Merge pull request #346 from dingquanyu/permutation

Update validation 

openfold/data/data_modules.py

@@ -23,6 +23,7 @@ import tempfile
 from openfold.utils.tensor_utils import (
     tensor_tree_map,
 )
+import random
 
 
 @contextlib.contextmanager
@@ -368,15 +369,15 @@ class OpenFoldSingleMultimerDataset(torch.utils.data.Dataset):
         """
         super(OpenFoldSingleMultimerDataset, self).__init__()
         self.data_dir = data_dir
-
+        self.mmcif_data_cache_path=mmcif_data_cache_path
         self.chain_data_cache = None
         if chain_data_cache_path is not None:
             with open(chain_data_cache_path, "r") as fp:
                 self.chain_data_cache = json.load(fp)
             assert isinstance(self.chain_data_cache, dict)
 
-        if mmcif_data_cache_path is not None:
-            with open(mmcif_data_cache_path,"r") as infile:
+        if self.mmcif_data_cache_path is not None:
+            with open(self.mmcif_data_cache_path,"r") as infile:
                 self.mmcif_data_cache = json.load(infile)
             assert isinstance(self.mmcif_data_cache,dict)
 
@@ -413,13 +414,16 @@ class OpenFoldSingleMultimerDataset(torch.utils.data.Dataset):
                 c for c in self._chain_ids if c in chains_to_include
             ]
 
-        if self.mmcif_data_cache is not None:
-
+        if self.mmcif_data_cache_path is not None:
             self._mmcifs = list(self.mmcif_data_cache.keys())
-            self._mmcif_id_to_idx_dict = {
+        elif self.mmcif_data_cache_path is None and self.alignment_dir is not None:
+            self._mmcifs = [i.split("_")[0] for i in os.listdir(self.alignment_dir)]
+        else:
+            raise ValueError("You must provide at least one of the mmcif_data_cache or alignment_dir")
+        self._mmcif_id_to_idx_dict = {
                 mmcif: i for i, mmcif in enumerate(self._mmcifs)
             }
-
+        
         # changed template_featurizer to hmmsearch for now just to run the test
         template_featurizer = templates.HmmsearchHitFeaturizer(
             mmcif_dir=template_mmcif_dir,
@@ -470,9 +474,6 @@ class OpenFoldSingleMultimerDataset(torch.utils.data.Dataset):
 
     def __getitem__(self, idx):
         mmcif_id = self.idx_to_mmcif_id(idx)
-        chains = self.mmcif_data_cache[mmcif_id]['chain_ids']
-        print(f"mmcif_id is :{mmcif_id} idx:{idx} and has {len(chains)}chains")
-
         alignment_index = None
         if(self.mode == 'train' or self.mode == 'eval'):
             path = os.path.join(self.data_dir, f"{mmcif_id}")
@@ -715,17 +716,18 @@ class OpenFoldMultimerDataset(torch.utils.data.Dataset):
 
     def filter_samples(self,dataset_idx):
             dataset = self.datasets[dataset_idx]
-            mmcif_data_cache = dataset.mmcif_data_cache
+            mmcif_data_cache = dataset.mmcif_data_cache if hasattr(dataset,"mmcif_data_cache") else None
             selected_idx = []
-            for i in range(len(mmcif_data_cache)):
-                    mmcif_id = dataset.idx_to_mmcif_id(i)
-                    chains = mmcif_data_cache[mmcif_id]['chain_ids']
-                    mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
-                    if deterministic_multimer_train_filter(mmcif_data_cache_entry,
-                                                           max_resolution=9,
-                                                           minimum_number_of_residues=5):
-                        selected_idx.append(i)
-            
+            if mmcif_data_cache is not None:
+                for i in range(len(mmcif_data_cache)):
+                        mmcif_id = dataset.idx_to_mmcif_id(i)
+                        mmcif_data_cache_entry = mmcif_data_cache[mmcif_id]
+                        if deterministic_multimer_train_filter(mmcif_data_cache_entry,
+                                                            max_resolution=9,
+                                                            minimum_number_of_residues=5):
+                            selected_idx.append(i)
+            else:
+                selected_idx = list(range(len(dataset._mmcif_id_to_idx_dict)))
             return selected_idx
     
     def __getitem__(self, idx):
@@ -746,6 +748,7 @@ class OpenFoldMultimerDataset(torch.utils.data.Dataset):
         self.datapoints = []
         for dataset_idx in dataset_choices:
             selected_idx = self.filter_samples(dataset_idx)
+            random.shuffle(selected_idx)
             if len(selected_idx)<self.epoch_len:
                 self.epoch_len = len(selected_idx)
             logging.info(f"self.epoch_len is {self.epoch_len}")
@@ -849,7 +852,6 @@ class OpenFoldMultimerDataLoader(torch.utils.data.DataLoader):
         self.stage = stage
         
         self.generator = generator
-        print('initialised a multimer dataloader')
     def __iter__(self):
         it = super().__iter__()
 
@@ -1092,6 +1094,7 @@ class OpenFoldMultimerDataModule(OpenFoldDataModule):
                  template_mmcif_dir: str, max_template_date: str, 
                  train_data_dir: Optional[str] = None,
                  train_mmcif_data_cache_path:Optional[str]  = None,
+                 val_mmcif_data_cache_path:Optional[str] = None,
                  **kwargs):
         super(OpenFoldMultimerDataModule,self).__init__(config, 
                                                    template_mmcif_dir, 
@@ -1099,6 +1102,7 @@ class OpenFoldMultimerDataModule(OpenFoldDataModule):
                                                    train_data_dir,**kwargs)
         self.train_mmcif_data_cache_path = train_mmcif_data_cache_path
         self.training_mode = self.train_data_dir is not None
+        self.val_mmcif_data_cache_path = val_mmcif_data_cache_path
 
     def setup(self):
         # Most of the arguments are the same for the three datasets 
@@ -1167,6 +1171,7 @@ class OpenFoldMultimerDataModule(OpenFoldDataModule):
                 self.eval_dataset = dataset_gen(
                     data_dir=self.val_data_dir,
                     alignment_dir=self.val_alignment_dir,
+                    mmcif_data_cache_path=self.val_mmcif_data_cache_path,
                     filter_path=None,
                     max_template_hits=self.config.eval.max_template_hits,
                     mode="eval",
@@ -1206,7 +1211,6 @@ class OpenFoldMultimerDataModule(OpenFoldDataModule):
             batch_size=1,
             num_workers=self.config.data_module.data_loaders.num_workers,
         )
-        print(f"generated training dataloader")
         return dl
 
 class DummyDataset(torch.utils.data.Dataset):

train_openfold.py

@@ -509,6 +509,10 @@ if __name__ == "__main__":
         "--val_alignment_dir", type=str, default=None,
         help="Directory containing precomputed validation alignments"
     )
+    parser.add_argument(
+        "--val_mmcif_data_cache_path", type=str, default=None,
+        help="path to the json file which records all the information of mmcif structures used during validation"
+    )
     parser.add_argument(
         "--kalign_binary_path", type=str, default='/usr/bin/kalign',
         help="Path to the kalign binary"