Add Transition transformation

.vscode/settings.json

@@ -1,3 +1,5 @@
 {
-    "python.defaultInterpreterPath": "${workspaceFolder}/.pixi/envs/dev/bin/python"
+    "python.defaultInterpreterPath": "${workspaceFolder}/.pixi/envs/dev/bin/python",
+    "python-envs.defaultEnvManager": "renan-r-santos.pixi-code:pixi",
+    "python-envs.defaultPackageManager": "renan-r-santos.pixi-code:pixi"
 }

CHANGELOG.md

@@ -4,6 +4,8 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
 ## [Unreleased]
+### Added
+- `geom.transform.transition()` for determining the transition-state geometry between two geometries via `StereoCondensedReactionGraph`.
 
 ## [0.0.19] - 2026-07-17
 ### Added

pixi.toml

@@ -36,7 +36,6 @@ ipykernel = "*"
 
 [feature.dev.pypi-dependencies]
 keepachangelog = "*"
-xyzrender = ">=0.3.1, <0.4"
 
 [feature.docs.dependencies]
 sphinx = "*"
@@ -51,6 +50,7 @@ dev = { features = ["dev", "docs"], solve-group = "default"}
 [pypi-dependencies]
 stereomolgraph = ">=0.0.22b0"
 irmsd = "==0.1.1"
+xyzrender = ">=0.3.1, <0.4"
 
 [feature.dev.tasks]
 # Manage pyproject.toml with uv

src/automol/geom/__init__.py

@@ -5,6 +5,7 @@
 from .core import (
     Geometry,
     from_rdkit_mol,
+    from_stereo_mol_graph,
     from_xyz_block,
     from_xyz_file,
     hill_formula,
@@ -23,6 +24,7 @@
 )
 from .internal import angles, bonds, dihedrals, set_distance
 from .properties import adjacency_matrix, center_of_mass, distance_keys, distance_matrix
+from .transform import transition
 from .vibration import (
     harmonic_zpv,
     mass_weight_vector,
@@ -45,6 +47,7 @@
     "distance_matrix",
     "eckart_frame",
     "from_rdkit_mol",
+    "from_stereo_mol_graph",
     "from_xyz_block",
     "from_xyz_file",
     "harmonic_zpv",
@@ -62,6 +65,7 @@
     "set_distance",
     "stereo_mol_graph",
     "transform",
+    "transition",
     "translational_normal_modes",
     "vibrational_analysis",
     "view",

src/automol/geom/core.py

@@ -217,6 +217,12 @@ def stereo_mol_graph(geo: Geometry) -> StereoMolGraph:
     return StereoMolGraph.from_geometry(sm_geo)  # ty:ignore[invalid-argument-type]
 
 
+def from_stereo_mol_graph(smg: StereoMolGraph, *, charge: int = 0) -> Geometry:
+    """Instantiate a Geometry from a StereoMolGraph."""
+    mol = smg.to_rdmol(charge=charge)
+    return from_rdkit_mol(mol)
+
+
 def hill_formula(geo: Geometry) -> str:
     """Render the molecular formula in Hill order."""
     counts = Counter(s.capitalize() for s in geo.symbols)

src/automol/geom/transform.py

@@ -6,6 +6,9 @@
 import numpy as np
 from numpy.typing import ArrayLike
 from scipy.spatial.transform import Rotation
+from stereomolgraph import StereoCondensedReactionGraph
+
+from .core import from_stereo_mol_graph, stereo_mol_graph
 
 if TYPE_CHECKING:
     from .core import Geometry
@@ -93,3 +96,39 @@ def rotate(
     mask = slice(None) if keys is None else list(keys)
     geo.coordinates[mask] = rot.apply(geo.coordinates[mask])
     return geo
+
+
+def transition(geo1: "Geometry", geo2: "Geometry") -> "Geometry":
+    """Determine the transition geometry between two geometries.
+
+    Parameters
+    ----------
+    geo1
+        Initial geometry.
+    geo2
+        Final geometry.
+
+    Returns
+    -------
+        Geometry.
+    """
+    if geo1.spin != geo2.spin:
+        msg = f"Geometries must have the same spin: {geo1.spin} != {geo2.spin}"
+        raise ValueError(msg)
+
+    smg1 = stereo_mol_graph(geo1)
+    smg2 = stereo_mol_graph(geo2)
+    scrg = StereoCondensedReactionGraph.from_graphs(smg1, smg2)
+
+    active_h = [a for a in scrg.active_atoms() if scrg.get_atom_type(a) == 1]
+    for h in active_h:
+        scrg.set_atom_attribute(h, "atom_type", 8)
+
+    ts_smg = scrg.ts()
+    ts_geo = from_stereo_mol_graph(ts_smg)
+    ts_geo.spin = geo1.spin
+
+    for h in active_h:
+        ts_geo.symbols[h] = "H"
+
+    return ts_geo

tests/test_transform.py

@@ -1,6 +1,7 @@
 """Geometry transform tests."""
 
 import numpy as np
+import pytest
 from scipy.spatial.transform import Rotation
 
 from automol import Geometry, geom
@@ -58,3 +59,45 @@ def test__rotate_in_place(water: Geometry) -> None:
     result = geom.transform.rotate(water, rot, in_place=True)
     assert result is water
     assert np.allclose(water.coordinates, expected)
+
+
+def test__transition_raises_for_mismatched_spin(water: Geometry) -> None:
+    """Test that transition() rejects geometries with different spins."""
+    water_triplet = water.model_copy(update={"spin": 2})
+    assert water.spin != water_triplet.spin
+    with pytest.raises(ValueError, match="spin"):
+        geom.transform.transition(water, water_triplet)
+
+
+def test__transition_identity(water: Geometry) -> None:
+    """Test the (degenerate) transition between a geometry and itself."""
+    ts_geo = geom.transform.transition(water, water)
+    assert ts_geo.symbols == water.symbols
+    assert ts_geo.spin == water.spin
+    assert ts_geo.coordinates.shape == water.coordinates.shape
+    assert np.all(np.isfinite(ts_geo.coordinates))
+
+
+def test__transition_hydrogen_abstraction() -> None:
+    """Test the transition geometry for an H-abstraction reaction.
+
+    F-H + Cl -> F + H-Cl: the migrating H atom breaks its bond to F and forms
+    a new bond to Cl.
+    """
+    reactant = Geometry(
+        symbols=["F", "H", "Cl"],
+        coordinates=[[0, 0, 0], [0.92, 0, 0], [3.5, 0, 0]],
+        charge=0,
+        spin=0,
+    )
+    product = Geometry(
+        symbols=["F", "H", "Cl"],
+        coordinates=[[0, 0, 0], [3.0, 0, 0], [4.27, 0, 0]],
+        charge=0,
+        spin=0,
+    )
+    ts_geo = geom.transform.transition(reactant, product)
+    assert ts_geo.symbols == reactant.symbols
+    assert ts_geo.spin == reactant.spin
+    assert ts_geo.coordinates.shape == reactant.coordinates.shape
+    assert np.all(np.isfinite(ts_geo.coordinates))