Remove special handling for target entities

Since we no longer create Entities for templates,
all entities are "target" entities, so there is no
need to keep a separate list for these.

modelcif/__init__.py

@@ -76,7 +76,6 @@ def __init__(self, title=None, id='model', database=None,
 
         self.entities = []
         self.asym_units = []
-        self.target_entities = []
         self.templates = []
         self.template_segments = []
         self.template_transformations = []
@@ -109,8 +108,6 @@ def _before_write(self):
         self.entities = list(_remove_identical(self._all_entities()))
         self.template_transformations = list(_remove_identical(
             self._all_template_transformations()))
-        self.target_entities = list(_remove_identical(
-            self._all_target_entities()))
         self.data_groups = list(_remove_identical(
             self._all_data_groups()))
         self.data = list(_remove_identical(
@@ -124,7 +121,7 @@ def _before_write(self):
 
     def _add_missing_reference_sequence(self):
         """If any TargetReference has no sequence, use that of the Entity"""
-        for e in self.entities + self.target_entities:
+        for e in self.entities:
             for r in e.references:
                 if r.sequence is None:
                     r.sequence = "".join(comp.code_canonical
@@ -160,13 +157,6 @@ def _all_citations(self):
             (software.citation for software in self._all_software()
              if software.citation)))
 
-    def _all_target_entities(self):
-        """Iterate over all Entities that are used for targets rather than
-           templates."""
-        return (itertools.chain(
-            self.target_entities,
-            (asym.entity for asmb in self.assemblies for asym in asmb)))
-
     def _all_software(self):
         """Utility method used by ihm.dumper to get all Software. To initially
            populate this list from all Software referenced in the system,
@@ -223,7 +213,6 @@ def _all_asym_in_assemblies():
             self.asym_units, _all_asym_in_assemblies())
 
     def _all_entities(self):
-        # Note that template entities are not included by default
         return itertools.chain(
             self.entities,
             (asym.entity for asym in self.asym_units))
@@ -250,7 +239,7 @@ def _all_data_in_files():
         return itertools.chain(
             self.data,
             self.templates,
-            self.target_entities,
+            self.entities,
             self.alignments,
             (model for group, model in self._all_models()),
             _all_data_in_groups(),

modelcif/dumper.py

@@ -103,10 +103,6 @@ def dump(self, system, writer):
 
 class _TargetRefDBDumper(Dumper):
     def dump(self, system, writer):
-        # Since target_entities is a *subset* of all entities, they may not
-        # be ordered by ID. Sort them so the output is prettier.
-        entities = sorted(system.target_entities,
-                          key=operator.attrgetter('_id'))
         with writer.loop(
                 "_ma_target_ref_db_details",
                 ["target_entity_id", "db_name", "db_name_other_details",
@@ -115,7 +111,7 @@ def dump(self, system, writer):
                  "ncbi_taxonomy_id", "organism_scientific",
                  "seq_db_sequence_version_date",
                  "seq_db_sequence_checksum"]) as lp:
-            for e in entities:
+            for e in system.entities:
                 for r in e.references:
                     if r.align_begin is None:
                         db_begin = min(a.db_begin for a in r._get_alignments())
@@ -167,12 +163,10 @@ def dump(self, system, writer):
 
 class _TargetEntityDumper(Dumper):
     def dump(self, system, writer):
-        entities = sorted(system.target_entities,
-                          key=operator.attrgetter('_id'))
         with writer.loop(
                 "_ma_target_entity",
                 ["entity_id", "data_id", "origin"]) as lp:
-            for e in entities:
+            for e in system.entities:
                 lp.write(entity_id=e._id, data_id=e._data_id,
                          origin="reference database" if e.references
                          else "designed")

test/test_dumper.py

@@ -173,7 +173,7 @@ def test_data_dumper(self):
         """Test DataDumper"""
         system = modelcif.System()
         entity = modelcif.Entity("DMA", description='test entity')
-        system.target_entities.append(entity)
+        system.entities.append(entity)
         # Template and target use same entity here (but different data IDs)
         template = modelcif.Template(
             entity, asym_id="A", model_num=1, name="test template",
@@ -206,7 +206,7 @@ def test_data_group_dumper(self):
         tgt_e1._data_id = 1
         tgt_e2._data_id = 2
         tgt_e3._data_id = 3
-        system.target_entities.extend((tgt_e1, tgt_e2, tgt_e3))
+        system.entities.extend((tgt_e1, tgt_e2, tgt_e3))
         dg12 = modelcif.data.DataGroup((tgt_e1, tgt_e2))
         p = modelcif.protocol.Protocol()
         p.steps.append(modelcif.protocol.ModelingStep(
@@ -516,7 +516,7 @@ class CustomRef(modelcif.reference.TargetReference):
 
         e1 = modelcif.Entity('ACGT', references=[ref1, ref2, ref3, ref4, ref5])
         e1._id = 1
-        system.target_entities.append(e1)
+        system.entities.append(e1)
 
         dumper = modelcif.dumper._TargetRefDBDumper()
         dumper.finalize(system)
@@ -844,7 +844,7 @@ def test_target_entity_dumper(self):
         e1 = modelcif.Entity("D")
         e1._id = 42
         e1._data_id = 99
-        system.target_entities.append(e1)
+        system.entities.append(e1)
 
         a1 = modelcif.AsymUnit(e1, 'foo')
         a1._id = 'X'

test/test_main.py

@@ -17,7 +17,7 @@ def test_all_data(self):
         s = modelcif.System()
         e1 = modelcif.Entity("D")
         e2 = modelcif.Entity("M")
-        s.target_entities.extend((e1, e2))
+        s.entities.extend((e1, e2))
 
         e3 = modelcif.Entity("A")
         s.data.extend((e1, e3))
@@ -86,24 +86,6 @@ def test_all_data_groups(self):
         d = s._all_data_groups()
         self.assertEqual(list(d), [e1, e1, e2])
 
-    def test_all_target_entities(self):
-        """Test _all_target_entities() method"""
-        s = modelcif.System()
-        e1 = modelcif.Entity("D")
-        e2 = modelcif.Entity("M")
-        s.target_entities.extend((e1, e2))
-
-        template_e = modelcif.Entity("M")
-        s.entities.extend((e1, e2, template_e))
-
-        asym = modelcif.AsymUnit(e1, 'foo')
-        s.asym_units.append(asym)
-        s.assemblies.append(modelcif.Assembly((asym,)))
-
-        te = s._all_target_entities()
-        # List may contain duplicates, but no template entities
-        self.assertEqual(list(te), [e1, e2, e1])
-
     def test_all_template_transformations(self):
         """Test _all_template_transformations() method"""
         s = modelcif.System()