Attention: big changes in __init__.py, almost no changes in import_pdb.py

and export_pdb.py

1. With respect to the propositions made by Campbell and Sebastian
(see http://projects.blender.org/tracker/?func=detail&group_id=153&aid=29226&atid=469)
I changed the code. The PDB IO has now the preset option in the file dialog
of the importer and exporter.

2. Furthermore, I have put all properties into one group, which is located
in bpy.contect.scene. 

3. Some code cleaning

Soon, I will put in a new option (next days): the user can decide whether the 
panel is always, once or never shown after a PDB file is loaded. Note that
the panel is essential for me and also my students. It helps quickly modifying
PDB structures.

Blendphys 

3 files changed, 258 insertions, 205 deletions

diff --git a/io_mesh_pdb/__init__.py b/io_mesh_pdb/__init__.py
index c32382f4..539c299b 100644
--- a/io_mesh_pdb/__init__.py
+++ b/io_mesh_pdb/__init__.py
@@ -71,94 +71,89 @@ class CLASS_atom_pdb_panel(Panel):
 
     def draw(self, context):
         layout = self.layout
-        scn    = bpy.context.scene
+        scn    = context.scene.atom_pdb[0]
 
         row = layout.row()
         row.label(text="Outputs and custom data file")
-
         box = layout.box()
         row = box.row()
         row.label(text="Custom data file")
         row = box.row()
         col = row.column()
-        col.prop(scn, "atom_pdb_datafile")
+        col.prop(scn, "datafile")
         col.operator("atom_pdb.datafile_apply")
         row = box.row()
         col = row.column(align=True)
-        col.prop(scn, "atom_pdb_PDB_file")
-
+        col.prop(scn, "PDB_file")
         row = layout.row()
         row.label(text="Reload structure")
-
         box = layout.box()
         row = box.row()
         col = row.column()
-        col.prop(scn, "use_atom_pdb_mesh")
+        col.prop(scn, "use_mesh")
         col = row.column()
         col.label(text="Scaling factors")
         row = box.row()
         col = row.column(align=True)  
-        col.active = scn.use_atom_pdb_mesh   
-        col.prop(scn, "atom_pdb_mesh_azimuth")
-        col.prop(scn, "atom_pdb_mesh_zenith")
+        col.active = scn.use_mesh   
+        col.prop(scn, "mesh_azimuth")
+        col.prop(scn, "mesh_zenith")
         col = row.column(align=True)
-        col.prop(scn, "atom_pdb_scale_ballradius")
-        col.prop(scn, "atom_pdb_scale_distances")
+        col.prop(scn, "scale_ballradius")
+        col.prop(scn, "scale_distances")
         row = box.row()
         col = row.column()  
-        col.prop(scn, "use_atom_pdb_sticks")
+        col.prop(scn, "use_sticks")
         row = box.row()        
-        row.active = scn.use_atom_pdb_sticks
+        row.active = scn.use_sticks
         col = row.column(align=True)
-        col.prop(scn, "atom_pdb_sticks_sectors")
-        col.prop(scn, "atom_pdb_sticks_radius")
-        col.prop(scn, "atom_pdb_sticks_unit_length")
+        col.prop(scn, "sticks_sectors")
+        col.prop(scn, "sticks_radius")
+        col.prop(scn, "sticks_unit_length")
         col = row.column(align=True)        
-        col.prop(scn, "use_atom_pdb_sticks_color")        
-        col.prop(scn, "use_atom_pdb_sticks_smooth")
-        col.prop(scn, "use_atom_pdb_sticks_bonds")
+        col.prop(scn, "use_sticks_color")        
+        col.prop(scn, "use_sticks_smooth")
+        col.prop(scn, "use_sticks_bonds")
         row = box.row()        
-        row.active = scn.use_atom_pdb_sticks
+        row.active = scn.use_sticks
         col = row.column(align=True)
         col = row.column(align=True)
-        col.active = scn.use_atom_pdb_sticks and scn.use_atom_pdb_sticks_bonds 
-        col.prop(scn, "atom_pdb_sticks_dist")        
+        col.active = scn.use_sticks and scn.use_sticks_bonds 
+        col.prop(scn, "sticks_dist")        
         row = box.row()
-        row.prop(scn, "use_atom_pdb_center")
+        row.prop(scn, "use_center")
         row = box.row()
         col = row.column()
-        col.prop(scn, "use_atom_pdb_cam")
-        col.prop(scn, "use_atom_pdb_lamp")
+        col.prop(scn, "use_camera")
+        col.prop(scn, "use_lamp")
         col = row.column()
         col.operator("atom_pdb.button_reload")
-        col.prop(scn, "atom_pdb_number_atoms")
+        col.prop(scn, "number_atoms")
         row = box.row()
         row.operator("atom_pdb.button_distance")
-        row.prop(scn, "atom_pdb_distance")
-
+        row.prop(scn, "distance")
         row = layout.row()
         row.label(text="Modify atom radii")
-        
         box = layout.box()
         row = box.row()
         row.label(text="All changes concern:")
         row = box.row()
-        row.prop(scn, "atom_pdb_radius_how")
+        row.prop(scn, "radius_how")
         row = box.row()
         row.label(text="1. Change type of radii")
         row = box.row()
-        row.prop(scn, "atom_pdb_radius_type")
+        row.prop(scn, "radius_type")
         row = box.row()
         row.label(text="2. Change atom radii in pm")
         row = box.row()
-        row.prop(scn, "atom_pdb_radius_pm_name")
+        row.prop(scn, "radius_pm_name")
         row = box.row()
-        row.prop(scn, "atom_pdb_radius_pm")
+        row.prop(scn, "radius_pm")
         row = box.row()
         row.label(text="3. Change atom radii by scale")
         row = box.row()
         col = row.column()
-        col.prop(scn, "atom_pdb_radius_all")
+        col.prop(scn, "radius_all")
         col = row.column(align=True)
         col.operator( "atom_pdb.radius_all_bigger" )
         col.operator( "atom_pdb.radius_all_smaller" )
@@ -177,124 +172,114 @@ class CLASS_atom_pdb_panel(Panel):
             row.operator( "atom_pdb.separate_atom" )
 
