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Internal updates due to Sire API fixes #203

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merged 3 commits into from
Nov 13, 2023
Merged

Internal updates due to Sire API fixes #203

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c011e22
Sire.IO.AmberRst7.box_angles now returns correct units.
lohedges Nov 13, 2023
84660b2
Now cursor.rotate rotates velocities too.
lohedges Nov 13, 2023
90c476f
Still need to apply units to angles.
lohedges Nov 13, 2023
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5 changes: 2 additions & 3 deletions python/BioSimSpace/Sandpit/Exscientia/Trajectory/_trajectory.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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())
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9 changes: 8 additions & 1 deletion python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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:
Expand All @@ -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:
Expand Down
5 changes: 2 additions & 3 deletions python/BioSimSpace/Trajectory/_trajectory.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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())
Expand Down
14 changes: 12 additions & 2 deletions python/BioSimSpace/_SireWrappers/_system.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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:
Expand All @@ -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:
Expand Down
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