From 605e2d159cda3fd369928e2823ed254565c8d34a Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Mon, 3 Jul 2023 18:25:14 +0100
Subject: [PATCH 01/17] Backport fix from PR #125. [ci skip]

---
 .github/workflows/devel.yaml                        | 10 +++++-----
 .github/workflows/pr.yaml                           | 10 +++++-----
 python/BioSimSpace/Process/_gromacs.py              | 13 +++++++++----
 python/BioSimSpace/Process/_openmm.py               | 10 +++++++---
 .../Sandpit/Exscientia/Process/_openmm.py           |  8 +++++++-
 .../Sandpit/Exscientia/Protocol/_config.py          |  8 +++++++-
 python/BioSimSpace/_Config/_config.py               | 12 ++++++++++--
 7 files changed, 50 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml
index 797741d97..c94a3cc27 100644
--- a/.github/workflows/devel.yaml
+++ b/.github/workflows/devel.yaml
@@ -13,7 +13,7 @@ jobs:
       max-parallel: 9
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
         platform:
           - { name: "windows", os: "windows-latest", shell: "pwsh" }
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
@@ -22,14 +22,14 @@ jobs:
           # Exclude all but the latest Python from all but Linux
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.8"
+            python-version: "3.9"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.8"
+            python-version: "3.9"
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.9"
+            python-version: "3.10"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.9"
+            python-version: "3.10"
     environment:
       name: biosimspace-build
     defaults:
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 6a4f15459..5e9268b58 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -12,7 +12,7 @@ jobs:
       max-parallel: 9
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
         platform:
           - { name: "windows", os: "windows-latest", shell: "pwsh" }
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
@@ -22,14 +22,14 @@ jobs:
           # but Linux
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.8"
+            python-version: "3.9"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.8"
+            python-version: "3.9"
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.9"
+            python-version: "3.10"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.9"
+            python-version: "3.10"
     environment:
       name: biosimspace-build
     defaults:
diff --git a/python/BioSimSpace/Process/_gromacs.py b/python/BioSimSpace/Process/_gromacs.py
index a3a3dd77a..5994f4e2e 100644
--- a/python/BioSimSpace/Process/_gromacs.py
+++ b/python/BioSimSpace/Process/_gromacs.py
@@ -286,10 +286,15 @@ def _generate_config(self):
         """Generate GROMACS configuration file strings."""
 
         # Check whether the system contains periodic box information.
-        # For now, well 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 self._system._sire_object.propertyKeys():
-            has_box = True
+        space_prop = self._property_map.get("space", "space")
+        if space_prop in self._system._sire_object.propertyKeys():
+            try:
+                # Make sure that we have a periodic box. The system will now have
+                # a default cartesian space.
+                box = self._system._sire_object.property(space_prop)
+                has_box = box.isPeriodic()
+            except:
+                has_box = False
         else:
             _warnings.warn("No simulation box found. Assuming gas phase simulation.")
             has_box = False
diff --git a/python/BioSimSpace/Process/_openmm.py b/python/BioSimSpace/Process/_openmm.py
index dc3bd8d2a..54af93ab6 100644
--- a/python/BioSimSpace/Process/_openmm.py
+++ b/python/BioSimSpace/Process/_openmm.py
@@ -283,10 +283,14 @@ def _generate_config(self):
         prop = self._property_map.get("space", "space")
 
         # Check whether the system contains periodic box information.
-        # 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 prop in self._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 = self._system._sire_object.property(prop)
+                has_box = box.isPeriodic()
+            except:
+                has_box = False
         else:
             _warnings.warn("No simulation box found. Assuming gas phase simulation.")
             has_box = False
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py
index a440a46d9..dcea9a2b5 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py
@@ -285,7 +285,13 @@ def _generate_config(self):
         # 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 prop in self._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 = self._system._sire_object.property(prop)
+                has_box = box.isPeriodic()
+            except:
+                has_box = False
         else:
             _warnings.warn("No simulation box found. Assuming gas phase simulation.")
             has_box = False
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py b/python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py
index 987cbb520..e71e1369d 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py
@@ -39,7 +39,13 @@ def __init__(self, system, protocol, explicit_dummies=False):
     def _has_box(self):
         """Return whether the current system has a box."""
         if "space" in self.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 = self.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
diff --git a/python/BioSimSpace/_Config/_config.py b/python/BioSimSpace/_Config/_config.py
index b372ca7e6..d8b5ce7ee 100644
--- a/python/BioSimSpace/_Config/_config.py
+++ b/python/BioSimSpace/_Config/_config.py
@@ -91,10 +91,18 @@ def hasBox(self):
         """
         space_prop = self._property_map.get("space", "space")
         if space_prop in self._system._sire_object.propertyKeys():
-            return True
+            try:
+                # Make sure that we have a periodic box. The system will now have
+                # a default cartesian space.
+                box = self._system._sire_object.property(space_prop)
+                has_box = box.isPeriodic()
+            except:
+                has_box = False
         else:
+            has_box = False
             _warnings.warn("No simulation box found. Assuming gas phase simulation.")
-            return False
+
+        return has_box
 
     def hasWater(self):
         """

From cbfef2e759728802e1f5ee89bd8e797085e6300e Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Fri, 7 Jul 2023 13:59:47 +0100
Subject: [PATCH 02/17] Backport fixes from PR #128. [ci skip]

---
 demo/interactive_md.ipynb                       | 10 +++++-----
 python/BioSimSpace/Process/_amber.py            | 15 +++++++++++++--
 python/BioSimSpace/Process/_gromacs.py          | 15 +++++++++++++--
 python/BioSimSpace/Process/_namd.py             | 16 ++++++++++++++--
 python/BioSimSpace/Process/_openmm.py           | 17 ++++++++++++++---
 python/BioSimSpace/Process/_plumed.py           |  8 +++++++-
 python/BioSimSpace/Process/_somd.py             | 15 +++++++++++++--
 .../Sandpit/Exscientia/Process/_amber.py        | 15 +++++++++++++--
 .../Sandpit/Exscientia/Process/_gromacs.py      | 15 +++++++++++++--
 .../Sandpit/Exscientia/Process/_namd.py         | 16 ++++++++++++++--
 .../Sandpit/Exscientia/Process/_openmm.py       | 17 ++++++++++++++---
 .../Sandpit/Exscientia/Process/_plumed.py       |  8 +++++++-
 .../Sandpit/Exscientia/Process/_somd.py         | 15 +++++++++++++--
 13 files changed, 153 insertions(+), 29 deletions(-)

diff --git a/demo/interactive_md.ipynb b/demo/interactive_md.ipynb
index 0b826f4bc..34f2293ff 100644
--- a/demo/interactive_md.ipynb
+++ b/demo/interactive_md.ipynb
@@ -336,14 +336,14 @@
    "outputs": [],
    "source": [
     "# Search the system for a residue named ALA. Since there is a single match, we take the first result.\n",
-    "residue = system.search(\"resname ALA\")[0]\n",
+    "atoms = system.search(\"resname ALA\")\n",
     "\n",
     "# Get the indices of the atoms in the molecule, relative to the original system.\n",
-    "indices = [system.getIndex(x) for x in residue.getAtoms()]\n",
+    "indices = [system.getIndex(atom) for atom in atoms]\n",
     "\n",
     "# Compute the RMSD for each frame and plot the result.\n",
     "BSS.Notebook.plot(\n",
-    "    y=process.getTrajectory().rmsd(frame=0, atoms=indices),\n",
+    "    y=process.getTrajectory(backend=\"mdtraj\").rmsd(frame=0, atoms=indices),\n",
     "    xlabel=\"Frame\",\n",
     "    ylabel=\"RMSD\",\n",
     ")"
@@ -352,7 +352,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -366,7 +366,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.10.11"
   }
  },
  "nbformat": 4,
diff --git a/python/BioSimSpace/Process/_amber.py b/python/BioSimSpace/Process/_amber.py
index 8533d325d..e755cf16c 100644
--- a/python/BioSimSpace/Process/_amber.py
+++ b/python/BioSimSpace/Process/_amber.py
@@ -461,13 +461,18 @@ def getCurrentSystem(self):
         """
         return self.getSystem(block=False)
 
-    def getTrajectory(self, block="AUTO"):
+    def getTrajectory(self, backend="AUTO", block="AUTO"):
         """
         Return a trajectory object.
 
         Parameters
         ----------
 
+        backend : str
+            The backend to use for trajectory parsing. To see supported backends,
+            run BioSimSpace.Trajectory.backends(). Using "AUTO" will try each in
+            sequence.
+
         block : bool
             Whether to block until the process has finished running.
 
@@ -478,6 +483,12 @@ def getTrajectory(self, block="AUTO"):
             The latest trajectory object.
         """
 
+        if not isinstance(backend, str):
+            raise TypeError("'backend' must be of type 'str'")
+
+        if not isinstance(block, (bool, str)):
+            raise TypeError("'block' must be of type 'bool' or 'str'")
+
         # Wait for the process to finish.
         if block is True:
             self.wait()
@@ -489,7 +500,7 @@ def getTrajectory(self, block="AUTO"):
             _warnings.warn("The process exited with an error!")
 
         try:
-            return _Trajectory.Trajectory(process=self)
+            return _Trajectory.Trajectory(process=self, backend=backend)
 
         except:
             return None
diff --git a/python/BioSimSpace/Process/_gromacs.py b/python/BioSimSpace/Process/_gromacs.py
index 5994f4e2e..98626325a 100644
--- a/python/BioSimSpace/Process/_gromacs.py
+++ b/python/BioSimSpace/Process/_gromacs.py
@@ -659,13 +659,18 @@ def getCurrentSystem(self):
         """
         return self.getSystem(block=False)
 
-    def getTrajectory(self, block="AUTO"):
+    def getTrajectory(self, backend="AUTO", block="AUTO"):
         """
         Return a trajectory object.
 
         Parameters
         ----------
 
+        backend : str
+            The backend to use for trajectory parsing. To see supported backends,
+            run BioSimSpace.Trajectory.backends(). Using "AUTO" will try each in
+            sequence.
+
         block : bool
             Whether to block until the process has finished running.
 
@@ -676,6 +681,12 @@ def getTrajectory(self, block="AUTO"):
             The latest trajectory object.
         """
 
+        if not isinstance(backend, str):
+            raise TypeError("'backend' must be of type 'str'")
+
+        if not isinstance(block, (bool, str)):
+            raise TypeError("'block' must be of type 'bool' or 'str'")
+
         # Wait for the process to finish.
         if block is True:
             self.wait()
@@ -695,7 +706,7 @@ def getTrajectory(self, block="AUTO"):
             else:
                 self._traj_file = traj_file
 
-            return _Trajectory.Trajectory(process=self)
+            return _Trajectory.Trajectory(process=self, backend=backend)
 
         except:
             return None
diff --git a/python/BioSimSpace/Process/_namd.py b/python/BioSimSpace/Process/_namd.py
index bb2b76d6c..571051e5c 100644
--- a/python/BioSimSpace/Process/_namd.py
+++ b/python/BioSimSpace/Process/_namd.py
@@ -813,13 +813,18 @@ def getCurrentSystem(self):
         """
         return self.getSystem(block=False)
 
-    def getTrajectory(self, block="AUTO"):
+    def getTrajectory(self, backend="AUTO", block="AUTO"):
         """
         Return a trajectory object.
 
         Parameters
         ----------
 
+        backend : str
+            The backend to use for trajectory parsing. To see supported backends,
+            run BioSimSpace.Trajectory.backends(). Using "AUTO" will try each in
+            sequence.
+
         block : bool
             Whether to block until the process has finished running.
 
@@ -829,6 +834,13 @@ def getTrajectory(self, block="AUTO"):
         trajectory : :class:`Trajectory <BioSimSpace.Trajectory>`
             The latest trajectory object.
         """
+
+        if not isinstance(backend, str):
+            raise TypeError("'backend' must be of type 'str'")
+
+        if not isinstance(block, (bool, str)):
+            raise TypeError("'block' must be of type 'bool' or 'str'")
+
         # Wait for the process to finish.
         if block is True:
             self.wait()
@@ -840,7 +852,7 @@ def getTrajectory(self, block="AUTO"):
             _warnings.warn("The process exited with an error!")
 
         try:
-            return _Trajectory.Trajectory(process=self)
+            return _Trajectory.Trajectory(process=self, backend=backend)
 
         except:
             return None
diff --git a/python/BioSimSpace/Process/_openmm.py b/python/BioSimSpace/Process/_openmm.py
index 54af93ab6..7a3f80a4d 100644
--- a/python/BioSimSpace/Process/_openmm.py
+++ b/python/BioSimSpace/Process/_openmm.py
@@ -1109,7 +1109,7 @@ def _generate_config(self):
 
             # Create a dummy PLUMED input file so that we can bind PLUMED
             # analysis functions to this process.
-            self._plumed = _Plumed(self._work_dir)
+            self._plumed = _Plumed(str(self._work_dir))
             plumed_config, auxillary_files = self._plumed.createConfig(
                 self._system, self._protocol, self._property_map
             )
@@ -1350,13 +1350,18 @@ def getCurrentSystem(self):
         """
         return self.getSystem(block=False)
 
-    def getTrajectory(self, block="AUTO"):
+    def getTrajectory(self, backend="AUTO", block="AUTO"):
         """
         Return a trajectory object.
 
         Parameters
         ----------
 
+        backend : str
+            The backend to use for trajectory parsing. To see supported backends,
+            run BioSimSpace.Trajectory.backends(). Using "AUTO" will try each in
+            sequence.
+
         block : bool
             Whether to block until the process has finished running.
 
@@ -1367,6 +1372,12 @@ def getTrajectory(self, block="AUTO"):
             The latest trajectory object.
         """
 
+        if not isinstance(backend, str):
+            raise TypeError("'backend' must be of type 'str'")
+
+        if not isinstance(block, (bool, str)):
+            raise TypeError("'block' must be of type 'bool' or 'str'")
+
         # Wait for the process to finish.
         if block is True:
             self.wait()
@@ -1380,7 +1391,7 @@ def getTrajectory(self, block="AUTO"):
         if not _os.path.isfile(self._traj_file):
             return None
         else:
-            return _Trajectory.Trajectory(process=self)
+            return _Trajectory.Trajectory(process=self, backend=backend)
 
     def getFrame(self, index):
         """
diff --git a/python/BioSimSpace/Process/_plumed.py b/python/BioSimSpace/Process/_plumed.py
index d113f1c22..9f3dfd52e 100644
--- a/python/BioSimSpace/Process/_plumed.py
+++ b/python/BioSimSpace/Process/_plumed.py
@@ -106,6 +106,10 @@ def __init__(self, work_dir):
                     "PLUMED version >= 2.5 is required."
                 )
 
+            # Store the major and minor versions.
+            self._plumed_major = major
+            self._plumed_minor = minor
+
         else:
             raise _Exceptions.IncompatibleError("Could not determine PLUMED version!")
 
@@ -377,7 +381,9 @@ def _createMetadynamicsConfig(self, system, protocol, property_map={}):
 
                 # The funnel collective variable requires an auxiliary file for
                 # PLUMED versions < 2.7.
-                if self._plumed_version < 2.7:
+                if self._plumed_major < 2 or (
+                    self._plumed_major < 3 and self._plumed_minor < 7
+                ):
                     aux_file = "ProjectionOnAxis.cpp"
                     self._config.append(f"LOAD FILE={aux_file}")
                     aux_file = (
diff --git a/python/BioSimSpace/Process/_somd.py b/python/BioSimSpace/Process/_somd.py
index 4d9d5e5e8..27582b2e5 100644
--- a/python/BioSimSpace/Process/_somd.py
+++ b/python/BioSimSpace/Process/_somd.py
@@ -585,13 +585,18 @@ def getCurrentSystem(self):
         """
         return self.getSystem(block=False)
 
-    def getTrajectory(self, block="AUTO"):
+    def getTrajectory(self, backend="AUTO", block="AUTO"):
         """
         Return a trajectory object.
 
