diff --git a/io_mesh_pdb/__init__.py b/io_mesh_pdb/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..69046b848de3f1e35a43285bc3e9f48f2cb01b8e
--- /dev/null
+++ b/io_mesh_pdb/__init__.py
@@ -0,0 +1,574 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+
+bl_info = {
+ "name": "PDB Atomic Blender",
+ "description": "Loading and manipulating atoms from PDB files",
+ "author": "Clemens Barth",
+ "version": (1,0),
+ "blender": (2,6),
+ "api": 31236,
+ "location": "File -> Import -> PDB (.pdb), Panel: View 3D - Tools",
+ "warning": "",
+ "wiki_url": "http://development.root-1.de/Atomic_Blender.php",
+ "tracker_url": "http://projects.blender.org/tracker/"
+ "index.php?func=detail&aid=29226&group_id=153&atid=468",
+ "category": "Import-Export"
+}
+
+
+import bpy
+from bpy_extras.io_utils import ImportHelper
+from bpy.props import (StringProperty,
+ BoolProperty,
+ EnumProperty,
+ IntProperty,
+ FloatProperty)
+
+
+# TODO, allow reload
+from . import import_pdb
+
+# -----------------------------------------------------------------------------
+# GUI
+
+# The panel, which is loaded after the file has been
+# chosen via the menu 'File -> Import'
+class CLASS_atom_pdb_panel(bpy.types.Panel):
+ bl_label = "PDB - Atomic Blender"
+ #bl_space_type = "PROPERTIES"
+ #bl_region_type = "WINDOW"
+ #bl_context = "physics"
+ # This could be also an option ... :
+ bl_space_type = "VIEW_3D"
+ bl_region_type = "TOOL_PROPS"
+
+ # This 'poll thing' has taken 3 hours of a hard search and understanding.
+ # I explain it in the following from my point of view:
+ #
+ # Before this class is entirely treaten (here: drawing the panel) the
+ # poll method is called first. Basically, some conditions are
+ # checked before other things in the class are done afterwards. If a
+ # condition is not valid, one returns 'False' such that nothing further
+ # is done. 'True' means: 'Go on'
+ #
+ # In the case here, it is verified if the ATOM_PDB_FILEPATH variable contains
+ # a name. If not - and this is the case directly after having started the
+ # script - the panel does not appear because 'False' is returned. However,
+ # as soon as a file has been chosen, the panel appears because
+ # ATOM_PDB_FILEPATH contains a name.
+ #
+ # Please, correct me if I'm wrong.
+ @classmethod
+ def poll(self, context):
+ if import_pdb.ATOM_PDB_FILEPATH == "":
+ return False
+ else:
+ return True
+
+ def draw(self, context):
+ layout = self.layout
+ scn = bpy.context.scene
+
+ row = layout.row()
+ row.label(text="Custom data file")
+ row = layout.row()
+ col = row.column()
+ col.prop(scn, "atom_pdb_datafile")
+ col.operator("atom_pdb.datafile_apply")
+ row = layout.row()
+ col = row.column(align=True)
+ col.prop(scn, "atom_pdb_PDB_file")
+
+ layout.separator()
+
+ row = layout.row()
+ col = row.column(align=True)
+ col.prop(scn, "use_atom_pdb_mesh")
+ col.prop(scn, "atom_pdb_mesh_azimuth")
+ col.prop(scn, "atom_pdb_mesh_zenith")
+
+
+ col = row.column(align=True)
+ col.label(text="Scaling factors")
+ col.prop(scn, "atom_pdb_scale_ballradius")
+ col.prop(scn, "atom_pdb_scale_distances")
+ row = layout.row()
+ col = row.column()
+ col.prop(scn, "use_atom_pdb_sticks")
