Don't create segments for ResidueFeature

ResidueFeature's mmCIF table already explicitly
lists the seq_id range, asym_id and entity_id
used by the restraint; it doesn't use segment_id.
Thus, we shouldn't create a segment for each
such feature. Closes #175.

Author: benmwebb

ihm/__init__.py

@@ -626,16 +626,17 @@ def _all_citations(self):
     def _all_entity_ranges(self):
         """Iterate over all Entity ranges in the system (these may be
            :class:`Entity`, :class:`AsymUnit`, :class:`EntityRange` or
-           :class:`AsymUnitRange` objects).
+           :class:`AsymUnitRange` objects) that will be given a unique ID.
            Note that we don't include self.entities or self.asym_units here,
            as we only want ranges that were actually used.
+           We also don't include ranges used in ResidueFeature, as that
+           explicitly states the range in the mmCIF table, not by reference to
+           ``ihm_entity_poly_segment``.
            Duplicates may be present."""
         return (itertools.chain(
             (sm.asym_unit for sm in self._all_starting_models()),
             (seg.asym_unit for seg in self._all_segments()),
             (comp for a in self._all_assemblies() for comp in a),
-            (comp for f in self._all_features()
-                for comp in f._all_entities_or_asyms()),
             (d.asym_unit for d in self._all_densities())))
 
     def _all_multi_state_schemes(self):

test/test_dumper.py

@@ -3091,11 +3091,15 @@ def test_entity_poly_segment_dumper(self):
         a1._id = 'X'
         system.entities.extend((e1, e2, e3))
         system.asym_units.append(a1)
-        res1 = e2.residue(1)
-        res2 = e2.residue(2)
-        system.orphan_features.append(ihm.restraint.ResidueFeature([e2]))
-        system.orphan_features.append(ihm.restraint.ResidueFeature([res2]))
-        system.orphan_features.append(ihm.restraint.NonPolyFeature([e3]))
+        rng1 = a1(1,2)
+        rng2 = a1(3,4)
+
+        s1 = ihm.representation.ResidueSegment(
+            rng1, starting_model=None,
+            rigid=False, primitive='sphere')
+        r1 = ihm.representation.Representation((s1,), name='foo',
+                                               details='bar')
+        system.orphan_representations.append(r1)
 
         system._make_complete_assembly()
 
@@ -3107,14 +3111,11 @@ def test_entity_poly_segment_dumper(self):
         # e1 isn't directly used in anything (a1 is used instead, in the
         # assembly) so should have no range ID
         self.assertFalse(hasattr(e1, '_range_id'))
-        self.assertEqual(a1._range_id, 1)
-        # e2 is use, in a ResidueFeature, so should have a range ID
-        self.assertEqual(e2._range_id, 2)
-        # non-polymers don't have ranges
-        self.assertEqual(e3._range_id, None)
-        # res2 should have been assigned a range, but not res1
-        self.assertFalse(hasattr(res1, '_range_id'))
-        self.assertEqual(res2._range_id, 3)
+        self.assertEqual(a1._range_id, 2)
+        # rng1 is use, in a ResidueSegment, so should have a range ID
+        self.assertEqual(rng1._range_id, 1)
+        # rng2 is not in use
+        self.assertFalse(hasattr(rng2, '_range_id'))
 
         out = _get_dumper_output(dumper, system)
         self.assertEqual(out, """#
@@ -3125,9 +3126,8 @@ def test_entity_poly_segment_dumper(self):
 _ihm_entity_poly_segment.seq_id_end
 _ihm_entity_poly_segment.comp_id_begin
 _ihm_entity_poly_segment.comp_id_end
-1 1 1 4 ALA ASP
-2 2 1 3 ALA GLY
-3 2 2 2 CYS CYS
+1 1 1 2 ALA HIS
+2 1 1 4 ALA ASP
 #
 """)
 
@@ -3142,8 +3142,12 @@ def test_entity_poly_segment_dumper_bad_range(self):
             # Disable construction-time check so that we
             # can see dump time check
             e1._range_check = False
-            system.orphan_features.append(
-                ihm.restraint.ResidueFeature([e1(*badrng)]))
+            s1 = ihm.representation.ResidueSegment(
+                e1(*badrng), starting_model=None,
+                rigid=False, primitive='sphere')
+            r1 = ihm.representation.Representation((s1,), name='foo',
+                                                   details='bar')
+            system.orphan_representations.append(r1)
             e1._range_check = True
 
             dumper = ihm.dumper._EntityDumper()

test/test_main.py

@@ -11,6 +11,7 @@
 import ihm.model
 import ihm.source
 import ihm.flr
+import ihm.restraint
 import ihm.multi_state_scheme
 
 
@@ -1172,6 +1173,7 @@ class MockObject:
         s.asym_units.append(a1)
         e1rng = e1(1, 3)
         a1rng = a1(1, 2)
+        a1rng2 = a1(3, 4)
 
         sm1 = MockObject()
         sm1.asym_unit = e1rng
@@ -1184,6 +1186,10 @@ class MockObject:
         rep.append(seg1)
         s.orphan_representations.append(rep)
 
+        # Ranges listed in ResidueFeature should not be included
+        # in _all_entity_ranges()
+        s.orphan_features.append(ihm.restraint.ResidueFeature([a1rng2]))
+
         asmb1 = ihm.Assembly([e1, a1])
         s.orphan_assemblies.append(asmb1)