Update code/add_3Dalignment.py

code/add_3Dalignment.py

@@ -207,18 +207,20 @@ def get_alignments_3D(identifier, model_num, pdb_path, pdbSequence, source, chai
                         coords.append([line[31:38].strip(), line[39:46].strip(), line[47:54].strip()])
                         resnums_for_sasa.append(line[22:26].strip())
 
-        f = open(Path(path_3D_alignment / f'{identifier}_{pdbID}_{str(chain)}_alignment.txt'),"w")
+        #f = open(Path(path_3D_alignment / f'{identifier}_{pdbID}_{str(chain)}_alignment.txt'),"w")
 
         aligner.mode = 'local'
         aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
         aligner.open_gap_score = -11
         aligner.extend_gap_score = -1
         alignments = aligner.align(pdbSequence, atomSequence)
+        st.write(' here is 3D alignments')
+        st.write(alignments)
         alignments = (list(alignments))
-        for alignment in alignments:
-            f.write(str(alignment))
-            f.write('\n')
-            f.write('\n')
+        #for alignment in alignments:
+        #    f.write(str(alignment))
+        #    f.write('\n')
+        #    f.write('\n')
         return alignments, coords, resnums_for_sasa
     elif mode==2:
             atomSequence = ''