+ col = row.column(align=True)
+ col.prop(scn, "atom_pdb_sticks_sectors")
+ col.prop(scn, "atom_pdb_sticks_radius")
+
+ row = layout.row()
+ row.prop(scn, "use_atom_pdb_center")
+
+ row = layout.row()
+ col = row.column()
+ col.prop(scn, "use_atom_pdb_cam")
+ col.prop(scn, "use_atom_pdb_lamp")
+ col = row.column()
+ col.operator("atom_pdb.button_reload")
+
+ # TODO, use lanel() instead
+ col.prop(scn, "atom_pdb_number_atoms")
+
+ layout.separator()
+
+ row = layout.row()
+ row.operator("atom_pdb.button_distance")
+ row.prop(scn, "atom_pdb_distance")
+ layout.separator()
+
+ row = layout.row()
+ row.label(text="All changes concern:")
+ row = layout.row()
+ row.prop(scn, "atom_pdb_radius_how")
+
+ row = layout.row()
+ row.label(text="1. Change type of radii")
+ row = layout.row()
+ row.prop(scn, "atom_pdb_radius_type")
+
+ row = layout.row()
+ row.label(text="2. Change atom radii in pm")
+ row = layout.row()
+ row.prop(scn, "atom_pdb_radius_pm_name")
+ row = layout.row()
+ row.prop(scn, "atom_pdb_radius_pm")
+
+ row = layout.row()
+ row.label(text="3. Change atom radii by scale")
+ row = layout.row()
+ col = row.column()
+ col.prop(scn, "atom_pdb_radius_all")
+ col = row.column(align=True)
+ col.operator( "atom_pdb.radius_all_bigger" )
+ col.operator( "atom_pdb.radius_all_smaller" )
+
+ if bpy.context.mode == 'EDIT_MESH':
+
+ layout.separator()
+ row = layout.row()
+ row.operator( "atom_pdb.separate_atom" )
+
+
+class CLASS_atom_pdb_IO(bpy.types.PropertyGroup):
+
+ def Callback_radius_type(self, context):
+ scnn = bpy.context.scene
+ import_pdb.DEF_atom_pdb_radius_type(
+ scnn.atom_pdb_radius_type,
+ scnn.atom_pdb_radius_how,
+ )
+
+ def Callback_radius_pm(self, context):
+ scnn = bpy.context.scene
+ import_pdb.DEF_atom_pdb_radius_pm(
+ scnn.atom_pdb_radius_pm_name,
+ scnn.atom_pdb_radius_pm,
+ scnn.atom_pdb_radius_how,
+ )
+
+ # In the file dialog window
+ scn = bpy.types.Scene
+ scn.use_atom_pdb_cam = BoolProperty(
+ name="Camera", default=False,
+ description="Do you need a camera?")
+ scn.use_atom_pdb_lamp = BoolProperty(
+ name="Lamp", default=False,
+ description = "Do you need a lamp?")
+ scn.use_atom_pdb_mesh = BoolProperty(
+ name = "Mesh balls", default=False,
+ description = "Do you want to use mesh balls instead of NURBS?")
+ scn.atom_pdb_mesh_azimuth = IntProperty(
+ name = "Azimuth", default=32, min=0,
+ description = "Number of sectors (azimuth)")
+ scn.atom_pdb_mesh_zenith = IntProperty(
+ name = "Zenith", default=32, min=0,
+ description = "Number of sectors (zenith)")
+ scn.atom_pdb_scale_ballradius = FloatProperty(
+ name = "Balls", default=1.0, min=0.0,
+ description = "Scale factor for all atom radii")
+ scn.atom_pdb_scale_distances = FloatProperty (
+ name = "Distances", default=1.0, min=0.0,
+ description = "Scale factor for all distances")
+ scn.use_atom_pdb_center = BoolProperty(
+ name = "Object to origin", default=True,
+ description = "Shall the object first put into the global origin "
+ "before applying the offsets on the left?")
+ scn.use_atom_pdb_sticks = BoolProperty(
+ name="Use sticks", default=False,
+ description="Do you want to display also the sticks?")
