Some of the Xtal-related functions are improved.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@486 a2be9bc6-48de-4e38-9406-05402d4bc13c

diff --git a/Scripts/crystal.rb b/Scripts/crystal.rb
index b034cc4..0bdf3cf 100755 (executable)
--- a/Scripts/crystal.rb
+++ b/Scripts/crystal.rb
@@ -1755,9 +1755,10 @@ end
 
   def cmd_unit_cell
     mol = self
+       new_box = nil
     hash = Dialog.run("Unit Cell") {
          @mol = mol
-         @box = @mol.box
+         @box = @mol.box.dup
          @box_save = nil
          
          def set_cell_value(item1)
@@ -1932,12 +1933,31 @@ end
                -1, -1)
          set_attr(0, :action=>lambda { |it|
            if set_box_value(it)
-                 @mol.box = @box
+                 new_box = @box
                  end_modal(it)
                end
          } )
          update_values(nil)
        }
+       if hash[:status] == 0
+         if new_box != nil
+           h = Dialog.run(" ") {
+                 layout(1,
+                   item(:text, :title=>"Do you want to keep the fractional coordinates?"),
+                       item(:radio, :title=>"Yes, convert the cartesian coordinates so that the fractional coordinates will be unchanged.",
+                         :tag=>"yes", :value=>1),
+                       item(:radio, :title=>"No, keep the cartesian coordinates unchanged.", :tag=>"no"))
+                 radio_group("yes", "no")
+               }
+               if h[:status] == 0
+                 yes = h["yes"] != 0
+                 new_box.push(yes)
+                 mol.box = new_box
+               end
+         else
+           mol.box = nil
+         end
+       end
   end
 
 
@@ -2292,6 +2312,34 @@ def cmd_show_periodic_image
        }
 end
 
+def has_expanded_atoms
+  atoms.find { |ap| ap.symop != nil }
+end
+
+def cmd_remove_expanded_atoms
+  mol = self
+  return unless mol.has_expanded_atoms
+  hash = Dialog.run("Remove Expanded Atoms") {
+    layout(1,
+         item(:radio, :title=>"Remove all expanded atoms.", :tag=>"all", :value=>1),
+         item(:radio, :title=>"Keep the expanded atoms that are in the same fragment with original atoms.", :tag=>"partial"))
+       radio_group("all", "partial")
+  }
+  if hash[:status] == 0
+    if hash["all"] == 1
+         rm = mol.atom_group { |ap| ap.symop != nil }
+       else
+         rm = IntGroup[]
+         mol.each_fragment { |f|
+           if !f.find { |i| mol.atoms[i].symop == nil }
+                 rm.add(f)
+               end
+         }
+       end
+       mol.remove(rm)
+  end
+end
+
 end
 
 require_cell = lambda { |m| m && m.cell != nil }
@@ -2299,10 +2347,11 @@ require_cell = lambda { |m| m && m.cell != nil }
 register_menu("Xtal\tUnit Cell...", :cmd_unit_cell)
 register_menu("Xtal\tSymmetry Operations...", :cmd_symmetry_operations)
 register_menu("Xtal\t-", nil)
-register_menu("Xtal\tShow Periodic Image...", :cmd_show_periodic_image, require_cell)
-register_menu("Xtal\tComplete by Symmetry", :complete_by_symmetry, require_cell)
+register_menu("Xtal\tComplete by Symmetry", :complete_by_symmetry, lambda { |m| m && (m.cell != nil || m.nsymmetries > 1) } )
 register_menu("Xtal\tCreate Packing Diagram...", :create_packing_diagram, require_cell)
+register_menu("Xtal\tShow Periodic Image...", :cmd_show_periodic_image, require_cell)
+register_menu("Xtal\tRemove Expanded Atoms...", :cmd_remove_expanded_atoms, lambda { |m| m && m.has_expanded_atoms } )
 register_menu("Xtal\t-", nil)
-register_menu("Xtal\tBest-fit Planes...", :cmd_plane, :non_empty)
 register_menu("Xtal\tBonds and Angles with Sigma...", :cmd_bond_angle_with_sigma, :non_empty)
+register_menu("Xtal\tBest-fit Planes...", :cmd_plane, :non_empty)
 register_menu("Xtal\tShow ORTEP...", :cmd_show_ortep, :non_empty)

diff --git a/Scripts/loadsave.rb b/Scripts/loadsave.rb
index bed2c53..acbcf51 100755 (executable)
--- a/Scripts/loadsave.rb
+++ b/Scripts/loadsave.rb
@@ -915,7 +915,7 @@ end_of_header
                          puts "#{n1} bonds are guessed." if verbose
                        end
                        if exbonds.length > 0
-                         h = Dialog.run {
+                         h = Dialog.run("CIF Import: Symmetry Expansion") {
                            layout(1,
                                  item(:text, :title=>"There are bonds including symmetry related atoms.\nWhat do you want to do?"),
                                  item(:radio, :title=>"Expand only atoms that are included in those extra bonds.", :tag=>"atoms_only"),