Fix endstate validation handling in PointMutationExecutor (#866)

* fix endstate validation handling * added a test to catch regressions like this Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
choderalab · Sep 14, 2021 · c1f5769 · c1f5769
1 parent 410ca4f
commit c1f5769
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Showing 2 changed files with 35 additions and 13 deletions.
diff --git a/perses/app/relative_point_mutation_setup.py b/perses/app/relative_point_mutation_setup.py
@@ -330,9 +330,9 @@ def __init__(self,
             else:
                 subtracted_valence_energy = geometry_engine.reverse_final_context_reduced_potential - geometry_engine.reverse_atoms_with_positions_reduced_potential
 
-
-            if conduct_endstate_validation and repartitioned_endstate is None:
-                zero_state_error, one_state_error = validate_endstate_energies(forward_htf._topology_proposal, forward_htf, added_valence_energy, subtracted_valence_energy, beta=beta, ENERGY_THRESHOLD=ENERGY_THRESHOLD)
+            if conduct_endstate_validation and generate_unmodified_hybrid_topology_factory:
+                htf = self.get_complex_htf() if is_complex else self.get_apo_htf()
+                zero_state_error, one_state_error = validate_endstate_energies(htf._topology_proposal, htf, added_valence_energy, subtracted_valence_energy, beta=beta, ENERGY_THRESHOLD=ENERGY_THRESHOLD)
                 if zero_state_error > ENERGY_THRESHOLD:
                     _logger.warning(f"Reduced potential difference of the nonalchemical and alchemical Lambda = 0 state is above the threshold ({ENERGY_THRESHOLD}): {zero_state_error}")
                 if one_state_error > ENERGY_THRESHOLD:

diff --git a/perses/tests/test_relative_point_mutation_setup.py b/perses/tests/test_relative_point_mutation_setup.py
@@ -1,14 +1,36 @@
 def test_PointMutationExecutor():
     from pkg_resources import resource_filename
+    from simtk import unit
+
     from perses.app.relative_point_mutation_setup import PointMutationExecutor
+
+    pdb_filename = resource_filename("perses", "data/ala_vacuum.pdb")
+    PointMutationExecutor(
+        pdb_filename,
+        "1",
+        "2",
+        "ASP",
+        ionic_strength=0.15 * unit.molar,
+        flatten_torsions=True,
+        flatten_exceptions=True,
+        conduct_endstate_validation=False,
+    )
+
+
+def test_PointMutationExecutor_endstate_validation():
+    from pkg_resources import resource_filename
     from simtk import unit
-    pdb_filename = resource_filename('perses', 'data/ala_vacuum.pdb')
-    solvent_delivery = PointMutationExecutor(pdb_filename,
-                            '1',
-                            '2',
-                            'ASP',
-                            ionic_strength=0.15*unit.molar,
-                            flatten_torsions=True,
-                            flatten_exceptions=True,
-                            conduct_endstate_validation=False
-                           )
+
+    from perses.app.relative_point_mutation_setup import PointMutationExecutor
+
+    pdb_filename = resource_filename("perses", "data/ala_vacuum.pdb")
+    PointMutationExecutor(
+        pdb_filename,
+        "1",
+        "2",
+        "ASP",
+        ionic_strength=0.15 * unit.molar,
+        flatten_torsions=False,
+        flatten_exceptions=False,
+        conduct_endstate_validation=True,
+    )