adding addtional toppar file for modified nucleobases

cbc-univie · May 25, 2023 · 3acaaff · 3acaaff
1 parent e7587ec
commit 3acaaff
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Showing 2 changed files with 6 additions and 8 deletions.
diff --git a/transformato/system.py b/transformato/system.py
@@ -139,7 +139,6 @@ def mol_to_nx(mol: Chem.Mol):
 
             return preprocessing._mol_to_nx_full_weight(mol)
         except ModuleNotFoundError:
-
             G = nx.Graph()
 
             for atom in mol.GetAtoms():
@@ -245,9 +244,8 @@ def _read_parameters(
             parameter_files += (f"{toppar_dir}/par_all36_lipid.prm",)
             parameter_files += (f"{toppar_dir}/top_all36_lipid.rtf",)
             parameter_files += (f"{toppar_dir}/toppar_water_ions.str",)
-            parameter_files += (
-                f"{toppar_dir}/toppar_all36_prot_na_combined.str",
-            )  # if modified aminoacids are needed
+            parameter_files += (f"{toppar_dir}/toppar_all36_prot_na_combined.str",)
+            parameter_files += (f"{toppar_dir}/toppar_all36_na_rna_modified.str",)
             # if os.path.isfile(f"{toppar_dir}/toppar_all36_moreions.str"):
             #     parameter_files += (f"{toppar_dir}/toppar_all36_moreions.str",)
 
@@ -397,7 +395,6 @@ def _create_sdf_file(self) -> str:
         return f"{file_path}/step3_input_reduced.sdf"
 
     def _return_small_molecule(self) -> Chem.rdchem.Mol:
-
         charmm_gui_env = self.charmm_gui_base + "waterbox"
         possible_files = []
         for ending in ["sdf", "mol", "mol2"]:

diff --git a/transformato/tests/test_point_mutation.py b/transformato/tests/test_point_mutation.py
@@ -30,10 +30,11 @@
     reason="Skipping tests that cannot pass in github actions",
 )
 def test_point_mutation_reduced_system():
+
     configuration = load_config_yaml(
-        config=f"/site/raid3/johannes/h2u/data/config/H2U_1_cano-H2U_1_mod.yaml",
-        input_dir="/site/raid3/johannes/h2u/data",
-        output_dir=f"/site/raid3/johannes",
+        config=f"{get_testsystems_dir()}/config/H2U_1_mod-H2U_1_cano.yaml",
+        input_dir=get_testsystems_dir(),
+        output_dir=get_test_output_dir(),
     )
 
     s1 = SystemStructure(configuration, "structure1")