         Parameters
         ----------
 
+        backend : str
+            The backend to use for trajectory parsing. To see supported backends,
+            run BioSimSpace.Trajectory.backends(). Using "AUTO" will try each in
+            sequence.
+
         block : bool
             Whether to block until the process has finished running.
 
@@ -602,6 +607,12 @@ def getTrajectory(self, block="AUTO"):
             The latest trajectory object.
         """
 
+        if not isinstance(backend, str):
+            raise TypeError("'backend' must be of type 'str'")
+
+        if not isinstance(block, (bool, str)):
+            raise TypeError("'block' must be of type 'bool' or 'str'")
+
         # Wait for the process to finish.
         if block is True:
             self.wait()
@@ -613,7 +624,7 @@ def getTrajectory(self, block="AUTO"):
             _warnings.warn("The process exited with an error!")
 
         try:
-            return _Trajectory.Trajectory(process=self)
+            return _Trajectory.Trajectory(process=self, backend=backend)
 
         except:
             return None
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py
index 10ea8de6f..7595ff33f 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py
@@ -708,13 +708,18 @@ def getCurrentSystem(self):
         """
         return self.getSystem(block=False)
 
-    def getTrajectory(self, block="AUTO"):
+    def getTrajectory(self, backend="AUTO", block="AUTO"):
         """
         Return a trajectory object.
 
         Parameters
         ----------
 
+        backend : str
+            The backend to use for trajectory parsing. To see supported backends,
+            run BioSimSpace.Trajectory.backends(). Using "AUTO" will try each in
+            sequence.
+
         block : bool
             Whether to block until the process has finished running.
 
@@ -725,6 +730,12 @@ def getTrajectory(self, block="AUTO"):
             The latest trajectory object.
         """
 
+        if not isinstance(backend, str):
+            raise TypeError("'backend' must be of type 'str'")
+
+        if not isinstance(block, (bool, str)):
+            raise TypeError("'block' must be of type 'bool' or 'str'")
+
         # Wait for the process to finish.
         if block is True:
             self.wait()
@@ -736,7 +747,7 @@ def getTrajectory(self, block="AUTO"):
             _warnings.warn("The process exited with an error!")
 
         try:
-            return _Trajectory.Trajectory(process=self)
+            return _Trajectory.Trajectory(process=self, backend=backend)
 
         except:
             return None
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py
index 2a53e58a9..4695d7af1 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py
@@ -704,13 +704,18 @@ def getCurrentSystem(self):
         """
         return self.getSystem(block=False)
 
-    def getTrajectory(self, block="AUTO"):
+    def getTrajectory(self, backend="AUTO", block="AUTO"):
         """
         Return a trajectory object.
 
         Parameters
         ----------
 
+        backend : str
+            The backend to use for trajectory parsing. To see supported backends,
+            run BioSimSpace.Trajectory.backends(). Using "AUTO" will try each in
+            sequence.
+
         block : bool
             Whether to block until the process has finished running.
 
@@ -721,6 +726,12 @@ def getTrajectory(self, block="AUTO"):
             The latest trajectory object.
         """
 
+        if not isinstance(backend, str):
+            raise TypeError("'backend' must be of type 'str'")
+
+        if not isinstance(block, (bool, str)):
+            raise TypeError("'block' must be of type 'bool' or 'str'")
+
         # Wait for the process to finish.
         if block is True:
             self.wait()
@@ -740,7 +751,7 @@ def getTrajectory(self, block="AUTO"):
             else:
                 self._traj_file = traj_file
 
-            return _Trajectory.Trajectory(process=self)
+            return _Trajectory.Trajectory(process=self, backend=backend)
 
         except:
             return None
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_namd.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_namd.py
index ac6dfaa7a..db585adaf 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Process/_namd.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Process/_namd.py
@@ -811,13 +811,18 @@ def getCurrentSystem(self):
         """
         return self.getSystem(block=False)
 
-    def getTrajectory(self, block="AUTO"):
+    def getTrajectory(self, backend="AUTO", block="AUTO"):
         """
         Return a trajectory object.
 
         Parameters
         ----------
 
+        backend : str
+            The backend to use for trajectory parsing. To see supported backends,
+            run BioSimSpace.Trajectory.backends(). Using "AUTO" will try each in
+            sequence.
+
         block : bool
             Whether to block until the process has finished running.
 
@@ -827,6 +832,13 @@ def getTrajectory(self, block="AUTO"):
         trajectory : :class:`Trajectory <BioSimSpace.Trajectory>`
             The latest trajectory object.
         """
+
+        if not isinstance(backend, str):
+            raise TypeError("'backend' must be of type 'str'")
+
+        if not isinstance(block, (bool, str)):
+            raise TypeError("'block' must be of type 'bool' or 'str'")
+
         # Wait for the process to finish.
         if block is True:
             self.wait()
@@ -838,7 +850,7 @@ def getTrajectory(self, block="AUTO"):
             _warnings.warn("The process exited with an error!")
 
         try:
-            return _Trajectory.Trajectory(process=self)
+            return _Trajectory.Trajectory(process=self, backend=backend)
 
         except:
             return None
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py
index dcea9a2b5..d6a1d42fd 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py
@@ -1109,7 +1109,7 @@ def _generate_config(self):
 
             # Create a dummy PLUMED input file so that we can bind PLUMED
             # analysis functions to this process.
-            self._plumed = _Plumed(self._work_dir)
+            self._plumed = _Plumed(str(self._work_dir))
             plumed_config, auxillary_files = self._plumed.createConfig(
                 self._system, self._protocol, self._property_map
             )
@@ -1350,13 +1350,18 @@ def getCurrentSystem(self):
         """
         return self.getSystem(block=False)
 
-    def getTrajectory(self, block="AUTO"):
+    def getTrajectory(self, backend="AUTO", block="AUTO"):
         """
         Return a trajectory object.
 
         Parameters
         ----------
 
+        backend : str
+            The backend to use for trajectory parsing. To see supported backends,
+            run BioSimSpace.Trajectory.backends(). Using "AUTO" will try each in
+            sequence.
+
         block : bool
             Whether to block until the process has finished running.
 
@@ -1367,6 +1372,12 @@ def getTrajectory(self, block="AUTO"):
             The latest trajectory object.
         """
 
+        if not isinstance(backend, str):
+            raise TypeError("'backend' must be of type 'str'")
+
+        if not isinstance(block, (bool, str)):
+            raise TypeError("'block' must be of type 'bool' or 'str'")
+
         # Wait for the process to finish.
         if block is True:
             self.wait()
@@ -1380,7 +1391,7 @@ def getTrajectory(self, block="AUTO"):
         if not _os.path.isfile(self._traj_file):
             return None
         else:
-            return _Trajectory.Trajectory(process=self)
+            return _Trajectory.Trajectory(process=self, backend=backend)
 
     def getFrame(self, index):
         """
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_plumed.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_plumed.py
index d113f1c22..9f3dfd52e 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Process/_plumed.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Process/_plumed.py
@@ -106,6 +106,10 @@ def __init__(self, work_dir):
                     "PLUMED version >= 2.5 is required."
                 )
 
+            # Store the major and minor versions.
+            self._plumed_major = major
+            self._plumed_minor = minor
+
         else:
             raise _Exceptions.IncompatibleError("Could not determine PLUMED version!")
 
@@ -377,7 +381,9 @@ def _createMetadynamicsConfig(self, system, protocol, property_map={}):
 
                 # The funnel collective variable requires an auxiliary file for
                 # PLUMED versions < 2.7.
-                if self._plumed_version < 2.7:
+                if self._plumed_major < 2 or (
+                    self._plumed_major < 3 and self._plumed_minor < 7
+                ):
                     aux_file = "ProjectionOnAxis.cpp"
                     self._config.append(f"LOAD FILE={aux_file}")
                     aux_file = (
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_somd.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_somd.py
index fbc1351c1..97882c198 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Process/_somd.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Process/_somd.py
@@ -600,13 +600,18 @@ def getCurrentSystem(self):
         """
         return self.getSystem(block=False)
 
-    def getTrajectory(self, block="AUTO"):
+    def getTrajectory(self, backend="AUTO", block="AUTO"):
         """
         Return a trajectory object.
 
         Parameters
         ----------
 
+        backend : str
+            The backend to use for trajectory parsing. To see supported backends,
+            run BioSimSpace.Trajectory.backends(). Using "AUTO" will try each in
+            sequence.
+
         block : bool
             Whether to block until the process has finished running.
 
@@ -617,6 +622,12 @@ def getTrajectory(self, block="AUTO"):
             The latest trajectory object.
         """
 
+        if not isinstance(backend, str):
+            raise TypeError("'backend' must be of type 'str'")
+
+        if not isinstance(block, (bool, str)):
+            raise TypeError("'block' must be of type 'bool' or 'str'")
+
         # Wait for the process to finish.
         if block is True:
             self.wait()
@@ -628,7 +639,7 @@ def getTrajectory(self, block="AUTO"):
             _warnings.warn("The process exited with an error!")
 
         try:
-            return _Trajectory.Trajectory(process=self)
+            return _Trajectory.Trajectory(process=self, backend=backend)
 
         except:
             return None

From d9c37e65f8b9706b16b0a7704e206b7a8025b76b Mon Sep 17 00:00:00 2001
From: "William (Zhiyi) Wu" <zwu@exscientia.co.uk>
Date: Thu, 13 Jul 2023 16:58:22 +0100
Subject: [PATCH 03/17] Fix the extract in the gmx.process

Update Sandpit_exs.yml

Signed-off-by: Zhiyi Wu <zwu@exscientia.ai>
Update Sandpit_exs.yml

Signed-off-by: Zhiyi Wu <zwu@exscientia.ai>
---
 .github/workflows/Sandpit_exs.yml                         | 6 ++----
 python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py | 2 +-
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/Sandpit_exs.yml b/.github/workflows/Sandpit_exs.yml
index 99616ce0e..1548f0d79 100644
--- a/.github/workflows/Sandpit_exs.yml
+++ b/.github/workflows/Sandpit_exs.yml
@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macOS-latest",]
-        python-version: ["3.8", ]
+        python-version: ["3.8",]
 
     steps:
       - uses: actions/checkout@v2
@@ -35,12 +35,10 @@ jobs:
 
       - name: Install dependency
         run: |
-          mamba install -c conda-forge -c openbiosim/label/main biosimspace python=3.8 ambertools gromacs "sire=2023.2.2" alchemlyb pytest pyarrow "typing-extensions!=4.6.0" openff-interchange pint=0.21 "rdkit<2023" "jaxlib>0.3.7" tqdm
+          mamba install -c conda-forge -c openbiosim/label/main biosimspace python=3.8 ambertools gromacs "sire=2023.3" "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
-          # Before the new alchemlyb is released
-          python -m pip install git+https://github.com/alchemistry/alchemlyb.git
 
       - name: Install the dev version
         run: |
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py
index 4695d7af1..a772e9090 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py
@@ -57,7 +57,7 @@
 _alchemlyb = _try_import("alchemlyb")
 
 if _have_imported(_alchemlyb):
-    from alchemlyb.parsing.amber import extract as _extract
+    from alchemlyb.parsing.gmx import extract as _extract
 
 from .. import _gmx_exe
 from .. import _isVerbose

From 64183f8c8bcb45cc3d2be7bb435c2943247bc45a Mon Sep 17 00:00:00 2001
From: Miroslav Suruzhon <36005076+msuruzhon@users.noreply.github.com>
Date: Mon, 31 Jul 2023 16:54:39 +0100
Subject: [PATCH 04/17] Fixed squash and unsquash in the case of explicit
 dummies (#18)

---
 .github/workflows/Sandpit_exs.yml             |  4 +-
 .../Sandpit/Exscientia/Align/_squash.py       | 87 +++++++++++++++----
 tests/Sandpit/Exscientia/Align/test_squash.py | 64 ++++++++++++--
 3 files changed, 130 insertions(+), 25 deletions(-)

diff --git a/.github/workflows/Sandpit_exs.yml b/.github/workflows/Sandpit_exs.yml
index 1548f0d79..4f7f9fad2 100644
--- a/.github/workflows/Sandpit_exs.yml
+++ b/.github/workflows/Sandpit_exs.yml
@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macOS-latest",]
-        python-version: ["3.8",]
+        python-version: ["3.10",]
 
     steps:
       - uses: actions/checkout@v2
@@ -35,7 +35,7 @@ jobs:
 
       - name: Install dependency
         run: |
-          mamba install -c conda-forge -c openbiosim/label/main biosimspace python=3.8 ambertools gromacs "sire=2023.3" "alchemlyb>=2.1" pytest openff-interchange pint=0.21 rdkit "jaxlib>0.3.7" tqdm
+          mamba install -c conda-forge -c openbiosim/label/main biosimspace python=3.10 ambertools gromacs "sire=2023.3" "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
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py b/python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py
index 6bc62793c..5193cfc83 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py
@@ -113,9 +113,30 @@ def _squash_molecule(molecule, explicit_dummies=False):
         return molecule
 
     if explicit_dummies:
-        # We make sure we use the same coordinates at both endstates.
+        # Get the common core atoms
+        atom_mapping0_common = _squashed_atom_mapping(
+            molecule,
+            is_lambda1=False,
+            explicit_dummies=explicit_dummies,
+            environment=False,
+            dummies=False,
+        )
+        atom_mapping1_common = _squashed_atom_mapping(
+            molecule,
+            is_lambda1=True,
+            explicit_dummies=explicit_dummies,
+            environment=False,
+            dummies=False,
+        )
+        if set(atom_mapping0_common) != set(atom_mapping1_common):
+            raise RuntimeError("The MCS atoms don't match between the two endstates")
+        common_atoms = set(atom_mapping0_common)
+
+        # We make sure we use the same coordinates for the common core at both endstates.
         c = molecule.copy()._sire_object.cursor()
-        c["coordinates1"] = c["coordinates0"]
+        for i, atom in enumerate(c.atoms()):
+            if i in common_atoms:
+                atom["coordinates1"] = atom["coordinates0"]
         molecule = _Molecule(c.commit())
 
     # Generate a "system" from the molecule at lambda = 0 and another copy at lambda = 1.
@@ -269,20 +290,38 @@ def _unsquash_molecule(molecule, squashed_molecules, explicit_dummies=False):
     molecule : BioSimSpace._SireWrappers.Molecule
          The output updated merged molecule.
     """
-    # Get the atom mapping and combine it with the lambda=0 molecule being prioritised
+    # Get the common core atoms
+    atom_mapping0_common = _squashed_atom_mapping(
+        molecule,
+        is_lambda1=False,
+        explicit_dummies=explicit_dummies,
+        environment=False,
+        dummies=False,
+    )
+    atom_mapping1_common = _squashed_atom_mapping(
+        molecule,
+        is_lambda1=True,
+        explicit_dummies=explicit_dummies,
+        environment=False,
+        dummies=False,
+    )
+    if set(atom_mapping0_common) != set(atom_mapping1_common):
+        raise RuntimeError("The MCS atoms don't match between the two endstates")
+    common_atoms = set(atom_mapping0_common)
+
+    # Get the atom mapping from both endstates
     atom_mapping0 = _squashed_atom_mapping(
         molecule, is_lambda1=False, explicit_dummies=explicit_dummies
     )
     atom_mapping1 = _squashed_atom_mapping(
         molecule, is_lambda1=True, explicit_dummies=explicit_dummies
     )
-    atom_mapping = {**atom_mapping1, **atom_mapping0}
     update_velocity = squashed_molecules[0]._sire_object.hasProperty("velocity")
 
