Merge pull request #164 from fjclark/bugfix_somd_pert_files

Ensure that SOMD ABFE pert files are always correct
OpenBioSim · Sep 1, 2023 · e26d2d0 · e26d2d0
2 parents 6fdda73 + c37f9e2
commit e26d2d0
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Showing 2 changed files with 21 additions and 2 deletions.
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_somd.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_somd.py
@@ -1269,6 +1269,9 @@ def atom_sorting_criteria(atom):
                     # Get the perturbed atom.
                     atom = mol.atom(idx)
 
+                    # Start atom record.
+                    file.write("    atom\n")
+
                     # Only require the initial Lennard-Jones properties.
                     LJ0 = atom.property("LJ0")
 
@@ -3002,8 +3005,8 @@ def sort_dihedrals(dihedrals, idx):
                             # End improper record.
                             file.write("    endimproper\n")
 
-            # End molecule record.
-            file.write("endmolecule\n")
+        # End molecule record.
+        file.write("endmolecule\n")
 
     # Finally, convert the molecule to the lambda = 0 state.
 

diff --git a/tests/Sandpit/Exscientia/Protocol/test_config.py b/tests/Sandpit/Exscientia/Protocol/test_config.py
@@ -373,12 +373,16 @@ def test_turn_on_restraint(self, system_and_restraint):
                 assert atom in pert_text
             # Check perturbations are correct
             lines = [
+                "molecule LIG",
+                "atom",
                 "initial_type   C1",
                 "final_type     C1",
                 "initial_LJ     3.48065 0.08688",
                 "final_LJ       3.48065 0.08688",
                 "initial_charge -0.13000",
                 "final_charge   -0.13000",
+                "endatom",
+                "endmolecule",
             ]
             for line in lines:
                 assert line in pert_text
@@ -413,12 +417,16 @@ def test_discharge(self, system_and_restraint):
                 assert atom in pert_text
             # Check perturbations are correct
             lines = [
+                "molecule LIG",
+                "atom",
                 "initial_type   C1",
                 "final_type     C1",
                 "initial_LJ     3.48065 0.08688",
                 "final_LJ       3.48065 0.08688",
                 "initial_charge -0.13000",
                 "final_charge   -0.00000",
+                "endatom",
+                "endmolecule",
             ]
             for line in lines:
                 assert line in pert_text
@@ -453,12 +461,16 @@ def test_vanish(self, system_and_restraint):
                 assert atom in pert_text
             # Check perturbations are correct
             lines = [
+                "molecule LIG",
+                "atom",
                 "initial_type   C1",
                 "final_type     du",
                 "initial_LJ     3.48065 0.08688",
                 "final_LJ       0.00000 0.00000",
                 "initial_charge -0.00000",
                 "final_charge   -0.00000",
+                "endatom",
+                "endmolecule",
             ]
             for line in lines:
                 assert line in pert_text
@@ -493,12 +505,16 @@ def test_discharge_and_vanish(self, system_and_restraint):
                 assert atom in pert_text
             # Check perturbations are correct
             lines = [
+                "molecule LIG",
+                "atom",
                 "initial_type   C1",
                 "final_type     du",
                 "initial_LJ     3.48065 0.08688",
                 "final_LJ       0.00000 0.00000",
                 "initial_charge -0.13000",
                 "final_charge   0.00000",
+                "endatom",
+                "endmolecule",
             ]
             for line in lines:
                 assert line in pert_text