,
@@ -605,6 +632,7 @@ class OpenFoldDataModule(pl.LightningDataModule):
             if(self.distillation_data_dir is not None):
                 distillation_dataset = dataset_gen(
                     data_dir=self.distillation_data_dir,
+                    chain_data_cache_path=self.distillation_chain_data_cache_path,
                     alignment_dir=self.distillation_alignment_dir,
                     filter_path=self.distillation_filter_path,
                     max_template_hits=self.config.train.max_template_hits,
@@ -620,16 +648,9 @@ class OpenFoldDataModule(pl.LightningDataModule):
                 datasets = [train_dataset, distillation_dataset]
                 d_prob = self.config.train.distillation_prob
                 probabilities = [1. - d_prob, d_prob]
-                chain_data_cache_paths = [
-                    self.train_chain_data_cache_path,
-                    self.distillation_chain_data_cache_path,
-                ]
             else:
                 datasets = [train_dataset]
-                probabilities = [1.]   
-                chain_data_cache_paths = [
-                    self.train_chain_data_cache_path,
-                ]
+                probabilities = [1.]
 
             generator = None
             if(self.batch_seed is not None):
@@ -640,7 +661,6 @@ class OpenFoldDataModule(pl.LightningDataModule):
                 datasets=datasets,
                 probabilities=probabilities,
                 epoch_len=self.train_epoch_len,
-                chain_data_cache_paths=chain_data_cache_paths,
                 generator=generator,
                 _roll_at_init=False,
             )