Fixing PDBize

modules/io/pymod/__init__.py

@@ -357,14 +357,25 @@ def _PDBize(biounit, asu, seqres=None, min_polymer_size=10,
     return atom_pos_wrong
 
   chain_names='ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz'
+  cur_chain_name = 0
+  water_chain = mol.ChainHandle()
+  ligand_chain = mol.ChainHandle()
+  a_pos_wrong = False
+  pdb_bu = mol.CreateEntity()
+  edi = pdb_bu.EditXCS(mol.BUFFERED_EDIT)
+  chains = biounit.GetChainList()
+  c_intvls = biounit.GetChainIntervalList()
+  o_intvls = biounit.GetOperationsIntervalList()
   # create list of operations
   # for cartesian products, operations are stored in a list, multiplied with
   # the next list of operations and re-stored... until all lists of operations
   # are multiplied in an all-against-all manner.
   operations = biounit.GetOperations()
+  for i in range(0,len(c_intvls)):
     trans_matrices = list()
-  if len(operations) > 0:
-    for op in operations[0]:
+    l_operations = operations[o_intvls[i][0]:o_intvls[i][1]]
+    if len(l_operations) > 0:
+      for op in l_operations[0]:
         rot = geom.Mat4()
         rot.PasteRotation(op.rotation)
         trans = geom.Mat4()
@@ -372,9 +383,9 @@ def _PDBize(biounit, asu, seqres=None, min_polymer_size=10,
         tr = geom.Mat4()
         tr = trans * rot
         trans_matrices.append(tr)
-    for op_n in range(1, len(operations)):
+      for op_n in range(1, len(l_operations)):
         tmp_ops = list()
-      for o in operations[op_n]:
+        for o in l_operations[op_n]:
           rot = geom.Mat4()
           rot.PasteRotation(o.rotation)
           trans = geom.Mat4()
@@ -386,15 +397,9 @@ def _PDBize(biounit, asu, seqres=None, min_polymer_size=10,
             tmp_ops.append(tp)
         trans_matrices = tmp_ops
     # select chains into a view as basis for each transformation
-  assu = asu.Select('cname=' + ','.join(biounit.GetChainList()))
+    assu = asu.Select('cname='+','.join(chains[c_intvls[i][0]:c_intvls[i][1]]))
     # use each transformation on the view, store as entity and transform, PDBize
     # the result while adding everything to one large entity
-  pdb_bu = mol.CreateEntity()
-  edi = pdb_bu.EditXCS(mol.BUFFERED_EDIT)
-  cur_chain_name = 0
-  water_chain = mol.ChainHandle()
-  ligand_chain = mol.ChainHandle()
-  a_pos_wrong = False
     for tr in trans_matrices:
       # do a PDBize, add each new entity to the end product
       for chain in assu.chains:

modules/io/tests/test_io_mmcif.py

@@ -201,7 +201,7 @@ class TestMMCifInfo(unittest.TestCase):
     pdb_ent, t = info.GetBioUnits()[0].PDBize(ent, transformation=True)
     self.assertAlmostEquals(pdb_ent.GetCenterOfAtoms()[0], -915.8, 1)
     self.assertAlmostEquals(pdb_ent.GetCenterOfAtoms()[1], -952.345, 2)
-    self.assertAlmostEquals(pdb_ent.GetCenterOfAtoms()[2], 3221.74, 2)
+    self.assertAlmostEquals(pdb_ent.GetCenterOfAtoms()[2], 3221.75, 2)
     self.assertEquals(geom.Equal(t,
                                  geom.Mat4(1,0,0,-920.462,
                                            0,1,0,-966.654,