Warn, not fail, on nonsequential fragments

Follow existing PMI behavior when we encounter
non-sequential fragments - that is, pretend they
cover their entire sequence without gaps. Emit
a warning to make the user aware.

modules/mmcif/pyext/src/data.py

@@ -13,6 +13,7 @@
 import ihm.reference
 import operator
 import inspect
+import warnings
 
 
 # Map from IMP ResidueType to ihm ChemComp
@@ -52,9 +53,10 @@ def get_molecule(h):
 def _check_sequential(fragment, resinds):
     for i in range(1, len(resinds)):
         if resinds[i - 1] + 1 != resinds[i]:
-            raise ValueError(
-                "%s: non-sequential residue indices are not supported"
-                % str(fragment))
+            warnings.warn(
+                "%s: non-sequential residue indices; mmCIF bead will cover "
+                "indices [%d-%d]"
+                % (str(fragment), resinds[0], resinds[-1]))
 
 
 def _get_all_state_provenance(state_h, top_h, types):

modules/mmcif/test/test_data.py

@@ -379,13 +379,20 @@ def test_coordinate_handler_get_structure_particles(self):
         self.assertIsInstance(ps[1], IMP.atom.Atom)
         self.assertIsInstance(ps[2], IMP.atom.Fragment)
 
-        # Non-sequential fragments are not supported
+    def test_coordinate_handler_get_structure_particles_nonseq(self):
+        """Test get_structure_particles() with non-sequential fragment"""
+        m = IMP.Model()
+        top = IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
         frag = IMP.atom.Fragment.setup_particle(IMP.Particle(m), [5, 6, 7, 9])
         IMP.core.XYZR.setup_particle(
             frag, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(1, 2, 3), 4))
         IMP.atom.Mass.setup_particle(frag, 1.0)
         top.add_child(frag)
-        self.assertRaises(ValueError, ch.get_structure_particles, top)
+        ch = IMP.mmcif.data._CoordinateHandler(None, None)
+        with self.assertWarns(UserWarning):
+            ps = ch.get_structure_particles(top)
+        self.assertEqual(len(ps), 1)
+        self.assertIsInstance(ps[0], IMP.atom.Fragment)
 
     def test_coordinate_handler_add_chain(self):
         """Test CoordinateHandler.add_chain()"""