Merge branch 'move_things2utils' of github.com:OpenFreeEnergy/openfe-…

…gromacs into move_things2utils
OpenFreeEnergy · Oct 1, 2024 · be2158e · be2158e
2 parents c84ea90 + 33de6fd
commit be2158e
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Showing 2 changed files with 10 additions and 4 deletions.
diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py
@@ -919,7 +919,9 @@ def _execute(
             output_dict["edr_em"] = shared_basepath / output_settings_em.edr_file
             output_dict["log_em"] = shared_basepath / output_settings_em.log_file
             output_dict["cpt_em"] = shared_basepath / output_settings_em.cpt_file
-            output_dict["grompp_mdp_em"] = shared_basepath / output_settings_em.grompp_mdp_file
+            output_dict["grompp_mdp_em"] = (
+                shared_basepath / output_settings_em.grompp_mdp_file
+            )
 
         # ToDo: Should we disallow running MD without EM?
         # Run NVT
@@ -956,7 +958,9 @@ def _execute(
             output_dict["edr_nvt"] = shared_basepath / output_settings_nvt.edr_file
             output_dict["log_nvt"] = shared_basepath / output_settings_nvt.log_file
             output_dict["cpt_nvt"] = shared_basepath / output_settings_nvt.cpt_file
-            output_dict["grompp_mdp_nvt"] = shared_basepath / output_settings_nvt.grompp_mdp_file
+            output_dict["grompp_mdp_nvt"] = (
+                shared_basepath / output_settings_nvt.grompp_mdp_file
+            )
 
         # Run NPT MD simulation
         if sim_settings_npt.nsteps > 0:
@@ -996,6 +1000,8 @@ def _execute(
             output_dict["edr_npt"] = shared_basepath / output_settings_npt.edr_file
             output_dict["log_npt"] = shared_basepath / output_settings_npt.log_file
             output_dict["cpt_npt"] = shared_basepath / output_settings_npt.cpt_file
-            output_dict["grompp_mdp_nvt"] = shared_basepath / output_settings_nvt.grompp_mdp_file
+            output_dict["grompp_mdp_nvt"] = (
+                shared_basepath / output_settings_nvt.grompp_mdp_file
+            )
 
         return output_dict
diff --git a/openfe_gromacs/protocols/gromacs_md/md_settings.py b/openfe_gromacs/protocols/gromacs_md/md_settings.py
@@ -267,7 +267,7 @@ class OutputSettings(SettingsBaseModel):
     """
     grompp_mdp_file: str = "mdout_em.mdp"
     """
-    Filename for the mdp file that gmx grompp outputs. This file contains 
+    Filename for the mdp file that gmx grompp outputs. This file contains
     comment lines, as well as the input that gmx grompp has read.
     Default 'mdout_em.mdp'
     """