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Fix issues #241, #242, and #243 #244

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merged 3 commits into from
Feb 19, 2024
Merged

Fix issues #241, #242, and #243 #244

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5cc7dea
Remove redundant parmed import and references to parmed files.
lohedges Feb 19, 2024
1730723
Expose FreeEnergyMixin protocols. [closes #243]
lohedges Feb 19, 2024
1cfa0bd
Remove shared properties when loading perturbable systems.
lohedges Feb 19, 2024
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20 changes: 19 additions & 1 deletion python/BioSimSpace/IO/_io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -566,7 +566,7 @@ def readMolecules(
prop = property_map.get("time", "time")
time = system.property(prop)
system.removeSharedProperty(prop)
system.setProperties(prop, time)
system.setProperty(prop, time)
except:
pass

Expand Down Expand Up @@ -1148,6 +1148,24 @@ def readPerturbableSystem(top0, coords0, top1, coords1, property_map={}):
# Update the molecule in the original system.
system0.updateMolecules(mol)

# 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 = system0._sire_object.property(prop)
system0._sire_object.removeSharedProperty(prop)
system0._sire_object.setProperty(prop, space)

# Time.
prop = property_map.get("time", "time")
time = system0._sire_object.property(prop)
system0._sire_object.removeSharedProperty(prop)
system0._sire_object.setProperty(prop, time)
except:
pass

return system0


Expand Down
7 changes: 1 addition & 6 deletions python/BioSimSpace/Parameters/_Protocol/_openforcefield.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,6 @@

import os as _os

_parmed = _try_import("parmed")
import queue as _queue
import subprocess as _subprocess

Expand Down Expand Up @@ -189,10 +188,6 @@ def run(self, molecule, work_dir=None, queue=None):
else:
is_smiles = False

# The following is adapted from the Open Force Field examples, where an
# OpenFF system is converted to AMBER format files using ParmEd:
# https://github.com/openforcefield/openff-toolkit/blob/master/examples/using_smirnoff_in_amber_or_gromacs/convert_to_amber_gromacs.ipynb

if is_smiles:
# Convert SMILES string to an OpenFF molecule.
try:
Expand Down Expand Up @@ -353,7 +348,7 @@ def run(self, molecule, work_dir=None, queue=None):
if par_mol.nMolecules() == 1:
par_mol = par_mol.getMolecules()[0]
except Exception as e:
msg = "Failed to read molecule from: 'parmed.prmtop', 'parmed.inpcrd'"
msg = "Failed to read molecule from: 'interchange.prmtop', 'interchange.inpcrd'"
if _isVerbose():
msg += ": " + getattr(e, "message", repr(e))
raise IOError(msg) from e
Expand Down
3 changes: 2 additions & 1 deletion python/BioSimSpace/Process/_amber.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@
from .._Config import Amber as _AmberConfig
from .._Exceptions import IncompatibleError as _IncompatibleError
from .._Exceptions import MissingSoftwareError as _MissingSoftwareError
from ..Protocol._free_energy_mixin import _FreeEnergyMixin
from ..Protocol._position_restraint_mixin import _PositionRestraintMixin
from .._SireWrappers import System as _System
from ..Types._type import Type as _Type
Expand Down Expand Up @@ -126,7 +127,7 @@ def __init__(
)

# Catch unsupported protocols.
if isinstance(protocol, _Protocol.FreeEnergy):
if isinstance(protocol, _FreeEnergyMixin):
raise _IncompatibleError(
"Unsupported protocol: '%s'" % self._protocol.__class__.__name__
)
Expand Down
29 changes: 20 additions & 9 deletions python/BioSimSpace/Process/_gromacs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,7 @@
from .. import _isVerbose
from .._Config import Gromacs as _GromacsConfig
from .._Exceptions import MissingSoftwareError as _MissingSoftwareError
from ..Protocol._free_energy_mixin import _FreeEnergyMixin
from ..Protocol._position_restraint_mixin import _PositionRestraintMixin
from .._SireWrappers import System as _System
from ..Types._type import Type as _Type
Expand Down Expand Up @@ -232,7 +233,7 @@ def _setup(self):
# Create a copy of the system.
system = self._system.copy()

if isinstance(self._protocol, _Protocol.FreeEnergy):
if isinstance(self._protocol, _FreeEnergyMixin):
# Check that the system contains a perturbable molecule.
if self._system.nPerturbableMolecules() == 0:
raise ValueError(
Expand Down Expand Up @@ -2544,10 +2545,15 @@ def _getFinalFrame(self):
space_prop in old_system._sire_object.propertyKeys()
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
)
# Get the original space.
box = old_system._sire_object.property("space")

