Update code/add_3Dalignment.py

code/add_3Dalignment.py

@@ -269,7 +269,10 @@ def get_alignments_3D(identifier, model_num, pdb_path, pdbSequence, source, chai
         aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
         aligner.open_gap_score = -11
         aligner.extend_gap_score = -1
-                    
+
+
+
+        atomSequence = convert_non_standard_amino_acids(atomSequence)
         print('HERE LASTLY')
         print(pdbSequence)
         print(atomSequence)
@@ -309,7 +312,7 @@ def get_alignments_3D(identifier, model_num, pdb_path, pdbSequence, source, chai
             aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
             aligner.open_gap_score = -11
             aligner.extend_gap_score = -1
-
+            atomSequence = convert_non_standard_amino_acids(atomSequence)
             alignments = aligner.align(pdbSequence, atomSequence)
             alignments = (list(alignments))