Merge pull request #356 from OpenBioSim/sync_exscientia

Synchronise with Exscientia remote

.github/workflows/Sandpit_exs.yml

@@ -33,7 +33,7 @@ jobs:
 
       - name: Install dependency
         run: |
-          conda install -c conda-forge -c openbiosim/label/main biosimspace python=3.10 ambertools gromacs "sire=2024.1.0" "alchemlyb>=2.1" pytest openff-interchange pint=0.21 rdkit "jaxlib>0.3.7" tqdm
+          conda install -c conda-forge -c openbiosim/label/main biosimspace python=3.10 ambertools gromacs "sire=2024.2.0" "alchemlyb>=2.1" pytest openff-interchange pint=0.21 rdkit "jaxlib>0.3.7" tqdm
           python -m pip install git+https://github.com/Exscientia/MDRestraintsGenerator.git
           # For the testing of BSS.FreeEnergy.AlchemicalFreeEnergy.analysis
           python -m pip install https://github.com/alchemistry/alchemtest/archive/master.zip

python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py

@@ -47,6 +47,7 @@
 from sire.legacy import Units as _SireUnits
 from sire.legacy import Vol as _SireVol
 
+from ..Units.Length import angstrom
 from .._Utils import _assert_imported, _have_imported, _try_import
 
 # alchemlyb isn't available on all variants of Python that we support, so we
@@ -355,7 +356,13 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
         # For now, we'll not attempt to generate a box if the system property
         # is missing. If no box is present, we'll assume a non-periodic simulation.
         if "space" in system._sire_object.propertyKeys():
-            has_box = True
+            try:
+                # Make sure that we have a periodic box. The system will now have
+                # a default cartesian space.
+                box = system._sire_object.property("space")
+                has_box = box.isPeriodic()
+            except:
+                has_box = False
         else:
             _warnings.warn("No simulation box found. Assuming gas phase simulation.")
             has_box = False
@@ -2174,15 +2181,17 @@ def _add_position_restraints(self, config_options):
                     for idx, mol_idx in enumerate(mol_idxs):
                         # Get the indices of any restrained atoms in this molecule,
                         # making sure that indices are relative to the molecule.
-                        if restraint is not None:
+                        if restraint is None:
+                            atom_idxs = []
+                        elif self._system.getMolecule(mol_idx).isLipid():
+                            atom_idxs = []
+                        else:
                             atom_idxs = self._system.getRestraintAtoms(
                                 restraint,
                                 mol_index=mol_idx,
                                 is_absolute=False,
                                 allow_zero_matches=True,
                             )
-                        else:
-                            atom_idxs = []
 
                         if self._system.getMolecule(mol_idx).isAlchemicalIon():
                             alch_ion = self._system.getMolecule(mol_idx).getAtoms()
@@ -2696,8 +2705,22 @@ def _getFinalFrame(self):
                     )
 
             # If this is a vacuum simulation, then translate the centre of mass
-            # of the system back to the origin.
-            if not space_prop in old_system._sire_object.propertyKeys():
+            # of the system back to the middle of the box to preserve PBC.
+            if old_system.getBox() == (None, None):
+                try:
+                    old_box = old_system._sire_object.property(space_prop)
+                except:
+                    old_box = None
+                box = _SireVol.PeriodicBox(_SireMaths.Vector(9999, 9999, 9999))
+                old_system._sire_object.setProperty(space_prop, box)
+                com = [angstrom * 9999 / 2 for _ in range(3)]
+                old_system.translate([x for x in com])
+                old_system._sire_object.make_whole()
+                old_system.translate([-x for x in com])
+                if old_box is None:
+                    old_system._sire_object.removeProperty(space_prop)
+                else:
+                    old_system._sire_object.setProperty(space_prop, old_box)
                 com = old_system._getCenterOfMass()
                 old_system.translate([-x for x in com])
 
@@ -2813,9 +2836,23 @@ def _getFrame(self, time):
                             )
 
