Update code/add_3Dalignment.py

code/add_3Dalignment.py

@@ -215,18 +215,11 @@ 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))
     pdbSequence = convert_non_standard_amino_acids(pdbSequence)
-    print('AFTER')
-    print((pdbSequence))
     if mode == 1:
-        print('mode')
         if source != 'MODBASE':
-            print('spırce')
             # Step 1: Fetch the PDB file
             pdb_url = f"https://files.rcsb.org/download/{pdbID}.pdb"
-            print('pdb_url')
             response = requests.get(pdb_url)
             response.raise_for_status()  # Check for a successful response
             
@@ -237,8 +230,7 @@ def get_alignments_3D(identifier, model_num, pdbSequence, source, chain, pdbID,
             atomSequence = ''.join([three_to_one(i[3]) for i in atoms])
             coords = [[i[6] ,i[7] ,i[8]] for i in atoms]
             resnums_for_sasa = [i[5] for i in atoms]
-            print('NEW')
-            print(atomSequence)
+
         else:
             pdb_url = f"https://files.rcsb.org/download/{pdbID}.pdb"
             
@@ -281,8 +273,6 @@ 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)
-        print(' here is 3D alignments')
-        print(alignments)
         alignments = (list(alignments))
         #for alignment in alignments:
         #    f.write(str(alignment))