Fixes for multimer config features and cropping

openfold/config.py

@@ -156,6 +156,10 @@ def model_config(
     elif "multimer" in name:
         c.update(multimer_config_update.copy_and_resolve_references())
 
+        # Not used in multimer
+        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):
             #c.model.input_embedder.num_msa = 252
@@ -681,6 +685,52 @@ multimer_config_update = mlc.ConfigDict({
     },
     "data": {
         "common": {
+            "feat": {
+                "aatype": [NUM_RES],
+                "all_atom_mask": [NUM_RES, None],
+                "all_atom_positions": [NUM_RES, None, None],
+                # "all_chains_entity_ids": [],  # TODO: Resolve missing features, remove processed msa feats
+                # "all_crops_all_chains_mask": [],
+                # "all_crops_all_chains_positions": [],
+                # "all_crops_all_chains_residue_ids": [],
+                "assembly_num_chains": [],
+                "asym_id": [NUM_RES],
+                "atom14_atom_exists": [NUM_RES, None],
+                "atom37_atom_exists": [NUM_RES, None],
+                "bert_mask": [NUM_MSA_SEQ, NUM_RES],
+                "cluster_bias_mask": [NUM_MSA_SEQ],
+                "cluster_profile": [NUM_MSA_SEQ, NUM_RES, None],
+                "cluster_deletion_mean": [NUM_MSA_SEQ, NUM_RES],
+                "deletion_matrix": [NUM_MSA_SEQ, NUM_RES],
+                "deletion_mean": [NUM_RES],
+                "entity_id": [NUM_RES],
+                "entity_mask": [NUM_RES],
+                "extra_deletion_matrix": [NUM_EXTRA_SEQ, NUM_RES],
+                "extra_msa": [NUM_EXTRA_SEQ, NUM_RES],
+                "extra_msa_mask": [NUM_EXTRA_SEQ, NUM_RES],
+                # "mem_peak": [],
+                "msa": [NUM_MSA_SEQ, NUM_RES],
+                "msa_feat": [NUM_MSA_SEQ, NUM_RES, None],
+                "msa_mask": [NUM_MSA_SEQ, NUM_RES],
+                "msa_profile": [NUM_RES, None],
+                "num_alignments": [],
+                "num_templates": [],
+                # "queue_size": [],
+                "residue_index": [NUM_RES],
+                "residx_atom14_to_atom37": [NUM_RES, None],
+                "residx_atom37_to_atom14": [NUM_RES, None],
+                "resolution": [],
+                "seq_length": [],
+                "seq_mask": [NUM_RES],
+                "sym_id": [NUM_RES],
+                "target_feat": [NUM_RES, None],
+                "template_aatype": [NUM_TEMPLATES, NUM_RES],
+                "template_all_atom_mask": [NUM_TEMPLATES, NUM_RES, None],
+                "template_all_atom_positions": [
+                    NUM_TEMPLATES, NUM_RES, None, None,
+                ],
+                "true_msa": [NUM_MSA_SEQ, NUM_RES]
+            },
             "max_recycling_iters": 20,
             "unsupervised_features": [
                     "aatype",
@@ -741,7 +791,6 @@ 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
@@ -785,8 +834,7 @@ 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/feature_pipeline.py

@@ -78,7 +78,8 @@ def np_example_to_features(
 ):
     np_example = dict(np_example)
 
-    num_res = int(np_example["seq_length"][0])
+    seq_length = np_example["seq_length"]
+    num_res = int(seq_length[0]) if seq_length.ndim != 0 else int(seq_length)
     cfg, feature_names = make_data_config(config, mode=mode, num_res=num_res)
 
     if "deletion_matrix_int" in np_example:

openfold/data/input_pipeline_multimer.py

@@ -31,11 +31,6 @@ def nonensembled_transform_fns(common_cfg, mode_cfg):
         data_transforms.make_atom14_masks,
     ]
 
-    if(common_cfg.use_templates):
-        transforms.extend([
-            data_transforms.make_pseudo_beta("template_"),
-        ])
-
     return transforms
 
 

openfold/data/msa_pairing.py

@@ -274,9 +274,8 @@ def _correct_post_merged_feats(
 ) -> Mapping[str, np.ndarray]:
     """Adds features that need to be computed/recomputed post merging."""
 
-    num_res = np_example['aatype'].shape[0]
     np_example['seq_length'] = np.asarray(
-        [num_res] * num_res,
+        np_example['aatype'].shape[0],
         dtype=np.int32
     )
     np_example['num_alignments'] = np.asarray(