Clarify map_manager.is_compatible_model(model) means this model can b…

…e used with this map manager

cctbx/maptbx/box.py

@@ -79,7 +79,8 @@ def __init__(self,
     assert self._map_manager.map_data().accessor().origin()  ==  (0, 0, 0)
     if model is not None:
       assert isinstance(model, mmtbx.model.manager)
-      assert map_manager.is_compatible_model(model)
+      assert map_manager.is_compatible_model(model,
+        require_match_unit_cell_crystal_symmetry=True)
 
     self._force_wrapping = wrapping
     if wrapping is None:
@@ -629,7 +630,8 @@ def __init__(self, map_manager,
     assert resolution is not None
     if model is not None:
       assert isinstance(model, mmtbx.model.manager)
-      assert map_manager.is_compatible_model(model)
+      assert map_manager.is_compatible_model(model,
+        require_match_unit_cell_crystal_symmetry=True)
     if self.map_manager().wrapping():  # map must be entire unit cell
       assert map_manager.unit_cell_grid == map_manager.map_data().all()
 

iotbx/map_manager.py

@@ -1926,7 +1926,7 @@ def is_compatible_ncs_object(self, ncs_object, tol = 0.001):
     return ok
 
   def is_compatible_model(self, model,
-       require_match_unit_cell_crystal_symmetry=True,
+       require_match_unit_cell_crystal_symmetry = False,
         absolute_angle_tolerance = 0.01,
         absolute_length_tolerance = 0.01,
         shift_tol = 0.001):
@@ -1940,13 +1940,12 @@ def is_compatible_model(self, model,
         2. model current symmetry does not match map original or current
         3. model has a shift_cart (shift applied) different than map shift_cart
 
-      NOTE: a True result does not mean that the model crystal_symmetry matches
-      the map crystal_symmetry.  It does mean that it is reasonable to set the
-      model crystal_symmetry to match the map ones.
-
       If require_match_unit_cell_crystal_symmetry is True, then they are
-      different if anything is different. If it is False, allow original
-       symmetries do not have to match
+      incompatible if anything is different.
+
+      If require_match_unit_cell_crystal_symmetry is False, original
+       symmetries do not have to match.  Model crystal_symmetry can match
+       the unit_cell_crystal_symmetry or crystal_symmetry of the map.
     '''
 
     ok=None
@@ -1983,6 +1982,8 @@ def is_compatible_model(self, model,
     text_map_uc=str(map_uc).replace("\n"," ")
     text_map=str(map_sym).replace("\n"," ")
 
+    assert map_sym # map_sym should always should be there. model_sym could be missing
+
     if require_match_unit_cell_crystal_symmetry and map_uc and (
       not model_uc) and (
        not map_sym.is_similar_symmetry(map_uc,
@@ -1998,7 +1999,7 @@ def is_compatible_model(self, model,
         "\n%s\n. Current map symmetry is: \n%s\n " %(
          text_map_uc,text_map)
 
-    elif  model_uc and map_uc and (
+    elif model_sym and model_uc and map_uc and (
         (not map_uc.is_similar_symmetry(map_sym,
         absolute_angle_tolerance = absolute_angle_tolerance,
         absolute_length_tolerance = absolute_length_tolerance,))
@@ -2014,31 +2015,41 @@ def is_compatible_model(self, model,
         absolute_angle_tolerance = absolute_angle_tolerance,
         absolute_length_tolerance = absolute_length_tolerance,
          ) ) ):
-       ok=False# model and map_manager symmetries present and do not match
+       ok=False # model and map_manager uc present and some symmetries do not match
        text="Model original symmetry: \n%s\n and current symmetry :\n%s\n" %(
           text_model_uc,text_model)+\
           "do not match map unit_cell symmetry:"+\
          " \n%s\n and map current symmetry: \n%s\n symmetry" %(
            text_map_uc,text_map)
-    elif model_sym and map_uc and (not model_sym.is_similar_symmetry(map_uc,
+    elif map_uc and model_sym and (not model_sym.is_similar_symmetry(map_uc,
         absolute_angle_tolerance = absolute_angle_tolerance,
         absolute_length_tolerance = absolute_length_tolerance,
         )) and (not
               model_sym.is_similar_symmetry(map_sym,
         absolute_angle_tolerance = absolute_angle_tolerance,
         absolute_length_tolerance = absolute_length_tolerance,
         )):
-       ok=False# model does not match either map symmetry
+       ok=False # model does not match either map symmetry
        text="Model current symmetry: \n%s\n" %(
           text_model)+\
           " does not match map unit_cell symmetry:"+\
            " \n%s\n or map current symmetry: \n%s\n" %(
            text_map_uc,text_map)
+    elif model_sym and (not model_uc) and (not map_uc) and (
+           not model_sym.is_similar_symmetry(map_sym,
+        absolute_angle_tolerance = absolute_angle_tolerance,
+        absolute_length_tolerance = absolute_length_tolerance,
+        )):
+       ok=False # model has no uc and model symmetry does not match map symmetry
+       text="Model current symmetry: \n%s\n" %(
+          text_model)+\
+          " does not match map symmetry: \n%s\n" %( text_map)
 
     elif require_match_unit_cell_crystal_symmetry and (
         not model_sym) and (not model_uc):
        ok=False # model does not have any symmetry so it does not match
        text="Model has no symmetry and cannot match any map"
+
     elif (not model_sym) and (not model_uc):
        ok=True # model does not have any symmetry so anything is ok
        text="Model has no symmetry and can match any map symmetry"

iotbx/map_model_manager.py

@@ -948,7 +948,8 @@ def add_model_by_id(self, model, model_id,
 
     if model and \
       self.map_manager() and (
-         not self.map_manager().is_compatible_model(model)):
+         not self.map_manager().is_compatible_model(model,
+          require_match_unit_cell_crystal_symmetry=True)):
       # needs shifting
       self.shift_any_model_to_match(model,
          set_unit_cell_crystal_symmetry = True)
@@ -7894,7 +7895,8 @@ def density_at_model_sites(self,
      "There is no map with id='%s' available for density_at_model_sites" %(
          map_id))
 
-    assert self.map_manager().is_compatible_model(model) # model must match
+    assert self.map_manager().is_compatible_model(model,
+       require_match_unit_cell_crystal_symmetry=True) # model must match
 
     if selection_string:
       sel = model.selection(selection_string)
@@ -7938,7 +7940,8 @@ def map_model_cc(self,
          map_id))
 
 
-    if not self.map_manager().is_compatible_model(model): # model must match
+    if not self.map_manager().is_compatible_model(model,
+        require_match_unit_cell_crystal_symmetry=True): # model must match
       print("Setting model crystal symmetry to match map", file = self.log)
       model = model.deep_copy()
       model.set_crystal_symmetry(self.map_manager().crystal_symmetry())
@@ -8632,7 +8635,8 @@ def generate_map(self,
         log = null_out())
 
     if have_map_manager:  #  make sure model matches
-      if not self.map_manager().is_compatible_model(model):
+      if not self.map_manager().is_compatible_model(model,
+          require_match_unit_cell_crystal_symmetry=True):
          self.shift_any_model_to_match(model,
          set_unit_cell_crystal_symmetry = True)