 
-class CLASS_atom_pdb_IO(bpy.types.PropertyGroup):
+# The properties (gadgets) in the panel. They all go to scene
+# during initialization (see end) 
+class CLASS_atom_pdb_Properties(bpy.types.PropertyGroup):
 
     def Callback_radius_type(self, context):
-        scnn = bpy.context.scene
+        scn = bpy.context.scene.atom_pdb[0]
         import_pdb.DEF_atom_pdb_radius_type(
-                scnn.atom_pdb_radius_type,
-                scnn.atom_pdb_radius_how,
-                )
+                scn.radius_type,
+                scn.radius_how,)
 
     def Callback_radius_pm(self, context):
-        scnn = bpy.context.scene
+        scn = bpy.context.scene.atom_pdb[0]
         import_pdb.DEF_atom_pdb_radius_pm(
-                scnn.atom_pdb_radius_pm_name,
-                scnn.atom_pdb_radius_pm,
-                scnn.atom_pdb_radius_how,
-                )
+                scn.radius_pm_name,
+                scn.radius_pm,
+                scn.radius_how,)
 
     # In the file dialog window - Import
-    scn = bpy.types.Scene
-    scn.use_atom_pdb_cam = BoolProperty(
+    use_camera = BoolProperty(
         name="Camera", default=False,
         description="Do you need a camera?")
-    scn.use_atom_pdb_lamp = BoolProperty(
+    use_lamp = BoolProperty(
         name="Lamp", default=False,
         description = "Do you need a lamp?")
-    scn.use_atom_pdb_mesh = BoolProperty(
+    use_mesh = BoolProperty(
         name = "Mesh balls", default=False,
         description = "Use mesh balls instead of NURBS")
-    scn.atom_pdb_mesh_azimuth = IntProperty(
-        name = "Azimuth", default=32, min=0,
+    mesh_azimuth = IntProperty(
+        name = "Azimuth", default=32, min=1,
         description = "Number of sectors (azimuth)")
-    scn.atom_pdb_mesh_zenith = IntProperty(
-        name = "Zenith", default=32, min=0,
+    mesh_zenith = IntProperty(
+        name = "Zenith", default=32, min=1,
         description = "Number of sectors (zenith)")
-    scn.atom_pdb_scale_ballradius = FloatProperty(
-        name = "Balls", default=1.0, min=0.0,
+    scale_ballradius = FloatProperty(
+        name = "Balls", default=1.0, min=0.0001,
         description = "Scale factor for all atom radii")
-    scn.atom_pdb_scale_distances = FloatProperty (
-        name = "Distances", default=1.0, min=0.0,
+    scale_distances = FloatProperty (
+        name = "Distances", default=1.0, min=0.0001,
         description = "Scale factor for all distances")
-    scn.use_atom_pdb_center = BoolProperty(
+    use_center = BoolProperty(
         name = "Object to origin", default=True,
         description = "Put the object into the global origin")
-    scn.use_atom_pdb_sticks = BoolProperty(
+    use_sticks = BoolProperty(
         name="Use sticks", default=True,
         description="Do you want to display the sticks?")
-    scn.atom_pdb_sticks_sectors = IntProperty(
-        name = "Sector", default=20, min=0,
+    sticks_sectors = IntProperty(
+        name = "Sector", default=20, min=1,
         description="Number of sectors of a stick")
-    scn.atom_pdb_sticks_radius = FloatProperty(
-        name = "Radius", default=0.1, min=0.0,
+    sticks_radius = FloatProperty(
+        name = "Radius", default=0.1, min=0.0001,
         description ="Radius of a stick")
-    scn.atom_pdb_sticks_unit_length = FloatProperty(
-        name = "Unit", default=0.2, min=0,
+    sticks_unit_length = FloatProperty(
+        name = "Unit", default=0.2, min=0.0001,
         description = "Length of the unit of a stick in Angstrom")        
-    scn.use_atom_pdb_sticks_color = BoolProperty(
+    use_sticks_color = BoolProperty(
