Update code/pdb_featureVector.py

code/pdb_featureVector.py

@@ -1382,7 +1382,8 @@ def pdb(input_set, mode, impute):
         modbase_only = None
         data['uniprotSequence'] = data['uniprotSequence'].str.replace('U', 'C')
         data['pdbSequence'] = data['pdbSequence'].str.replace('U', 'C')
-
+        st.write('after')
+        st.write(data)
         for i in data.index:
             id_ = data.at[i, 'pdbID'].lower()
             up_id_ = data.at[i, 'uniprotID']
@@ -1404,11 +1405,13 @@ def pdb(input_set, mode, impute):
 
             alignments = get_alignments_3D(uniprotID, 'nan', pdb_path, pdbSequence, source, chain, pdbID, mode, Path(path_to_output_files / '3D_alignment'), file_format = 'gzip')
             mutPos = data.at[i, 'mutationPositionOnPDB']
+            st.write('mutpos', mutPos)
             try:
                 coordMut = get_coords(mutPos, alignments, 'nan', 'nan', mode)[0]
             except:
                 ValueError
                 coordMut = 'nan'
+            st.write('coordMut', coordMut)
             try:
                 sasa_pos = get_coords(mutPos, alignments, 'nan', 'nan', mode)[2]
                 data.at[i, 'sasa'] = sasa(data.at[i, 'source'], data.at[i, 'pdbID'], data.at[i, 'uniprotID'], sasa_pos,
@@ -1416,6 +1419,8 @@ def pdb(input_set, mode, impute):
             except:
                 ValueError
                 data.at[i, 'sasa'] = 'nan'  # mutation position is nan
+            st.write('data')
+            st.write(data)
             for annot in annotation_list:
                 annotx = []
                 try:
@@ -1481,7 +1486,8 @@ def pdb(input_set, mode, impute):
             k = pd.Series((key, str(list(set(val)))))
             interface_dataframe = interface_dataframe.append(k, ignore_index=True)
         interface_dataframe.columns = ['uniprotID', 'positions']
-
+        st.write('sasa')
+        st.write(data)
         if len(data) == 0:
             data = pd.DataFrame(
                 columns=['uniprotID', 'wt', 'mut', 'pos', 'composition', 'polarity', 'volume', 'granthamScore',