Added sequence-embedding mode config.

- Added configuration options in `config.py` for toggling seq-emb mode
- Added list for specifying features to be used in seq-emb mode.

openfold/config.py

@@ -247,6 +247,7 @@ config = mlc.ConfigDict(
                     "rigidgroups_gt_frames": [NUM_RES, None, None, None],
                     "seq_length": [],
                     "seq_mask": [NUM_RES],
+                    "seq_embedding": [NUM_RES, None],
                     "target_feat": [NUM_RES, None],
                     "template_aatype": [NUM_TEMPLATES, NUM_RES],
                     "template_all_atom_mask": [NUM_TEMPLATES, NUM_RES, None],
@@ -298,9 +299,20 @@ config = mlc.ConfigDict(
                     "deletion_matrix",
                     "no_recycling_iters",
                 ],
+                "seqemb_features": [
+                    "seq_embedding"
+                ],
                 "use_templates": templates_enabled,
                 "use_template_torsion_angles": embed_template_torsion_angles,
             },
+            "seqemb_mode": {
+                "enabled": False, # If True, use seq emb instead of MSA
+                "seqemb_config": {
+                    "max_msa_clusters": 0,
+                    "max_extra_msa": 0,
+                    "max_distillation_msa_clusters": 0
+                },
+            },
             "supervised": {
                 "clamp_prob": 0.9,
                 "supervised_features": [