-    # Even though the two molecules should have the same coordinates, they might be PBC wrapped differently.
+    # Even though the common core of the two molecules should have the same coordinates,
+    # they might be PBC wrapped differently.
     # Here we take the first common core atom and translate the second molecule.
     if len(squashed_molecules) == 2:
-        common_atoms = set(atom_mapping0.keys()) & set(atom_mapping1.keys())
         first_common_atom = list(sorted(common_atoms))[0]
         pertatom0 = squashed_molecules.getAtom(atom_mapping0[first_common_atom])
         pertatom1 = squashed_molecules.getAtom(atom_mapping1[first_common_atom])
@@ -292,25 +331,39 @@ def _unsquash_molecule(molecule, squashed_molecules, explicit_dummies=False):
 
     # Update the coordinates and velocities.
     siremol = molecule.copy()._sire_object.edit()
-    for merged_atom_idx, squashed_atom_idx in atom_mapping.items():
+    for merged_atom_idx in range(molecule.nAtoms()):
+        # Get the relevant atom indices
         merged_atom = siremol.atom(_SireMol.AtomIdx(merged_atom_idx))
-        squashed_atom = squashed_molecules.getAtom(squashed_atom_idx)
+        if merged_atom_idx in atom_mapping0:
+            squashed_atom_idx0 = atom_mapping0[merged_atom_idx]
+        else:
+            squashed_atom_idx0 = atom_mapping1[merged_atom_idx]
+        if merged_atom_idx in atom_mapping1:
+            squashed_atom_idx1 = atom_mapping1[merged_atom_idx]
+            apply_translation_vec = True
+        else:
+            squashed_atom_idx1 = atom_mapping0[merged_atom_idx]
+            apply_translation_vec = False
 
-        # Update the coordinates.
-        coordinates = squashed_atom._sire_object.property("coordinates")
+        # Get the coordinates.
+        squashed_atom0 = squashed_molecules.getAtom(squashed_atom_idx0)
+        squashed_atom1 = squashed_molecules.getAtom(squashed_atom_idx1)
+        coordinates0 = squashed_atom0._sire_object.property("coordinates")
+        coordinates1 = squashed_atom1._sire_object.property("coordinates")
 
         # Apply the translation if the atom is coming from the second molecule.
-        if len(squashed_molecules) == 2 and squashed_atom_idx in atom_mapping1.values():
-            coordinates -= translation_vec
+        if len(squashed_molecules) == 2 and apply_translation_vec:
+            coordinates1 -= translation_vec
 
-        siremol = merged_atom.setProperty("coordinates0", coordinates).molecule()
-        siremol = merged_atom.setProperty("coordinates1", coordinates).molecule()
+        siremol = merged_atom.setProperty("coordinates0", coordinates0).molecule()
+        siremol = merged_atom.setProperty("coordinates1", coordinates1).molecule()
 
         # Update the velocities.
         if update_velocity:
-            velocities = squashed_atom._sire_object.property("velocity")
-            siremol = merged_atom.setProperty("velocity0", velocities).molecule()
-            siremol = merged_atom.setProperty("velocity1", velocities).molecule()
+            velocities0 = squashed_atom0._sire_object.property("velocity")
+            velocities1 = squashed_atom1._sire_object.property("velocity")
+            siremol = merged_atom.setProperty("velocity0", velocities0).molecule()
+            siremol = merged_atom.setProperty("velocity1", velocities1).molecule()
 
     return _Molecule(siremol.commit())
 
diff --git a/tests/Sandpit/Exscientia/Align/test_squash.py b/tests/Sandpit/Exscientia/Align/test_squash.py
index 132cfdacf..bfcc29656 100644
--- a/tests/Sandpit/Exscientia/Align/test_squash.py
+++ b/tests/Sandpit/Exscientia/Align/test_squash.py
@@ -1,9 +1,22 @@
+import os
 import pickle
+
+import numpy as np
 import pytest
+import sire
+from sire.maths import Vector
 
 import BioSimSpace.Sandpit.Exscientia as BSS
 
-from tests.Sandpit.Exscientia.conftest import has_amber
+# Make sure AMBER is installed.
+if BSS._amber_home is not None:
+    exe = "%s/bin/sander" % BSS._amber_home
+    if os.path.isfile(exe):
+        has_amber = True
+    else:
+        has_amber = False
+else:
+    has_amber = False
 
 
 @pytest.fixture(scope="session")
@@ -30,6 +43,20 @@ def perturbed_system():
     return system
 
 
+@pytest.fixture(scope="session")
+def dual_topology_system():
+    mol_smiles = ["c1ccccc1", "c1ccccc1C"]
+    mols = [BSS.Parameters.gaff(smi).getMolecule() for smi in mol_smiles]
+    pertmol = BSS.Align.merge(mols[0], mols[1], mapping={0: 0})
+    c = pertmol._sire_object.cursor()
+    # Translate all atoms so that we have different coordinates between both endstates
+    for atom in c.atoms():
+        atom["coordinates1"] = atom["coordinates0"] + Vector(1, 1, 1)
+    pertmol = BSS._SireWrappers.Molecule(c.commit())
+    system = pertmol.toSystem()
+    return system
+
+
 @pytest.fixture
 def perturbed_tripeptide():
     return pickle.load(
@@ -118,21 +145,46 @@ def test_squashed_atom_mapping_explicit(perturbed_tripeptide, is_lambda1):
 
 @pytest.mark.skipif(has_amber is False, reason="Requires AMBER to be installed.")
 @pytest.mark.parametrize("explicit", [False, True])
-def test_unsquash(perturbed_system, explicit):
+def test_unsquash(dual_topology_system, explicit):
     squashed_system, mapping = BSS.Align._squash._squash(
-        perturbed_system, explicit_dummies=explicit
+        dual_topology_system, explicit_dummies=explicit
     )
     new_perturbed_system = BSS.Align._squash._unsquash(
-        perturbed_system, squashed_system, mapping, explicit_dummies=explicit
+        dual_topology_system, squashed_system, mapping, explicit_dummies=explicit
     )
     assert [
         mol0.nAtoms() == mol1.nAtoms()
-        for mol0, mol1 in zip(perturbed_system, new_perturbed_system)
+        for mol0, mol1 in zip(dual_topology_system, new_perturbed_system)
     ]
     assert [
         mol0.isPerturbable() == mol1.isPerturbable()
-        for mol0, mol1 in zip(perturbed_system, new_perturbed_system)
+        for mol0, mol1 in zip(dual_topology_system, new_perturbed_system)
     ]
+    if explicit:
+        # Check that we have loaded the correct coordinates
+        coords0_before = sire.io.get_coords_array(
+            dual_topology_system[0]._sire_object, map={"coordinates": "coordinates0"}
+        )
+        coords1_before = sire.io.get_coords_array(
+            dual_topology_system[0]._sire_object, map={"coordinates": "coordinates1"}
+        )
+        coords0_after = sire.io.get_coords_array(
+            new_perturbed_system[0]._sire_object, map={"coordinates": "coordinates0"}
+        )
+        coords1_after = sire.io.get_coords_array(
+            new_perturbed_system[0]._sire_object, map={"coordinates": "coordinates1"}
+        )
+
+        # The coordinates at the first endstate should be completely preserved
+        # Because in this case they are either common core, or separate dummies at lambda = 0
+        assert np.allclose(coords0_before, coords0_after)
+
+        # The coordinates at the first endstate should be partially preserved
+        # The common core must have the same coordinates as lambda = 0
+        # Here this is just a single atom in the beginning
+        # The extra atoms which are dummies at lambda = 0 have separate coordinates here
+        assert np.allclose(coords0_before[:1, :], coords1_after[:1, :])
+        assert np.allclose(coords1_before[1:, :], coords1_after[1:, :])
 
 
 @pytest.mark.parametrize("explicit", [False, True])

From 1f1802a99b4d773c449f7ac59e4654e5418c002b Mon Sep 17 00:00:00 2001
From: Zhiyi Wu <zwu@exscientia.ai>
Date: Wed, 16 Aug 2023 09:13:17 +0100
Subject: [PATCH 05/17] Make the saveMetric method more robust (#19)

Co-authored-by: William (Zhiyi) Wu <zwu@exscientia.co.uk>
---
 .../Sandpit/Exscientia/Process/_process.py    | 12 ++++++++-
 .../Sandpit/Exscientia/Process/test_amber.py  | 26 ++++++++++++++-----
 .../Exscientia/Process/test_gromacs.py        | 14 ++++++++++
 3 files changed, 45 insertions(+), 7 deletions(-)

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_process.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_process.py
index fd9c5db95..7809ab9ee 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Process/_process.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Process/_process.py
@@ -29,6 +29,7 @@
 import collections as _collections
 import glob as _glob
 import os as _os
+import traceback
 
 import pandas as pd
 
@@ -910,7 +911,16 @@ def wait(self, max_time=None):
 
         # The process isn't running.
         if not self.isRunning():
-            self.saveMetric()
+            try:
+                self.saveMetric()
+            except Exception:
+                exception_info = traceback.format_exc()
+                with open(f"{self.workDir()}/{self._name}.err", 'a+') as f:
+                    f.write("Exception Information during saveMetric():\n")
+                    f.write("======================\n")
+                    f.write(exception_info)
+                    f.write("\n\n")
+
             return
 
         if max_time is not None:
diff --git a/tests/Sandpit/Exscientia/Process/test_amber.py b/tests/Sandpit/Exscientia/Process/test_amber.py
index 86b0bb4ac..489f5bd84 100644
--- a/tests/Sandpit/Exscientia/Process/test_amber.py
+++ b/tests/Sandpit/Exscientia/Process/test_amber.py
@@ -320,14 +320,11 @@ def test_parse_fep_output(system, protocol):
         assert len(records_sc1) != 0
 
 
-@pytest.mark.skipif(
-    has_amber is False or has_pyarrow is False,
-    reason="Requires AMBER and pyarrow to be installed.",
-)
+
 class TestsaveMetric:
     @staticmethod
     @pytest.fixture()
-    def setup(system):
+    def alchemical_system(system):
         # Copy the system.
         system_copy = system.copy()
 
@@ -335,10 +332,15 @@ def setup(system):
         mol = system_copy[0]
         mol = BSS.Align.decouple(mol)
         system_copy.updateMolecule(0, mol)
+        return system_copy
+
 
+    @staticmethod
+    @pytest.fixture()
+    def setup(alchemical_system):
         # Create a process using any system and the protocol.
         process = BSS.Process.Amber(
-            system_copy,
+            alchemical_system,
             BSS.Protocol.FreeEnergy(temperature=298 * BSS.Units.Temperature.kelvin),
         )
         shutil.copyfile(
@@ -348,6 +350,18 @@ def setup(system):
         process.saveMetric()
         return process
 
+    def test_error_alchemlyb_extract(self, alchemical_system):
+        # Create a process using any system and the protocol.
+        process = BSS.Process.Amber(
+            alchemical_system,
+            BSS.Protocol.FreeEnergy(temperature=298 * BSS.Units.Temperature.kelvin),
+        )
+        process.wait()
+        with open(process.workDir() + '/amber.err', 'r') as f:
+            text = f.read()
+            assert 'Exception Information' in text
+
+
     def test_metric_parquet_exist(self, setup):
         assert Path(f"{setup.workDir()}/metric.parquet").exists()
 
diff --git a/tests/Sandpit/Exscientia/Process/test_gromacs.py b/tests/Sandpit/Exscientia/Process/test_gromacs.py
index ea08bf52f..1a42967c5 100644
--- a/tests/Sandpit/Exscientia/Process/test_gromacs.py
+++ b/tests/Sandpit/Exscientia/Process/test_gromacs.py
@@ -341,6 +341,20 @@ def test_u_nk_parquet(self, setup):
         df = pd.read_parquet(f"{setup.workDir()}/u_nk.parquet")
         assert df.shape == (1001, 20)
 
+    def test_error_alchemlyb_extract(self, perturbable_system, monkeypatch):
+        def extract(*args):
+            raise ValueError('alchemlyb.parsing.gmx.extract failed.')
+        monkeypatch.setattr('alchemlyb.parsing.gmx.extract', extract)
+        # Create a process using any system and the protocol.
+        process = BSS.Process.Gromacs(
+            perturbable_system,
+            BSS.Protocol.FreeEnergy(temperature=298 * BSS.Units.Temperature.kelvin),
+        )
+        process.wait()
+        with open(process.workDir() + '/gromacs.err', 'r') as f:
+            text = f.read()
+            assert 'Exception Information' in text
+
 
 @pytest.mark.skipif(
     has_amber is False

From f32838635e41ba8983b0a72ee00c7b1fee710cef Mon Sep 17 00:00:00 2001
From: Miroslav Suruzhon <36005076+msuruzhon@users.noreply.github.com>
Date: Fri, 1 Sep 2023 13:06:42 +0100
Subject: [PATCH 06/17] Merge some recent bugfixes (#24)

---
 .github/workflows/Sandpit_exs.yml             |  2 +-
 python/BioSimSpace/Convert/_convert.py        | 19 +++++++++++++--
 python/BioSimSpace/IO/_io.py                  | 23 +++++++++++++++++++
 .../Sandpit/Exscientia/Align/_squash.py       |  3 +++
 .../Sandpit/Exscientia/Convert/_convert.py    | 19 +++++++++++++--
 .../BioSimSpace/Sandpit/Exscientia/IO/_io.py  | 23 +++++++++++++++++++
 .../Sandpit/Exscientia/Process/_amber.py      | 13 +++++++----
 .../Exscientia/_SireWrappers/_system.py       | 17 --------------
 python/BioSimSpace/_SireWrappers/_system.py   | 17 --------------
 .../Exscientia/Process/test_gromacs.py        |  9 ++++----
 .../Process/test_position_restraint.py        | 16 ++++++-------
 11 files changed, 106 insertions(+), 55 deletions(-)

diff --git a/.github/workflows/Sandpit_exs.yml b/.github/workflows/Sandpit_exs.yml
index 4f7f9fad2..f55d08ace 100644
--- a/.github/workflows/Sandpit_exs.yml
+++ b/.github/workflows/Sandpit_exs.yml
@@ -35,7 +35,7 @@ jobs:
 
       - name: Install dependency
         run: |
-          mamba install -c conda-forge -c openbiosim/label/main biosimspace python=3.10 ambertools gromacs "sire=2023.3" "alchemlyb>=2.1" pytest openff-interchange pint=0.21 rdkit "jaxlib>0.3.7" tqdm
+          mamba install -c conda-forge -c openbiosim/label/main biosimspace python=3.10 ambertools gromacs "sire=2023.3" "alchemlyb>=2.1" pytest openff-interchange pint=0.21 rdkit "jaxlib>0.3.7" tqdm pyarrow=12.0.1
           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
diff --git a/python/BioSimSpace/Convert/_convert.py b/python/BioSimSpace/Convert/_convert.py
index 68a2910b3..3025e165f 100644
--- a/python/BioSimSpace/Convert/_convert.py
+++ b/python/BioSimSpace/Convert/_convert.py
@@ -49,6 +49,7 @@
 
 import sire.legacy.Mol as _SireMol
 import sire.legacy.System as _SireSystem
+import sire.legacy.Vol as _SireVol
 
 import sire.system as _NewSireSystem
 
@@ -205,14 +206,28 @@ def to(obj, format="biosimspace", property_map={}):
                 try:
                     obj = obj.toSystem()
                 except:
-                    # Otherwise, convert residues/atoms to a molecule.
+                    # Otherwise, convert residues/atoms to a molecule, then a system.
                     try:
-                        obj = obj.toMolecule()
+                        obj = obj.toMolecule().toSystem()
                     except:
                         raise _ConversionError(
                             "Unable to convert object to OpenMM format!"
                         )
 
+            # Get the user-defined space property name.
+            prop = property_map.get("space", "space")
+
+            # Try to get the space property. Use an infinite cartesian space
+            # if none is present.
+            try:
+                space = obj._sire_object.property(prop)
+            except:
+                space = _SireVol.Cartesian()
+
+            # Set a shared space property.
+            obj._sire_object.addSharedProperty(prop)
+            obj._sire_object.setSharedProperty(prop, space)
+
             # Now try to convert the object to OpenMM format.
             try:
                 return _sire_convert.to(
diff --git a/python/BioSimSpace/IO/_io.py b/python/BioSimSpace/IO/_io.py
index c36696051..36b4e548f 100644
--- a/python/BioSimSpace/IO/_io.py
+++ b/python/BioSimSpace/IO/_io.py
@@ -523,6 +523,29 @@ def readMolecules(
                 else:
                     raise IOError(msg) from None
 