         name="Color", default=True,
         description="The sticks appear in the color of the atoms")
-    scn.use_atom_pdb_sticks_smooth = BoolProperty(
+    use_sticks_smooth = BoolProperty(
         name="Smooth", default=False,
         description="The sticks are round (sectors are not visible)")     
-    scn.use_atom_pdb_sticks_bonds = BoolProperty(
+    use_sticks_bonds = BoolProperty(
         name="Bonds", default=False,
         description="Show double and tripple bonds.")
-    scn.atom_pdb_sticks_dist = FloatProperty(
+    sticks_dist = FloatProperty(
         name="Distance", default = 1.1, min=1.0, max=3.0,
         description="Distance between sticks measured in stick diameter")        
-    scn.atom_pdb_atomradius = EnumProperty(
+    atomradius = EnumProperty(
         name="Type of radius",
         description="Choose type of atom radius",
         items=(('0', "Pre-defined", "Use pre-defined radius"),
                ('1', "Atomic", "Use atomic radius"),
                ('2', "van der Waals", "Use van der Waals radius")),
-               default='0',)
-
-    # In the file dialog window - Export
-    scn.atom_pdb_export_type = EnumProperty(
-        name="Type of Objects",
-        description="Choose type of objects",
-        items=(('0', "All", "Export all active objects"),
-               ('1', "Elements", "Export only those active objects which have a proper element name")),
-               default='1',)    
-    
+               default='0',)  
     # In the panel
-    scn.atom_pdb_datafile = StringProperty(
+    datafile = StringProperty(
         name = "", description="Path to your custom data file",
         maxlen = 256, default = "", subtype='FILE_PATH')
-    scn.atom_pdb_PDB_file = StringProperty(
+    PDB_file = StringProperty(
         name = "PDB file", default="",
         description = "Path of the PDB file")
-    scn.atom_pdb_number_atoms = StringProperty(name="",
+    number_atoms = StringProperty(name="",
         default="Number", description = "This output shows "
         "the number of atoms which have been loaded")
-    scn.atom_pdb_distance = StringProperty(
+    distance = StringProperty(
         name="", default="Distance (A)",
         description="Distance of 2 objects in Angstrom")
-    scn.atom_pdb_radius_how = EnumProperty(
+    radius_how = EnumProperty(
         name="",
         description="Which objects shall be modified?",
         items=(('ALL_ACTIVE',"all active objects", "in the current layer"),
                ('ALL_IN_LAYER',"all"," in active layer(s)")),
                default='ALL_ACTIVE',)
-    scn.atom_pdb_radius_type = EnumProperty(
+    radius_type = EnumProperty(
         name="Type",
         description="Which type of atom radii?",
         items=(('0',"predefined", "Use pre-defined radii"),
                ('1',"atomic", "Use atomic radii"),
                ('2',"van der Waals","Use van der Waals radii")),
                default='0',update=Callback_radius_type)
-    scn.atom_pdb_radius_pm_name = StringProperty(
+    radius_pm_name = StringProperty(
         name="", default="Atom name",
         description="Put in the name of the atom (e.g. Hydrogen)")
-    scn.atom_pdb_radius_pm = FloatProperty(
-        name="", default=100.0, min=0.0,
+    radius_pm = FloatProperty(
+        name="", default=100.0, min=0.01,
         description="Put in the radius of the atom (in pm)",
         update=Callback_radius_pm)
-    scn.atom_pdb_radius_all = FloatProperty(
-        name="Scale", default = 1.05, min=1.0,
+    radius_all = FloatProperty(
+        name="Scale", default = 1.05, min=1.0, max=5.0,
         description="Put in the scale factor")
 
