Note that add_structure() works with mmCIF too

pyext/src/topology/__init__.py

@@ -13,7 +13,8 @@
    like Molecule.get_atomic_residues() and Molecule.get_non_atomic_residues().
    These functions all return Python sets for easy set arithmetic using
    & (and), | (or), - (difference)
- * Molecule.add_structure() to add structural information from a PDB file.
+ * Molecule.add_structure() to add structural information from an mmCIF
+   or PDB file.
  * Molecule.add_representation() to create a representation unit - here you
    can choose bead resolutions as well as alternate representations like
    densities or ideal helices.
@@ -548,7 +549,7 @@ def add_structure(self, pdb_fn, chain_id, res_range=[],
                       soft_check=False):
         """Read a structure and store the coordinates.
         @return the atomic residues (as a set)
-        @param pdb_fn     The file to read
+        @param pdb_fn     The file to read (in PDB or mmCIF format)
         @param chain_id   Chain ID to read
         @param res_range  Add only a specific set of residues from the PDB
                           file. res_range[0] is the starting and res_range[1]

test/test_hierarchy_construction.py

@@ -9,9 +9,14 @@
 class Tests(IMP.test.TestCase):
     def test_hierarchy_construction(self):
         """Test construction of a hierarchy"""
+        self._test_hierarchy_internal(self.get_input_file_name("mini.pdb"))
 
+    def test_hierarchy_construction_mmcif(self):
+        """Test construction of a hierarchy using mmCIF inputs"""
+        self._test_hierarchy_internal(self.get_input_file_name("mini.cif"))
+
+    def _test_hierarchy_internal(self, pdbfile):
         # input parameter
-        pdbfile = self.get_input_file_name("mini.pdb")
         fastafile = self.get_input_file_name("mini.fasta")
 
         components = ["Rpb1", "Rpb2" ]
@@ -32,6 +37,7 @@ def test_hierarchy_construction(self):
             mol.add_representation(mol.get_non_atomic_residues(),
                                    resolutions=[10])
         hier = simo.build()
+        self.assertEqual(len(IMP.atom.get_leaves(hier)), 12)
 
         ev = IMP.pmi.restraints.stereochemistry.ExcludedVolumeSphere(
                                         included_objects=hier, resolution=10)