+    # Add a file format shared property.
+    prop = property_map.get("fileformat", "fileformat")
+    system.addSharedProperty(prop)
+    system.setSharedProperty(prop, system.property(prop))
+
+    # Remove "space" and "time" shared properties since this causes incorrect
+    # behaviour when extracting molecules and recombining them to make other
+    # systems.
+    try:
+        # Space.
+        prop = property_map.get("space", "space")
+        space = system.property(prop)
+        system.removeSharedProperty(prop)
+        system.setProperty(prop, space)
+
+        # Time.
+        prop = property_map.get("time", "time")
+        time = system.property(prop)
+        system.removeSharedProperty(prop)
+        system.setProperties(prop, time)
+    except:
+        pass
+
     return _System(system)
 
 
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py b/python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py
index 5193cfc83..a7377f7b1 100644
--- 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/python/BioSimSpace/Sandpit/Exscientia/Convert/_convert.py b/python/BioSimSpace/Sandpit/Exscientia/Convert/_convert.py
index 68a2910b3..3025e165f 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Convert/_convert.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Convert/_convert.py
@@ -49,6 +49,7 @@
 
 import sire.legacy.Mol as _SireMol
 import sire.legacy.System as _SireSystem
+import sire.legacy.Vol as _SireVol
 
 import sire.system as _NewSireSystem
 
@@ -205,14 +206,28 @@ def to(obj, format="biosimspace", property_map={}):
                 try:
                     obj = obj.toSystem()
                 except:
-                    # Otherwise, convert residues/atoms to a molecule.
+                    # Otherwise, convert residues/atoms to a molecule, then a system.
                     try:
-                        obj = obj.toMolecule()
+                        obj = obj.toMolecule().toSystem()
                     except:
                         raise _ConversionError(
                             "Unable to convert object to OpenMM format!"
                         )
 
+            # Get the user-defined space property name.
+            prop = property_map.get("space", "space")
+
+            # Try to get the space property. Use an infinite cartesian space
+            # if none is present.
+            try:
+                space = obj._sire_object.property(prop)
+            except:
+                space = _SireVol.Cartesian()
+
+            # Set a shared space property.
+            obj._sire_object.addSharedProperty(prop)
+            obj._sire_object.setSharedProperty(prop, space)
+
             # Now try to convert the object to OpenMM format.
             try:
                 return _sire_convert.to(
diff --git a/python/BioSimSpace/Sandpit/Exscientia/IO/_io.py b/python/BioSimSpace/Sandpit/Exscientia/IO/_io.py
index c36696051..36b4e548f 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/IO/_io.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/IO/_io.py
@@ -523,6 +523,29 @@ def readMolecules(
                 else:
                     raise IOError(msg) from None
 
+    # Add a file format shared property.
+    prop = property_map.get("fileformat", "fileformat")
+    system.addSharedProperty(prop)
+    system.setSharedProperty(prop, system.property(prop))
+
+    # Remove "space" and "time" shared properties since this causes incorrect
+    # behaviour when extracting molecules and recombining them to make other
+    # systems.
+    try:
+        # Space.
+        prop = property_map.get("space", "space")
+        space = system.property(prop)
+        system.removeSharedProperty(prop)
+        system.setProperty(prop, space)
+
+        # Time.
+        prop = property_map.get("time", "time")
+        time = system.property(prop)
+        system.removeSharedProperty(prop)
+        system.setProperties(prop, time)
+    except:
+        pass
+
     return _System(system)
 
 
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py
index 7595ff33f..742ad8459 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py
@@ -27,6 +27,7 @@
 __all__ = ["Amber"]
 
 import os
+import shutil
 from pathlib import Path as _Path
 
 from .._Utils import _try_import
@@ -303,9 +304,11 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
         if coord_file is not None:
             try:
                 file = _os.path.splitext(coord_file)[0]
-                _IO.saveMolecules(file, system, "rst7", property_map=self._property_map)
+                _IO.saveMolecules(file, system, "rst", property_map=self._property_map)
+                # To keep the file extension the same.
+                shutil.move(f"{file}.rst", f"{file}.rst7")
             except Exception as e:
-                msg = "Failed to write system to 'RST7' format."
+                msg = "Failed to write system to 'rst7' format."
                 if _isVerbose():
                     raise IOError(msg) from e
                 else:
@@ -315,9 +318,11 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
         if ref_file is not None:
             try:
                 file = _os.path.splitext(ref_file)[0]
-                _IO.saveMolecules(file, system, "rst7", property_map=self._property_map)
+                _IO.saveMolecules(file, system, "rst", property_map=self._property_map)
+                # To keep the file extension the same.
+                shutil.move(f"{file}.rst", f"{file}.rst7")
             except Exception as e:
-                msg = "Failed to write system to 'RST7' format."
+                msg = "Failed to write system to 'rst7' format."
                 if _isVerbose():
                     raise IOError(msg) from e
                 else:
diff --git a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
index 701cf81d2..8793472ef 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
@@ -136,23 +136,6 @@ def __init__(self, system):
         # Initialise the iterator counter.
         self._iter_count = 0
 
-        # Copy any fileformat property to each molecule.
-        if "fileformat" in self._sire_object.propertyKeys():
-            fileformat = self._sire_object.property("fileformat")
-            for num in self._mol_nums:
-                edit_mol = self._sire_object[num].edit()
-                edit_mol = edit_mol.setProperty("fileformat", fileformat)
-                self._sire_object.update(edit_mol.commit())
-        else:
-            # If a molecule has a fileformat property, use the first
-            # that we find.
-            for mol in self:
-                if mol._sire_object.hasProperty("fileformat"):
-                    self._sire_object.setProperty(
-                        "fileformat", mol._sire_object.property("fileformat")
-                    )
-                    break
-
         # Reset the index mappings.
         self._reset_mappings()
 
diff --git a/python/BioSimSpace/_SireWrappers/_system.py b/python/BioSimSpace/_SireWrappers/_system.py
index 140a66f5b..14ef3ba65 100644
--- a/python/BioSimSpace/_SireWrappers/_system.py
+++ b/python/BioSimSpace/_SireWrappers/_system.py
@@ -136,23 +136,6 @@ def __init__(self, system):
         # Initialise the iterator counter.
         self._iter_count = 0
 
-        # Copy any fileformat property to each molecule.
-        if "fileformat" in self._sire_object.propertyKeys():
-            fileformat = self._sire_object.property("fileformat")
-            for num in self._mol_nums:
-                edit_mol = self._sire_object[num].edit()
-                edit_mol = edit_mol.setProperty("fileformat", fileformat)
-                self._sire_object.update(edit_mol.commit())
-        else:
-            # If a molecule has a fileformat property, use the first
-            # that we find.
-            for mol in self:
-                if mol._sire_object.hasProperty("fileformat"):
-                    self._sire_object.setProperty(
-                        "fileformat", mol._sire_object.property("fileformat")
-                    )
-                    break
-
         # Reset the index mappings.
         self._reset_mappings()
 
diff --git a/tests/Sandpit/Exscientia/Process/test_gromacs.py b/tests/Sandpit/Exscientia/Process/test_gromacs.py
index 1a42967c5..8d7f6c4fd 100644
--- a/tests/Sandpit/Exscientia/Process/test_gromacs.py
+++ b/tests/Sandpit/Exscientia/Process/test_gromacs.py
@@ -343,17 +343,18 @@ def test_u_nk_parquet(self, setup):
 
     def test_error_alchemlyb_extract(self, perturbable_system, monkeypatch):
         def extract(*args):
-            raise ValueError('alchemlyb.parsing.gmx.extract failed.')
-        monkeypatch.setattr('alchemlyb.parsing.gmx.extract', extract)
+            raise ValueError("alchemlyb.parsing.gmx.extract failed.")
+
+        monkeypatch.setattr("alchemlyb.parsing.gmx.extract", extract)
         # Create a process using any system and the protocol.
         process = BSS.Process.Gromacs(
             perturbable_system,
             BSS.Protocol.FreeEnergy(temperature=298 * BSS.Units.Temperature.kelvin),
         )
         process.wait()
-        with open(process.workDir() + '/gromacs.err', 'r') as f:
+        with open(process.workDir() + "/gromacs.err", "r") as f:
             text = f.read()
-            assert 'Exception Information' in text
+            assert "Exception Information" in text
 
 
 @pytest.mark.skipif(
diff --git a/tests/Sandpit/Exscientia/Process/test_position_restraint.py b/tests/Sandpit/Exscientia/Process/test_position_restraint.py
index 45697b9ed..aa720c470 100644
--- a/tests/Sandpit/Exscientia/Process/test_position_restraint.py
+++ b/tests/Sandpit/Exscientia/Process/test_position_restraint.py
@@ -5,6 +5,7 @@
 
 import pandas as pd
 import pytest
+from sire.legacy.IO import AmberRst
 
 import BioSimSpace.Sandpit.Exscientia as BSS
 from BioSimSpace.Sandpit.Exscientia.Units.Energy import kj_per_mol
@@ -121,8 +122,8 @@ def test_gromacs(protocol, system, ref_system, tmp_path):
 
 
 @pytest.mark.skipif(
-    has_gromacs is False or has_openff is False,
-    reason="Requires AMBER and openff to be installed",
+    has_openff is False,
+    reason="Requires openff to be installed",
 )
 def test_amber(protocol, system, ref_system, tmp_path):
     proc = BSS.Process.Amber(
@@ -137,12 +138,11 @@ def test_amber(protocol, system, ref_system, tmp_path):
 
     # We have generated a separate restraint reference
     assert os.path.exists(proc._ref_file)
-    contents_ref, contents_rst = (
-        open(proc._ref_file).readlines(),
-        open(proc._rst_file).readlines(),
-    )
-    diff = list(unified_diff(contents_ref, contents_rst))
-    assert len(diff)
+
+    ref = AmberRst(proc._ref_file).getFrame(0)
+    rst = AmberRst(proc._rst_file).getFrame(0)
+
+    assert ref != rst
 
     # We are pointing the reference to the correct file
     assert f"{proc._work_dir}/{proc.getArgs()['-ref']}" == proc._ref_file

From 24bbaa05d3241635d6946d589a64b68f366cb327 Mon Sep 17 00:00:00 2001
From: Miroslav Suruzhon <msuruzhon@exscientia.co.uk>
Date: Mon, 4 Sep 2023 15:03:10 +0100
Subject: [PATCH 07/17] Revert "Merge some recent bugfixes (#24)"

This reverts commit f32838635e41ba8983b0a72ee00c7b1fee710cef.
---
 .github/workflows/Sandpit_exs.yml             |  2 +-
 python/BioSimSpace/Convert/_convert.py        | 19 ++-------------
 python/BioSimSpace/IO/_io.py                  | 23 -------------------
 .../Sandpit/Exscientia/Align/_squash.py       |  3 ---
 .../Sandpit/Exscientia/Convert/_convert.py    | 19 ++-------------
 .../BioSimSpace/Sandpit/Exscientia/IO/_io.py  | 23 -------------------
 .../Sandpit/Exscientia/Process/_amber.py      | 13 ++++-------
 .../Exscientia/_SireWrappers/_system.py       | 17 ++++++++++++++
 python/BioSimSpace/_SireWrappers/_system.py   | 17 ++++++++++++++
 .../Exscientia/Process/test_gromacs.py        |  9 ++++----
 .../Process/test_position_restraint.py        | 16 ++++++-------
 11 files changed, 55 insertions(+), 106 deletions(-)

diff --git a/.github/workflows/Sandpit_exs.yml b/.github/workflows/Sandpit_exs.yml
index f55d08ace..4f7f9fad2 100644
--- a/.github/workflows/Sandpit_exs.yml
+++ b/.github/workflows/Sandpit_exs.yml
@@ -35,7 +35,7 @@ jobs:
 
       - name: Install dependency
         run: |
-          mamba install -c conda-forge -c openbiosim/label/main biosimspace python=3.10 ambertools gromacs "sire=2023.3" "alchemlyb>=2.1" pytest openff-interchange pint=0.21 rdkit "jaxlib>0.3.7" tqdm pyarrow=12.0.1
+          mamba install -c conda-forge -c openbiosim/label/main biosimspace python=3.10 ambertools gromacs "sire=2023.3" "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
diff --git a/python/BioSimSpace/Convert/_convert.py b/python/BioSimSpace/Convert/_convert.py
index 3025e165f..68a2910b3 100644
--- a/python/BioSimSpace/Convert/_convert.py
+++ b/python/BioSimSpace/Convert/_convert.py
@@ -49,7 +49,6 @@
 
 import sire.legacy.Mol as _SireMol
 import sire.legacy.System as _SireSystem
-import sire.legacy.Vol as _SireVol
 
 import sire.system as _NewSireSystem
 
@@ -206,28 +205,14 @@ def to(obj, format="biosimspace", property_map={}):
                 try:
                     obj = obj.toSystem()
                 except:
-                    # Otherwise, convert residues/atoms to a molecule, then a system.
+                    # Otherwise, convert residues/atoms to a molecule.
                     try:
-                        obj = obj.toMolecule().toSystem()
+                        obj = obj.toMolecule()
                     except:
                         raise _ConversionError(
                             "Unable to convert object to OpenMM format!"
                         )
 
-            # Get the user-defined space property name.
-            prop = property_map.get("space", "space")
-
-            # Try to get the space property. Use an infinite cartesian space
-            # if none is present.
-            try:
-                space = obj._sire_object.property(prop)
-            except:
-                space = _SireVol.Cartesian()
-
-            # Set a shared space property.
-            obj._sire_object.addSharedProperty(prop)
-            obj._sire_object.setSharedProperty(prop, space)
-
             # Now try to convert the object to OpenMM format.
             try:
                 return _sire_convert.to(
diff --git a/python/BioSimSpace/IO/_io.py b/python/BioSimSpace/IO/_io.py
index 36b4e548f..c36696051 100644
--- a/python/BioSimSpace/IO/_io.py
+++ b/python/BioSimSpace/IO/_io.py
@@ -523,29 +523,6 @@ def readMolecules(
                 else:
                     raise IOError(msg) from None
 
-    # Add a file format shared property.
-    prop = property_map.get("fileformat", "fileformat")
-    system.addSharedProperty(prop)
-    system.setSharedProperty(prop, system.property(prop))
-
-    # Remove "space" and "time" shared properties since this causes incorrect
-    # behaviour when extracting molecules and recombining them to make other
-    # systems.
-    try:
-        # Space.
-        prop = property_map.get("space", "space")
-        space = system.property(prop)
-        system.removeSharedProperty(prop)
-        system.setProperty(prop, space)
-
-        # Time.
-        prop = property_map.get("time", "time")
-        time = system.property(prop)
-        system.removeSharedProperty(prop)
-        system.setProperties(prop, time)
-    except:
-        pass
-
     return _System(system)
 
 
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py b/python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py
index a7377f7b1..5193cfc83 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py
@@ -353,9 +353,6 @@ 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/python/BioSimSpace/Sandpit/Exscientia/Convert/_convert.py b/python/BioSimSpace/Sandpit/Exscientia/Convert/_convert.py
index 3025e165f..68a2910b3 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Convert/_convert.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Convert/_convert.py
@@ -49,7 +49,6 @@
 
 import sire.legacy.Mol as _SireMol
 import sire.legacy.System as _SireSystem
-import sire.legacy.Vol as _SireVol
 
 import sire.system as _NewSireSystem
 
@@ -206,28 +205,14 @@ def to(obj, format="biosimspace", property_map={}):
                 try:
                     obj = obj.toSystem()
                 except:
-                    # Otherwise, convert residues/atoms to a molecule, then a system.
+                    # Otherwise, convert residues/atoms to a molecule.
                     try:
-                        obj = obj.toMolecule().toSystem()
+                        obj = obj.toMolecule()
                     except:
                         raise _ConversionError(
                             "Unable to convert object to OpenMM format!"
                         )
 
