From 70e844fa927eb1dfdd78eb4e13c5ba50ceeaa1d3 Mon Sep 17 00:00:00 2001
From: taivu1998 <46636857+taivu1998@users.noreply.github.com>
Date: Sun, 10 May 2026 04:39:17 -0700
Subject: [PATCH] Fix batched multimer template embeddings

---
 openfold/model/embedders.py |  8 +--
 tests/test_template.py      | 97 +++++++++++++++++++++++++++++++++++++
 2 files changed, 102 insertions(+), 3 deletions(-)

diff --git a/openfold/model/embedders.py b/openfold/model/embedders.py
index 8915ab190..dcd48edd2 100644
--- a/openfold/model/embedders.py
+++ b/openfold/model/embedders.py
@@ -911,7 +911,7 @@ def forward(self,
         for i in range(n_templ):
             idx = batch["template_aatype"].new_tensor(i)
             single_template_feats = tensor_tree_map(
-                lambda t: torch.index_select(t, templ_dim, idx),
+                lambda t: torch.index_select(t, templ_dim, idx).squeeze(templ_dim),
                 batch,
             )
 
@@ -944,7 +944,9 @@ def forward(self,
                 single_template_feats["template_aatype"],
             )
             points = rigid.translation
-            rigid_vec = rigid[..., None].inverse().apply_to_point(points)
+            rigid_vec = rigid[..., None].inverse().apply_to_point(
+                points[..., None, :]
+            )
             unit_vector = rigid_vec.normalized()
 
             pair_act = self.template_pair_embedder(
@@ -968,7 +970,7 @@ def forward(self,
             template_embeds.append(single_template_embeds)
 
         template_embeds = dict_multimap(
-            partial(torch.cat, dim=templ_dim),
+            partial(torch.stack, dim=templ_dim),
             template_embeds,
         )
 
diff --git a/tests/test_template.py b/tests/test_template.py
index ae65b7cb2..df2009b30 100644
--- a/tests/test_template.py
+++ b/tests/test_template.py
@@ -16,10 +16,13 @@
 import torch
 import numpy as np
 import unittest
+from openfold.config import model_config
+from openfold.model.embedders import TemplateEmbedderMultimer
 from openfold.model.template import (
     TemplatePointwiseAttention,
     TemplatePairStack,
 )
+from openfold.np import residue_constants
 import tests.compare_utils as compare_utils
 from tests.config import consts
 from tests.data_utils import random_template_feats
@@ -194,6 +197,100 @@ def template_iteration_fn(x):
         compare_utils.assert_max_abs_diff_small(out_gt, out_repro, consts.eps)
 
 
+class TestTemplateEmbedderMultimer(unittest.TestCase):
+    def test_batched_template_embedding_shape(self):
+        torch.manual_seed(0)
+        batch_size = 2
+        n_templ = 2
+        n_res = 8
+
+        config = model_config("model_1_multimer_v3")
+        config.model.template.template_pair_stack.no_blocks = 1
+        config.model.template.template_pair_stack.blocks_per_ckpt = None
+
+        embedder = TemplateEmbedderMultimer(config.model.template)
+        embedder.eval()
+
+        aatype = torch.full(
+            (batch_size, n_templ, n_res),
+            residue_constants.restype_order["A"],
+            dtype=torch.long,
+        )
+        atom_positions = torch.zeros(
+            batch_size,
+            n_templ,
+            n_res,
+            residue_constants.atom_type_num,
+            3,
+        )
+        atom_mask = torch.zeros(
+            batch_size,
+            n_templ,
+            n_res,
+            residue_constants.atom_type_num,
+        )
+
+        n_idx = residue_constants.atom_order["N"]
+        ca_idx = residue_constants.atom_order["CA"]
+        c_idx = residue_constants.atom_order["C"]
+        cb_idx = residue_constants.atom_order["CB"]
+        residue_positions = torch.arange(n_res, dtype=torch.float32)
+
+        atom_positions[..., n_idx, 0] = residue_positions
+        atom_positions[..., ca_idx, 0] = residue_positions
+        atom_positions[..., ca_idx, 1] = 1.0
+        atom_positions[..., c_idx, 0] = residue_positions
+        atom_positions[..., c_idx, 2] = 1.0
+        atom_positions[..., cb_idx, 0] = residue_positions
+        atom_positions[..., cb_idx, 1] = 1.0
+        atom_positions[..., cb_idx, 2] = 1.0
+        atom_mask[..., [n_idx, ca_idx, c_idx, cb_idx]] = 1.0
+
+        batch = {
+            "template_aatype": aatype,
+            "template_all_atom_positions": atom_positions,
+            "template_all_atom_mask": atom_mask,
+        }
+        z = torch.randn(batch_size, n_res, n_res, config.globals.c_z)
+        padding_mask_2d = torch.ones(batch_size, n_res, n_res)
+        asym_id = torch.tensor(
+            [[1] * (n_res // 2) + [2] * (n_res - n_res // 2)]
+            * batch_size
+        )
+        multichain_mask_2d = asym_id[..., None] == asym_id[..., None, :]
+
+        with torch.no_grad():
+            out = embedder(
+                batch,
+                z,
+                padding_mask_2d,
+                templ_dim=1,
+                chunk_size=None,
+                multichain_mask_2d=multichain_mask_2d,
+                use_lma=False,
+                inplace_safe=False,
+            )
+
+        self.assertEqual(
+            out["template_pair_embedding"].shape,
+            (batch_size, n_res, n_res, config.globals.c_z),
+        )
+        self.assertEqual(
+            out["template_single_embedding"].shape,
+            (batch_size, n_templ, n_res, config.globals.c_m),
+        )
+        self.assertEqual(
+            out["template_mask"].shape,
+            (batch_size, n_templ, n_res),
+        )
+        self.assertTrue(
+            torch.isfinite(out["template_pair_embedding"]).all().item()
+        )
+        self.assertTrue(
+            torch.isfinite(out["template_single_embedding"]).all().item()
+        )
+
+
 class Template(unittest.TestCase):
     @classmethod
     def setUpClass(cls):