Merge pull request #338 from OpenBioSim/feature_remove_space

Add method to remove the space property from a system. [ci skip]

python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py

@@ -1670,6 +1670,9 @@ def setBox(self, box, angles=3 * [_Angle(90, "degree")], property_map={}):
         if len(box) != 3:
             raise ValueError("'angles' must contain three items.")
 
+        if not isinstance(property_map, dict):
+            raise TypeError("'property_map' must be of type 'dict'.")
+
         # Convert sizes to Anstrom.
         vec = [x.angstroms().value() for x in box]
 
@@ -1720,6 +1723,9 @@ def getBox(self, property_map={}):
             The box vector angles: yz, xz, and xy.
         """
 
+        if not isinstance(property_map, dict):
+            raise TypeError("'property_map' must be of type 'dict'.")
+
         # Get the "space" property and convert to a list of BioSimSpace.Type.Length
         # objects.
         try:
@@ -1751,6 +1757,28 @@ def getBox(self, property_map={}):
 
         return box, angles
 
+    def removeBox(self, property_map={}):
+        """
+        Remove the simulation box from the system.
+
+        Parameters
+        ----------
+
+        property_map : dict
+            A dictionary that maps system "properties" to their user defined
+            values. This allows the user to refer to properties with their
+            own naming scheme, e.g. { "charge" : "my-charge" }
+        """
+
+        if not isinstance(property_map, dict):
+            raise TypeError("'property_map' must be of type 'dict'")
+
+        # Remove the "space" property.
+        try:
+            self._sire_object.removeProperty(property_map.get("space", "space"))
+        except:
+            pass
+
     def makeWhole(self, property_map={}):
         """
         Make all molecules in the system "whole", i.e. unwrap any molecules that have

python/BioSimSpace/_SireWrappers/_system.py

@@ -1587,6 +1587,9 @@ def setBox(self, box, angles=3 * [_Angle(90, "degree")], property_map={}):
         if len(box) != 3:
             raise ValueError("'angles' must contain three items.")
 
+        if not isinstance(property_map, dict):
+            raise TypeError("'property_map' must be of type 'dict'")
+
         # Convert sizes to Anstrom.
         vec = [x.angstroms().value() for x in box]
 
@@ -1637,6 +1640,9 @@ def getBox(self, property_map={}):
             The box vector angles: yz, xz, and xy.
         """
 
+        if not isinstance(property_map, dict):
+            raise TypeError("'property_map' must be of type 'dict'")
+
         # Get the "space" property and convert to a list of BioSimSpace.Type.Length
         # objects.
         try:
@@ -1668,6 +1674,28 @@ def getBox(self, property_map={}):
 
         return box, angles
 
+    def removeBox(self, property_map={}):
+        """
+        Remove the simulation box from the system.
+
+        Parameters
+        ----------
+
+        property_map : dict
+            A dictionary that maps system "properties" to their user defined
+            values. This allows the user to refer to properties with their
+            own naming scheme, e.g. { "charge" : "my-charge" }
+        """
+
+        if not isinstance(property_map, dict):
+            raise TypeError("'property_map' must be of type 'dict'")
+
+        # Remove the "space" property.
+        try:
+            self._sire_object.removeProperty(property_map.get("space", "space"))
+        except:
+            pass
+
     def makeWhole(self, property_map={}):
         """
         Make all molecules in the system "whole", i.e. unwrap any molecules that have

tests/Sandpit/Exscientia/_SireWrappers/test_system.py

@@ -494,3 +494,17 @@ def test_set_water_property_preserve(system):
 
     # Make sure the property is preserved.
     assert system[-1]._sire_object.hasProperty("test")
+
+
+def test_remove_box(system):
+    # Make a copy of the system.
+    system = system.copy()
+
+    # Make sure the box is present.
+    assert "space" in system._sire_object.propertyKeys()
+
+    # Remove the box.
+    system.removeBox()
+
+    # Make sure the box is removed.
+    assert not "space" in system._sire_object.propertyKeys()

tests/_SireWrappers/test_system.py

@@ -484,3 +484,17 @@ def test_set_water_property_preserve(system):
 
     # Make sure the property is preserved.
     assert system[-1]._sire_object.hasProperty("test")
+
+
+def test_remove_box(system):
+    # Make a copy of the system.
+    system = system.copy()
+
+    # Make sure the box is present.
+    assert "space" in system._sire_object.propertyKeys()
+
+    # Remove the box.
+    system.removeBox()
+
+    # Make sure the box is removed.
+    assert not "space" in system._sire_object.propertyKeys()