Update code/add_3Dalignment.py

code/add_3Dalignment.py

@@ -10,13 +10,13 @@ from Bio import Align
 import gzip
 from pathlib import Path
 from Bio.Align import substitution_matrices
+from Bio.PDB.Polypeptide import *
 aligner = Align.PairwiseAligner()
 import requests
 from Bio.PDB import PDBParser, PPBuilder
 from io import StringIO
 
 
-from Bio.PDB.Polypeptide import *
 
 
 def convert_non_standard_amino_acids(sequence):
@@ -260,13 +260,7 @@ def get_alignments_3D(identifier, model_num, pdb_path, pdbSequence, source, chai
                         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())
-        print('In 3D Alignments')
-        print('atomSequence')
-        print(atomSequence)
-        print('coords')
-        print(coords)
-        print('resnums_for_sasa')
-        print(resnums_for_sasa)
+
         aligner.mode = 'local'
         aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
         aligner.open_gap_score = -11
@@ -275,14 +269,10 @@ def get_alignments_3D(identifier, model_num, pdb_path, pdbSequence, source, chai
 
 
         atomSequence = convert_non_standard_amino_acids(atomSequence)
-        print('HERE LASTLY')
-        print(pdbSequence)
-        print(atomSequence)
-        print(aligner.align(pdbSequence, atomSequence))
+
         alignments = aligner.align(pdbSequence, atomSequence)
         alignments = (list(alignments))
-        print('alignments')
-        print(alignments)
+
         return alignments, coords, resnums_for_sasa
     elif mode==2:
             atomSequence = ''