-            # Get the user-defined space property name.
-            prop = property_map.get("space", "space")
-
-            # Try to get the space property. Use an infinite cartesian space
-            # if none is present.
-            try:
-                space = obj._sire_object.property(prop)
-            except:
-                space = _SireVol.Cartesian()
-
-            # Set a shared space property.
-            obj._sire_object.addSharedProperty(prop)
-            obj._sire_object.setSharedProperty(prop, space)
-
             # Now try to convert the object to OpenMM format.
             try:
                 return _sire_convert.to(
diff --git a/python/BioSimSpace/Sandpit/Exscientia/IO/_io.py b/python/BioSimSpace/Sandpit/Exscientia/IO/_io.py
index 36b4e548f..c36696051 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/IO/_io.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/IO/_io.py
@@ -523,29 +523,6 @@ def readMolecules(
                 else:
                     raise IOError(msg) from None
 
-    # Add a file format shared property.
-    prop = property_map.get("fileformat", "fileformat")
-    system.addSharedProperty(prop)
-    system.setSharedProperty(prop, system.property(prop))
-
-    # Remove "space" and "time" shared properties since this causes incorrect
-    # behaviour when extracting molecules and recombining them to make other
-    # systems.
-    try:
-        # Space.
-        prop = property_map.get("space", "space")
-        space = system.property(prop)
-        system.removeSharedProperty(prop)
-        system.setProperty(prop, space)
-
-        # Time.
-        prop = property_map.get("time", "time")
-        time = system.property(prop)
-        system.removeSharedProperty(prop)
-        system.setProperties(prop, time)
-    except:
-        pass
-
     return _System(system)
 
 
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py
index 742ad8459..7595ff33f 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py
@@ -27,7 +27,6 @@
 __all__ = ["Amber"]
 
 import os
-import shutil
 from pathlib import Path as _Path
 
 from .._Utils import _try_import
@@ -304,11 +303,9 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
         if coord_file is not None:
             try:
                 file = _os.path.splitext(coord_file)[0]
-                _IO.saveMolecules(file, system, "rst", property_map=self._property_map)
-                # To keep the file extension the same.
-                shutil.move(f"{file}.rst", f"{file}.rst7")
+                _IO.saveMolecules(file, system, "rst7", property_map=self._property_map)
             except Exception as e:
-                msg = "Failed to write system to 'rst7' format."
+                msg = "Failed to write system to 'RST7' format."
                 if _isVerbose():
                     raise IOError(msg) from e
                 else:
@@ -318,11 +315,9 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
         if ref_file is not None:
             try:
                 file = _os.path.splitext(ref_file)[0]
-                _IO.saveMolecules(file, system, "rst", property_map=self._property_map)
-                # To keep the file extension the same.
-                shutil.move(f"{file}.rst", f"{file}.rst7")
+                _IO.saveMolecules(file, system, "rst7", property_map=self._property_map)
             except Exception as e:
-                msg = "Failed to write system to 'rst7' format."
+                msg = "Failed to write system to 'RST7' format."
                 if _isVerbose():
                     raise IOError(msg) from e
                 else:
diff --git a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
index 8793472ef..701cf81d2 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
@@ -136,6 +136,23 @@ def __init__(self, system):
         # Initialise the iterator counter.
         self._iter_count = 0
 
+        # Copy any fileformat property to each molecule.
+        if "fileformat" in self._sire_object.propertyKeys():
+            fileformat = self._sire_object.property("fileformat")
+            for num in self._mol_nums:
+                edit_mol = self._sire_object[num].edit()
+                edit_mol = edit_mol.setProperty("fileformat", fileformat)
+                self._sire_object.update(edit_mol.commit())
+        else:
+            # If a molecule has a fileformat property, use the first
+            # that we find.
+            for mol in self:
+                if mol._sire_object.hasProperty("fileformat"):
+                    self._sire_object.setProperty(
+                        "fileformat", mol._sire_object.property("fileformat")
+                    )
+                    break
+
         # Reset the index mappings.
         self._reset_mappings()
 
diff --git a/python/BioSimSpace/_SireWrappers/_system.py b/python/BioSimSpace/_SireWrappers/_system.py
index 14ef3ba65..140a66f5b 100644
--- a/python/BioSimSpace/_SireWrappers/_system.py
+++ b/python/BioSimSpace/_SireWrappers/_system.py
@@ -136,6 +136,23 @@ def __init__(self, system):
         # Initialise the iterator counter.
         self._iter_count = 0
 
+        # Copy any fileformat property to each molecule.
+        if "fileformat" in self._sire_object.propertyKeys():
+            fileformat = self._sire_object.property("fileformat")
+            for num in self._mol_nums:
+                edit_mol = self._sire_object[num].edit()
+                edit_mol = edit_mol.setProperty("fileformat", fileformat)
+                self._sire_object.update(edit_mol.commit())
+        else:
+            # If a molecule has a fileformat property, use the first
+            # that we find.
+            for mol in self:
+                if mol._sire_object.hasProperty("fileformat"):
+                    self._sire_object.setProperty(
+                        "fileformat", mol._sire_object.property("fileformat")
+                    )
+                    break
+
         # Reset the index mappings.
         self._reset_mappings()
 
diff --git a/tests/Sandpit/Exscientia/Process/test_gromacs.py b/tests/Sandpit/Exscientia/Process/test_gromacs.py
index 8d7f6c4fd..1a42967c5 100644
--- a/tests/Sandpit/Exscientia/Process/test_gromacs.py
+++ b/tests/Sandpit/Exscientia/Process/test_gromacs.py
@@ -343,18 +343,17 @@ def test_u_nk_parquet(self, setup):
 
     def test_error_alchemlyb_extract(self, perturbable_system, monkeypatch):
         def extract(*args):
-            raise ValueError("alchemlyb.parsing.gmx.extract failed.")
-
-        monkeypatch.setattr("alchemlyb.parsing.gmx.extract", extract)
+            raise ValueError('alchemlyb.parsing.gmx.extract failed.')
+        monkeypatch.setattr('alchemlyb.parsing.gmx.extract', extract)
         # Create a process using any system and the protocol.
         process = BSS.Process.Gromacs(
             perturbable_system,
             BSS.Protocol.FreeEnergy(temperature=298 * BSS.Units.Temperature.kelvin),
         )
         process.wait()
-        with open(process.workDir() + "/gromacs.err", "r") as f:
+        with open(process.workDir() + '/gromacs.err', 'r') as f:
             text = f.read()
-            assert "Exception Information" in text
+            assert 'Exception Information' in text
 
 
 @pytest.mark.skipif(
diff --git a/tests/Sandpit/Exscientia/Process/test_position_restraint.py b/tests/Sandpit/Exscientia/Process/test_position_restraint.py
index aa720c470..45697b9ed 100644
--- a/tests/Sandpit/Exscientia/Process/test_position_restraint.py
+++ b/tests/Sandpit/Exscientia/Process/test_position_restraint.py
@@ -5,7 +5,6 @@
 
 import pandas as pd
 import pytest
-from sire.legacy.IO import AmberRst
 
 import BioSimSpace.Sandpit.Exscientia as BSS
 from BioSimSpace.Sandpit.Exscientia.Units.Energy import kj_per_mol
@@ -122,8 +121,8 @@ def test_gromacs(protocol, system, ref_system, tmp_path):
 
 
 @pytest.mark.skipif(
-    has_openff is False,
-    reason="Requires openff to be installed",
+    has_gromacs is False or has_openff is False,
+    reason="Requires AMBER and openff to be installed",
 )
 def test_amber(protocol, system, ref_system, tmp_path):
     proc = BSS.Process.Amber(
@@ -138,11 +137,12 @@ def test_amber(protocol, system, ref_system, tmp_path):
 
     # We have generated a separate restraint reference
     assert os.path.exists(proc._ref_file)
-
-    ref = AmberRst(proc._ref_file).getFrame(0)
-    rst = AmberRst(proc._rst_file).getFrame(0)
-
-    assert ref != rst
+    contents_ref, contents_rst = (
+        open(proc._ref_file).readlines(),
+        open(proc._rst_file).readlines(),
+    )
+    diff = list(unified_diff(contents_ref, contents_rst))
+    assert len(diff)
 
     # We are pointing the reference to the correct file
     assert f"{proc._work_dir}/{proc.getArgs()['-ref']}" == proc._ref_file

From f9bed330ff5cfa2850b0a5865052b3ccd9ecfb53 Mon Sep 17 00:00:00 2001
From: Miroslav Suruzhon <36005076+msuruzhon@users.noreply.github.com>
Date: Mon, 18 Sep 2023 11:10:01 +0100
Subject: [PATCH 08/17] Added some fixes to the solvation (#25)

Co-authored-by: Lester Hedges <lester.hedges@gmail.com>
---
 python/BioSimSpace/Convert/_convert.py        | 19 +++++++++++++--
 python/BioSimSpace/IO/_io.py                  | 23 +++++++++++++++++++
 .../Sandpit/Exscientia/Convert/_convert.py    | 19 +++++++++++++--
 .../BioSimSpace/Sandpit/Exscientia/IO/_io.py  | 23 +++++++++++++++++++
 .../Exscientia/_SireWrappers/_system.py       | 17 --------------
 python/BioSimSpace/_SireWrappers/_system.py   | 17 --------------
 6 files changed, 80 insertions(+), 38 deletions(-)

diff --git a/python/BioSimSpace/Convert/_convert.py b/python/BioSimSpace/Convert/_convert.py
index 68a2910b3..3025e165f 100644
--- a/python/BioSimSpace/Convert/_convert.py
+++ b/python/BioSimSpace/Convert/_convert.py
@@ -49,6 +49,7 @@
 
 import sire.legacy.Mol as _SireMol
 import sire.legacy.System as _SireSystem
+import sire.legacy.Vol as _SireVol
 
 import sire.system as _NewSireSystem
 
@@ -205,14 +206,28 @@ def to(obj, format="biosimspace", property_map={}):
                 try:
                     obj = obj.toSystem()
                 except:
-                    # Otherwise, convert residues/atoms to a molecule.
+                    # Otherwise, convert residues/atoms to a molecule, then a system.
                     try:
-                        obj = obj.toMolecule()
+                        obj = obj.toMolecule().toSystem()
                     except:
                         raise _ConversionError(
                             "Unable to convert object to OpenMM format!"
                         )
 
+            # Get the user-defined space property name.
+            prop = property_map.get("space", "space")
+
+            # Try to get the space property. Use an infinite cartesian space
+            # if none is present.
+            try:
+                space = obj._sire_object.property(prop)
+            except:
+                space = _SireVol.Cartesian()
+
+            # Set a shared space property.
+            obj._sire_object.addSharedProperty(prop)
+            obj._sire_object.setSharedProperty(prop, space)
+
             # Now try to convert the object to OpenMM format.
             try:
                 return _sire_convert.to(
diff --git a/python/BioSimSpace/IO/_io.py b/python/BioSimSpace/IO/_io.py
index c36696051..36b4e548f 100644
--- a/python/BioSimSpace/IO/_io.py
+++ b/python/BioSimSpace/IO/_io.py
@@ -523,6 +523,29 @@ def readMolecules(
                 else:
                     raise IOError(msg) from None
 
+    # Add a file format shared property.
+    prop = property_map.get("fileformat", "fileformat")
+    system.addSharedProperty(prop)
+    system.setSharedProperty(prop, system.property(prop))
+
+    # Remove "space" and "time" shared properties since this causes incorrect
+    # behaviour when extracting molecules and recombining them to make other
+    # systems.
+    try:
+        # Space.
+        prop = property_map.get("space", "space")
+        space = system.property(prop)
+        system.removeSharedProperty(prop)
+        system.setProperty(prop, space)
+
+        # Time.
+        prop = property_map.get("time", "time")
+        time = system.property(prop)
+        system.removeSharedProperty(prop)
+        system.setProperties(prop, time)
+    except:
+        pass
+
     return _System(system)
 
 
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Convert/_convert.py b/python/BioSimSpace/Sandpit/Exscientia/Convert/_convert.py
index 68a2910b3..3025e165f 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Convert/_convert.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Convert/_convert.py
@@ -49,6 +49,7 @@
 
 import sire.legacy.Mol as _SireMol
 import sire.legacy.System as _SireSystem
+import sire.legacy.Vol as _SireVol
 
 import sire.system as _NewSireSystem
 
@@ -205,14 +206,28 @@ def to(obj, format="biosimspace", property_map={}):
                 try:
                     obj = obj.toSystem()
                 except:
-                    # Otherwise, convert residues/atoms to a molecule.
+                    # Otherwise, convert residues/atoms to a molecule, then a system.
                     try:
-                        obj = obj.toMolecule()
+                        obj = obj.toMolecule().toSystem()
                     except:
                         raise _ConversionError(
                             "Unable to convert object to OpenMM format!"
                         )
 
+            # Get the user-defined space property name.
+            prop = property_map.get("space", "space")
+
+            # Try to get the space property. Use an infinite cartesian space
+            # if none is present.
+            try:
+                space = obj._sire_object.property(prop)
+            except:
+                space = _SireVol.Cartesian()
+
+            # Set a shared space property.
+            obj._sire_object.addSharedProperty(prop)
+            obj._sire_object.setSharedProperty(prop, space)
+
             # Now try to convert the object to OpenMM format.
             try:
                 return _sire_convert.to(
diff --git a/python/BioSimSpace/Sandpit/Exscientia/IO/_io.py b/python/BioSimSpace/Sandpit/Exscientia/IO/_io.py
index c36696051..36b4e548f 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/IO/_io.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/IO/_io.py
@@ -523,6 +523,29 @@ def readMolecules(
                 else:
                     raise IOError(msg) from None
 
+    # Add a file format shared property.
+    prop = property_map.get("fileformat", "fileformat")
+    system.addSharedProperty(prop)
+    system.setSharedProperty(prop, system.property(prop))
+
+    # Remove "space" and "time" shared properties since this causes incorrect
+    # behaviour when extracting molecules and recombining them to make other
+    # systems.
+    try:
+        # Space.
+        prop = property_map.get("space", "space")
+        space = system.property(prop)
+        system.removeSharedProperty(prop)
+        system.setProperty(prop, space)
+
+        # Time.
+        prop = property_map.get("time", "time")
+        time = system.property(prop)
+        system.removeSharedProperty(prop)
+        system.setProperties(prop, time)
+    except:
+        pass
+
     return _System(system)
 
 
diff --git a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
index 701cf81d2..8793472ef 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
@@ -136,23 +136,6 @@ def __init__(self, system):
         # Initialise the iterator counter.
         self._iter_count = 0
 
-        # Copy any fileformat property to each molecule.
-        if "fileformat" in self._sire_object.propertyKeys():
-            fileformat = self._sire_object.property("fileformat")
-            for num in self._mol_nums:
-                edit_mol = self._sire_object[num].edit()
-                edit_mol = edit_mol.setProperty("fileformat", fileformat)
-                self._sire_object.update(edit_mol.commit())
-        else:
-            # If a molecule has a fileformat property, use the first
-            # that we find.
-            for mol in self:
-                if mol._sire_object.hasProperty("fileformat"):
-                    self._sire_object.setProperty(
-                        "fileformat", mol._sire_object.property("fileformat")
-                    )
-                    break
-
         # Reset the index mappings.
         self._reset_mappings()
 
diff --git a/python/BioSimSpace/_SireWrappers/_system.py b/python/BioSimSpace/_SireWrappers/_system.py
index 140a66f5b..14ef3ba65 100644
--- a/python/BioSimSpace/_SireWrappers/_system.py
+++ b/python/BioSimSpace/_SireWrappers/_system.py
@@ -136,23 +136,6 @@ def __init__(self, system):
         # Initialise the iterator counter.
         self._iter_count = 0
 
