feat: pyo3 bindings (MWE)

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## 7.1.0
+
+### Added
+- Use libdx for TRC and file conversion capabilities; conversion to/from SDF, to/from XYZ, and
+  `perceive_bonds` and `perceive_formal_charges` member functions on TRCS are now available
+
 ## 7.0.0
 
 No new changes since 7.0.0rc3.

examples/exess-interaction-energy/05_exess_interaction_energy.py

@@ -14,7 +14,7 @@
 
 from pathlib import Path
 
-from rush import RunOpts, exess, prepare
+from rush import RunOpts, exess, get_fragments_near_fragment, prepare
 
 # ===== Example 1: Fragment-based interaction energy =====
 print("=" * 60)
@@ -80,7 +80,7 @@
 
 # Step 2: Find ligand fragment index + nearby pocket
 lig_idx = trc.residues.seqs.index("MK1")
-frag_idcs = trc.topology.get_fragments_near_fragment(lig_idx, 5.0) + [lig_idx]
+frag_idcs = get_fragments_near_fragment(trc.topology, lig_idx, 5.0) + [lig_idx]
 
 # Step 3: Run interaction energy
 

examples/exess-qmmm/06_exess_qmmm.py

@@ -19,12 +19,13 @@
 """
 
 import json
-from itertools import batched
 from pathlib import Path
 
-from rush import RunOpts, Topology, exess
+import numpy as np
+
+from rush import TRC, RunOpts, Topology, exess
 from rush.exess import Trajectory
-from rush.mol import Element, Fragment, Residue, Residues
+from rush.mol import Element
 
 DATA_DIR = Path(__file__).parent / "data"
 OUTPUT_DIR = Path(__file__).parent / "qmmm-outputs"
@@ -72,7 +73,8 @@
 out_traj = res.geometries
 
 # Load topology for atom info
-topology = Topology.from_json(topology_path)
+with open(topology_path) as f:
+    topology = Topology.from_dict(json.load(f))
 assert topology.fragments, "Topology lost its fragments!"
 
 n_atoms = len(topology.symbols)
@@ -119,6 +121,10 @@ def geometry_to_xyz(syms, geom, frame_label=""):
     return "\n".join(lines)
 
 
+# NOTE: topology.geometry is an (N,3) numpy array, but out_traj geometries
+# from the server are flat lists. geometry_to_xyz handles the flat format.
+
+
 # Build all frames as XYZ strings
 all_frames_xyz = []
 for i, geom in enumerate(out_traj):
@@ -337,38 +343,23 @@ def geometry_to_xyz(syms, geom, frame_label=""):
 print("Example 2: Minimal QM/MM (two water molecules)")
 print("=" * 60)
 
-topology = Topology(
+trc = TRC(
     symbols=[Element.O, Element.H, Element.H, Element.O, Element.H, Element.H],
     geometry=[
-        0.0000,
-        0.0000,
-        0.0000,
-        0.7570,
-        0.5860,
-        0.0000,
-        -0.7570,
-        0.5860,
-        0.0000,
-        2.8000,
-        0.0000,
-        0.0000,
-        3.5570,
-        0.5860,
-        0.0000,
-        2.0430,
-        0.5860,
-        0.0000,
+        [0.0000, 0.0000, 0.0000],
+        [0.7570, 0.5860, 0.0000],
+        [-0.7570, 0.5860, 0.0000],
+        [2.8000, 0.0000, 0.0000],
+        [3.5570, 0.5860, 0.0000],
+        [2.0430, 0.5860, 0.0000],
     ],
-    fragments=[Fragment([0, 1, 2]), Fragment([3, 4, 5])],
-)
-
-residues = Residues(
-    residues=[Residue([0, 1, 2]), Residue([3, 4, 5])],
-    seqs=["HOH", "HOH"],
+    fragments=[[0, 1, 2], [3, 4, 5]],
+    residues=[[0, 1, 2], [3, 4, 5]],
+    residue_seqs=["HOH", "HOH"],
 )
 
 run2 = exess.qmmm(
-    (topology, residues),
+    trc,
     n_timesteps=100,
     trajectory=Trajectory(include_waters=True),
     mm_fragments=[],
@@ -386,10 +377,11 @@ def geometry_to_xyz(syms, geom, frame_label=""):
 out_traj = res2.geometries
 
 print("Atoms at First Step")
-for atom_x, atom_y, atom_z in batched(topology.geometry, 3):
-    print(f"  x: {atom_x:>7.4f}, y: {atom_y:>7.4f}, z: {atom_z:>7.4f}")
+for x, y, z in trc.topology.geometry:
+    print(f"  x: {x:>7.4f}, y: {y:>7.4f}, z: {z:>7.4f}")
 
-topology.geometry = out_traj[-1]
+final_geom = np.array(out_traj[-1], dtype=np.float32).reshape(-1, 3)
+final_trc = TRC(symbols=list(trc.topology.symbols), geometry=final_geom.tolist())
 print("Atoms at Final Step")
-for atom_x, atom_y, atom_z in batched(topology.geometry, 3):
-    print(f"  x: {atom_x:>7.4f}, y: {atom_y:>7.4f}, z: {atom_z:>7.4f}")
+for x, y, z in final_trc.topology.geometry:
+    print(f"  x: {x:>7.4f}, y: {y:>7.4f}, z: {z:>7.4f}")

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rush-py"
-version = "7.0.0"
+version = "7.1.0"
 description = "Python client for QDX's Rush platform"
 readme = "README.md"
 requires-python = ">=3.12"
@@ -11,6 +11,7 @@ authors = [
 dependencies = [
   "gql~=4.0",
   "h5py~=3.14",
+  "libqdx~=0.8.0",
   "numpy>=1.26,<3",
   "rdkit~=2025.9.2",
   "matplotlib~=3.10",

src/rush/__init__.py

@@ -17,24 +17,24 @@
 )
 from .mol import (
     TRC,
+    Topology,
+    Residues,
+    Chains,
+    AlphaHelices,
     AminoAcidSeq,
     AtomRef,
+    BetaSheets,
     Bond,
     BondOrder,
-    Chain,
     ChainRef,
-    Chains,
     Element,
-    FormalCharge,
-    Fragment,
     FragmentRef,
-    PartialCharge,
-    Residue,
-    ResidueId,
+    HelixClass,
     ResidueRef,
-    Residues,
-    SchemaVersion,
-    Topology,
+    Stereochemistry,
+    StrandSense,
+    AtomCheckStrictness,
+    get_fragments_near_fragment,
 )
 from .objects import (
     ObjectID,
@@ -87,26 +87,24 @@
     "ObjectID",
     "TRCPaths",
     "TRCRef",
-    # Core structures
+    # Core types
     "TRC",
     "Topology",
     "Residues",
     "Chains",
-    # Chemistry types
     "Element",
     "Bond",
     "BondOrder",
-    "FormalCharge",
-    "PartialCharge",
-    "Fragment",
-    "FragmentRef",
+    "Stereochemistry",
+    "HelixClass",
+    "StrandSense",
+    "AlphaHelices",
+    "BetaSheets",
+    "AtomCheckStrictness",
     "AminoAcidSeq",
-    "SchemaVersion",
-    # Indices and records
     "AtomRef",
-    "Residue",
     "ResidueRef",
-    "ResidueId",
-    "Chain",
     "ChainRef",
+    "FragmentRef",
+    "get_fragments_near_fragment",
 ]