New function of GRM to accomodate shifting coordinates for us and ext…

…ernal forcefields.

cctbx/geometry_restraints/base_geometry.py

@@ -60,6 +60,13 @@ def select(self, selection=None, iselection=None):
     Given selection return manager only with selected atoms and restraints
     """
     raise NotImplementedError
+  def shift_sites_cart(self, shift):
+    """
+    Sometimes coordinates of the model are shifted (e.g. in boxing with map).
+    In case any element of restraints cares, do what is appropriate here.
+    """
+    raise NotImplementedError
+
   def discard_symmetry(self, new_unit_cell):
     return self
   def add_angles_in_place(self, additional_angle_proxies):

cctbx/geometry_restraints/manager.py

@@ -438,6 +438,10 @@ def get_n_seq():
     result.set_source(source = self.get_source())
     return result
 
+  def shift_sites_cart(self, shift):
+    # just a stub from RSR. Proper treatment can be implemented here.
+    self.remove_reference_coordinate_restraints_in_place()
+
   def discard_symmetry(self, new_unit_cell):
     assert self.site_symmetry_table is not None #XXX lazy
     assert self.shell_sym_tables is not None #XXX lazy

mmtbx/refinement/real_space/individual_sites.py

@@ -344,15 +344,10 @@ def refine(self,
       new_unit_cell = box.xray_structure_box.unit_cell()
       geo_box = self.geometry_restraints_manager.select(box.selection)
       geo_box = geo_box.discard_symmetry(new_unit_cell=new_unit_cell)
-      geo_box.remove_reference_coordinate_restraints_in_place() # disaster happens otherwise
+      geo_box.shift_sites_cart(box.shift_cart) # disaster happens otherwise
       map_box = box.map_box
       sites_cart_box = box.xray_structure_box.sites_cart()
 
-      # When using the Schrodinger force field, move the whole structure as the
-      # selected atoms are environment aware.
-      if geo_box.get_source() == 'SCHRODINGER':
-        geo_box.shift_cart(box.shift_cart)
-
       rsr_simple_refiner = simple(
         target_map                  = map_box,
         selection                   = sel,
@@ -377,8 +372,6 @@ def refine(self,
         iselection, sites_cart_refined)
       self.xray_structure.set_sites_cart(sites_cart_moving)
       self.sites_cart = self.xray_structure.sites_cart()
-      if geo_box.get_source() == 'SCHRODINGER':
-        geo_box.shift_cart(shift_back)
     else: # NCS constraints are present
       # select on xrs, grm, ncs_groups
       grm = self.geometry_restraints_manager.select(selection)