Seed fixes for multimer data pipeline

openfold/config.py

@@ -155,8 +155,6 @@ def model_config(
         c.loss.tm.weight = 0.1
     elif "multimer" in name:
         c.update(multimer_config_update.copy_and_resolve_references())
-        del c.model.template.template_pointwise_attention
-        del c.loss.fape.backbone
 
         # TODO: Change max_msa_clusters and max_extra_msa to multimer feats within model
         if re.fullmatch("^model_[1-5]_multimer(_v2)?$", name):
@@ -354,6 +352,8 @@ config = mlc.ConfigDict(
                 "max_templates": 4,
                 "crop": False,
                 "crop_size": None,
+                "spatial_crop_prob": None,
+                "interface_threshold": None,
                 "supervised": False,
                 "uniform_recycling": False,
             },
@@ -367,6 +367,8 @@ config = mlc.ConfigDict(
                 "max_templates": 4,
                 "crop": False,
                 "crop_size": None,
+                "spatial_crop_prob": None,
+                "interface_threshold": None,
                 "supervised": True,
                 "uniform_recycling": False,
             },
@@ -381,6 +383,8 @@ config = mlc.ConfigDict(
                 "shuffle_top_k_prefiltered": 20,
                 "crop": True,
                 "crop_size": 256,
+                "spatial_crop_prob": 0.,
+                "interface_threshold": None,
                 "supervised": True,
                 "clamp_prob": 0.9,
                 "max_distillation_msa_clusters": 1000,
@@ -709,7 +713,9 @@ multimer_config_update = mlc.ConfigDict({
         "train": {
             "max_msa_clusters": 508,
             "max_extra_msa": 2048,
-            "crop_size": 640
+            "crop_size": 640,
+            "spatial_crop_prob": 0.5,
+            "interface_threshold": 10.
         },
     },
     "model": {
@@ -735,6 +741,7 @@ multimer_config_update = mlc.ConfigDict({
                 "tri_mul_first": True,
                 "fuse_projection_weights": True
             },
+            "template_pointwise_attention": None,  # Not used in Multimer
             "c_t": c_t,
             "c_z": c_z,
             "use_unit_vector": True
@@ -778,7 +785,8 @@ multimer_config_update = mlc.ConfigDict({
                 "clamp_distance": 30.0,
                 "loss_unit_distance": 20.0,
                 "weight": 0.5
-            }
+            },
+            "backbone": None  # Not used in Multimer
         },
         "masked_msa": {
             "num_classes": 22

openfold/data/data_modules.py

@@ -4,7 +4,7 @@ import json
 import logging
 import os
 import pickle
-from typing import Optional, Sequence, List, Any
+from typing import Optional, Sequence, Any
 
 import ml_collections as mlc
 import pytorch_lightning as pl
@@ -880,10 +880,7 @@ class OpenFoldMultimerDataLoader(torch.utils.data.DataLoader):
     def __init__(self, *args, config, stage="train", generator=None, **kwargs):
         super(OpenFoldMultimerDataLoader,self).__init__(*args, **kwargs)
         self.config = config
-        self.stage = stage    
-
-        if(generator is None):
-            generator = torch.Generator()
+        self.stage = stage
         
         self.generator = generator
         print('initialised a multimer dataloader')
@@ -1220,8 +1217,9 @@ class OpenFoldMultimerDataModule(OpenFoldDataModule):
             )
     
     def _gen_dataloader(self, stage):
-        generator = torch.Generator()
+        generator = None
         if(self.batch_seed is not None):
+            generator = torch.Generator()
             generator = generator.manual_seed(self.batch_seed)
 
         dataset = None

openfold/data/data_transforms.py

@@ -477,8 +477,9 @@ def make_masked_msa(protein, config, replace_fraction, seed):
 
     sh = protein["msa"].shape
 
-    g = torch.Generator(device=protein["msa"].device)
+    g = None
     if seed is not None:
+        g = torch.Generator(device=protein["msa"].device)
         g.manual_seed(seed)
     
     sample = torch.rand(sh, device=device, generator=g)

openfold/data/data_transforms_multimer.py

@@ -100,8 +100,9 @@ def make_masked_msa(batch, config, replace_fraction, seed, eps=1e-6):
     
     logits = torch.log(categorical_probs + eps)
     
-    g = torch.Generator(device=batch["msa"].device)
+    g = None
     if seed is not None:
+        g = torch.Generator(device=batch["msa"].device)
         g.manual_seed(seed)
 
     bert_msa = gumbel_max_sample(logits, generator=g)
@@ -262,8 +263,9 @@ def sample_msa(batch, max_seq, max_extra_msa_seq, seed, inf=1e6):
     Returns:
         Protein with sampled msa.
     """
-    g = torch.Generator(device=batch["msa"].device)
+    g = None
     if seed is not None:
+        g = torch.Generator(device=batch["msa"].device)
         g.manual_seed(seed)
 
     # Sample uniformly among sequences with at least one non-masked position.
@@ -417,8 +419,9 @@ def random_crop_to_size(
 ):
     """Crop randomly to `crop_size`, or keep as is if shorter than that."""
     # We want each ensemble to be cropped the same way
-    g = torch.Generator(device=protein["seq_length"].device)
+    g = None
     if seed is not None:
+        g = torch.Generator(device=protein["seq_length"].device)
         g.manual_seed(seed)
 
     use_spatial_crop = torch.rand((1,),

openfold/data/input_pipeline_multimer.py

@@ -13,8 +13,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from functools import partial
-
+import random
 import torch
 
 from openfold.data import (
@@ -75,13 +74,44 @@ def ensembled_transform_fns(common_cfg, mode_cfg, ensemble_seed):
     transforms.append(data_transforms_multimer.nearest_neighbor_clusters())
     transforms.append(data_transforms_multimer.create_msa_feat)
 
+    crop_feats = dict(common_cfg.feat)
+
+    if mode_cfg.fixed_size:
+        transforms.append(data_transforms.select_feat(list(crop_feats)))
+
+        if mode_cfg.crop:
+            transforms.append(
+                data_transforms_multimer.random_crop_to_size(
+                    crop_size=mode_cfg.crop_size,
+                    max_templates=mode_cfg.max_templates,
+                    shape_schema=crop_feats,
+                    spatial_crop_prob=mode_cfg.spatial_crop_prob,
+                    interface_threshold=mode_cfg.interface_threshold,
+                    subsample_templates=mode_cfg.subsample_templates,
+                    seed=ensemble_seed + 1,
+                )
+            )
+        transforms.append(
+            data_transforms.make_fixed_size(
+                shape_schema=crop_feats,
+                msa_cluster_size=pad_msa_clusters,
+                extra_msa_size=mode_cfg.max_extra_msa,
+                num_res=mode_cfg.crop_size,
+                num_templates=mode_cfg.max_templates,
+            )
+        )
+    else:
+        transforms.append(
+            data_transforms.crop_templates(mode_cfg.max_templates)
+        )
+
     return transforms
 
 
 def process_tensors_from_config(tensors, common_cfg, mode_cfg):
     """Based on the config, apply filters and transformations to the data."""
 
-    ensemble_seed = torch.Generator().seed()
+    ensemble_seed = random.randint(0, torch.iinfo(torch.int32).max)
 
     def wrap_ensemble_fn(data, i):
         """Function to be mapped over the ensemble dimension."""