Fixed PBC fixing when unsquashing for dummy atoms (#20)

OpenBioSim · Sep 18, 2023 · f1f5276 · f1f5276
1 parent f9bed33
commit f1f5276
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diff --git a/python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py b/python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py
@@ -353,6 +353,9 @@ def _unsquash_molecule(molecule, squashed_molecules, explicit_dummies=False):
 
         # Apply the translation if the atom is coming from the second molecule.
         if len(squashed_molecules) == 2 and apply_translation_vec:
+            # This is a dummy atom so we need to translate coordinates0 as well
+            if squashed_atom_idx0 == squashed_atom_idx1:
+                coordinates0 -= translation_vec
             coordinates1 -= translation_vec
 
         siremol = merged_atom.setProperty("coordinates0", coordinates0).molecule()

diff --git a/tests/Sandpit/Exscientia/_SireWrappers/test_system.py b/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
@@ -1,5 +1,6 @@
 import math
 import pytest
+import platform
 
 import BioSimSpace.Sandpit.Exscientia as BSS
 
@@ -262,6 +263,10 @@ def test_get_box(system):
         assert math.isclose(a0.value(), a1.value(), rel_tol=1e-4)
 
 
+@pytest.mark.skipif(
+    platform != "Linux",
+    reason="Temporarily skipping test for macOS because the fixed sire 2023.2.3 has not been built for it",
+)
 def test_set_box(system):
     # Generate box dimensions and angles for a truncated octahedron.
     box, angles = BSS.Box.truncatedOctahedron(30 * BSS.Units.Length.angstrom)