Unicode support: more base changes

cootbx/interactive_edit.py

@@ -5,6 +5,8 @@
 import os
 import sys
 
+from libtbx.utils import to_str
+
 t_wait = 250 # in milliseconds
 
 #-----------------------------------------------------------------------
@@ -110,7 +112,7 @@ def __init__ (self, pdb_file, map_file, needs_rebuild=False) :
     toolbar.insert(maps_button, -1)
     maps_button.connect("clicked", self.OnNewMaps)
     maps_button.show()
-    self._imol = read_pdb(pdb_file)
+    self._imol = read_pdb(to_str(pdb_file))
     set_molecule_bonds_colour_map_rotation(self._imol, 30)
     self._map_mols = []
     self.load_maps(map_file)
@@ -130,9 +132,9 @@ def load_maps (self, map_file) :
         close_molecule(imol)
     else :
       set_colour_map_rotation_for_map(10)
-    print "Loading %s" % map_file
+    print "Loading %s" % to_str(map_file)
     self._map_mols = []
-    map_imol = auto_read_make_and_draw_maps(map_file)
+    map_imol = auto_read_make_and_draw_maps(to_str(map_file))
     if (isinstance(map_imol, int)) :
       # XXX this may be dangerous, but auto_read_make_and_draw_maps only returns
       # the last imol

cootbx/ligand_checklist.py

@@ -4,6 +4,8 @@
 import os
 import sys
 
+from libtbx.utils import to_str
+
 t_wait = 250
 
 def start_coot_and_wait (
@@ -29,6 +31,7 @@ def start_coot_and_wait (
   base_script = __file__.replace(".pyc", ".py")
   ligand_xyzs = []
   for pdb_file in ligand_files :
+    pdb_file = to_str(pdb_file)
     pdb_in = file_reader.any_file(pdb_file, force_type="pdb")
     pdb_in.assert_file_type("pdb")
     coords = pdb_in.file_object.atoms().extract_xyz()
@@ -39,10 +42,10 @@ def start_coot_and_wait (
   f.write("\n")
   f.write("import coot\n")
   cootbx.write_disable_nomenclature_errors(f)
-  f.write("read_pdb(\"%s\")\n" % pdb_file)
-  f.write("auto_read_make_and_draw_maps(\"%s\")\n" % map_file)
+  f.write("read_pdb(\"%s\")\n" % to_str(pdb_file))
+  f.write("auto_read_make_and_draw_maps(\"%s\")\n" % to_str(map_file))
   for cif_file in cif_files :
-    f.write("read_cif_dictionary(\"%s\")\n" % cif_file)
+    f.write("read_cif_dictionary(\"%s\")\n" % to_str(cif_file))
   f.write("m = manager(%s)\n" % str(ligand_info))
   f.close()
   make_header("Ligand selection in Coot", log)
@@ -77,7 +80,7 @@ def __init__ (self, ligand_file_info) :
     self.ligand_file_info = ligand_file_info
     self.ligand_imols = []
     for file_name, cc, xyz in ligand_file_info :
-      self.ligand_imols.append(read_pdb(file_name))
+      self.ligand_imols.append(read_pdb(to_str(file_name)))
     self.window = gtk.Window(gtk.WINDOW_TOPLEVEL)
     self.window.set_default_size(300, 200)
     self.window.set_title(title)

cootbx/view_refinement.py

@@ -1,6 +1,8 @@
 
 from __future__ import division
 
+from libtbx.utils import to_str
+
 def load_refinement (
     pdb_file,
     map_file,
@@ -23,20 +25,20 @@ def load_refinement (
             script_dir = os.path.dirname(script_file)
             if (script_dir != "") :
               os.chdir(script_dir)
-  read_pdb(pdb_file)
+  read_pdb(to_str(pdb_file))
   if (peaks_file is not None) and (os.path.isfile(peaks_file)) :
-    imol = read_pdb(peaks_file)
+    imol = read_pdb(to_str(peaks_file))
     set_mol_displayed(imol, False)
-  auto_read_make_and_draw_maps(map_file)
+  auto_read_make_and_draw_maps(to_str(map_file))
   if (have_anom_map) :
-    imol = make_and_draw_map(map_file,"ANOM","PHANOM","",0,0)
+    imol = make_and_draw_map(to_str(map_file),"ANOM","PHANOM","",0,0)
     set_contour_level_in_sigma(imol, 3.0)
     if (have_residual_map) :
       set_map_colour(imol, 0.0, 1.0, 1.0)
       set_map_displayed(imol, False)
     else :
       set_map_colour(imol, 1.0, 1.0, 0.0)
   if (have_residual_map) :
-    imol = make_and_draw_map(map_file,"ANOMDIFF","PHANOMDIFF","",0,1)
+    imol = make_and_draw_map(to_str(map_file),"ANOMDIFF","PHANOMDIFF","",0,1)
     set_contour_level_in_sigma(imol, 3.0)
     set_map_colour(imol, 1.0, 1.0, 0.0)

cootbx/watch_file.py

@@ -2,6 +2,8 @@
 from __future__ import division
 import os.path
 
+from libtbx.utils import to_str
+
 class watch_model (object) :
   """
   Simple filesystem-only automatic loader for PDB files.  Once invoked with
@@ -22,9 +24,9 @@ def check_file (self) :
       if file_mtime > self.last_mtime :
         if self.model_imol is not None :
           clear_and_update_molecule_from_file(self.model_imol,
-            self.file_name)
+            to_str(self.file_name))
         else :
-          self.model_imol = read_pdb(self.file_name)
+          self.model_imol = read_pdb(to_str(self.file_name))
         self.last_mtime = file_mtime
 
 
@@ -56,16 +58,16 @@ def update_files (self) :
     import coot # import dependency
     if (self.model_imol is not None) :
       clear_and_update_molecule_from_file(self.model_imol,
-        self.pdb_file)
+                                          to_str(self.pdb_file))
     else :
-      self.model_imol = read_pdb(self.pdb_file)
+      self.model_imol = read_pdb(to_str(self.pdb_file))
     if (len(self.map_imols) > 0) :
       set_colour_map_rotation_for_map(0)
       for imol in self._map_mols :
         close_molecule(imol)
     else :
       set_colour_map_rotation_for_map(10)
-    map_imol = auto_read_make_and_draw_maps(self.map_file)
+    map_imol = auto_read_make_and_draw_maps(to_str(self.map_file))
     if (isinstance(map_imol, int)) :
       # XXX this may be dangerous, but auto_read_make_and_draw_maps only returns
       # the last imol

cootbx/xmlrpc_server.py

@@ -16,6 +16,8 @@
 import traceback
 import os
 
+from libtbx.utils import to_str
+
 try :
   import coot_python
 except Exception, e :
@@ -94,7 +96,7 @@ def update_model (self, pdb_file) :
     """
     import coot
     if (self.current_imol is None) :
-      self.current_imol = read_pdb(pdb_file)
+      self.current_imol = read_pdb(to_str(pdb_file))
     else :
       clear_and_update_molecule_from_file(self.current_imol,
         pdb_file)