Merge pull request #203 from OpenBioSim/fix_sire_api_updates

Internal updates due to Sire API fixes
OpenBioSim · Nov 13, 2023 · d1d0acb · d1d0acb
2 parents 621149b + 90c476f
commit d1d0acb
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Showing 4 changed files with 24 additions and 9 deletions.
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Trajectory/_trajectory.py b/python/BioSimSpace/Sandpit/Exscientia/Trajectory/_trajectory.py
@@ -1120,11 +1120,10 @@ def _split_molecules(frame, pdb, reference, work_dir, property_map={}):
 
     # 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.
+        # Get the box dimensions and angles.
         degree = _SireUnits.degree
         dimensions = [x.value() for x in frame.box_dimensions()]
-        angles = [x.value() * degree for x in frame.box_angles()]
+        angles = [x.to(degree) * 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())

diff --git a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
@@ -1228,7 +1228,10 @@ def rotateBoxVectors(
         try:
             prop_name = property_map.get("velocity", "velocity")
             cursor = cursor.rotate(
-                center=center, matrix=rotation_matrix, map={"coordinates": prop_name}
+                center=center,
+                matrix=rotation_matrix,
+                rotate_velocities=False,
+                map={"coordinates": prop_name},
             )
         except:
             pass
@@ -1241,12 +1244,14 @@ def rotateBoxVectors(
                 cursor = cursor.rotate(
                     center=center,
                     matrix=rotation_matrix,
+                    rotate_velocities=False,
                     map={"coordinates": prop_name},
                 )
                 prop_name = property_map.get("coordinates", "coordinates") + "1"
                 cursor = cursor.rotate(
                     center=center,
                     matrix=rotation_matrix,
+                    rotate_velocities=False,
                     map={"coordinates": prop_name},
                 )
             except:
@@ -1258,12 +1263,14 @@ def rotateBoxVectors(
                 cursor = cursor.rotate(
                     center=center,
                     matrix=rotation_matrix,
+                    rotate_velocities=False,
                     map={"coordinates": prop_name},
                 )
                 prop_name = property_map.get("velocity", "velocity") + "1"
                 cursor = cursor.rotate(
                     center=center,
                     matrix=rotation_matrix,
+                    rotate_velocities=False,
                     map={"coordinates": prop_name},
                 )
             except:

diff --git a/python/BioSimSpace/Trajectory/_trajectory.py b/python/BioSimSpace/Trajectory/_trajectory.py
@@ -1120,11 +1120,10 @@ def _split_molecules(frame, pdb, reference, work_dir, property_map={}):
 
     # 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.
+        # Get the box dimensions and angles.
         degree = _SireUnits.degree
         dimensions = [x.value() for x in frame.box_dimensions()]
-        angles = [x.value() * degree for x in frame.box_angles()]
+        angles = [x.to(degree) * 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())

diff --git a/python/BioSimSpace/_SireWrappers/_system.py b/python/BioSimSpace/_SireWrappers/_system.py
@@ -1167,7 +1167,10 @@ def rotateBoxVectors(
         try:
             prop_name = property_map.get("coordinates", "coordinates")
             cursor = cursor.rotate(
-                center=center, matrix=rotation_matrix, map={"coordinates": prop_name}
+                center=center,
+                matrix=rotation_matrix,
+                rotate_velocities=False,
+                map={"coordinates": prop_name},
             )
         except:
             pass
@@ -1176,7 +1179,10 @@ def rotateBoxVectors(
         try:
             prop_name = property_map.get("velocity", "velocity")
             cursor = cursor.rotate(
-                center=center, matrix=rotation_matrix, map={"coordinates": prop_name}
+                center=center,
+                matrix=rotation_matrix,
+                rotate_velocities=False,
+                map={"coordinates": prop_name},
             )
         except:
             pass
@@ -1189,12 +1195,14 @@ def rotateBoxVectors(
                 cursor = cursor.rotate(
                     center=center,
                     matrix=rotation_matrix,
+                    rotate_velocities=False,
                     map={"coordinates": prop_name},
                 )
                 prop_name = property_map.get("coordinates", "coordinates") + "1"
                 cursor = cursor.rotate(
                     center=center,
                     matrix=rotation_matrix,
+                    rotate_velocities=False,
                     map={"coordinates": prop_name},
                 )
             except:
@@ -1206,12 +1214,14 @@ def rotateBoxVectors(
                 cursor = cursor.rotate(
                     center=center,
                     matrix=rotation_matrix,
+                    rotate_velocities=False,
                     map={"coordinates": prop_name},
                 )
                 prop_name = property_map.get("velocity", "velocity") + "1"
                 cursor = cursor.rotate(
                     center=center,
                     matrix=rotation_matrix,
+                    rotate_velocities=False,
                     map={"coordinates": prop_name},
                 )
             except: