Merge pull request #173 from OpenBioSim/fix_172

Fix issue #172
OpenBioSim · Sep 20, 2023 · e3014dc · e3014dc
2 parents 65045f0 + a2619d8
commit e3014dc
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Showing 14 changed files with 173 additions and 36 deletions.
diff --git a/python/BioSimSpace/Process/_amber.py b/python/BioSimSpace/Process/_amber.py
@@ -442,9 +442,10 @@ def getSystem(self, block="AUTO"):
             # Update the box information in the original system.
             if "space" in new_system._sire_object.propertyKeys():
                 box = new_system._sire_object.property("space")
-                old_system._sire_object.setProperty(
-                    self._property_map.get("space", "space"), box
-                )
+                if box.isPeriodic():
+                    old_system._sire_object.setProperty(
+                        self._property_map.get("space", "space"), box
+                    )
 
             return old_system
 

diff --git a/python/BioSimSpace/Process/_gromacs.py b/python/BioSimSpace/Process/_gromacs.py
@@ -2537,9 +2537,10 @@ def _getFrame(self, time):
                     and space_prop in new_system._sire_object.propertyKeys()
                 ):
                     box = new_system._sire_object.property("space")
-                    old_system._sire_object.setProperty(
-                        self._property_map.get("space", "space"), box
-                    )
+                    if box.isPeriodic():
+                        old_system._sire_object.setProperty(
+                            self._property_map.get("space", "space"), box
+                        )
 
                 # If this is a vacuum simulation, then translate the centre of mass
                 # of the system back to the origin.

diff --git a/python/BioSimSpace/Process/_namd.py b/python/BioSimSpace/Process/_namd.py
@@ -789,9 +789,10 @@ def getSystem(self, block="AUTO"):
                 # Update the box information in the original system.
                 if "space" in new_system._sire_object.propertyKeys():
                     box = new_system._sire_object.property("space")
-                    old_system._sire_object.setProperty(
-                        self._property_map.get("space", "space"), box
-                    )
+                    if box.isPeriodic():
+                        old_system._sire_object.setProperty(
+                            self._property_map.get("space", "space"), box
+                        )
 
                 return old_system
 

diff --git a/python/BioSimSpace/Process/_openmm.py b/python/BioSimSpace/Process/_openmm.py
@@ -1318,9 +1318,10 @@ def getSystem(self, block="AUTO"):
                 # Update the box information in the original system.
                 if "space" in new_system._sire_object.propertyKeys():
                     box = new_system._sire_object.property("space")
-                    old_system._sire_object.setProperty(
-                        self._property_map.get("space", "space"), box
-                    )
+                    if box.isPeriodic():
+                        old_system._sire_object.setProperty(
+                            self._property_map.get("space", "space"), box
+                        )
 
                 return old_system
 

diff --git a/python/BioSimSpace/Process/_somd.py b/python/BioSimSpace/Process/_somd.py
@@ -540,6 +540,13 @@ def getSystem(self, block="AUTO"):
 
             new_system = _IO.readMolecules(self._restart_file)
 
+            # Try loading the trajectory file to get the box information.
+            try:
+                frame = self.getTrajectory().getFrames(-1)
+                box = frame._sire_object.property("space")
+            except:
+                box = None
+
             # Since SOMD requires specific residue and water naming we copy the
             # coordinates back into the original system.
             old_system = self._system.copy()
@@ -564,8 +571,7 @@ def getSystem(self, block="AUTO"):
             self._mapping = mapping
 
             # Update the box information in the original system.
-            if "space" in new_system._sire_object.propertyKeys():
-                box = new_system._sire_object.property("space")
+            if box and box.isPeriodic():
                 old_system._sire_object.setProperty(
                     self._property_map.get("space", "space"), box
                 )

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py
@@ -693,9 +693,10 @@ def getSystem(self, block="AUTO"):
             # Update the box information in the original system.
             if "space" in new_system._sire_object.propertyKeys():
                 box = new_system._sire_object.property("space")
-                old_system._sire_object.setProperty(
-                    self._property_map.get("space", "space"), box
-                )
+                if box.isPeriodic():
+                    old_system._sire_object.setProperty(
+                        self._property_map.get("space", "space"), box
+                    )
 
             return old_system
 

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py
@@ -2597,9 +2597,10 @@ def _getFrame(self, time):
                     and space_prop in new_system._sire_object.propertyKeys()
                 ):
                     box = new_system._sire_object.property("space")
-                    old_system._sire_object.setProperty(
-                        self._property_map.get("space", "space"), box
-                    )
+                    if box.isPeriodic():
+                        old_system._sire_object.setProperty(
+                            self._property_map.get("space", "space"), box
+                        )
 
                 # If this is a vacuum simulation, then translate the centre of mass
                 # of the system back to the origin.

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_namd.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_namd.py
@@ -787,9 +787,10 @@ def getSystem(self, block="AUTO"):
                 # Update the box information in the original system.
                 if "space" in new_system._sire_object.propertyKeys():
                     box = new_system._sire_object.property("space")
-                    old_system._sire_object.setProperty(
-                        self._property_map.get("space", "space"), box
-                    )
+                    if box.isPeriodic():
+                        old_system._sire_object.setProperty(
+                            self._property_map.get("space", "space"), box
+                        )
 
                 return old_system
 

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_openmm.py
@@ -1322,9 +1322,10 @@ def getSystem(self, block="AUTO"):
                 # Update the box information in the original system.
                 if "space" in new_system._sire_object.propertyKeys():
                     box = new_system._sire_object.property("space")
-                    old_system._sire_object.setProperty(
-                        self._property_map.get("space", "space"), box
-                    )
+                    if box.isPeriodic():
+                        old_system._sire_object.setProperty(
+                            self._property_map.get("space", "space"), box
+                        )
 
                 return old_system
 

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_somd.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_somd.py
@@ -559,6 +559,13 @@ def getSystem(self, block="AUTO"):
 
             new_system = _IO.readMolecules(self._restart_file)
 
