Update code/add_3Dalignment.py

code/add_3Dalignment.py

@@ -217,8 +217,13 @@ def get_coords(annot, alignments, coords, resnums_for_sasa, mode):
 def get_alignments_3D(identifier, model_num, pdbSequence, source, chain, pdbID, mode,file_format = 'gzip'):
     print('I am here get alignments 3D')
     print(type(mode))
+    print((uniprotSequence))
+    print((pdbSequence))
     uniprotSequence = convert_non_standard_amino_acids(uniprotSequence) 
-    pdbSequence = convert_non_standard_amino_acids(pdbSequence) 
+    pdbSequence = convert_non_standard_amino_acids(pdbSequence)
+    print('AFTER')
+    print((uniprotSequence))
+    print((pdbSequence))
     if mode == 1:
         print('mode')
         if source != 'MODBASE':
@@ -280,8 +285,8 @@ def get_alignments_3D(identifier, model_num, pdbSequence, source, chain, pdbID,
         aligner.open_gap_score = -11
         aligner.extend_gap_score = -1
         alignments = aligner.align(pdbSequence, atomSequence)
-        st.write(' here is 3D alignments')
-        st.write(alignments)
+        print(' here is 3D alignments')
+        print(alignments)
         alignments = (list(alignments))
         #for alignment in alignments:
         #    f.write(str(alignment))