-        # Copy any fileformat property to each molecule.
-        if "fileformat" in self._sire_object.propertyKeys():
-            fileformat = self._sire_object.property("fileformat")
-            for num in self._mol_nums:
-                edit_mol = self._sire_object[num].edit()
-                edit_mol = edit_mol.setProperty("fileformat", fileformat)
-                self._sire_object.update(edit_mol.commit())
-        else:
-            # If a molecule has a fileformat property, use the first
-            # that we find.
-            for mol in self:
-                if mol._sire_object.hasProperty("fileformat"):
-                    self._sire_object.setProperty(
-                        "fileformat", mol._sire_object.property("fileformat")
-                    )
-                    break
-
         # Reset the index mappings.
         self._reset_mappings()
 

From f1f52769fe43e6654caec03f537a1fe8aee69bdd Mon Sep 17 00:00:00 2001
From: "William (Zhiyi) Wu" <zwu@exscientia.co.uk>
Date: Mon, 18 Sep 2023 18:22:35 +0800
Subject: [PATCH 09/17] Fixed PBC fixing when unsquashing for dummy atoms (#20)

---
 python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py | 3 +++
 tests/Sandpit/Exscientia/_SireWrappers/test_system.py  | 5 +++++
 2 files changed, 8 insertions(+)

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py b/python/BioSimSpace/Sandpit/Exscientia/Align/_squash.py
index 5193cfc83..a7377f7b1 100644
--- 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
index 86d4e0f85..c5e6978c6 100644
--- 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)

From 55bb6fcae20ab7dae5a4e8aa8f8914cec4dab121 Mon Sep 17 00:00:00 2001
From: Zhiyi Wu <zwu@exscientia.ai>
Date: Mon, 21 Aug 2023 18:33:43 +0800
Subject: [PATCH 10/17] Have amber process write binary RST file instead of
 text rst7 file (#22)

Co-authored-by: William (Zhiyi) Wu <zwu@exscientia.co.uk>
---
 .../Sandpit/Exscientia/Process/_amber.py         | 13 +++++++++----
 .../Process/test_position_restraint.py           | 16 ++++++++--------
 2 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py
index 7595ff33f..742ad8459 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py
@@ -27,6 +27,7 @@
 __all__ = ["Amber"]
 
 import os
+import shutil
 from pathlib import Path as _Path
 
 from .._Utils import _try_import
@@ -303,9 +304,11 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
         if coord_file is not None:
             try:
                 file = _os.path.splitext(coord_file)[0]
-                _IO.saveMolecules(file, system, "rst7", property_map=self._property_map)
+                _IO.saveMolecules(file, system, "rst", property_map=self._property_map)
+                # To keep the file extension the same.
+                shutil.move(f"{file}.rst", f"{file}.rst7")
             except Exception as e:
-                msg = "Failed to write system to 'RST7' format."
+                msg = "Failed to write system to 'rst7' format."
                 if _isVerbose():
                     raise IOError(msg) from e
                 else:
@@ -315,9 +318,11 @@ def _write_system(self, system, coord_file=None, topol_file=None, ref_file=None)
         if ref_file is not None:
             try:
                 file = _os.path.splitext(ref_file)[0]
-                _IO.saveMolecules(file, system, "rst7", property_map=self._property_map)
+                _IO.saveMolecules(file, system, "rst", property_map=self._property_map)
+                # To keep the file extension the same.
+                shutil.move(f"{file}.rst", f"{file}.rst7")
             except Exception as e:
-                msg = "Failed to write system to 'RST7' format."
+                msg = "Failed to write system to 'rst7' format."
                 if _isVerbose():
                     raise IOError(msg) from e
                 else:
diff --git a/tests/Sandpit/Exscientia/Process/test_position_restraint.py b/tests/Sandpit/Exscientia/Process/test_position_restraint.py
index 45697b9ed..aa720c470 100644
--- a/tests/Sandpit/Exscientia/Process/test_position_restraint.py
+++ b/tests/Sandpit/Exscientia/Process/test_position_restraint.py
@@ -5,6 +5,7 @@
 
 import pandas as pd
 import pytest
+from sire.legacy.IO import AmberRst
 
 import BioSimSpace.Sandpit.Exscientia as BSS
 from BioSimSpace.Sandpit.Exscientia.Units.Energy import kj_per_mol
@@ -121,8 +122,8 @@ def test_gromacs(protocol, system, ref_system, tmp_path):
 
 
 @pytest.mark.skipif(
-    has_gromacs is False or has_openff is False,
-    reason="Requires AMBER and openff to be installed",
+    has_openff is False,
+    reason="Requires openff to be installed",
 )
 def test_amber(protocol, system, ref_system, tmp_path):
     proc = BSS.Process.Amber(
@@ -137,12 +138,11 @@ def test_amber(protocol, system, ref_system, tmp_path):
 
     # We have generated a separate restraint reference
     assert os.path.exists(proc._ref_file)
-    contents_ref, contents_rst = (
-        open(proc._ref_file).readlines(),
-        open(proc._rst_file).readlines(),
-    )
-    diff = list(unified_diff(contents_ref, contents_rst))
-    assert len(diff)
+
+    ref = AmberRst(proc._ref_file).getFrame(0)
+    rst = AmberRst(proc._rst_file).getFrame(0)
+
+    assert ref != rst
 
     # We are pointing the reference to the correct file
     assert f"{proc._work_dir}/{proc.getArgs()['-ref']}" == proc._ref_file

From 591a535542b7d9a83326c8b0f5b7eda07de29b16 Mon Sep 17 00:00:00 2001
From: "William (Zhiyi) Wu" <zwu@exscientia.co.uk>
Date: Mon, 18 Sep 2023 21:47:50 +0800
Subject: [PATCH 11/17] remove skip

---
 tests/Sandpit/Exscientia/_SireWrappers/test_system.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/tests/Sandpit/Exscientia/_SireWrappers/test_system.py b/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
index c5e6978c6..55e7a96d9 100644
--- a/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
+++ b/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
@@ -263,10 +263,6 @@ 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)

From e82f367d0108f2d8dd6e83f755fe850b92540f9b Mon Sep 17 00:00:00 2001
From: "William (Zhiyi) Wu" <zwu@exscientia.co.uk>
Date: Mon, 18 Sep 2023 21:48:26 +0800
Subject: [PATCH 12/17] fix import

---
 tests/Sandpit/Exscientia/_SireWrappers/test_system.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/Sandpit/Exscientia/_SireWrappers/test_system.py b/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
index 55e7a96d9..86d4e0f85 100644
--- a/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
+++ b/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
@@ -1,6 +1,5 @@
 import math
 import pytest
-import platform
 
 import BioSimSpace.Sandpit.Exscientia as BSS
 

From d5e28e8afea9a3a7e1b9ab3830cb505768fc0397 Mon Sep 17 00:00:00 2001
From: Zhiyi Wu <zwu@exscientia.ai>
Date: Tue, 19 Sep 2023 17:36:43 +0800
Subject: [PATCH 13/17] Fix test in devel (#27)

Co-authored-by: William (Zhiyi) Wu <zwu@exscientia.co.uk>
---
 tests/Sandpit/Exscientia/_SireWrappers/test_system.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/Sandpit/Exscientia/_SireWrappers/test_system.py b/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
index 86d4e0f85..f715ee05a 100644
--- a/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
+++ b/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
@@ -274,7 +274,7 @@ def test_set_box(system):
 
     # Store the expected box dimensions and angles.
     expected_box = [30, 30, 30] * BSS.Units.Length.angstrom
-    expected_angles = [70.5288, 109.4712, 70.5288] * BSS.Units.Angle.degree
+    expected_angles = [109.4712, 109.4712, 109.4712] * BSS.Units.Angle.degree
 
     # Check that the box dimensions match.
     for b0, b1 in zip(box, expected_box):

From 20da673bfd6b7ecf0a359106b06293a654a3dcd1 Mon Sep 17 00:00:00 2001
From: Zhiyi Wu <zwu@exscientia.ai>
Date: Tue, 19 Sep 2023 21:14:44 +0800
Subject: [PATCH 14/17] Fix the tests such that it no longer require the
 working directory to be the root directory (#28)

Co-authored-by: William (Zhiyi) Wu <zwu@exscientia.co.uk>
---
 .../Sandpit/Exscientia/Align/test_decouple.py |  5 ++++-
 .../Sandpit/Exscientia/Align/test_make_ml.py  |  5 ++++-
 tests/Sandpit/Exscientia/Align/test_squash.py |  3 ++-
 .../Exscientia/Convert/test_convert.py        |  5 ++++-
 .../FreeEnergy/test_alchemical_free_energy.py |  9 ++++++--
 tests/Sandpit/Exscientia/Gateway/test_file.py |  5 ++++-
 .../Exscientia/Gateway/test_fileset.py        | 11 +++++-----
 tests/Sandpit/Exscientia/Gateway/test_node.py |  3 ++-
 .../Sandpit/Exscientia/IO/test_file_cache.py  |  3 ++-
 tests/Sandpit/Exscientia/IO/test_tuple.py     |  3 ++-
 tests/Sandpit/Exscientia/MD/test_md.py        | 11 ++++++----
 .../Sandpit/Exscientia/Process/test_amber.py  | 18 ++++++++--------
 .../Exscientia/Process/test_dummy_protocol.py |  5 ++++-
 .../Exscientia/Process/test_gromacs.py        | 16 ++++++++------
 tests/Sandpit/Exscientia/Process/test_namd.py |  7 ++++---
 .../Sandpit/Exscientia/Process/test_openmm.py |  5 ++++-
 tests/Sandpit/Exscientia/Process/test_somd.py |  7 +++++--
 .../Sandpit/Exscientia/Stream/test_stream.py  |  5 ++++-
 .../Exscientia/Trajectory/test_trajectory.py  | 21 +++++++++++--------
 .../Exscientia/_SireWrappers/test_bond.py     |  5 ++++-
 .../Exscientia/_SireWrappers/test_molecule.py |  5 ++++-
 .../_SireWrappers/test_properties.py          |  3 ++-
 .../_SireWrappers/test_search_result.py       |  5 ++++-
 .../Exscientia/_SireWrappers/test_system.py   |  5 ++++-
 tests/conftest.py                             |  4 ++++
 25 files changed, 118 insertions(+), 56 deletions(-)

diff --git a/tests/Sandpit/Exscientia/Align/test_decouple.py b/tests/Sandpit/Exscientia/Align/test_decouple.py
index 210bdd816..150938ddd 100644
--- a/tests/Sandpit/Exscientia/Align/test_decouple.py
+++ b/tests/Sandpit/Exscientia/Align/test_decouple.py
@@ -6,6 +6,7 @@
 
 from BioSimSpace.Sandpit.Exscientia.Align._decouple import decouple
 import BioSimSpace.Sandpit.Exscientia as BSS
+from tests.conftest import root_fp
 
 # Store the tutorial URL.
 url = BSS.tutorialUrl()
@@ -14,7 +15,9 @@
 @pytest.fixture(scope="session")
 def mol():
     # Alanin-dipeptide.
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])[0]
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )[0]
 
 
 def test_sanity(mol):
diff --git a/tests/Sandpit/Exscientia/Align/test_make_ml.py b/tests/Sandpit/Exscientia/Align/test_make_ml.py
index 908fd3ee5..b2c2a54e9 100644
--- a/tests/Sandpit/Exscientia/Align/test_make_ml.py
+++ b/tests/Sandpit/Exscientia/Align/test_make_ml.py
@@ -2,6 +2,7 @@
 
 import BioSimSpace.Sandpit.Exscientia as BSS
 from BioSimSpace.Sandpit.Exscientia.Align import make_ml
+from tests.conftest import root_fp
 
 # Store the tutorial URL.
 url = BSS.tutorialUrl()
@@ -9,7 +10,9 @@
 
 @pytest.fixture
 def mol():
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])[0]
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )[0]
 
 
 @pytest.fixture
diff --git a/tests/Sandpit/Exscientia/Align/test_squash.py b/tests/Sandpit/Exscientia/Align/test_squash.py
index bfcc29656..0f01bf088 100644
--- a/tests/Sandpit/Exscientia/Align/test_squash.py
+++ b/tests/Sandpit/Exscientia/Align/test_squash.py
@@ -7,6 +7,7 @@
 from sire.maths import Vector
 
 import BioSimSpace.Sandpit.Exscientia as BSS
+from tests.conftest import root_fp
 
 # Make sure AMBER is installed.
 if BSS._amber_home is not None:
@@ -60,7 +61,7 @@ def dual_topology_system():
 @pytest.fixture
 def perturbed_tripeptide():
     return pickle.load(
-        open("tests/Sandpit/Exscientia/input/merged_tripeptide.pickle", "rb")
+        open(f"{root_fp}/Sandpit/Exscientia/input/merged_tripeptide.pickle", "rb")
     )
 
 
diff --git a/tests/Sandpit/Exscientia/Convert/test_convert.py b/tests/Sandpit/Exscientia/Convert/test_convert.py
index 220f48b51..e444c3144 100644
--- a/tests/Sandpit/Exscientia/Convert/test_convert.py
+++ b/tests/Sandpit/Exscientia/Convert/test_convert.py
@@ -3,11 +3,14 @@
 from sire.legacy import Mol as SireMol
 
 import BioSimSpace.Sandpit.Exscientia as BSS
+from tests.conftest import root_fp
 
 
 @pytest.fixture(scope="session")
 def system():
-    return BSS.IO.readMolecules(["tests/input/ala.crd", "tests/input/ala.top"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.crd", f"{root_fp}/input/ala.top"]
+    )
 
 
 def test_system(system):
diff --git a/tests/Sandpit/Exscientia/FreeEnergy/test_alchemical_free_energy.py b/tests/Sandpit/Exscientia/FreeEnergy/test_alchemical_free_energy.py
index 5c2b8f952..873c654d5 100644
--- a/tests/Sandpit/Exscientia/FreeEnergy/test_alchemical_free_energy.py
+++ b/tests/Sandpit/Exscientia/FreeEnergy/test_alchemical_free_energy.py
@@ -14,6 +14,7 @@
     has_gromacs,
     url,
 )
+from tests.conftest import root_fp
 
 import BioSimSpace.Sandpit.Exscientia as BSS
 from BioSimSpace.Sandpit.Exscientia.Protocol import FreeEnergyEquilibration
@@ -133,7 +134,9 @@ class TestAnalysePARQUET:
     @pytest.fixture(scope="class")
     def data(tmp_path_factory):
         outdir = tmp_path_factory.mktemp("out")
-        shutil.copytree("tests/Sandpit/Exscientia/input/parquet", outdir / "parquet")
+        shutil.copytree(
+            f"{root_fp}/Sandpit/Exscientia/input/parquet", outdir / "parquet"
+        )
         return str(outdir / "parquet")
 
     def test_analyse(self, data):
@@ -153,7 +156,9 @@ class Test_gmx_ABFE:
     @staticmethod
     @pytest.fixture(scope="class")
     def freenrg():
-        m = BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])[0]
+        m = BSS.IO.readMolecules(
+            [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+        )[0]
         decouple_m = decouple(m)
         solvated = BSS.Solvent.tip3p(
             molecule=decouple_m, box=3 * [3 * BSS.Units.Length.nanometer]
diff --git a/tests/Sandpit/Exscientia/Gateway/test_file.py b/tests/Sandpit/Exscientia/Gateway/test_file.py
index e36faf36f..ea098822d 100644
--- a/tests/Sandpit/Exscientia/Gateway/test_file.py
+++ b/tests/Sandpit/Exscientia/Gateway/test_file.py
@@ -1,6 +1,7 @@
 import pytest
 
 from BioSimSpace.Sandpit.Exscientia.Gateway import File
+from tests.conftest import root_fp
 
 
 def test_no_arguments():
@@ -10,7 +11,9 @@ def test_no_arguments():
         f = File()
 
