Pass clone representation to ProtocolOutput

If we clone a subunit, pass the original
representation to ProtocolOutput again so it
is also cloned in the mmCIF output.

pyext/src/topology/__init__.py

@@ -319,6 +319,8 @@ def build(self, **kwargs):
                     mol._build_protocol_output()
                 for mol in reversed(self.molecules[molname]):
                     mol.build(protocol_output=False, **kwargs)
+                for mol in self.molecules[molname]:
+                    mol._finalize_build()
             self.built = True
         return self.hier
 
@@ -795,6 +797,17 @@ def _build_protocol_output(self):
                                           asym_name=self._name_with_copy,
                                           alphabet=self.alphabet)
 
+    def _finalize_build(self):
+        # For clones, pass the representation of the original molecule
+        # to ProtocolOutput
+        if self.mol_to_clone:
+            rephandler = _RepresentationHandler(
+                self._name_with_copy, list(self._all_protocol_output()),
+                self.mol_to_clone._pdb_elements)
+            for res in self.mol_to_clone.residues:
+                if res.hier:
+                    rephandler(res)
+
     def build(self, protocol_output=True):
         """Create all parts of the IMP hierarchy
         including Atoms, Residues, and Fragments/Representations and,
@@ -883,7 +896,11 @@ def build(self, protocol_output=True):
                         # otherwise just store what you found
                         new_hier = IMP.atom.Hierarchy(new_p)
                     res.hier = new_hier
-                    rephandler(res)
+                    # Clones will be handled in _finalize_build() instead
+                    # (can't handle them here as the parent of the clone
+                    # isn't built yet)
+                    if self.mol_to_clone is None:
+                        rephandler(res)
                 else:
                     res.hier = None
             self._represented = IMP.pmi.tools.OrderedSet(

test/test_mmcif.py

@@ -2048,6 +2048,63 @@ def test_model_repr_dump_rigid(self):
 1 1 1 Nup84 A 1 sphere 1 rigid by-residue . .
 2 1 1 Nup84 A 2 sphere . flexible by-feature 1 .
 #
+""")
+
+    def test_model_repr_dump_clone(self):
+        """Test ModelRepresentationDumper with clones"""
+        m = IMP.Model()
+        s = IMP.pmi.topology.System(m)
+        po = IMP.pmi.mmcif.ProtocolOutput()
+        s.add_protocol_output(po)
+        state = s.create_state()
+        nup84 = state.create_molecule("Nup84", "MELS", "A")
+        nup84.add_structure(self.get_input_file_name('test.nup84.pdb'), 'A')
+        nup84.add_representation(nup84.get_atomic_residues(), resolutions=[1])
+        nup84.add_representation(nup84.get_non_atomic_residues(),
+                                 resolutions=[10])
+        clone = nup84.create_clone("B")
+        _ = s.build()
+        dof = IMP.pmi.dof.DegreesOfFreedom(m)
+        dof.create_rigid_body(nup84.get_atomic_residues())
+        fh = StringIO()
+        w = ihm.format.CifWriter(fh)
+        self.assign_entity_asym_ids(po.system)
+        self.assign_range_ids(po.system)
+        # Need this to assign starting model details
+        ihm.dumper._StartingModelDumper().finalize(po.system)
+        d = ihm.dumper._ModelRepresentationDumper()
+        d.finalize(po.system)
+        d.dump(po.system, w)
+        r, = po.system.orphan_representations
+        self.assertEqual([f.asym_unit.seq_id_range for f in r],
+                         [(1, 2), (3, 4), (1, 2), (3, 4)])
+        out = fh.getvalue()
+        self.assertEqual(out, """#
+loop_
+_ihm_model_representation.id
+_ihm_model_representation.name
+_ihm_model_representation.details
+1 'Default representation' .
+#
+#
+loop_
+_ihm_model_representation_details.id
+_ihm_model_representation_details.representation_id
+_ihm_model_representation_details.entity_id
+_ihm_model_representation_details.entity_description
+_ihm_model_representation_details.entity_asym_id
+_ihm_model_representation_details.entity_poly_segment_id
+_ihm_model_representation_details.model_object_primitive
+_ihm_model_representation_details.starting_model_id
+_ihm_model_representation_details.model_mode
+_ihm_model_representation_details.model_granularity
+_ihm_model_representation_details.model_object_count
+_ihm_model_representation_details.description
+1 1 1 Nup84 A 1 sphere 1 rigid by-residue . .
+2 1 1 Nup84 A 2 sphere . flexible by-feature 1 .
+3 1 1 Nup84 B 1 sphere 2 rigid by-residue . .
+4 1 1 Nup84 B 2 sphere . flexible by-feature 1 .
+#
 """)
 
     def test_flush(self):