 
@@ -305,12 +290,12 @@ class CLASS_atom_pdb_datafile_apply(Operator):
     bl_description = "Use color and radii values stored in the custom file"
 
     def execute(self, context):
-        scn    = bpy.context.scene
+        scn    = bpy.context.scene.atom_pdb[0]
 
-        if scn.atom_pdb_datafile == "":
+        if scn.datafile == "":
             return {'FINISHED'}
 
-        import_pdb.DEF_atom_pdb_custom_datafile(scn.atom_pdb_datafile)
+        import_pdb.DEF_atom_pdb_custom_datafile(scn.datafile)
 
         # TODO, move this into 'import_pdb' and call the function
         for obj in bpy.context.selected_objects:
@@ -338,7 +323,7 @@ class CLASS_atom_pdb_separate_atom(Operator):
     bl_description = "Separate the atom you have chosen"
 
     def execute(self, context):
-        scn    = bpy.context.scene
+        scn = bpy.context.scene.atom_pdb[0]
 
         # Get first all important properties from the atom which the user
         # has chosen: location, color, scale
@@ -365,7 +350,7 @@ class CLASS_atom_pdb_separate_atom(Operator):
         current_layers=bpy.context.scene.layers
 
         if "Vacancy" not in name:
-            if scn.use_atom_pdb_mesh == False:
+            if scn.use_mesh == False:
                 bpy.ops.surface.primitive_nurbs_surface_sphere_add(
                                     view_align=False, enter_editmode=False,
                                     location=loc_vec+loc_obj_vec,
@@ -373,8 +358,8 @@ class CLASS_atom_pdb_separate_atom(Operator):
                                     layers=current_layers)
             else:
                 bpy.ops.mesh.primitive_uv_sphere_add(
-                                segments=scn.atom_pdb_mesh_azimuth,
-                                ring_count=scn.atom_pdb_mesh_zenith,
+                                segments=scn.mesh_azimuth,
+                                ring_count=scn.mesh_zenith,
                                 size=1, view_align=False, enter_editmode=False,
                                 location=loc_vec+loc_obj_vec,
                                 rotation=(0, 0, 0),
@@ -410,7 +395,7 @@ class CLASS_atom_pdb_distance_button(Operator):
     bl_description = "Measure the distance between two objects (only in Object Mode)"
 
     def execute(self, context):
-        scn    = bpy.context.scene
+        scn    = bpy.context.scene.atom_pdb[0]
         dist   = import_pdb.DEF_atom_pdb_distance()
 
         if dist != "N.A.":
@@ -422,7 +407,7 @@ class CLASS_atom_pdb_distance_button(Operator):
            dist   = dist + " A"
 
         # Put the distance into the string of the output field.
-        scn.atom_pdb_distance = dist
+        scn.distance = dist
         return {'FINISHED'}
 
 
@@ -433,10 +418,10 @@ class CLASS_atom_pdb_radius_all_bigger_button(Operator):
     bl_description = "Increase the radii of the atoms"
 
     def execute(self, context):
-        scn = bpy.context.scene
+        scn = bpy.context.scene.atom_pdb[0]
         import_pdb.DEF_atom_pdb_radius_all(
-                scn.atom_pdb_radius_all,
-                scn.atom_pdb_radius_how,
+                scn.radius_all,
+                scn.radius_how,
                 )
         return {'FINISHED'}
 
