Also combine overlapping ranges into segments

With atomic models, subsequent atoms in the same residue will overlap the range of the last representation segment, not just end up contiguous with it. Combine these into one segment.
salilab · Sep 15, 2023 · bf3f62d · bf3f62d
1 parent 6bbfeae
commit bf3f62d
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/modules/mmcif/pyext/src/data.py b/modules/mmcif/pyext/src/data.py
@@ -254,7 +254,7 @@ def start_new_segment():
         elif (type(particle) == type(self.particles[0])  # noqa: E721
               and is_res == self.is_res
               and is_atom == self.is_atom
-              and resrange[0] == self.residue_range[1] + 1
+              and resrange[0] <= self.residue_range[1] + 1
               and starting_model == self.starting_model
               and self._same_rigid_body(rigid_body)):
             # Continue an existing segment

diff --git a/modules/mmcif/test/test_data.py b/modules/mmcif/test/test_data.py
@@ -354,11 +354,11 @@ def test_coordinate_handler_add_chain(self):
         # One residue with atomic representation
         residue = IMP.atom.Residue.setup_particle(IMP.Particle(m),
                                                   IMP.atom.ALA, 4)
-        atom = IMP.atom.Atom.setup_particle(IMP.Particle(m),
-                                            IMP.atom.AT_CA)
-        IMP.core.XYZR.setup_particle(
-            atom, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(1, 2, 3), 4))
-        residue.add_child(atom)
+        for att in (IMP.atom.AT_CA, IMP.atom.AT_O):
+            atom = IMP.atom.Atom.setup_particle(IMP.Particle(m), att)
+            IMP.core.XYZR.setup_particle(
+                atom, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(1, 2, 3), 4))
+            residue.add_child(atom)
         top.add_child(residue)
         # Two beads each spanning two residues
         frag = IMP.atom.Fragment.setup_particle(IMP.Particle(m), [5, 6])