Merge pull request #302 from OpenBioSim/fix_301

Fix issue #301

Author: lohedges

doc/source/changelog.rst

@@ -24,6 +24,7 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
 * Preserve molecule name when reading from SDF format and on conversion to RDKit.
 * Handle missing velocity data for ``AMBER`` RST7 files with only a few atoms.
 * Preserve SDF metadata when converting to ``RDKIt`` format.
+* Fixed unbound local variable when simulation lambda value is not in ``lambda_windows`` array.
 
 `2024.4.0 <https://github.com/openbiosim/sire/compare/2024.3.1...2024.4.0>`__ - Feb 2025
 ----------------------------------------------------------------------------------------

src/sire/mol/_dynamics.py

@@ -437,15 +437,18 @@ def _exit_dynamics_block(
                     # lambda windows list
                     try:
                         lambda_index = lambda_windows.index(sim_lambda_value)
+                        has_lambda_index = True
                     except:
-                        num_energy_neighbours = num_lambda_windows
-                        lambda_index = i
+                        has_lambda_index = False
 
                     for i, (lambda_value, rest2_scale) in enumerate(
                         zip(lambda_windows, rest2_scale_factors)
                     ):
                         if lambda_value != sim_lambda_value:
-                            if abs(lambda_index - i) <= num_energy_neighbours:
+                            if (
+                                not has_lambda_index
+                                or abs(lambda_index - i) <= num_energy_neighbours
+                            ):
                                 self._omm_mols.set_lambda(
                                     lambda_value,
                                     rest2_scale=rest2_scale,