Update code/alphafold_featureVector.py

code/alphafold_featureVector.py

@@ -607,11 +607,8 @@ def alphafold(input_set, mode, impute):
                                               pdbSequence, Path(path_to_output_files / 'alignment_files'))
 
                 pdb_alignStatus = mutation_position_on_pdb(alignment_list, uniprot_matched.at[i, 'pos'])[0]
-                st.write('alignment_list---')
                 info_per_model[mod]['pdb_alignStatus'] = pdb_alignStatus
-                st.write(alignment_list)
-                st.write(uniprot_matched.at[i, 'pos'])
-                st.write(pdb_alignStatus)
+
                 mutationPositionOnPDB = mutation_position_on_pdb(alignment_list, uniprot_matched.at[i, 'pos'])[1]
                 info_per_model[mod]['mutationPositionOnPDB'] = mutationPositionOnPDB
                 startGap = mutation_position_on_pdb(alignment_list, uniprot_matched.at[i, 'pos'])[2]
@@ -629,7 +626,6 @@ def alphafold(input_set, mode, impute):
                     info_per_model[mod][annot] = annotation_pos_on_pdb_
 
                 
-                st.write('Downloading the model from ASCARIS dataset.')
                 pdb_path = hf_hub_download(repo_id="HuBioDataLab/AlphafoldStructures", filename=f"AF-{uniprotID}-F{mod}-model_v4.pdb.gz",repo_type = 'dataset')
                 
 
@@ -637,7 +633,6 @@ def alphafold(input_set, mode, impute):
                 #    file_content = f.read()
                 #    st.write(file_content)
 
-                st.write('Download complete.')
                 
                 
                 #st.write(get_alignments_3D(uniprotID, mod, pdb_path, pdbSequence, 'nan', 'nan', 'nan', mode, Path(path_to_output_files / '3D_alignment'),
@@ -648,14 +643,11 @@ def alphafold(input_set, mode, impute):
 
 
                 pdbSequence = convert_non_standard_amino_acids(pdbSequence)
-                st.write(pdbSequence)
-            
-                st.write('Hello I am in 3Dalignment')                
+           
     
                 atomSequence = ''
                 coords = []
                 resnums_for_sasa = []
-                st.write('Hello I am in 3Dalignment GZIP')
                 with gzip.open(pdb_path, mode='rb') as f:
                     
                     for line in f:
@@ -668,7 +660,6 @@ def alphafold(input_set, mode, impute):
                             atomSequence += threeToOne(line[17:20].strip())
                             coords.append([line[31:38].strip(), line[39:46].strip(), line[47:54].strip()])
                             resnums_for_sasa.append(line[22:26].strip())
-                st.write('o-complee')
                 #f = open(Path(path_3D_alignment / f'{identifier}_{str(model_num)}_3Dalignment.txt'),"w")
                 aligner.mode = 'local'
                 aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
@@ -681,7 +672,6 @@ def alphafold(input_set, mode, impute):
                 #                     'gzip') != None:
                 
                 if alignments != None:
-                    st.write('I am here')
                     #alignments, coords, resnums_for_sasa = get_alignments_3D(uniprotID, mod, pdb_path, pdbSequence, 'nan',
                     #                                                        'nan', 'nan', mode, Path(path_to_output_files / '3D_alignment'),
                     #                                                       'gzip')
@@ -693,10 +683,8 @@ def alphafold(input_set, mode, impute):
                     #fullID = f'AF-{uniprotID}-F{mod}-model_v4.pdb.gz'
                     #st.write(fullID)
                     run_freesasa(pdb_path, Path(path_to_output_files / f'freesasa_files/AF-{uniprotID}-F{mod}.txt'), include_hetatms=True,outdir=None, force_rerun=False)
-                    st.write('Calculated')
                     #calculate_freesasa(uniprotID, mod, existing_free_sasa, alphafold_path, path_to_output_files)
                     if (mutationPositionOnPDB != 'nan'):
-                        st.write('Here1')
                         if (int(mutationPositionOnPDB) <= 1400):
                             try:
                                 coordMut = get_coords(mutationPositionOnPDB, alignments, coords, resnums_for_sasa, mode)[0]
@@ -707,12 +695,7 @@ def alphafold(input_set, mode, impute):
                             coordMut = np.NaN
 
                         sasa_pos = get_coords(mutationPositionOnPDB, alignments, coords, resnums_for_sasa, mode)[2]
-                        st.write('sasa_pos', sasa_pos)
-                        st.write('existing_free_sasa', existing_free_sasa)
-                        st.write('existing_free_sasa', existing_free_sasa)
 
-
-                        st.write('all', list(Path(path_to_output_files / 'freesasa_files').glob("*")))
                         
                     
                         if sasa_pos != np.NaN:
@@ -720,22 +703,20 @@ def alphafold(input_set, mode, impute):
                             for filename in  list(Path(path_to_output_files / 'freesasa_files').glob("*"))[1:]:
     
                                 try:
-                                    st.write(list(filter(None, str(filename).split('.')))[0].split('/')[-1].split('-')[1].upper())
                                     fname = list(filter(None, str(filename).split('.')))[0].split('/')[-1].split('-')[1].upper()
                                 except IndexError:
                                     
                                     st.write('IndexError')
                                     fname = ''
-                                st.write(uniprotID , fname, uniprotID == fname)
                                 if uniprotID == fname:
                                     files = open(filename, 'r')
                                     file = files.readlines()
                                     for k in file:
-
                                         if str(k.strip()[10:13].strip()) == str(sasa_pos):
                                             st.write('WHY ')
                                             st.write(str(k[4:7].strip()))
                                             st.write('WHY 2')
+                                            st.write('kk', k)
                                             sy.write('kk',k[4:7])
                                             residue = str(k[4:7].strip())