@@ -448,10 +433,10 @@ class CLASS_atom_pdb_radius_all_smaller_button(Operator):
     bl_description = "Decrease the radii of the atoms"
 
     def execute(self, context):
-        scn = bpy.context.scene
+        scn = bpy.context.scene.atom_pdb[0]
         import_pdb.DEF_atom_pdb_radius_all(
-                1.0/scn.atom_pdb_radius_all,
-                scn.atom_pdb_radius_how,
+                1.0/scn.radius_all,
+                scn.radius_how,
                 )
         return {'FINISHED'}
 
@@ -465,12 +450,11 @@ class CLASS_atom_pdb_radius_sticks_button(Operator):
 
     def execute(self, context):
         global ATOM_PDB_ERROR
-        
-        scn = bpy.context.scene
+        scn = bpy.context.scene.atom_pdb[0]
                 
         result = import_pdb.DEF_atom_pdb_radius_sticks(
-                     scn.atom_pdb_sticks_radius * 0.9,
-                     scn.atom_pdb_radius_how,
+                     scn.sticks_radius * 0.9,
+                     scn.radius_how,
                      )
                      
         if result == False:
@@ -487,154 +471,221 @@ class CLASS_atom_pdb_load_button(Operator):
     bl_description = "Load the structure again"
 
     def execute(self, context):
-        scn = bpy.context.scene
-
-        azimuth    = scn.atom_pdb_mesh_azimuth
-        zenith     = scn.atom_pdb_mesh_zenith
-        bradius    = scn.atom_pdb_scale_ballradius
-        bdistance  = scn.atom_pdb_scale_distances
-        radiustype = scn.atom_pdb_atomradius
-        center     = scn.use_atom_pdb_center
-        sticks     = scn.use_atom_pdb_sticks
-        sticks_col = scn.use_atom_pdb_sticks_color
-        sticks_sm  = scn.use_atom_pdb_sticks_smooth
-        ssector    = scn.atom_pdb_sticks_sectors
-        sradius    = scn.atom_pdb_sticks_radius
-        stick_bond = scn.use_atom_pdb_sticks_bonds
-        stick_dist = scn.atom_pdb_sticks_dist
-        stick_unit = scn.atom_pdb_sticks_unit_length
-        
-        cam        = scn.use_atom_pdb_cam
-        lamp       = scn.use_atom_pdb_lamp
-        mesh       = scn.use_atom_pdb_mesh
-        datafile   = scn.atom_pdb_datafile
+        scn = context.scene.atom_pdb[0]
         
-        # Execute main routine an other time ... from the panel
         atom_number = import_pdb.DEF_atom_pdb_main(
-                mesh, azimuth, zenith, bradius, radiustype, bdistance, 
-                sticks, sticks_col, sticks_sm, stick_bond, stick_unit,
-                stick_dist, ssector, sradius, center, cam, lamp, datafile)
-        scn.atom_pdb_number_atoms = str(atom_number) + " atoms"
+                      scn.use_mesh,
+                      scn.mesh_azimuth,
+                      scn.mesh_zenith,
+                      scn.scale_ballradius,
+                      scn.atomradius,
+                      scn.scale_distances,
+                      scn.use_sticks,
+                      scn.use_sticks_color,
+                      scn.use_sticks_smooth,
+                      scn.use_sticks_bonds,
+                      scn.sticks_unit_length,
+                      scn.sticks_dist,
+                      scn.sticks_sectors,
+                      scn.sticks_radius,
+                      scn.use_center,
+                      scn.use_camera,
+                      scn.use_lamp,
+                      scn.datafile)     
+                      
+        scn.number_atoms = str(atom_number) + " atoms"
 
         return {'FINISHED'}
 
 
-# This is the class for the file dialog.
+# This is the class for the file dialog of the importer.
 class ImportPDB(Operator, ImportHelper):
     bl_idname = "import_mesh.pdb"
     bl_label  = "Import Protein Data Bank(*.pdb)"
+    bl_options = {'PRESET', 'UNDO'}
 
     filename_ext = ".pdb"
     filter_glob  = StringProperty(default="*.pdb", options={'HIDDEN'},)
 
