Update code/add_3Dalignment.py

code/add_3Dalignment.py

@@ -214,13 +214,13 @@ def get_coords(annot, alignments, coords, resnums_for_sasa, mode):
             return np.NaN, np.NaN, np.NaN
 
 
-def get_alignments_3D(identifier, model_num, pdb_path, pdbSequence, source, chain, pdbID, mode, path_3D_alignment,file_format = 'gzip'):
+def get_alignments_3D(identifier, model_num, pdbSequence, source, chain, pdbID, mode, file_format = 'gzip'):
     print('In Function')
     pdbSequence = convert_non_standard_amino_acids(pdbSequence)
     print(pdbSequence)
     print(mode, source)
     if mode == 1:
-        if source == 'PDB':
+        if source != 'MODBASE':
             # Step 1: Fetch the PDB file
             pdb_url = f"https://files.rcsb.org/download/{pdbID}.pdb"
             response = requests.get(pdb_url)
@@ -233,7 +233,7 @@ def get_alignments_3D(identifier, model_num, pdb_path, pdbSequence, source, chai
             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]
-
+        """
         else:
             atomSequence = ''
             coords = []
@@ -244,7 +244,7 @@ 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())
-                
+        """        
         aligner.mode = 'local'
         aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
         aligner.open_gap_score = -11