# Only update the box if the space is periodic.
if box.isPeriodic():
box = new_system._sire_object.property("space")
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.
Expand Down Expand Up @@ -2655,11 +2661,16 @@ def _getFrame(self, time):
space_prop in old_system._sire_object.propertyKeys()
and space_prop in new_system._sire_object.propertyKeys()
):
box = new_system._sire_object.property("space")
# Get the original space.
box = old_system._sire_object.property("space")

# Only update the box if the space is periodic.
if box.isPeriodic():
old_system._sire_object.setProperty(
self._property_map.get("space", "space"), box
)
box = new_system._sire_object.property("space")
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.
Expand Down
20 changes: 19 additions & 1 deletion python/BioSimSpace/Sandpit/Exscientia/IO/_io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -566,7 +566,7 @@ def readMolecules(
prop = property_map.get("time", "time")
time = system.property(prop)
system.removeSharedProperty(prop)
system.setProperties(prop, time)
system.setProperty(prop, time)
except:
pass

Expand Down Expand Up @@ -1148,6 +1148,24 @@ def readPerturbableSystem(top0, coords0, top1, coords1, property_map={}):
# Update the molecule in the original system.
system0.updateMolecules(mol)

# 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 = system0._sire_object.property(prop)
system0._sire_object.removeSharedProperty(prop)
system0._sire_object.setProperty(prop, space)

# Time.
prop = property_map.get("time", "time")
time = system0._sire_object.property(prop)
system0._sire_object.removeSharedProperty(prop)
system0._sire_object.setPropery(prop, time)
except:
pass

return system0


Expand Down
7 changes: 1 addition & 6 deletions python/BioSimSpace/Sandpit/Exscientia/Parameters/_Protocol/_openforcefield.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,6 @@

import os as _os

_parmed = _try_import("parmed")
import queue as _queue
import subprocess as _subprocess

Expand Down Expand Up @@ -189,10 +188,6 @@ def run(self, molecule, work_dir=None, queue=None):
else:
is_smiles = False

# The following is adapted from the Open Force Field examples, where an
# OpenFF system is converted to AMBER format files using ParmEd:
# https://github.com/openforcefield/openff-toolkit/blob/master/examples/using_smirnoff_in_amber_or_gromacs/convert_to_amber_gromacs.ipynb

if is_smiles:
# Convert SMILES string to an OpenFF molecule.
try:
Expand Down Expand Up @@ -353,7 +348,7 @@ def run(self, molecule, work_dir=None, queue=None):
if par_mol.nMolecules() == 1:
par_mol = par_mol.getMolecules()[0]
except Exception as e:
msg = "Failed to read molecule from: 'parmed.prmtop', 'parmed.inpcrd'"
msg = "Failed to read molecule from: 'interchange.prmtop', 'interchange.inpcrd'"
if _isVerbose():
msg += ": " + getattr(e, "message", repr(e))
raise IOError(msg) from e
Expand Down
26 changes: 18 additions & 8 deletions python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2638,10 +2638,15 @@ def _getFinalFrame(self):
space_prop in old_system._sire_object.propertyKeys()
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
)
# Get the original space.
box = old_system._sire_object.property("space")

# Only update the box if the space is periodic.
if box.isPeriodic():
box = new_system._sire_object.property("space")
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.
Expand Down Expand Up @@ -2749,11 +2754,16 @@ def _getFrame(self, time):
space_prop in old_system._sire_object.propertyKeys()
and space_prop in new_system._sire_object.propertyKeys()
):
box = new_system._sire_object.property("space")
# Get the original space.
box = old_system._sire_object.property("space")

# Only update the box if the space is periodic.
if box.isPeriodic():
old_system._sire_object.setProperty(
self._property_map.get("space", "space"), box
)
box = new_system._sire_object.property("space")
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.
Expand Down
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