+    use_camera = BoolProperty(
+        name="Camera", default=False,
+        description="Do you need a camera?")
+    use_lamp = BoolProperty(
+        name="Lamp", default=False,
+        description = "Do you need a lamp?")
+    use_mesh = BoolProperty(
+        name = "Mesh balls", default=False,
+        description = "Use mesh balls instead of NURBS")
+    mesh_azimuth = IntProperty(
+        name = "Azimuth", default=32, min=1,
+        description = "Number of sectors (azimuth)")
+    mesh_zenith = IntProperty(
+        name = "Zenith", default=32, min=1,
+        description = "Number of sectors (zenith)")
+    scale_ballradius = FloatProperty(
+        name = "Balls", default=1.0, min=0.0001,
+        description = "Scale factor for all atom radii")
+    scale_distances = FloatProperty (
+        name = "Distances", default=1.0, min=0.0001,
+        description = "Scale factor for all distances")
+    use_center = BoolProperty(
+        name = "Object to origin", default=True,
+        description = "Put the object into the global origin")
+    use_sticks = BoolProperty(
+        name="Use sticks", default=True,
+        description="Do you want to display the sticks?")
+    sticks_sectors = IntProperty(
+        name = "Sector", default=20, min=1,
+        description="Number of sectors of a stick")
+    sticks_radius = FloatProperty(
+        name = "Radius", default=0.1, min=0.0001,
+        description ="Radius of a stick")
+    sticks_unit_length = FloatProperty(
+        name = "Unit", default=0.2, min=0.0001,
+        description = "Length of the unit of a stick in Angstrom")        
+    use_sticks_color = BoolProperty(
+        name="Color", default=True,
+        description="The sticks appear in the color of the atoms")
+    use_sticks_smooth = BoolProperty(
+        name="Smooth", default=False,
+        description="The sticks are round (sectors are not visible)")     
+    use_sticks_bonds = BoolProperty(
+        name="Bonds", default=False,
+        description="Show double and tripple bonds.")
+    sticks_dist = FloatProperty(
+        name="Distance", default = 1.1, min=1.0, max=3.0,
+        description="Distance between sticks measured in stick diameter")        
+    atomradius = EnumProperty(
+        name="Type of radius",
+        description="Choose type of atom radius",
+        items=(('0', "Pre-defined", "Use pre-defined radius"),
+               ('1', "Atomic", "Use atomic radius"),
+               ('2', "van der Waals", "Use van der Waals radius")),
+               default='0',)
+    datafile = StringProperty(
+        name = "", description="Path to your custom data file",
+        maxlen = 256, default = "", subtype='FILE_PATH')
+
     def draw(self, context):
         layout = self.layout
-        scn = bpy.context.scene
-
         row = layout.row()
-        row.prop(scn, "use_atom_pdb_cam")
-        row.prop(scn, "use_atom_pdb_lamp")
+        row.prop(self, "use_camera")
+        row.prop(self, "use_lamp")
         row = layout.row()
         col = row.column()
-        col.prop(scn, "use_atom_pdb_mesh")
+        col.prop(self, "use_mesh")
         col = row.column(align=True)
-        col.active = scn.use_atom_pdb_mesh
-        col.prop(scn, "atom_pdb_mesh_azimuth")
-        col.prop(scn, "atom_pdb_mesh_zenith")
-
+        col.active = self.use_mesh
+        col.prop(self, "mesh_azimuth")
+        col.prop(self, "mesh_zenith")
         row = layout.row()
         col = row.column()
         col.label(text="Scaling factors")
         col = row.column(align=True)
-        col.prop(scn, "atom_pdb_scale_ballradius")
-        col.prop(scn, "atom_pdb_scale_distances")
+        col.prop(self, "scale_ballradius")
+        col.prop(self, "scale_distances")
         row = layout.row()
         col = row.column()
-        col.prop(scn, "use_atom_pdb_sticks")
+        col.prop(self, "use_sticks")
         row = layout.row()        
-        row.active = scn.use_atom_pdb_sticks
+        row.active = self.use_sticks
         col = row.column()
-        col.prop(scn, "atom_pdb_sticks_sectors")
-        col.prop(scn, "atom_pdb_sticks_radius")
-        col.prop(scn, "atom_pdb_sticks_unit_length")
+        col.prop(self, "sticks_sectors")
+        col.prop(self, "sticks_radius")
+        col.prop(self, "sticks_unit_length")
         col = row.column(align=True)        
-        col.prop(scn, "use_atom_pdb_sticks_color")        
-        col.prop(scn, "use_atom_pdb_sticks_smooth")
-        col.prop(scn, "use_atom_pdb_sticks_bonds")
+        col.prop(self, "use_sticks_color")        
+        col.prop(self, "use_sticks_smooth")
+        col.prop(self, "use_sticks_bonds")
         row = layout.row()        
-        row.active = scn.use_atom_pdb_sticks
+        row.active = self.use_sticks
         col = row.column(align=True)
         col = row.column(align=True)
-        col.active = scn.use_atom_pdb_sticks and scn.use_atom_pdb_sticks_bonds 
-        col.prop(scn, "atom_pdb_sticks_dist")
-
+        col.active = self.use_sticks and self.use_sticks_bonds 
+        col.prop(self, "sticks_dist")
         row = layout.row()
-        row.prop(scn, "use_atom_pdb_center")
-
+        row.prop(self, "use_center")
         row = layout.row()
-        row.prop(scn, "atom_pdb_atomradius")
+        row.prop(self, "atomradius")
 
