Respect mapped SMILES

absolv/runner.py

@@ -1,4 +1,5 @@
 """Run calculations defined by a config."""
+
 import pathlib
 import tempfile
 import typing
@@ -219,7 +220,7 @@ def _run_phase_hremd(
         n_steps_per_cycle=protocol.production_protocol.n_steps_per_cycle,
         n_cycles=protocol.production_protocol.n_cycles,
         trajectory_interval=protocol.production_protocol.trajectory_interval,
-        trajectory_enforce_pbc=protocol.production_protocol.trajectory_enforce_pbc
+        trajectory_enforce_pbc=protocol.production_protocol.trajectory_enforce_pbc,
     )
 
     with tempfile.TemporaryDirectory() as tmp_dir:
@@ -254,7 +255,7 @@ def run_eq(
         config.temperature,
         prepared_system_a,
         platform,
-        None if output_dir is None else output_dir / "solvant-a",
+        None if output_dir is None else output_dir / "solvent-a",
     )
 
     dg_a, dg_a_std = results_a["ddG_kcal_mol"], results_a["ddG_error_kcal_mol"]
@@ -265,7 +266,7 @@ def run_eq(
         config.temperature,
         prepared_system_b,
         platform,
-        None if output_dir is None else output_dir / "solvant-b",
+        None if output_dir is None else output_dir / "solvent-b",
     )
 
     dg_b, dg_b_std = results_b["ddG_kcal_mol"], results_b["ddG_error_kcal_mol"]

absolv/setup.py

@@ -1,4 +1,5 @@
 """Setup systems ready for calculations."""
+
 import errno
 import functools
 import logging
@@ -9,6 +10,7 @@
 
 import numpy
 import openff.toolkit
+import openff.toolkit.utils.exceptions
 import openff.utilities
 import openmm
 
@@ -96,6 +98,17 @@ def _generate_input_file(
     )
 
 
+def _molecule_from_smiles(smiles: str) -> openff.toolkit.Molecule:
+    """Create a molecule from a SMILES string."""
+
+    try:
+        molecule = openff.toolkit.Molecule.from_mapped_smiles(smiles)
+    except (openff.toolkit.utils.exceptions.SmilesParsingError, ValueError):
+        molecule = openff.toolkit.Molecule.from_smiles(smiles)
+
+    return molecule
+
+
 def setup_system(
     components: list[tuple[str, int]],
     box_target_density: openmm.unit.Quantity = 0.95 * _G_PER_ML,
@@ -110,6 +123,9 @@ def setup_system(
             ``smiles_i`` is the SMILES representation of component `i` and
             ``count_i`` is the number of corresponding instances of that component
             to create.
+
+            If any SMILES is fully indexed an attempt will be made to create components
+            with the same atom ordering as the indices.
         box_target_density: Target mass density when approximating the box size for the
             final system with units compatible with g / mL.
         box_scale_factor: The amount to scale the approximate box size by.
@@ -139,7 +155,7 @@ def setup_system(
         if smiles in molecules:
             continue
 
-        molecule = openff.toolkit.Molecule.from_smiles(smiles)
+        molecule = _molecule_from_smiles(smiles)
         molecule.generate_conformers(n_conformers=1)
         molecule.name = f"component-{len(molecules)}.xyz"
         molecules[smiles] = molecule

absolv/tests/test_setup.py

@@ -7,6 +7,7 @@
 from absolv.setup import (
     _approximate_box_size_by_density,
     _generate_input_file,
+    _molecule_from_smiles,
     setup_system,
 )
 
@@ -53,6 +54,23 @@ def test_generate_input_file(monkeypatch):
     assert actual_input_file == expected_input_file
 
 
+@pytest.mark.parametrize(
+    "smiles, expected_order",
+    [
+        ("O", [8, 1, 1]),
+        ("[O:1]([H:2])[H:3]", [8, 1, 1]),
+        ("[H:2][O:1][H:3]", [8, 1, 1]),
+        ("[O:2]([H:1])[H:3]", [1, 8, 1]),
+        ("[O:2]([H])[H:3]", [8, 1, 1]),
+    ]
+)
+def test_molecule_from_smiles(smiles, expected_order):
+    molecule = _molecule_from_smiles(smiles)
+
+    assert [atom.atomic_number for atom in molecule.atoms] == expected_order
+
+
+
 def test_setup_system_packmol_missing(monkeypatch):
     monkeypatch.setattr(shutil, "which", lambda *_: None)