Update code/add_3Dalignment.py

code/add_3Dalignment.py

@@ -235,44 +235,23 @@ def get_alignments_3D(identifier, model_num, pdb_path, pdbSequence, source, chai
             resnums_for_sasa = [i[5] for i in atoms]
 
         else:
-            if line[0:7].strip() == 'ATOM' and line[13:15].strip() == 'CA':
-                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())
-            
-        """
-        atomSequence = ''
-        coords = []
-        resnums_for_sasa = []
-        with open(pdb_path, encoding="utf8") as f:
-            for line in f.readlines():
-                if source != 'MODBASE':
-                    if line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA' and line[21].upper() == chain.upper():
-                        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())
-                    elif line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA' and line[21] == ' ':
-                        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())
-                else:
+            atomSequence = ''
+            coords = []
+            resnums_for_sasa = []
+            with open(pdb_path, encoding="utf8") as f:
+                for line in f.readlines():
                     if line[0:7].strip() == 'ATOM' and line[13:15].strip() == 'CA':
                         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())
-        """
-        #f = open(Path(path_3D_alignment / f'{identifier}_{pdbID}_{str(chain)}_alignment.txt'),"w")
-
+                
         aligner.mode = 'local'
         aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
         aligner.open_gap_score = -11
         aligner.extend_gap_score = -1
         alignments = aligner.align(pdbSequence, atomSequence)
         alignments = (list(alignments))
-        #for alignment in alignments:
-        #    f.write(str(alignment))
-        #    f.write('\n')
-        #    f.write('\n')
+
         return alignments, coords, resnums_for_sasa
     elif mode==2:
             atomSequence = ''