Merge pull request #438 from OpenBioSim/backport_347

Backport fix from PR #437

Author: lohedges

python/BioSimSpace/IO/_io.py

@@ -592,7 +592,13 @@ def readMolecules(
 
 
 def saveMolecules(
-    filebase, system, fileformat, match_water=True, property_map={}, **kwargs
+    filebase,
+    system,
+    fileformat,
+    match_water=True,
+    save_velocities=True,
+    property_map={},
+    **kwargs,
 ):
     """
     Save a molecular system to file.
@@ -617,6 +623,9 @@ def saveMolecules(
         is being saved to a different file format to that from which it was
         loaded.
 
+    save_velocities : bool
+        Whether to write velocities to the output files.
+
     property_map : dict
         A dictionary that maps system "properties" to their user
         defined values. This allows the user to refer to properties
@@ -710,6 +719,10 @@ def saveMolecules(
     if not isinstance(match_water, bool):
         raise TypeError("'match_water' must be of type 'bool'.")
 
+    # Validate the save_velocities flag.
+    if not isinstance(save_velocities, bool):
+        raise TypeError("'save_velocities' must be of type 'bool'.")
+
     # Make a list of the matched file formats.
     formats = []
 
@@ -735,6 +748,11 @@ def saveMolecules(
     if _gmx_path is not None and ("GROMACS_PATH" not in _property_map):
         _property_map["GROMACS_PATH"] = _gmx_path
 
+    # If the user doesn't wish to save velocities, then remap the
+    # velocity property.
+    if not save_velocities:
+        _property_map["velocity"] = "null"
+
     # Get the directory name.
     dirname = _os.path.dirname(filebase)
 
@@ -861,7 +879,7 @@ def saveMolecules(
     return files
 
 
-def savePerturbableSystem(filebase, system, property_map={}):
+def savePerturbableSystem(filebase, system, save_velocities=True, property_map={}):
     """
     Save a system containing a perturbable molecule. This will be written in
     AMBER format, with a topology file for each end state of the perturbation,
@@ -877,6 +895,9 @@ def savePerturbableSystem(filebase, system, property_map={}):
     system : :class:`System <BioSimSpace._SireWrappers.System>`
         The molecular system.
 
+    save_velocities : bool
+        Whether to write velocities to the output files.
+
     property_map : dict
         A dictionary that maps system "properties" to their user defined
         values. This allows the user to refer to properties with their
@@ -907,6 +928,10 @@ def savePerturbableSystem(filebase, system, property_map={}):
             "or a list of 'BiSimSpace._SireWrappers.Molecule' types."
         )
 
+    # Validate the save_velocities flag.
+    if not isinstance(save_velocities, bool):
+        raise TypeError("'save_velocities' must be of type 'bool'.")
+
     # Validate the map.
     if not isinstance(property_map, dict):
         raise TypeError("'property_map' must be of type 'dict'")
@@ -926,6 +951,14 @@ def savePerturbableSystem(filebase, system, property_map={}):
     system0 = system.copy()
     system1 = system.copy()
 
+    # Create a copy of the property map.
+    property_map = property_map.copy()
+
+    # If the user doesn't wish to save velocities, then remap the
+    # velocity property.
+    if not save_velocities:
+        property_map["velocity"] = "null"
+
     # Update the perturbable molecule in each system.
     system0.updateMolecules(
         pert_mol._toRegularMolecule(property_map=property_map, is_lambda1=False)

python/BioSimSpace/Sandpit/Exscientia/IO/_io.py

@@ -592,7 +592,13 @@ def readMolecules(
 
 
 def saveMolecules(
-    filebase, system, fileformat, match_water=True, property_map={}, **kwargs
+    filebase,
+    system,
+    fileformat,
+    match_water=True,
+    save_velocities=True,
+    property_map={},
+    **kwargs,
 ):
     """
     Save a molecular system to file.
@@ -617,6 +623,9 @@ def saveMolecules(
         is being saved to a different file format to that from which it was
         loaded.
 
+    save_velocities : bool
+        Whether to write velocities to the output files.
+
     property_map : dict
         A dictionary that maps system "properties" to their user
         defined values. This allows the user to refer to properties
@@ -710,6 +719,10 @@ def saveMolecules(
     if not isinstance(match_water, bool):
         raise TypeError("'match_water' must be of type 'bool'.")
 
+    # Validate the save_velocities flag.
+    if not isinstance(save_velocities, bool):
+        raise TypeError("'save_velocities' must be of type 'bool'.")
+
     # Make a list of the matched file formats.
     formats = []
 
@@ -735,6 +748,11 @@ def saveMolecules(
     if _gmx_path is not None and ("GROMACS_PATH" not in _property_map):
         _property_map["GROMACS_PATH"] = _gmx_path
 
+    # If the user doesn't wish to save velocities, then remap the
+    # velocity property.
+    if not save_velocities:
+        _property_map["velocity"] = "null"
+
     # Get the directory name.
     dirname = _os.path.dirname(filebase)
 
@@ -861,7 +879,7 @@ def saveMolecules(
     return files
 
 
-def savePerturbableSystem(filebase, system, property_map={}):
+def savePerturbableSystem(filebase, system, save_velocities=True, property_map={}):
     """
     Save a system containing a perturbable molecule. This will be written in
     AMBER format, with a topology file for each end state of the perturbation,
@@ -877,6 +895,9 @@ def savePerturbableSystem(filebase, system, property_map={}):
     system : :class:`System <BioSimSpace._SireWrappers.System>`
         The molecular system.
 
+    save_velocities : bool
+        Whether to write velocities to the output files.
+
     property_map : dict
         A dictionary that maps system "properties" to their user defined
         values. This allows the user to refer to properties with their
@@ -907,6 +928,10 @@ def savePerturbableSystem(filebase, system, property_map={}):
             "or a list of 'BiSimSpace._SireWrappers.Molecule' types."
         )
 
+    # Validate the save_velocities flag.
+    if not isinstance(save_velocities, bool):
+        raise TypeError("'save_velocities' must be of type 'bool'.")
+
     # Validate the map.
     if not isinstance(property_map, dict):
         raise TypeError("'property_map' must be of type 'dict'")
@@ -926,6 +951,14 @@ def savePerturbableSystem(filebase, system, property_map={}):
     system0 = system.copy()
     system1 = system.copy()
 
+    # Create a copy of the property map.
+    property_map = property_map.copy()
+
+    # If the user doesn't wish to save velocities, then remap the
+    # velocity property.
+    if not save_velocities:
+        property_map["velocity"] = "null"
+
     # Update the perturbable molecule in each system.
     system0.updateMolecules(
         pert_mol._toRegularMolecule(property_map=property_map, is_lambda1=False)