 
-@pytest.mark.parametrize("value", ["tests/input/ala.crd", "tests/input/ala.top"])
+@pytest.mark.parametrize(
+    "value", [f"{root_fp}/input/ala.crd", f"{root_fp}/input/ala.top"]
+)
 def test_value(value):
     """Test whether object is initialised correctly and value is set."""
 
diff --git a/tests/Sandpit/Exscientia/Gateway/test_fileset.py b/tests/Sandpit/Exscientia/Gateway/test_fileset.py
index d2e1b0216..9b4bdf9e5 100644
--- a/tests/Sandpit/Exscientia/Gateway/test_fileset.py
+++ b/tests/Sandpit/Exscientia/Gateway/test_fileset.py
@@ -1,6 +1,7 @@
 import pytest
 
 from BioSimSpace.Sandpit.Exscientia.Gateway import FileSet
+from tests.conftest import root_fp
 
 
 def test_no_arguments():
@@ -13,11 +14,11 @@ def test_no_arguments():
 @pytest.mark.parametrize(
     "value",
     [
-        ["tests/input/ala.crd", "tests/input/ala.top"],
+        [f"{root_fp}/input/ala.crd", f"{root_fp}/input/ala.top"],
         [
-            "tests/input/alanin.pdb",
-            "tests/input/alanin.psf",
-            "tests/input/alanin.params",
+            f"{root_fp}/input/alanin.pdb",
+            f"{root_fp}/input/alanin.psf",
+            f"{root_fp}/input/alanin.params",
         ],
     ],
 )
@@ -58,7 +59,7 @@ def test_missing_files():
     # One file missing.
     with pytest.raises(IOError):
         f = FileSet(help="Help!")
-        f.setValue(["tests/input/amber/ala/ala.crd", "missing2.txt"])
+        f.setValue([f"{root_fp}/input/amber/ala/ala.crd", "missing2.txt"])
 
 
 @pytest.mark.parametrize("optional", [True, False])
diff --git a/tests/Sandpit/Exscientia/Gateway/test_node.py b/tests/Sandpit/Exscientia/Gateway/test_node.py
index 3d47cbd3a..61e9ff047 100644
--- a/tests/Sandpit/Exscientia/Gateway/test_node.py
+++ b/tests/Sandpit/Exscientia/Gateway/test_node.py
@@ -4,9 +4,10 @@
 import sys
 
 import BioSimSpace.Sandpit.Exscientia as BSS
+from tests.conftest import root_fp
 
 # Store the name of the test script.
-script_name = "tests/Gateway/node.py"
+script_name = f"{root_fp}/Gateway/node.py"
 
 # Store the name of the python interpreter.
 exe = sys.executable
diff --git a/tests/Sandpit/Exscientia/IO/test_file_cache.py b/tests/Sandpit/Exscientia/IO/test_file_cache.py
index cce3c62a8..92e0a8d91 100644
--- a/tests/Sandpit/Exscientia/IO/test_file_cache.py
+++ b/tests/Sandpit/Exscientia/IO/test_file_cache.py
@@ -6,6 +6,7 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
 
 from tests.Sandpit.Exscientia.conftest import has_amber, has_openff
+from tests.conftest import root_fp
 
 
 def test_file_cache():
@@ -18,7 +19,7 @@ def test_file_cache():
     BSS.IO._file_cache._cache = BSS.IO._file_cache._FixedSizeOrderedDict()
 
     # Load the molecular system.
-    s = BSS.IO.readMolecules(["tests/input/ala.crd", "tests/input/ala.top"])
+    s = BSS.IO.readMolecules([f"{root_fp}/input/ala.crd", f"{root_fp}/input/ala.top"])
 
     # Create a temporary working directory.
     tmp_dir = tempfile.TemporaryDirectory()
diff --git a/tests/Sandpit/Exscientia/IO/test_tuple.py b/tests/Sandpit/Exscientia/IO/test_tuple.py
index f4fc601bb..1f8700888 100644
--- a/tests/Sandpit/Exscientia/IO/test_tuple.py
+++ b/tests/Sandpit/Exscientia/IO/test_tuple.py
@@ -1,6 +1,7 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
+from tests.conftest import root_fp
 
 
 def test_tuple():
     """Check that we can read from a tuple of files."""
-    BSS.IO.readMolecules(("tests/input/ala.crd", "tests/input/ala.top"))
+    BSS.IO.readMolecules((f"{root_fp}/input/ala.crd", f"{root_fp}/input/ala.top"))
diff --git a/tests/Sandpit/Exscientia/MD/test_md.py b/tests/Sandpit/Exscientia/MD/test_md.py
index f479d9ab1..f2afe28db 100644
--- a/tests/Sandpit/Exscientia/MD/test_md.py
+++ b/tests/Sandpit/Exscientia/MD/test_md.py
@@ -3,6 +3,7 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
 
 from tests.Sandpit.Exscientia.conftest import url, has_amber, has_gromacs, has_namd
+from tests.conftest import root_fp
 
 
 @pytest.mark.skipif(has_amber is False, reason="Requires AMBER to be installed.")
@@ -13,7 +14,9 @@ def test_amber():
     protocol = BSS.Protocol.Minimisation(steps=100)
 
     # Load the molecular system.
-    system = BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    system = BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
     # Initialise the AMBER process.
     process = BSS.MD.run(system, protocol, name="test")
@@ -55,9 +58,9 @@ def test_namd():
     # Load the molecular system.
     system = BSS.IO.readMolecules(
         [
-            "tests/input/alanin.psf",
-            "tests/input/alanin.pdb",
-            "tests/input/alanin.params",
+            f"{root_fp}/input/alanin.psf",
+            f"{root_fp}/input/alanin.pdb",
+            f"{root_fp}/input/alanin.params",
         ]
     )
 
diff --git a/tests/Sandpit/Exscientia/Process/test_amber.py b/tests/Sandpit/Exscientia/Process/test_amber.py
index 489f5bd84..60168a707 100644
--- a/tests/Sandpit/Exscientia/Process/test_amber.py
+++ b/tests/Sandpit/Exscientia/Process/test_amber.py
@@ -10,12 +10,15 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
 
 from tests.Sandpit.Exscientia.conftest import url, has_amber, has_pyarrow
+from tests.conftest import root_fp
 
 
 @pytest.fixture(scope="session")
 def system():
     """Re-use the same molecuar system for each test."""
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
 
 @pytest.mark.skipif(
@@ -280,9 +283,9 @@ def test_parse_fep_output(system, protocol):
 
     # Assign the path to the output file.
     if isinstance(protocol, BSS.Protocol.FreeEnergy):
-        out_file = "tests/Sandpit/Exscientia/output/amber_fep.out"
+        out_file = f"{root_fp}/Sandpit/Exscientia/output/amber_fep.out"
     else:
-        out_file = "tests/Sandpit/Exscientia/output/amber_fep_min.out"
+        out_file = f"{root_fp}/Sandpit/Exscientia/output/amber_fep_min.out"
 
     # Copy the existing output file into the working directory.
     shutil.copyfile(out_file, process.workDir() + "/amber.out")
@@ -320,7 +323,6 @@ def test_parse_fep_output(system, protocol):
         assert len(records_sc1) != 0
 
 
-
 class TestsaveMetric:
     @staticmethod
     @pytest.fixture()
@@ -334,7 +336,6 @@ def alchemical_system(system):
         system_copy.updateMolecule(0, mol)
         return system_copy
 
-
     @staticmethod
     @pytest.fixture()
     def setup(alchemical_system):
@@ -344,7 +345,7 @@ def setup(alchemical_system):
             BSS.Protocol.FreeEnergy(temperature=298 * BSS.Units.Temperature.kelvin),
         )
         shutil.copyfile(
-            "tests/Sandpit/Exscientia/output/amber_fep.out",
+            f"{root_fp}/Sandpit/Exscientia/output/amber_fep.out",
             process.workDir() + "/amber.out",
         )
         process.saveMetric()
@@ -357,10 +358,9 @@ def test_error_alchemlyb_extract(self, alchemical_system):
             BSS.Protocol.FreeEnergy(temperature=298 * BSS.Units.Temperature.kelvin),
         )
         process.wait()
-        with open(process.workDir() + '/amber.err', 'r') as f:
+        with open(process.workDir() + "/amber.err", "r") as f:
             text = f.read()
-            assert 'Exception Information' in text
-
+            assert "Exception Information" in text
 
     def test_metric_parquet_exist(self, setup):
         assert Path(f"{setup.workDir()}/metric.parquet").exists()
diff --git a/tests/Sandpit/Exscientia/Process/test_dummy_protocol.py b/tests/Sandpit/Exscientia/Process/test_dummy_protocol.py
index a50c5e533..fa063d427 100644
--- a/tests/Sandpit/Exscientia/Process/test_dummy_protocol.py
+++ b/tests/Sandpit/Exscientia/Process/test_dummy_protocol.py
@@ -1,6 +1,7 @@
 import pytest
 
 from tests.Sandpit.Exscientia.conftest import has_amber, has_gromacs
+from tests.conftest import root_fp
 
 import BioSimSpace.Sandpit.Exscientia as BSS
 from BioSimSpace.Sandpit.Exscientia.Process._process import Process
@@ -9,7 +10,9 @@
 @pytest.fixture(scope="session")
 def system():
     """Re-use the same molecuar system for each test."""
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
 
 @pytest.mark.skipif(
diff --git a/tests/Sandpit/Exscientia/Process/test_gromacs.py b/tests/Sandpit/Exscientia/Process/test_gromacs.py
index 1a42967c5..7d4e57c49 100644
--- a/tests/Sandpit/Exscientia/Process/test_gromacs.py
+++ b/tests/Sandpit/Exscientia/Process/test_gromacs.py
@@ -27,12 +27,15 @@
     has_openff,
     has_pyarrow,
 )
+from tests.conftest import root_fp
 
 
 @pytest.fixture(scope="session")
 def system():
     """Re-use the same molecuar system for each test."""
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
 
 @pytest.fixture(scope="session")
@@ -254,7 +257,7 @@ def setup(perturbable_system):
         )
         process = BSS.Process.Gromacs(perturbable_system, protocol)
         shutil.copyfile(
-            "tests/Sandpit/Exscientia/output/gromacs.edr",
+            f"{root_fp}/Sandpit/Exscientia/output/gromacs.edr",
             process.workDir() + "/gromacs.edr",
         )
         shutil.copyfile(
@@ -343,17 +346,18 @@ def test_u_nk_parquet(self, setup):
 
     def test_error_alchemlyb_extract(self, perturbable_system, monkeypatch):
         def extract(*args):
-            raise ValueError('alchemlyb.parsing.gmx.extract failed.')
-        monkeypatch.setattr('alchemlyb.parsing.gmx.extract', extract)
+            raise ValueError("alchemlyb.parsing.gmx.extract failed.")
+
+        monkeypatch.setattr("alchemlyb.parsing.gmx.extract", extract)
         # Create a process using any system and the protocol.
         process = BSS.Process.Gromacs(
             perturbable_system,
             BSS.Protocol.FreeEnergy(temperature=298 * BSS.Units.Temperature.kelvin),
         )
         process.wait()
-        with open(process.workDir() + '/gromacs.err', 'r') as f:
+        with open(process.workDir() + "/gromacs.err", "r") as f:
             text = f.read()
-            assert 'Exception Information' in text
+            assert "Exception Information" in text
 
 
 @pytest.mark.skipif(
diff --git a/tests/Sandpit/Exscientia/Process/test_namd.py b/tests/Sandpit/Exscientia/Process/test_namd.py
index 5327a4a28..3ad97f742 100644
--- a/tests/Sandpit/Exscientia/Process/test_namd.py
+++ b/tests/Sandpit/Exscientia/Process/test_namd.py
@@ -3,6 +3,7 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
 
 from tests.Sandpit.Exscientia.conftest import url, has_namd
+from tests.conftest import root_fp
 
 
 @pytest.fixture(scope="session")
@@ -10,9 +11,9 @@ def system():
     """Re-use the same molecuar system for each test."""
     return BSS.IO.readMolecules(
         [
-            "tests/input/alanin.psf",
-            f"tests/input/alanin.pdb",
-            f"tests/input/alanin.params",
+            f"{root_fp}/input/alanin.psf",
+            f"{root_fp}/input/alanin.pdb",
+            f"{root_fp}/input/alanin.params",
         ]
     )
 
diff --git a/tests/Sandpit/Exscientia/Process/test_openmm.py b/tests/Sandpit/Exscientia/Process/test_openmm.py
index f4a55342b..10c9f0045 100644
--- a/tests/Sandpit/Exscientia/Process/test_openmm.py
+++ b/tests/Sandpit/Exscientia/Process/test_openmm.py
@@ -4,12 +4,15 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
 
 from tests.Sandpit.Exscientia.conftest import url, has_amber, has_gromacs, has_openff
+from tests.conftest import root_fp
 
 
 @pytest.fixture(scope="session")
 def system():
     """Re-use the same molecuar system for each test."""
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
 
 @pytest.mark.parametrize("restraint", ["backbone", "heavy", "all", "none"])
diff --git a/tests/Sandpit/Exscientia/Process/test_somd.py b/tests/Sandpit/Exscientia/Process/test_somd.py
index 11ecc6ba0..ca81a539c 100644
--- a/tests/Sandpit/Exscientia/Process/test_somd.py
+++ b/tests/Sandpit/Exscientia/Process/test_somd.py
@@ -12,6 +12,7 @@
 import warnings
 
 import BioSimSpace.Sandpit.Exscientia as BSS
+from tests.conftest import root_fp
 
 # Store the tutorial URL.
 url = BSS.tutorialUrl()
@@ -20,7 +21,9 @@
 @pytest.fixture(scope="session")
 def system():
     """Re-use the same molecuar system for each test."""
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
 
 @pytest.fixture(scope="session")
@@ -91,7 +94,7 @@ def test_pert_file():
     BSS.Process._somd._to_pert_file(mol)
 
     # Check that the files are the same.
-    assert filecmp.cmp("MORPH.pert", "tests/input/morph.pert")
+    assert filecmp.cmp("MORPH.pert", f"{root_fp}/input/morph.pert")
 
     # Remove the temporary perturbation file.
     os.remove("MORPH.pert")
diff --git a/tests/Sandpit/Exscientia/Stream/test_stream.py b/tests/Sandpit/Exscientia/Stream/test_stream.py
index bf40c3993..432110cbc 100644
--- a/tests/Sandpit/Exscientia/Stream/test_stream.py
+++ b/tests/Sandpit/Exscientia/Stream/test_stream.py
@@ -2,11 +2,14 @@
 import pytest
 
 import BioSimSpace.Sandpit.Exscientia as BSS
+from tests.conftest import root_fp
 
 
 @pytest.fixture
 def system(scope="session"):
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
 
 @pytest.fixture(autouse=True)
diff --git a/tests/Sandpit/Exscientia/Trajectory/test_trajectory.py b/tests/Sandpit/Exscientia/Trajectory/test_trajectory.py
index 667c0fea7..6711d806e 100644
--- a/tests/Sandpit/Exscientia/Trajectory/test_trajectory.py
+++ b/tests/Sandpit/Exscientia/Trajectory/test_trajectory.py
@@ -11,20 +11,23 @@ def wrap(arg):
 
 
 from tests.Sandpit.Exscientia.conftest import has_mdanalysis, has_mdtraj
+from tests.conftest import root_fp
 
 
 @pytest.fixture(scope="session")
 def system():
     """A system object with the same topology as the trajectories."""
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
 
