Handle intrascale merging for GLYCAM molecules.

Author: lohedges

src/BioSimSpace/Align/_merge.py

@@ -90,6 +90,7 @@ def merge(
         The merged molecule.
     """
     from sire.legacy import CAS as _SireCAS
+    from sire.legacy import IO as _SireIO
     from sire.legacy import MM as _SireMM
     from sire.legacy import Base as _SireBase
     from sire.legacy import Mol as _SireMol
@@ -1178,23 +1179,22 @@ def merge(
         edit_mol.set_property("connectivity0", conn0)
         edit_mol.set_property("connectivity1", conn1)
 
-    # Create the CLJNBPairs matrices.
-    ff = molecule0.property(ff0)
-
-    # Create the new intrascale matrices.
-    scale_factor_14 = _SireMM.CLJScaleFactor(
-        ff.electrostatic14_scale_factor(), ff.vdw14_scale_factor()
+    # Merge the intrascale properties of the two molecules.
+    merged_intrascale = _SireIO.mergeIntrascale(
+        molecule0.property("intrascale"),
+        molecule1.property("intrascale"),
+        edit_mol.info(),
+        mol0_merged_mapping,
+        mol1_merged_mapping,
     )
-    clj_nb_pairs0 = _SireMM.CLJNBPairs(conn0, scale_factor_14)
-    clj_nb_pairs1 = _SireMM.CLJNBPairs(conn1, scale_factor_14)
 
     # Store the two molecular components.
     edit_mol.set_property("molecule0", molecule0)
     edit_mol.set_property("molecule1", molecule1)
 
     # Set the "intrascale" properties.
-    edit_mol.set_property("intrascale0", clj_nb_pairs0)
-    edit_mol.set_property("intrascale1", clj_nb_pairs1)
+    edit_mol.set_property("intrascale0", merged_intrascale[0])
+    edit_mol.set_property("intrascale1", merged_intrascale[1])
 
     # Set the "forcefield" properties.
     edit_mol.set_property("forcefield0", molecule0.property(ff0))

tests/Align/test_align.py

@@ -74,10 +74,24 @@ def test_invalid_prematch(system0, system1, prematch):
         )
 
 
-def test_merge():
-    # Load the ligands.
-    s0 = BSS.IO.readMolecules([f"{url}/ligand31.prm7.bz2", f"{url}/ligand31.rst7.bz2"])
-    s1 = BSS.IO.readMolecules([f"{url}/ligand38.prm7.bz2", f"{url}/ligand38.rst7.bz2"])
+@pytest.mark.parametrize(
+    "s0_files,s1_files",
+    [
+        (
+            [f"{url}/ligand31.prm7.bz2", f"{url}/ligand31.rst7.bz2"],
+            [f"{url}/ligand38.prm7.bz2", f"{url}/ligand38.rst7.bz2"],
+        ),
+        pytest.param(
+            [f"{url}/glycam_M5.gro.bz2", f"{url}/glycam_M5.top.bz2"],
+            [f"{url}/glycam_M5G0.gro.bz2", f"{url}/glycam_M5G0.top.bz2"],
+            marks=pytest.mark.slow,
+        ),
+    ],
+)
+def test_merge(s0_files, s1_files):
+    # Load the molecules.
+    s0 = BSS.IO.readMolecules(s0_files)
+    s1 = BSS.IO.readMolecules(s1_files)
 
     # Extract the molecules.
     m0 = s0.getMolecules()[0]