+            # Try loading the trajectory file to get the box information.
+            try:
+                frame = self.getTrajectory().getFrames(-1)
+                box = frame._sire_object.property("space")
+            except:
+                box = None
+
             # Since SOMD requires specific residue and water naming we copy the
             # coordinates back into the original system.
             old_system = self._system.copy()
@@ -583,8 +590,7 @@ def getSystem(self, block="AUTO"):
             self._mapping = mapping
 
             # Update the box information in the original system.
-            if "space" in new_system._sire_object.propertyKeys():
-                box = new_system._sire_object.property("space")
+            if box and box.isPeriodic():
                 old_system._sire_object.setProperty(
                     self._property_map.get("space", "space"), box
                 )

diff --git a/python/BioSimSpace/Sandpit/Exscientia/Trajectory/_trajectory.py b/python/BioSimSpace/Sandpit/Exscientia/Trajectory/_trajectory.py
@@ -41,6 +41,8 @@
 from sire.legacy import Base as _SireBase
 from sire.legacy import IO as _SireIO
 from sire.legacy import Mol as _SireMol
+from sire.legacy import Units as _SireUnits
+from sire.legacy import Vol as _SireVol
 
 from sire import load as _sire_load
 from sire._load import _resolve_path
@@ -203,15 +205,25 @@ def getFrame(trajectory, topology, index, system=None, property_map={}):
     if system is not None:
         if is_sire and frame.current().num_molecules() > 1:
             try:
+                new_system = frame.current()._system
+
                 sire_system, _ = _SireIO.updateCoordinatesAndVelocities(
                     system._sire_object,
-                    frame.current()._system,
+                    new_system,
                     mapping,
                     False,
                     property_map,
                     {},
                 )
 
+                # Update the box information in the original system.
+                if "space" in new_system.propertyKeys():
+                    box = new_system.property("space")
+                    if box.isPeriodic():
+                        sire_system.setProperty(
+                            self._property_map.get("space", "space"), box
+                        )
+
                 new_system = _System(sire_system)
 
             except Exception as e:
@@ -261,6 +273,14 @@ def getFrame(trajectory, topology, index, system=None, property_map={}):
                     system._sire_object, new_system, mapping, False, property_map, {}
                 )
 
+                # Update the box information in the original system.
+                if "space" in new_system.propertyKeys():
+                    box = new_system.property("space")
+                    if box.isPeriodic():
+                        sire_system.setProperty(
+                            self._property_map.get("space", "space"), box
+                        )
+
                 new_system = _System(sire_system)
             except Exception as e:
                 msg = "Failed to copy trajectory coordinates/velocities into BioSimSpace system!"
@@ -762,15 +782,25 @@ def getFrames(self, indices=None):
             if self._system is not None:
                 if self._backend == "SIRE" and frame.current().num_molecules() > 1:
                     try:
+                        new_system = frame.current()._system
+
                         sire_system, _ = _SireIO.updateCoordinatesAndVelocities(
                             self._system._sire_object,
-                            frame.current()._system,
+                            new_system,
                             self._mapping,
                             False,
                             self._property_map,
                             {},
                         )
 
+                        # Update the box information in the original system.
+                        if "space" in new_system.propertyKeys():
+                            box = new_system.property("space")
+                            if box.isPeriodic():
+                                sire_system.setProperty(
+                                    self._property_map.get("space", "space"), box
+                                )
+
                         new_system = _System(sire_system)
                     except Exception as e:
                         msg = "Failed to copy trajectory coordinates/velocities into BioSimSpace system!"
@@ -828,6 +858,14 @@ def getFrames(self, indices=None):
                             {},
                         )
 
+                        # Update the box information in the original system.
+                        if "space" in new_system.propertyKeys():
+                            box = new_system.property("space")
+                            if box.isPeriodic():
+                                sire_system.setProperty(
+                                    self._property_map.get("space", "space"), box
+                                )
+
                         new_system = _System(sire_system)
                     except Exception as e:
                         msg = "Failed to copy trajectory coordinates/velocities into BioSimSpace system!"
@@ -1080,6 +1118,17 @@ def _split_molecules(frame, pdb, reference, work_dir, property_map={}):
     # Whether we've parsed as a PDB file.
     is_pdb = False
 
+    # Create a triclinic space from the information in the frame file.
+    if isinstance(frame, _SireIO.AmberRst7):
+        # Get the box dimensions and angles. Take the values, since the
+        # units are wrong.
+        degree = _SireUnits.degree
+        dimensions = [x.value() for x in frame.box_dimensions()]
+        angles = [x.value() * degree for x in frame.box_angles()]
+        box = _SireVol.TriclinicBox(*dimensions, *angles)
+    else:
+        box = _SireVol.TriclinicBox(frame.box_v1(), frame.box_v2(), frame.box_v3())
+
     if "PRM7" in formats:
         try:
             top = _SireIO.AmberPrm(reference._sire_object)
@@ -1154,6 +1203,9 @@ def _split_molecules(frame, pdb, reference, work_dir, property_map={}):
             else:
                 raise IOError(msg) from None
 
+    # Add the space property.
+    split_system.setProperty(property_map.get("space", "space"), box)
+
     return split_system