From 9e7e36876b92f52d0169b9a178508eaaa416e4d9 Mon Sep 17 00:00:00 2001
From: Ishaan Mathur <ishaan@evolutionaryscale.ai>
Date: Thu, 9 Oct 2025 18:30:46 +0000
Subject: [PATCH 1/2] syncing covalent bonds

---
 esm/sdk/base_forge_client.py             |  4 ++--
 esm/utils/msa/filter_sequences.py        |  5 +++-
 esm/utils/structure/input_builder.py     | 29 +++++++++++++++++++++++-
 esm/utils/structure/molecular_complex.py |  2 ++
 4 files changed, 36 insertions(+), 4 deletions(-)

diff --git a/esm/sdk/base_forge_client.py b/esm/sdk/base_forge_client.py
index ff05b541..2ed37633 100644
--- a/esm/sdk/base_forge_client.py
+++ b/esm/sdk/base_forge_client.py
@@ -128,7 +128,7 @@ async def _async_post(
         except Exception as e:
             raise ESMProteinError(
                 error_code=500,
-                error_msg=f"Failed to submit request to {endpoint}. Error: {e}",
+                error_msg=f"Failed to submit request to {endpoint}. Error: {str(e)}",
             )
 
     def _post(
@@ -158,5 +158,5 @@ def _post(
         except Exception as e:
             raise ESMProteinError(
                 error_code=500,
-                error_msg=f"Failed to submit request to {endpoint}. Error: {e}",
+                error_msg=f"Failed to submit request to {endpoint}. Error: {str(e)}",
             )
diff --git a/esm/utils/msa/filter_sequences.py b/esm/utils/msa/filter_sequences.py
index d44549d5..da860d27 100644
--- a/esm/utils/msa/filter_sequences.py
+++ b/esm/utils/msa/filter_sequences.py
@@ -1,3 +1,4 @@
+import os
 import tempfile
 from pathlib import Path
 
@@ -53,7 +54,9 @@ def hhfilter(
     qsc: float = -20.0,
     binary: str = "hhfilter",
 ) -> list[int]:
-    with tempfile.TemporaryDirectory(dir="/dev/shm") as tempdirname:
+    with tempfile.TemporaryDirectory(
+        dir="/dev/shm" if os.path.exists("/dev/shm") else None
+    ) as tempdirname:
         tempdir = Path(tempdirname)
         fasta_file = tempdir / "input.fasta"
         fasta_file.write_text(
diff --git a/esm/utils/structure/input_builder.py b/esm/utils/structure/input_builder.py
index 026912fc..e432b532 100644
--- a/esm/utils/structure/input_builder.py
+++ b/esm/utils/structure/input_builder.py
@@ -50,11 +50,22 @@ class PocketConditioning:
     contacts: list[tuple[str, int]]
 
 
+@dataclass
+class CovalentBond:
+    chain_id1: str
+    res_idx1: int
+    atom_idx1: int
+    chain_id2: str
+    res_idx2: int
+    atom_idx2: int
+
+
 @dataclass
 class StructurePredictionInput:
     sequences: Sequence[ProteinInput | RNAInput | DNAInput | LigandInput]
     pocket: PocketConditioning | None = None
     distogram_conditioning: list[DistogramConditioning] | None = None
+    covalent_bonds: list[CovalentBond] | None = None
 
 
 def serialize_structure_prediction_input(all_atom_input: StructurePredictionInput):
@@ -92,4 +103,20 @@ def create_chain_data(seq_input, chain_type: str) -> dict[str, Any]:
         else:
             raise ValueError(f"Unsupported sequence input type: {type(seq_input)}")
 
-    return {"sequences": sequences}
+    result: dict[str, Any] = {"sequences": sequences}
+
+    # Add covalent bonds if present
+    if all_atom_input.covalent_bonds is not None:
+        result["covalent_bonds"] = [
+            {
+                "chain_id1": bond.chain_id1,
+                "res_idx1": bond.res_idx1,
+                "atom_idx1": bond.atom_idx1,
+                "chain_id2": bond.chain_id2,
+                "res_idx2": bond.res_idx2,
+                "atom_idx2": bond.atom_idx2,
+            }
+            for bond in all_atom_input.covalent_bonds
+        ]
+
+    return result
diff --git a/esm/utils/structure/molecular_complex.py b/esm/utils/structure/molecular_complex.py
index 6b6da1ca..3b2ffe7e 100644
--- a/esm/utils/structure/molecular_complex.py
+++ b/esm/utils/structure/molecular_complex.py
@@ -35,6 +35,8 @@ class MolecularComplexResult:
     pair_chains_iptm: torch.Tensor | None = None
     output_embedding_sequence: torch.Tensor | None = None
     output_embedding_pair_pooled: torch.Tensor | None = None
+    residue_index: torch.Tensor | None = None
+    entity_id: torch.Tensor | None = None
 
 
 @dataclass

From a22356ca1c233249a0292b19e3450c2968375389 Mon Sep 17 00:00:00 2001
From: Ishaan Mathur <ishaan@evolutionaryscale.ai>
Date: Thu, 9 Oct 2025 18:46:47 +0000
Subject: [PATCH 2/2] bump version

---
 esm/__init__.py | 2 +-
 pixi.lock       | 4 ++--
 pyproject.toml  | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/esm/__init__.py b/esm/__init__.py
index 98a35b2d..3348d7f9 100644
--- a/esm/__init__.py
+++ b/esm/__init__.py
@@ -1 +1 @@
-__version__ = "3.2.2.post2"
+__version__ = "3.2.3"
diff --git a/pixi.lock b/pixi.lock
index 897f11a5..33ad120c 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -1726,8 +1726,8 @@ packages:
   requires_python: '>=3.8'
 - pypi: ./
   name: esm
-  version: 3.2.2.post2
-  sha256: 3f59a2977c85d35b4b1353902fa90e35d02acbabe6ffb506727bd406ec987ad1
+  version: 3.2.3
+  sha256: 7f3df1026fb23f4812615d3c4968f643f04d9cbf7735000615b011620ac83007
   requires_dist:
   - torch>=2.2.0
   - torchvision
diff --git a/pyproject.toml b/pyproject.toml
index 0dcc398d..923d306e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "esm"
-version = "3.2.2.post2"
+version = "3.2.3"
 description = "EvolutionaryScale open model repository"
 readme = "README.md"
 requires-python = ">=3.12,<3.13"