Merge pull request #497 from OpenBioSim/fix_496

Fix issue #496

Author: lohedges

python/BioSimSpace/Parameters/__init__.py

@@ -40,7 +40,7 @@
 
    import BioSimSpace as BSS
 
-   print(BSS.Parameters.force_fields())
+   print(BSS.Parameters.forceFields())
 
 Parameterise a molecule using GAFF.
 

python/BioSimSpace/Parameters/_parameters.py

@@ -74,7 +74,7 @@ def parameterise(
         string.
 
     forcefield : str
-        The force field. Run BioSimSpace.Parameters.force_fields() to get a
+        The force field. Run BioSimSpace.Parameters.forceFields() to get a
         list of the supported force fields.
 
     ensure_compatible : bool

python/BioSimSpace/Sandpit/Exscientia/Parameters/__init__.py

@@ -40,7 +40,7 @@
 
    import BioSimSpace as BSS
 
-   print(BSS.Parameters.force_fields())
+   print(BSS.Parameters.forceFields())
 
 Parameterise a molecule using GAFF.
 

python/BioSimSpace/Sandpit/Exscientia/Parameters/_parameters.py

@@ -74,7 +74,7 @@ def parameterise(
         string.
 
     forcefield : str
-        The force field. Run BioSimSpace.Parameters.force_fields() to get a
+        The force field. Run BioSimSpace.Parameters.forceFields() to get a
         list of the supported force fields.
 
     ensure_compatible : bool

python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py

@@ -983,9 +983,9 @@ def makeCompatibleWith(
                                 propty = mol1.property(_property_map[prop])
 
                                 # Try making it compatible with the original molecule.
-                                if hasattr(propty, "makeCompatibleWith"):
+                                if hasattr(propty, "make_compatible_with"):
                                     try:
-                                        propty = propty.makeCompatibleWith(
+                                        propty = propty.make_compatible_with(
                                             mol0, inv_matches
                                         )
                                     except Exception as e:
@@ -1188,9 +1188,9 @@ def makeCompatibleWith(
                         propty = mol.property(prop)
 
                         # Try making the property compatible with the original molecule.
-                        if hasattr(propty, "makeCompatibleWith"):
+                        if hasattr(propty, "make_compatible_with"):
                             try:
-                                propty = propty.makeCompatibleWith(mol0, inv_matches)
+                                propty = propty.make_compatible_with(mol0, inv_matches)
                             except Exception as e:
                                 msg = "Incompatible property: %s" % prop
                                 if _isVerbose():

python/BioSimSpace/_SireWrappers/_molecule.py

@@ -923,9 +923,9 @@ def makeCompatibleWith(
                                 propty = mol1.property(_property_map[prop])
 
                                 # Try making it compatible with the original molecule.
-                                if hasattr(propty, "makeCompatibleWith"):
+                                if hasattr(propty, "make_compatible_with"):
                                     try:
-                                        propty = propty.makeCompatibleWith(
+                                        propty = propty.make_compatible_with(
                                             mol0, inv_matches
                                         )
                                     except Exception as e:
@@ -1128,9 +1128,9 @@ def makeCompatibleWith(
                         propty = mol.property(prop)
 
                         # Try making the property compatible with the original molecule.
-                        if hasattr(propty, "makeCompatibleWith"):
+                        if hasattr(propty, "make_compatible_with"):
                             try:
-                                propty = propty.makeCompatibleWith(mol0, inv_matches)
+                                propty = propty.make_compatible_with(mol0, inv_matches)
                             except Exception as e:
                                 msg = "Incompatible property: %s" % prop
                                 if _isVerbose():

tests/Sandpit/Exscientia/_SireWrappers/test_molecule.py

@@ -143,3 +143,34 @@ def test_lipid(lipid):
         mol._sire_object = c.commit()
 
     assert mol.isLipid() is lipid
+
+
+@pytest.mark.skipif(has_amber is False, reason="Requires AMBER to be installed.")
+def test_makeCompatibleWith_regression():
+    """Test that makeCompatibleWith works correctly for a known regression case."""
+
+    import sire as sr
+
+    # Load the BACE protein.
+    protein_xtal = BSS.IO.readMolecules(BSS.IO.expand(url, "bace.pdb"))
+
+    # Remove waters.
+    protein = protein_xtal[0].extract(
+        [atom.index() for atom in protein_xtal[0].search("not resname WAT").atoms()]
+    )
+
+    # Parameterise with ff14SB.
+    protein = BSS.Parameters.ff14SB(
+        protein, work_dir="debug", ensure_compatible=False
+    ).getMolecule()
+
+    # Convert to a Sire System and compute the energy.
+    system = sr.system.System(protein.toSystem()._sire_object)
+    nrg_compatible = system.energy().value()
+
+    # Load in the tLEaP-generated system and compute the energy.
+    system = sr.load("debug/leap.crd", "debug/leap.top")
+    nrg_leap = system.energy().value()
+
+    # Make sure the energies are approximately equal.
+    assert nrg_compatible == pytest.approx(nrg_leap, rel=1e-5)

tests/_SireWrappers/test_molecule.py

@@ -115,3 +115,34 @@ def test_extract(system):
 
     # Make sure the numbers are different.
     assert partial_mol.number() != mol.number()
+
+
+@pytest.mark.skipif(has_amber is False, reason="Requires AMBER to be installed.")
+def test_makeCompatibleWith_regression():
+    """Test that makeCompatibleWith works correctly for a known regression case."""
+
+    import sire as sr
+
+    # Load the BACE protein.
+    protein_xtal = BSS.IO.readMolecules(BSS.IO.expand(url, "bace.pdb"))
+
+    # Remove waters.
+    protein = protein_xtal[0].extract(
+        [atom.index() for atom in protein_xtal[0].search("not resname WAT").atoms()]
+    )
+
+    # Parameterise with ff14SB.
+    protein = BSS.Parameters.ff14SB(
+        protein, work_dir="debug", ensure_compatible=False
+    ).getMolecule()
+
+    # Convert to a Sire System and compute the energy.
+    system = sr.system.System(protein.toSystem()._sire_object)
+    nrg_compatible = system.energy().value()
+
+    # Load in the tLEaP-generated system and compute the energy.
+    system = sr.load("debug/leap.crd", "debug/leap.top")
+    nrg_leap = system.energy().value()
+
+    # Make sure the energies are approximately equal.
+    assert nrg_compatible == pytest.approx(nrg_leap, rel=1e-5)