Merge branch 'devel' into feature_no_ghost_mods

Author: lohedges

README.rst

@@ -17,6 +17,16 @@
    :target: https://joss.theoj.org/papers/4ba84ad443693b5dded90e35bf5f8225
    :alt: Paper
 
+Survey
+------
+
+We are currently conducting a
+`survey <https://docs.google.com/forms/d/1zY0i3lLR9MhmohKjcu0wJp_CXJvBwcWoj6iG4p9LNKk/edit?ts=6836f566>`__
+to help us understand how BioSimSpace is being used and how we can improve it.
+The survey explores your molecular simulation tools and practices, identifies workflow challenges, and
+gathers feedback on the BioSimSpace simulation framework to guide its future development. If you have
+a few minutes, please fill it out!
+
 About
 -----
 

python/BioSimSpace/Process/_amber.py

@@ -745,31 +745,58 @@ def getFrame(self, index):
             # Create a copy of the existing system object.
             old_system = self._system.copy()
 
-            # Update the coordinates and velocities and return a mapping between
-            # the molecule indices in the two systems.
-            sire_system, mapping = _SireIO.updateCoordinatesAndVelocities(
-                old_system._sire_object,
-                new_system._sire_object,
-                self._mapping,
-                is_lambda1,
-                self._property_map,
-                self._property_map,
-            )
+            if isinstance(self._protocol, _Protocol._FreeEnergyMixin):
+                # Udpate the coordinates and velocities and return a mapping between
+                # the molecule indices in the two systems.
+                mapping = {
+                    _SireMol.MolIdx(x): _SireMol.MolIdx(x)
+                    for x in range(0, self._squashed_system.nMolecules())
+                }
+                (
+                    self._squashed_system._sire_object,
+                    _,
+                ) = _SireIO.updateCoordinatesAndVelocities(
+                    self._squashed_system._sire_object,
+                    new_system._sire_object,
+                    mapping,
+                    is_lambda1,
+                    self._property_map,
+                    self._property_map,
+                )
+
+                # Update the unsquashed system based on the updated squashed system.
+                old_system = _unsquash(
+                    old_system,
+                    self._squashed_system,
+                    self._mapping,
+                    explicit_dummies=self._explicit_dummies,
+                )
+
+            else:
+                # Update the coordinates and velocities and return a mapping between
+                # the molecule indices in the two systems.
+                sire_system, mapping = _SireIO.updateCoordinatesAndVelocities(
+                    old_system._sire_object,
+                    new_system._sire_object,
+                    self._mapping,
+                    is_lambda1,
+                    self._property_map,
+                    self._property_map,
+                )
 
-            # Update the underlying Sire object.
-            old_system._sire_object = sire_system
+                # Update the underlying Sire object.
+                old_system._sire_object = sire_system
 
-            # Store the mapping between the MolIdx in both systems so we don't
-            # need to recompute it next time.
-            self._mapping = mapping
+                # Store the mapping between the MolIdx in both systems so we don't
+                # need to recompute it next time.
+                self._mapping = mapping
 
             # Update the box information in the original system.
-            if self._has_box:
-                if "space" 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
-                    )
+            if "space" 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
+                )
 
             return old_system