Use chain sequence offset if provided

Get the sequence offset either from
the Chain object or from the sequence
determined from Residues and pass that
through to python-ihm's AsymUnit class.
(Currently, we only support offset==0.)

modules/mmcif/pyext/src/data.py

@@ -95,7 +95,6 @@ def __init__(self, system):
 
     def _get_sequence_from_residues(self, chain, seq_from_res):
         seq_id_begin, seq = seq_from_res
-        # todo: handle seq_id_begin != 1
         if not seq:
             raise ValueError("Chain %s has no sequence and no residues"
                              % chain)
@@ -107,14 +106,15 @@ def _get_sequence_from_residues(self, chain, seq_from_res):
                 "sequence from Residues, but the following residue indices "
                 "have no residue type (perhaps covered only by Fragments): %s"
                 % (chain, str(missing_seq)))
-        return tuple(seq)
+        return seq_id_begin - 1, tuple(seq)
 
     def add(self, chain, seq_from_res=None):
         sequence = chain.get_sequence()
+        offset = chain.get_sequence_offset()
         if sequence == '':
             if seq_from_res is not None:
-                sequence = self._get_sequence_from_residues(chain,
-                                                            seq_from_res)
+                offset, sequence = self._get_sequence_from_residues(
+                    chain, seq_from_res)
             else:
                 raise ValueError("Chain %s has no sequence" % chain)
         else:
@@ -127,7 +127,7 @@ def add(self, chain, seq_from_res=None):
             self._entities.append(entity)
             self._sequence_dict[sequence] = entity
         self[chain] = self._sequence_dict[sequence]
-        return self[chain]
+        return self[chain], offset
 
     def get_all(self):
         """Yield all entities"""
@@ -189,7 +189,7 @@ def _handle_chain(self, chain):
             name = map_key = chain.name
         return modeled, asym_id, map_key, name
 
-    def add(self, chain, entity):
+    def add(self, chain, entity, offset):
         """Add a chain (either an IMP Chain object for a modeled component,
            or a NonModeledChain object for a non-modeled component)"""
         modeled, asym_id, map_key, name = self._handle_chain(chain)
@@ -203,8 +203,13 @@ def add(self, chain, entity):
                     entity.description = \
                         component.name.split("@")[0].split(".")[0]
             self._all_components.append(component)
+            if offset != 0:
+                raise ValueError(
+                    "Non-zero chain sequence offsets are not "
+                    "currently handled")
             if modeled:
-                asym = ihm.AsymUnit(entity, name, id=asym_id)
+                asym = ihm.AsymUnit(entity, name, id=asym_id,
+                                    auth_seq_id_map=offset)
                 self.system.asym_units.append(asym)
                 component.asym_unit = asym
                 self._all_modeled_components.append(component)

modules/mmcif/pyext/src/util.py

@@ -269,8 +269,8 @@ def _add_state(self, state):
         self._state_by_name[state.name] = state
 
     def _add_chain(self, chain, seq_from_res):
-        entity = self._entities.add(chain, seq_from_res)
-        component = self._components.add(chain, entity)
+        entity, offset = self._entities.add(chain, seq_from_res)
+        component = self._components.add(chain, entity, offset)
         return component
 
     def add_rmf(self, filename, name=None, frame=0, states=None,

modules/mmcif/test/test_data.py

@@ -12,12 +12,16 @@ def add_attrs(r):
 
 
 class MockChain(object):
-    def __init__(self, name, sequence='', chain_type=IMP.atom.Protein):
+    def __init__(self, name, sequence='', chain_type=IMP.atom.Protein,
+                 offset=0):
         self.name = name
         self.sequence = sequence
         self.chain_type = chain_type
+        self.offset = offset
     def get_sequence(self):
         return self.sequence
+    def get_sequence_offset(self):
+        return self.offset
     def get_chain_type(self):
         return self.chain_type
 
@@ -102,9 +106,9 @@ def test_entity_naming(self):
         chain1 = MockChain("A.1@12")
         chain2 = MockChain("A.2@12")
         chain3 = MockChain(None)
-        comp1 = cm.add(chain1, entity1)
-        comp2 = cm.add(chain2, entity1)
-        comp3 = cm.add(chain3, entity2)
+        comp1 = cm.add(chain1, entity1, 0)
+        comp2 = cm.add(chain2, entity1, 0)
+        comp3 = cm.add(chain3, entity2, 0)
         self.assertEqual(chain1.name, "A.1@12")
         self.assertEqual(chain2.name, "A.2@12")
         self.assertIsNone(chain3.name)
@@ -118,10 +122,19 @@ def test_component_mapper_same_id_chain(self):
         entity2 = ihm.Entity("DEF")
         chain1 = MockChain("A")
         chain2 = MockChain("A")
-        comp1 = cm.add(chain1, entity1)
+        comp1 = cm.add(chain1, entity1, 0)
         self.assertEqual(cm[chain1], comp1)
         # Cannot add two chains with the same ID but different sequences
-        self.assertRaises(ValueError, cm.add, chain2, entity2)
+        self.assertRaises(ValueError, cm.add, chain2, entity2, 0)
+
+    def test_component_mapper_non_zero_offset(self):
+        """Test ComponentMapper given non-zero sequence offset"""
+        system = ihm.System()
+        cm = IMP.mmcif.data._ComponentMapper(system)
+        entity1 = ihm.Entity("ANC")
+        chain1 = MockChain("A")
+        # Non-zero offsets are not currently handled
+        self.assertRaises(ValueError, cm.add, chain1, entity1, 100)
 
     def test_component_mapper_get_all(self):
         """Test ComponentMapper get_all()"""
@@ -131,8 +144,8 @@ def test_component_mapper_get_all(self):
         entity2 = ihm.Entity("DEF")
         chain1 = MockChain("A")
         chain2 = MockChain("B")
-        comp1 = cm.add(chain1, entity1)
-        comp2 = cm.add(chain2, entity2)
+        comp1 = cm.add(chain1, entity1, 0)
+        comp2 = cm.add(chain2, entity2, 0)
         allc = cm.get_all()
         self.assertEqual(allc, [comp1, comp2])
         self.assertEqual(cm.get_all_modeled(), [])