Merge pull request #5 from dingquanyu/multimer-dataloader

added openfold multimer dataloader class and overwrite batch processing

openfold/data/data_modules.py

@@ -24,6 +24,9 @@ import tempfile
 from openfold.utils.tensor_utils import (
     tensor_tree_map,
 )
+import logging
+logger = logging.getLogger(__name__)
+
 @contextlib.contextmanager
 def temp_fasta_file(sequence_str):
     """function that create temparory fasta file used in multimer datapipeline"""
@@ -468,6 +471,7 @@ class OpenFoldSingleMultimerDataset(torch.utils.data.Dataset):
 
     def __getitem__(self, idx):
         mmcif_id = self.idx_to_mmcif_id(idx)
+        print(f"mmcif_id is :{mmcif_id}")
         chains = self.mmcif_data_cache[mmcif_id]['chain_ids']
         seqs = self.mmcif_data_cache[mmcif_id]['seqs']
         fasta_str = ""
@@ -599,7 +603,10 @@ def deterministic_multimer_train_filter(
     
     for seq in seqs:
         for aa in seq:
-            counts[aa] += 1
+            if aa not in restypes:
+                return False
+            else:
+                counts[aa] += 1
     largest_aa_count = max(counts.values())
     largest_single_aa_prop = largest_aa_count / total_len
     if(largest_single_aa_prop > max_single_aa_prop):
@@ -867,6 +874,52 @@ class OpenFoldDataLoader(torch.utils.data.DataLoader):
 
         return _batch_prop_gen(it)
 
+class OpenFoldMultimerDataLoader(OpenFoldDataLoader):
+    def __init__(self, *args, config, stage="train", generator=None, **kwargs):
+        super(OpenFoldMultimerDataLoader,self).__init__(*args, config=config, stage=stage, generator=generator, **kwargs)
+
+    def _add_batch_properties(self, batch):
+        samples = torch.multinomial(
+        self.prop_probs_tensor,
+        num_samples=1, # 1 per row
+        replacement=True,
+        generator=self.generator)
+
+        def process_samples(batch,samples):
+
+            aatype = batch["aatype"]
+            batch_dims = aatype.shape[:-2]
+            recycling_dim = aatype.shape[-1]
+            no_recycling = recycling_dim
+            for i, key in enumerate(self.prop_keys):
+                sample = int(samples[i][0])
+                sample_tensor = torch.tensor(
+                    sample, 
+                    device=aatype.device, 
+                    requires_grad=False
+                )
+                orig_shape = sample_tensor.shape
+                sample_tensor = sample_tensor.view(
+                    (1,) * len(batch_dims) + sample_tensor.shape + (1,)
+                )
+                sample_tensor = sample_tensor.expand(
+                    batch_dims + orig_shape + (recycling_dim,)
+                )
+                batch[key] = sample_tensor
+
+                if(key == "no_recycling_iters"):
+                    no_recycling = sample 
+            
+            resample_recycling = lambda t: t[..., :no_recycling + 1]
+            batch = tensor_tree_map(resample_recycling, batch)
+
+            return batch
+        
+        all_chain_features,ground_truth =batch
+        all_chain_features = process_samples(all_chain_features,samples)
+        ground_truth = [process_samples(i,samples) for i in ground_truth]
+        return (all_chain_features,ground_truth)
+
 
 class OpenFoldDataModule(pl.LightningDataModule):
     def __init__(self,
@@ -1123,7 +1176,6 @@ class OpenFoldMultimerDataModule(OpenFoldDataModule):
             train_dataset = dataset_gen(
                 data_dir=self.train_data_dir,
                 mmcif_data_cache_path=self.train_mmcif_data_cache_path,
-                chain_data_cache_path=self.train_chain_data_cache_path,
                 alignment_dir=self.train_alignment_dir,
                 filter_path=self.train_filter_path,
                 max_template_hits=self.config.train.max_template_hits,
@@ -1138,7 +1190,6 @@ class OpenFoldMultimerDataModule(OpenFoldDataModule):
             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,
@@ -1189,6 +1240,35 @@ class OpenFoldMultimerDataModule(OpenFoldDataModule):
                 max_template_hits=self.config.predict.max_template_hits,
                 mode="predict",
             )
+    
+    def _gen_dataloader(self, stage):
+        generator = torch.Generator()
+        if(self.batch_seed is not None):
+            generator = generator.manual_seed(self.batch_seed)
+
+        dataset = None
+        if(stage == "train"):
+            dataset = self.train_dataset
+            # Filter the dataset, if necessary
+            dataset.reroll()
+        elif(stage == "eval"):
+            dataset = self.eval_dataset
+        elif(stage == "predict"):
+            dataset = self.predict_dataset
+        else:
+            raise ValueError("Invalid stage")
+
+
+        dl = OpenFoldMultimerDataLoader(
+            dataset,
+            config=self.config,
+            stage=stage,
+            generator=generator,
+            batch_size=self.config.data_module.data_loaders.batch_size,
+            num_workers=self.config.data_module.data_loaders.num_workers,
+        )
+
+        return dl
 
 class DummyDataset(torch.utils.data.Dataset):
     def __init__(self, batch_path):