 @pytest.fixture(scope="session")
 def traj_sire(system):
     """A trajectory object using the Sire backend."""
     return BSS.Trajectory.Trajectory(
-        trajectory="tests/input/ala.trr",
-        topology="tests/input/ala.gro",
+        trajectory=f"{root_fp}/input/ala.trr",
+        topology=f"{root_fp}/input/ala.gro",
         system=system,
         backend="SIRE",
     )
@@ -34,8 +37,8 @@ def traj_sire(system):
 def traj_mdtraj(system):
     """A trajectory object using the MDTraj backend."""
     return BSS.Trajectory.Trajectory(
-        trajectory="tests/input/ala.trr",
-        topology="tests/input/ala.gro",
+        trajectory=f"{root_fp}/input/ala.trr",
+        topology=f"{root_fp}/input/ala.gro",
         system=system,
         backend="MDTRAJ",
     )
@@ -45,8 +48,8 @@ def traj_mdtraj(system):
 def traj_mdanalysis(system):
     """A trajectory object using the MDAnalysis backend."""
     return BSS.Trajectory.Trajectory(
-        trajectory="tests/input/ala.trr",
-        topology="tests/input/ala.tpr",
+        trajectory=f"{root_fp}/input/ala.trr",
+        topology=f"{root_fp}/input/ala.tpr",
         system=system,
         backend="MDANALYSIS",
     )
@@ -58,8 +61,8 @@ def traj_mdanalysis_pdb(system):
     new_system = system.copy()
     new_system._sire_object.setProperty("fileformat", wrap("PDB"))
     return BSS.Trajectory.Trajectory(
-        trajectory="tests/input/ala.trr",
-        topology="tests/input/ala.tpr",
+        trajectory=f"{root_fp}/input/ala.trr",
+        topology=f"{root_fp}/input/ala.tpr",
         system=new_system,
         backend="MDANALYSIS",
     )
diff --git a/tests/Sandpit/Exscientia/_SireWrappers/test_bond.py b/tests/Sandpit/Exscientia/_SireWrappers/test_bond.py
index bab5be6d8..861e49241 100644
--- a/tests/Sandpit/Exscientia/_SireWrappers/test_bond.py
+++ b/tests/Sandpit/Exscientia/_SireWrappers/test_bond.py
@@ -1,10 +1,13 @@
 import pytest
 
 import BioSimSpace.Sandpit.Exscientia as BSS
+from tests.conftest import root_fp
 
 
 def test_bonds():
-    system = BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    system = BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
     bonds = system.search("bonds")
 
diff --git a/tests/Sandpit/Exscientia/_SireWrappers/test_molecule.py b/tests/Sandpit/Exscientia/_SireWrappers/test_molecule.py
index f66f70db4..d19b385f8 100644
--- a/tests/Sandpit/Exscientia/_SireWrappers/test_molecule.py
+++ b/tests/Sandpit/Exscientia/_SireWrappers/test_molecule.py
@@ -3,11 +3,14 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
 
 from tests.Sandpit.Exscientia.conftest import url, has_amber, has_pyarrow
+from tests.conftest import root_fp
 
 
 @pytest.fixture(scope="session")
 def system():
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
 
 @pytest.mark.skipif(
diff --git a/tests/Sandpit/Exscientia/_SireWrappers/test_properties.py b/tests/Sandpit/Exscientia/_SireWrappers/test_properties.py
index 545bf249c..47bf616f1 100644
--- a/tests/Sandpit/Exscientia/_SireWrappers/test_properties.py
+++ b/tests/Sandpit/Exscientia/_SireWrappers/test_properties.py
@@ -1,8 +1,9 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
+from tests.conftest import root_fp
 
 
 def test_sire_properties():
-    s = BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    s = BSS.IO.readMolecules([f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"])
 
     m = s[0]._sire_object
 
diff --git a/tests/Sandpit/Exscientia/_SireWrappers/test_search_result.py b/tests/Sandpit/Exscientia/_SireWrappers/test_search_result.py
index 45903da4f..aae552377 100644
--- a/tests/Sandpit/Exscientia/_SireWrappers/test_search_result.py
+++ b/tests/Sandpit/Exscientia/_SireWrappers/test_search_result.py
@@ -1,6 +1,7 @@
 import pytest
 
 import BioSimSpace.Sandpit.Exscientia as BSS
+from tests.conftest import root_fp
 
 # Store the tutorial URL.
 url = BSS.tutorialUrl()
@@ -9,7 +10,9 @@
 @pytest.fixture(scope="session")
 def system():
     """Re-use the same molecuar system for each test."""
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
 
 @pytest.fixture(scope="session")
diff --git a/tests/Sandpit/Exscientia/_SireWrappers/test_system.py b/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
index f715ee05a..1d8948520 100644
--- a/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
+++ b/tests/Sandpit/Exscientia/_SireWrappers/test_system.py
@@ -4,12 +4,15 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
 
 from tests.Sandpit.Exscientia.conftest import url, has_amber, has_openff
+from tests.conftest import root_fp
 
 
 @pytest.fixture(scope="session")
 def system():
     """Re-use the same molecuar system for each test."""
-    return BSS.IO.readMolecules(["tests/input/ala.top", "tests/input/ala.crd"])
+    return BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )
 
 
 # Parameterise the function with a set of molecule indices.
diff --git a/tests/conftest.py b/tests/conftest.py
index 9c547f7c3..b303e6d82 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,3 +1,5 @@
+from pathlib import Path
+
 collect_ignore_glob = ["*/out_test*.py"]
 
 import os
@@ -55,3 +57,5 @@
 )
 
 has_mdrestraints_generator = _have_imported(MDRestraintsGenerator)
+
+root_fp = Path(__file__).parent.resolve()

From 3c4a23ddeb9b8d6e587612253eaf033dcc9acdf8 Mon Sep 17 00:00:00 2001
From: Zhiyi Wu <zwu@exscientia.ai>
Date: Tue, 19 Sep 2023 23:22:30 +0800
Subject: [PATCH 15/17] Add a function for marking the alchemical ion (#30)

Co-authored-by: William (Zhiyi) Wu <zwu@exscientia.co.uk>
---
 .../Sandpit/Exscientia/Align/_alch_ion.py     | 52 +++++++++++++++++++
 .../Exscientia/_SireWrappers/_molecule.py     | 12 +++++
 .../Exscientia/_SireWrappers/_system.py       | 27 ++++++++++
 .../Exscientia/Align/test_alchemical_ion.py   | 49 +++++++++++++++++
 4 files changed, 140 insertions(+)
 create mode 100644 python/BioSimSpace/Sandpit/Exscientia/Align/_alch_ion.py
 create mode 100644 tests/Sandpit/Exscientia/Align/test_alchemical_ion.py

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Align/_alch_ion.py b/python/BioSimSpace/Sandpit/Exscientia/Align/_alch_ion.py
new file mode 100644
index 000000000..14773adf6
--- /dev/null
+++ b/python/BioSimSpace/Sandpit/Exscientia/Align/_alch_ion.py
@@ -0,0 +1,52 @@
+import warnings
+
+from .._SireWrappers import Molecule as _Molecule
+
+
+def _mark_alchemical_ion(molecule):
+    """
+    Mark the ion molecule as being alchemical ion.
+
+    This enables one to use
+
+        * :meth:`~BioSimSpace.Sandpit.Exscientia._SireWrappers._system.System.getAlchemicalIon` to get the alchemical ion.
+        * :meth:`~BioSimSpace.Sandpit.Exscientia._SireWrappers._system.System.getAlchemicalIonIdx` to get the index of alchemical ion.
+        * :meth:`~BioSimSpace.Sandpit.Exscientia._SireWrappers._molecule.Molecule.isAlchemicalIon` to check if a molecule is an alchemical ion.
+
+
+    Parameters
+    ----------
+
+    molecule : BioSimSpace._SireWrappers.Molecule
+        The molecule to be marked as alchemical ion.
+
+    Returns
+    -------
+
+    alchemical_ion : BSS._SireWrappers.Molecule
+        The molecule marked as being alchemical ion.
+    """
+    # Validate input.
+
+    if not isinstance(molecule, _Molecule):
+        raise TypeError(
+            "'molecule' must be of type 'BioSimSpace._SireWrappers.Molecule'"
+        )
+
+    # Cannot decouple a perturbable molecule.
+    if molecule.isAlchemicalIon():
+        warnings.warn("'molecule' has already been marked as alchemical ion!")
+
+    # Create a copy of this molecule.
+    mol = _Molecule(molecule)
+    mol_sire = mol._sire_object
+
+    # Edit the molecule
+    mol_edit = mol_sire.edit()
+
+    mol_edit.setProperty("AlchemicalIon", True)
+
+    # Update the Sire molecule object of the new molecule.
+    mol._sire_object = mol_edit.commit()
+
+    return mol
diff --git a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py
index 005a68d63..05ca21681 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py
@@ -518,6 +518,18 @@ def isML(self):
         else:
             return False
 
+    def isAlchemicalIon(self):
+        """
+        Whether this molecule is marked as Alchemical Ion.
+
+        Returns
+        -------
+
+        isAlchemicalIon : bool
+            Whether the molecule is marked as Alchemical Ion.
+        """
+        return self._sire_object.hasProperty("AlchemicalIon")
+
     def isWater(self, property_map={}):
         """
         Whether this is a water molecule.
diff --git a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
index 8793472ef..280e01327 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
@@ -1115,6 +1115,33 @@ def nMLMolecules(self):
         """
         return len(self.getMLMolecules())
 
+    def getAlchemicalIon(self):
+        """
+        Return the Alchemical Ion in the system.
+
+        Returns
+        -------
+
+        molecule : [:class:`Molecule <BioSimSpace._SireWrappers.Molecule>`]
+            The Alchemical Ion or None if there isn't any.
+        """
+        try:
+            return self.search("mols with property AlchemicalIon").molecules()[0]
+        except:
+            return None
+
+    def getAlchemicalIonIdx(self):
+        """
+        Return the index of Alchemical Ion in the system.
+
+        Returns
+        -------
+
+        index : int
+            The index of Alchemical Ion in the system.
+        """
+        return self.getIndex(self.getAlchemicalIon())
+
     def repartitionHydrogenMass(
         self, factor=4, water="no", use_coordinates=False, property_map={}
     ):
diff --git a/tests/Sandpit/Exscientia/Align/test_alchemical_ion.py b/tests/Sandpit/Exscientia/Align/test_alchemical_ion.py
new file mode 100644
index 000000000..3b56be919
--- /dev/null
+++ b/tests/Sandpit/Exscientia/Align/test_alchemical_ion.py
@@ -0,0 +1,49 @@
+import pytest
+
+import BioSimSpace.Sandpit.Exscientia as BSS
+from BioSimSpace.Sandpit.Exscientia.Align._alch_ion import _mark_alchemical_ion
+from BioSimSpace.Sandpit.Exscientia._SireWrappers import Molecule
+
+from tests.conftest import root_fp
+
+
+@pytest.fixture
+def system():
+    mol = BSS.IO.readMolecules(
+        [f"{root_fp}/input/ala.top", f"{root_fp}/input/ala.crd"]
+    )[0]
+    system = BSS.Solvent.tip3p(mol, ion_conc=0.15, shell=2 * BSS.Units.Length.nanometer)
+    return system
+
+
+@pytest.fixture
+def alchemical_ion_system(system):
+    ion = system[-1]
+    ion = _mark_alchemical_ion(ion)
+    system.updateMolecules(ion)
+    return system
+
+
+@pytest.mark.parametrize(
+    "input_system,isalchem", [("system", False), ("alchemical_ion_system", True)]
+)
+def test_isAlchemicalIon(input_system, isalchem, request):
+    system = request.getfixturevalue(input_system)
+    assert system[-1].isAlchemicalIon() is isalchem
+
+
+@pytest.mark.parametrize(
+    "input_system,isalchem", [("system", None), ("alchemical_ion_system", True)]
+)
+def test_getAlchemicalIon(input_system, isalchem, request):
+    system = request.getfixturevalue(input_system)
+    ion = system.getAlchemicalIon()
+    if isalchem is None:
+        assert ion is None
+    else:
+        assert isinstance(ion, Molecule)
+
+
+def test_getAlchemicalIonIdx(alchemical_ion_system):
+    index = alchemical_ion_system.getAlchemicalIonIdx()
+    assert index == 680

From b9f1c84abe30e8bef5d55194565b5709b1919c56 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 12 Oct 2023 19:28:42 +0100
Subject: [PATCH 16/17] Increase distance tolerance.

This is not reproducibly satisfied on all platforms and Python variants.
---
 tests/Sandpit/Exscientia/Process/test_openmm.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/Sandpit/Exscientia/Process/test_openmm.py b/tests/Sandpit/Exscientia/Process/test_openmm.py
index 3c45e7fb9..aec8406af 100644
--- a/tests/Sandpit/Exscientia/Process/test_openmm.py
+++ b/tests/Sandpit/Exscientia/Process/test_openmm.py
@@ -70,7 +70,7 @@ def test_minimise(system, restraint):
     )
 
     # Run the process, check that it finished without error, and returns a system.
-    run_process(system, protocol, restraint=restraint, tolerance=0.05)
+    run_process(system, protocol, restraint=restraint, tolerance=0.1)
 
 
 @pytest.mark.parametrize("restraint", ["backbone", "heavy", "all", "none"])

From 4cceb23955057e204d64f19bcb084e699275a099 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 12 Oct 2023 19:29:29 +0100
Subject: [PATCH 17/17] Guard tests against missing packages.

---
 tests/Sandpit/Exscientia/Align/test_alchemical_ion.py       | 5 ++++-
 tests/Sandpit/Exscientia/Process/test_position_restraint.py | 4 ++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/tests/Sandpit/Exscientia/Align/test_alchemical_ion.py b/tests/Sandpit/Exscientia/Align/test_alchemical_ion.py
index 3b56be919..fa2a0aeb6 100644
--- a/tests/Sandpit/Exscientia/Align/test_alchemical_ion.py
+++ b/tests/Sandpit/Exscientia/Align/test_alchemical_ion.py
@@ -4,7 +4,7 @@
 from BioSimSpace.Sandpit.Exscientia.Align._alch_ion import _mark_alchemical_ion
 from BioSimSpace.Sandpit.Exscientia._SireWrappers import Molecule
 
-from tests.conftest import root_fp
+from tests.conftest import root_fp, has_gromacs
 
 
 @pytest.fixture
@@ -24,6 +24,7 @@ def alchemical_ion_system(system):
     return system
 
 
+@pytest.mark.skipif(has_gromacs is False, reason="Requires GROMACS to be installed.")
 @pytest.mark.parametrize(
     "input_system,isalchem", [("system", False), ("alchemical_ion_system", True)]
 )
@@ -32,6 +33,7 @@ def test_isAlchemicalIon(input_system, isalchem, request):
     assert system[-1].isAlchemicalIon() is isalchem
 
 
+@pytest.mark.skipif(has_gromacs is False, reason="Requires GROMACS to be installed.")
 @pytest.mark.parametrize(
     "input_system,isalchem", [("system", None), ("alchemical_ion_system", True)]
 )
@@ -44,6 +46,7 @@ def test_getAlchemicalIon(input_system, isalchem, request):
         assert isinstance(ion, Molecule)
 
 
+@pytest.mark.skipif(has_gromacs is False, reason="Requires GROMACS to be installed.")
 def test_getAlchemicalIonIdx(alchemical_ion_system):
     index = alchemical_ion_system.getAlchemicalIonIdx()
     assert index == 680
diff --git a/tests/Sandpit/Exscientia/Process/test_position_restraint.py b/tests/Sandpit/Exscientia/Process/test_position_restraint.py
index aa720c470..7355adc70 100644
--- a/tests/Sandpit/Exscientia/Process/test_position_restraint.py
+++ b/tests/Sandpit/Exscientia/Process/test_position_restraint.py
@@ -122,8 +122,8 @@ def test_gromacs(protocol, system, ref_system, tmp_path):
 
 
 @pytest.mark.skipif(
-    has_openff is False,
-    reason="Requires openff to be installed",
+    has_amber is False or has_openff is False,
+    reason="Requires AMBER and openff to be installed",
 )
 def test_amber(protocol, system, ref_system, tmp_path):
     proc = BSS.Process.Amber(