     def execute(self, context):
-        scn = bpy.context.scene
-
         # This is in order to solve this strange 'relative path' thing.
         import_pdb.ATOM_PDB_FILEPATH = bpy.path.abspath(self.filepath)
 
-        scn.atom_pdb_PDB_file = import_pdb.ATOM_PDB_FILEPATH
-
-        azimuth    = scn.atom_pdb_mesh_azimuth
-        zenith     = scn.atom_pdb_mesh_zenith
-        bradius    = scn.atom_pdb_scale_ballradius
-        bdistance  = scn.atom_pdb_scale_distances
-        radiustype = scn.atom_pdb_atomradius
-        center     = scn.use_atom_pdb_center
-        sticks     = scn.use_atom_pdb_sticks
-        sticks_col = scn.use_atom_pdb_sticks_color
-        sticks_sm  = scn.use_atom_pdb_sticks_smooth
-        ssector    = scn.atom_pdb_sticks_sectors
-        sradius    = scn.atom_pdb_sticks_radius
-        stick_bond = scn.use_atom_pdb_sticks_bonds
-        stick_dist = scn.atom_pdb_sticks_dist
-        stick_unit = scn.atom_pdb_sticks_unit_length
-                
-        cam        = scn.use_atom_pdb_cam
-        lamp       = scn.use_atom_pdb_lamp
-        mesh       = scn.use_atom_pdb_mesh
-        datafile   = scn.atom_pdb_datafile
-        
-        # Execute main routine
+        # Execute main routine                
         atom_number = import_pdb.DEF_atom_pdb_main(
-                mesh, azimuth, zenith, bradius, radiustype, bdistance, 
-                sticks, sticks_col, sticks_sm, stick_bond, stick_unit,
-                stick_dist, ssector, sradius, center, cam, lamp, datafile)
-
-        scn.atom_pdb_number_atoms = str(atom_number) + " atoms"
+                      self.use_mesh,
+                      self.mesh_azimuth,
+                      self.mesh_zenith,
+                      self.scale_ballradius,
+                      self.atomradius,
+                      self.scale_distances,
+                      self.use_sticks,
+                      self.use_sticks_color,
+                      self.use_sticks_smooth,
+                      self.use_sticks_bonds,
+                      self.sticks_unit_length,
+                      self.sticks_dist,
+                      self.sticks_sectors,
+                      self.sticks_radius,
+                      self.use_center,
+                      self.use_camera,
+                      self.use_lamp,
+                      self.datafile)        
+
+        # Copy the whole bunch of values into the property collection.
+        scn = context.scene.atom_pdb[0]
+        scn.use_mesh = self.use_mesh
+        scn.mesh_azimuth = self.mesh_azimuth
+        scn.mesh_zenith = self.mesh_zenith
+        scn.scale_ballradius = self.scale_ballradius
+        scn.atomradius = self.atomradius
+        scn.scale_distances = self.scale_distances
+        scn.use_sticks = self.use_sticks
+        scn.use_sticks_color = self.use_sticks_color
+        scn.use_sticks_smooth = self.use_sticks_smooth
+        scn.use_sticks_bonds = self.use_sticks_bonds
+        scn.sticks_unit_length = self.sticks_unit_length
+        scn.sticks_dist = self.sticks_dist
+        scn.sticks_sectors = self.sticks_sectors
+        scn.sticks_radius = self.sticks_radius
+        scn.use_center = self.use_center
+        scn.use_camera = self.use_camera
+        scn.use_lamp = self.use_lamp
+        scn.datafile = self.datafile
+        
+        scn.number_atoms = str(atom_number) + " atoms"
+        scn.PDB_file = import_pdb.ATOM_PDB_FILEPATH
 
