T018: deprecation warnings and images not showing (#334)

devtools/test_env.yml

@@ -29,7 +29,7 @@ dependencies:
   - pypdb
   - biopython<=1.77
   - biopandas
-  - rdkit==2021.09.5
+  - rdkit
   - openbabel
   - opencadd
   - biotite>=0.34.0

teachopencadd/talktorials/T018_automated_cadd_pipeline/utils/helpers/nglview.py

@@ -282,7 +282,7 @@ def _on_selection_change(change):
                 app.center.close()
 
             # NGL Viewer
-            app.center = viewer = nv.NGLWidget(default=True, gui=True)
+            app.center = viewer = nv.NGLWidget()
 
             with open(protein_filepath) as f:
                 prot_component = viewer.add_component(

teachopencadd/talktorials/T018_automated_cadd_pipeline/utils/helpers/pdb.py

@@ -3,9 +3,10 @@
 """
 
 from pathlib import Path  # for creating folders and handling local paths
+import warnings
 
-import pypdb  # for communicating with the RCSB Protein Data Bank (PDB) to fetch PDB files
 from biopandas.pdb import PandasPdb  # for working with PDB files
+import pypdb  # for communicating with the RCSB Protein Data Bank (PDB) to fetch PDB files
 from opencadd.structure.core import Structure  # for manipulating PDB files
 
 
@@ -84,7 +85,9 @@ def extract_molecule_from_pdb_file(molecule_name, input_filepath, output_filepat
     molecule_name = f"resname {molecule_name}" if molecule_name != "protein" else molecule_name
     extracted_structure = pdb_structure.select_atoms(molecule_name)
     if output_filepath is not None:
-        extracted_structure.write(Path(output_filepath).with_suffix(".pdb"))
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore")
+            extracted_structure.write(Path(output_filepath).with_suffix(".pdb"))
     return extracted_structure
 
 

teachopencadd/talktorials/T018_automated_cadd_pipeline/utils/ligand.py

@@ -81,12 +81,9 @@ def __repr__(self):
         return f"<Ligand CID: {self.cid}>"
 
     def __call__(self):
-        df = pd.DataFrame(columns=["smiles"])
-        df.loc[1] = self.smiles
-        PandasTools.AddMoleculeColumnToFrame(df, smilesCol="smiles")
-        romol = df.loc[1, "ROMol"]
-
-        return pd.concat({romol: self.dataframe}, names=["Structure"])
+        df = pd.DataFrame({"Value": [self.rdkit_obj]}, index=[""])
+        df.index.name = "Property"
+        return pd.concat([df, self.dataframe])
 
     def remove_counterion(self):
         """

teachopencadd/talktorials/T018_automated_cadd_pipeline/utils/protein.py

@@ -59,7 +59,7 @@ def __init__(self, identifier_type, identifier_value, protein_output_path):
                 identifier_value, Path(protein_output_path) / identifier_value
             )
 
-        self.file_content = pdb.read_pdb_file_content(identifier_type.value, identifier_value)
+        self.file_content = pdb.read_pdb_file_content("pdb_filepath", self.pdb_filepath)
 
         dict_of_dataframes = pdb.load_pdb_file_as_dataframe(self.file_content)
         for key, value in dict_of_dataframes.items():