Update code/alphafold_featureVector.py

code/alphafold_featureVector.py

@@ -587,9 +587,9 @@ def alphafold(input_set, mode, impute):
                 pdb_path = hf_hub_download(repo_id="HuBioDataLab/AlphafoldStructures", filename=f"AF-{uniprotID}-F{mod}-model_v4.pdb.gz",repo_type = 'dataset')
                 
 
-                with gzip.open(pdb_path, mode="rt") as f:
-                    file_content = f.read()
-                    st.write(file_content)
+                #with gzip.open(pdb_path, mode="rt") as f:
+                #    file_content = f.read()
+                #    st.write(file_content)
 
                 st.write('Download complete.')
                 
@@ -611,31 +611,19 @@ def alphafold(input_set, mode, impute):
                 atomSequence = ''
                 coords = []
                 resnums_for_sasa = []
-                if file_format == 'txt':
-                    st.write('Hello I am in 3Dalignment TXT')
-                    with open(name, encoding="utf8") as f:
-                        for line in f.readlines():
-                            if line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA':
-                                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())
-                            elif line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA' and line[21] == ' ':
-                                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())
-                elif file_format == 'gzip':
-                    st.write('Hello I am in 3Dalignment GZIP')
-                    with gzip.open(pdb_path, mode='rb') as f:
-                        for line in f:
-                            line = line.decode()
-                            if line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA':
-                                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())
-                            elif line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA' and line[21] == ' ':
-                                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('Hello I am in 3Dalignment GZIP')
+                with gzip.open(pdb_path, mode='rb') as f:
+                    for line in f:
+                        line = line.decode()
+                        if line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA':
+                            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())
+                        elif line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA' and line[21] == ' ':
+                            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")