         return {'FINISHED'}
 
 
 
-# This is the class for the file dialog.
+# This is the class for the file dialog of the exporter.
 class ExportPDB(Operator, ExportHelper):
     bl_idname = "export_mesh.pdb"
     bl_label  = "Export Protein Data Bank(*.pdb)"
-
     filename_ext = ".pdb"
-    filter_glob  = StringProperty(default="*.pdb", options={'HIDDEN'},)
+
+    filter_glob  = StringProperty(
+        default="*.pdb", options={'HIDDEN'},)
+
+    atom_pdb_export_type = EnumProperty(
+        name="Type of Objects",
+        description="Choose type of objects",
+        items=(('0', "All", "Export all active objects"),
+               ('1', "Elements", "Export only those active objects which have a proper element name")),
+               default='1',) 
 
     def draw(self, context):
         layout = self.layout
-        scn = bpy.context.scene
-
         row = layout.row()
-        row.prop(scn, "atom_pdb_export_type")
+        row.prop(self, "atom_pdb_export_type")
 
     def execute(self, context):
-        scn = bpy.context.scene
-
         # This is in order to solve this strange 'relative path' thing.
         export_pdb.ATOM_PDB_FILEPATH = bpy.path.abspath(self.filepath)
-        export_pdb.DEF_atom_pdb_export(scn.atom_pdb_export_type)
+        export_pdb.DEF_atom_pdb_export(self.atom_pdb_export_type)
 
         return {'FINISHED'}
 
@@ -668,7 +719,9 @@ def register():
     bpy.utils.register_module(__name__)
     bpy.types.INFO_MT_file_import.append(menu_func_import)
     bpy.types.INFO_MT_file_export.append(menu_func_export)
-
+    bpy.types.Scene.atom_pdb = bpy.props.CollectionProperty(type=CLASS_atom_pdb_Properties)    
+    bpy.context.scene.atom_pdb.add()
+    
 def unregister():
     bpy.utils.unregister_module(__name__)
     bpy.types.INFO_MT_file_import.remove(menu_func_import)
diff --git a/io_mesh_pdb/export_pdb.py b/io_mesh_pdb/export_pdb.py
index eadeb6c8..04b79fc5 100644
--- a/io_mesh_pdb/export_pdb.py
+++ b/io_mesh_pdb/export_pdb.py
@@ -25,7 +25,7 @@
 #
 #  Start of project              : 2011-08-31 by Clemens Barth
 #  First publication in Blender  : 2011-11-11
-#  Last modified                 : 2012-03-09
+#  Last modified                 : 2012-03-21
 #
 #  Acknowledgements: Thanks to ideasman, meta_androcto, truman, kilon,
 #  dairin0d, PKHG, Valter, etc
diff --git a/io_mesh_pdb/import_pdb.py b/io_mesh_pdb/import_pdb.py
index 45d858bf..0db76e92 100644
--- a/io_mesh_pdb/import_pdb.py
+++ b/io_mesh_pdb/import_pdb.py
@@ -25,7 +25,7 @@
 #
 #  Start of project              : 2011-08-31 by Clemens Barth
 #  First publication in Blender  : 2011-11-11
-#  Last modified                 : 2012-03-09
+#  Last modified                 : 2012-03-21
 #
 #  Acknowledgements: Thanks to ideasman, meta_androcto, truman, kilon,
 #  dairin0d, PKHG, Valter, etc