                 # If this is a vacuum simulation, then translate the centre of mass
-                # of the system back to the origin.
-                if not space_prop in old_system._sire_object.propertyKeys():
-                    com = new_system._getCenterOfMass()
+                # of the system back to the middle of the box to preserve PBC.
+                if old_system.getBox() == (None, None):
+                    try:
+                        old_box = old_system._sire_object.property(space_prop)
+                    except:
+                        old_box = None
+                    box = _SireVol.PeriodicBox(_SireMaths.Vector(9999, 9999, 9999))
+                    old_system._sire_object.setProperty(space_prop, box)
+                    com = [angstrom * 9999 / 2 for _ in range(3)]
+                    old_system.translate([x for x in com])
+                    old_system._sire_object.make_whole()
+                    old_system.translate([-x for x in com])
+                    if old_box is None:
+                        old_system._sire_object.removeProperty(space_prop)
+                    else:
+                        old_system._sire_object.setProperty(space_prop, old_box)
+                    com = old_system._getCenterOfMass()
                     old_system.translate([-x for x in com])
 
                 return old_system

python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py

@@ -189,7 +189,7 @@ def generateAmberConfig(self, extra_options=None, extra_lines=None):
 
         # Define some miscellaneous defaults.
         protocol_dict = {
-            "ntpr": 200,  # Interval between reporting energies.
+            "ntpr": self._report_interval,  # Interval between reporting energies.
             "ntwr": self._restart_interval,  # Interval between saving restart files.
             "ntwx": self._restart_interval,  # Trajectory sampling frequency.
             "ntxo": 2,  # Output coordinates as NetCDF.

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

@@ -518,6 +518,22 @@ def isDecoupled(self):
         else:
             return False
 
+    def isLipid(self):
+        """
+        Whether this molecule is decoupled, i.e. it can be used in a
+        free-energy decoupling simulation.
+
+        Returns
+        -------
+
+        is_decoupled : bool
+            Whether the molecule is decoupled.
+        """
+        if self._sire_object.hasProperty("lipid"):
+            return True
+        else:
+            return False
+
     def isML(self):
         """
         Whether this molecule is marked as ML molecule, i.e. it can be used in a

tests/Sandpit/Exscientia/Process/test_position_restraint.py

@@ -167,6 +167,37 @@ def test_gromacs(protocol, system, ref_system, tmp_path):
     assert len(diff)
 
 
+@pytest.mark.skipif(
+    has_gromacs is False or has_openff is False,
+    reason="Requires GROMACS and openff to be installed",
+)
+@pytest.mark.parametrize("lipid", [True, False])
+def test_gromacs_lipid(system, tmp_path, lipid):
+    protocol = BSS.Protocol.Minimisation(restraint="heavy")
+    if lipid:
+        molecule = system.getMolecule(0)
+        sire_obj = molecule._sire_object
+        c = sire_obj.cursor()
+        c["lipid"] = True
+        molecule._sire_object = c.commit()
+        system.updateMolecule(0, molecule)
+    BSS.Process.Gromacs(
+        system,
+        protocol,
+        reference_system=system,
+        work_dir=str(tmp_path),
+        ignore_warnings=True,
+    )
+    if lipid is False:
+        assert (tmp_path / "posre_0001.itp").is_file()
+        with open(tmp_path / "gromacs.top", "r") as f:
+            assert "posre_0001.itp" in f.read()
+    else:
+        assert not (tmp_path / "posre_0001.itp").is_file()
+        with open(tmp_path / "gromacs.top", "r") as f:
+            assert not "posre_0001.itp" in f.read()
+
+
 @pytest.mark.skipif(
     has_amber is False or has_openff is False,
     reason="Requires AMBER and openff to be installed",

tests/Sandpit/Exscientia/_SireWrappers/test_molecule.py

@@ -2,7 +2,7 @@
 
 import BioSimSpace.Sandpit.Exscientia as BSS
 
-from tests.Sandpit.Exscientia.conftest import url, has_amber, has_pyarrow
+from tests.Sandpit.Exscientia.conftest import url, has_amber, has_openff, has_pyarrow
 from tests.conftest import root_fp
 
 
@@ -126,3 +126,20 @@ def test_extract(system):
 
     # Make sure the numbers are different.
     assert partial_mol.number() != mol.number()
+
+
+@pytest.mark.parametrize("lipid", [True, False])
+@pytest.mark.skipif(
+    has_amber is False or has_openff is False,
+    reason="Requires AMBER and OpenFF to be installed.",
+)
+def test_lipid(lipid):
+    ff = "openff_unconstrained-2.0.0"
+    mol = BSS.Parameters.parameterise("c1ccccc1C", ff).getMolecule()
+    if lipid:
+        sire_obj = mol._sire_object
+        c = sire_obj.cursor()
+        c["lipid"] = lipid
+        mol._sire_object = c.commit()
+
+    assert mol.isLipid() is lipid