Merge pull request #61 from NDoering99/main

Remove ligand_processing_test.py and update imports in openmmdlanalysis_test.py and test_preprocessing.py

openmmdl/tests/openmmdl_analysis/openmmdlanalysis_test.py

@@ -5,9 +5,8 @@
 
 from pathlib import Path
 
-from openmmdl.openmmdl_analysis.preprocessing import process_pdb_file, convert_pdb_to_sdf
+from openmmdl.openmmdl_analysis.preprocessing import process_pdb_file, convert_pdb_to_sdf, increase_ring_indices, convert_ligand_to_smiles
 from openmmdl.openmmdl_analysis.rmsd_calculation import rmsd_for_atomgroups, RMSD_dist_frames
-from openmmdl.openmmdl_analysis.ligand_processing import increase_ring_indices, convert_ligand_to_smiles
 from openmmdl.openmmdl_analysis.interaction_gathering import characterize_complex, retrieve_plip_interactions, create_df_from_binding_site, process_frame, process_trajectory, fill_missing_frames
 from openmmdl.openmmdl_analysis.binding_mode_processing import gather_interactions, remove_duplicate_values, combine_subdict_values, filtering_values, unique_data_generation, df_iteration_numbering, update_values
 from openmmdl.openmmdl_analysis.markov_state_figure_generation import min_transition_calculation, binding_site_markov_network

openmmdl/tests/openmmdl_analysis/test_preprocessing.py

@@ -282,3 +282,35 @@ def test_extract_and_save_ligand_as_sdf():
 
     assert output_filename is not None
     os.remove("ligand_changed.sdf")
+
+test_data_directory = Path("openmmdl/tests/data/in")
+TEST_LIGAND_FILE = f"{test_data_directory}/CVV.sdf"
+TEST_OUTPUT_FILE = "CVV.smi"
+
+def test_increase_ring_indices():
+    # Test case 1: Check if ring indices are correctly increased
+    ring = [1, 2, 3]
+    lig_index = 10
+    result = increase_ring_indices(ring, lig_index)
+    assert result == [11, 12, 13]
+
+    # Test case 2: Check with a different lig_index
+    ring = [3, 4, 5]
+    lig_index = 20
+    result = increase_ring_indices(ring, lig_index)
+    assert result == [23, 24, 25]
+
+
+def test_convert_ligand_to_smiles():
+    # Convert the ligand structure to SMILES in the same directory as the input SDF file
+    convert_ligand_to_smiles(TEST_LIGAND_FILE, TEST_OUTPUT_FILE)
+
+    # Verify that the output SMILES file was created in the same directory as the input file
+    assert os.path.exists(TEST_OUTPUT_FILE)
+
+    # Optionally, you can also read and validate the content of the output SMILES file
+    with open(TEST_OUTPUT_FILE, "r") as smi_file:
+        smiles_lines = smi_file.readlines()
+        assert len(smiles_lines) > 0  # Check that there are SMILES representations
+
+