MMCIFParser: store models as ints.

Author: Lenna X. Peterson

Bio/PDB/MMCIFParser.py

@@ -34,7 +34,7 @@ def _build_structure(self, structure_id):
         b_factor_list=mmcif_dict["_atom_site.B_iso_or_equiv"]
         occupancy_list=mmcif_dict["_atom_site.occupancy"]
         fieldname_list=mmcif_dict["_atom_site.group_PDB"]
-        model_list = mmcif_dict["_atom_site.pdbx_PDB_model_num"]
+        model_list = [int(n) for n in mmcif_dict["_atom_site.pdbx_PDB_model_num"]]
         try:
             aniso_u11=mmcif_dict["_atom_site.aniso_U[1][1]"]
             aniso_u12=mmcif_dict["_atom_site.aniso_U[1][2]"]

Tests/test_MMCIF.py

@@ -47,7 +47,7 @@ def test_parser(self):
         for ppbuild in [PPBuilder(), CaPPBuilder()]:
             #==========================================================
             #First try allowing non-standard amino acids,
-            polypeptides = ppbuild.build_peptides(structure['1'], False)
+            polypeptides = ppbuild.build_peptides(structure[1], False)
             self.assertEqual(len(polypeptides), 1)
             pp = polypeptides[0]
             # Check the start and end positions
@@ -64,7 +64,7 @@ def test_parser(self):
             #Now try strict version with only standard amino acids
             #Should ignore MSE 151 at start, and then break the chain
             #at MSE 185, and MSE 214,215
-            polypeptides = ppbuild.build_peptides(structure['1'], True)
+            polypeptides = ppbuild.build_peptides(structure[1], True)
             self.assertEqual(len(polypeptides), 3)
             #First fragment
             pp = polypeptides[0]
@@ -99,7 +99,7 @@ def testModels(self):
         for ppbuild in [PPBuilder(), CaPPBuilder()]:
                 #==========================================================
                 #First try allowing non-standard amino acids,
-                polypeptides = ppbuild.build_peptides(structure['1'], False)
+                polypeptides = ppbuild.build_peptides(structure[1], False)
                 self.assertEqual(len(polypeptides), 1)
                 pp = polypeptides[0]
                 # Check the start and end positions
@@ -114,7 +114,7 @@ def testModels(self):
                                  str(s))
                 #==========================================================
                 #Now try strict version with only standard amino acids
-                polypeptides = ppbuild.build_peptides(structure['1'], True)
+                polypeptides = ppbuild.build_peptides(structure[1], True)
                 self.assertEqual(len(polypeptides), 1)
                 pp = polypeptides[0]
                 # Check the start and end positions