+ scn.atom_pdb_sticks_sectors = IntProperty(
+ name = "Sector", default=20, min=0,
+ description="Number of sectors of a stick")
+ scn.atom_pdb_sticks_radius = FloatProperty(
+ name = "Radius", default=0.1, min=0.0,
+ description ="Radius of a stick")
+ scn.atom_pdb_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 panel
+ scn.atom_pdb_datafile = StringProperty(
+ name = "", description="Path to your custom data file",
+ maxlen = 256, default = "", subtype='FILE_PATH')
+ scn.atom_pdb_PDB_file = StringProperty(
+ name = "Path to file", default="",
+ description = "Path of the PDB file")
+ # TODO, remove this property, its used for display only!
+ scn.atom_pdb_number_atoms = StringProperty(name="",
+ default="Number", description = "This output shows "
+ "the number of atoms which have been loaded")
+ scn.atom_pdb_distance = StringProperty(
+ name="", default="Distance (A)",
+ description="Distance of 2 objects in Angstrom")
+ scn.atom_pdb_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(
+ 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(
+ 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,
+ 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,
+ description="Put in the scale factor")
+
+
+# Button loading a custom data file
+class CLASS_atom_pdb_datafile_apply(bpy.types.Operator):
+ bl_idname = "atom_pdb.datafile_apply"
+ bl_label = "Apply"
+ bl_description = "Use color and radii values stored in a custom file"
+
+ def execute(self, context):
+ scn = bpy.context.scene
+
+ if scn.atom_pdb_datafile == "":
+ return {'FINISHED'}
+
+ import_pdb.DEF_atom_pdb_custom_datafile(scn.atom_pdb_datafile)
+
+ for obj in bpy.context.selected_objects:
+ if len(obj.children) != 0:
+ child = obj.children[0]
+ if child.type == "SURFACE" or child.type == "MESH":
+ for element in ATOM_PDB_ELEMENTS:
+ if element.name in obj.name:
+ child.scale = (element.radii[0],
+ element.radii[0],
+ element.radii[0])
+ child.active_material.diffuse_color = element.color
+ else:
+ if obj.type == "SURFACE" or obj.type == "MESH":
+ for element in ATOM_PDB_ELEMENTS:
+ if element.name in obj.name:
+ obj.scale = (element.radii[0],
+ element.radii[0],
+ element.radii[0])
+ obj.active_material.diffuse_color = element.color
+
+ return {'FINISHED'}
+
+
+# Button for measuring the distance of the active objects
+class CLASS_atom_pdb_separate_atom(bpy.types.Operator):
+ bl_idname = "atom_pdb.separate_atom"
+ bl_label = "Separate atom"
+ bl_description = "Separate the atom you have chosen"
+
+ def execute(self, context):
+ scn = bpy.context.scene
+
+ # Get first all important properties from the atom which the user
+ # has chosen: location, color, scale
+ obj = bpy.context.edit_object
+ name = obj.name
+ loc_obj_vec = obj.location
+ scale = obj.children[0].scale
+ material = obj.children[0].active_material
+
+ # Separate the vertex from the main mesh and create a new mesh.
+ bpy.ops.mesh.separate()
+ new_object = bpy.context.scene.objects[0]
+ # Keep in mind the coordinates <= We only need this
+ loc_vec = new_object.data.vertices[0].co
+
+ # And now, switch to the OBJECT mode such that we can ...
+ bpy.ops.object.mode_set(mode='OBJECT', toggle=False)
+ # ... delete the new mesh including the separated vertex
+ bpy.ops.object.select_all(action='DESELECT')
+ new_object.select = True
+ bpy.ops.object.delete()
+
+ # Create a new atom/vacancy at the position of the old atom
+ current_layers=bpy.context.scene.layers
+
+ if "Vacancy" not in name:
+ if scn.use_atom_pdb_mesh == False:
+ bpy.ops.surface.primitive_nurbs_surface_sphere_add(
+ view_align=False, enter_editmode=False,
+ location=loc_vec+loc_obj_vec,
+ rotation=(0.0, 0.0, 0.0),
+ layers=current_layers)
+ else:
+ bpy.ops.mesh.primitive_uv_sphere_add(
+ segments=scn.atom_pdb_mesh_azimuth,
+ ring_count=scn.atom_pdb_mesh_zenith,
+ size=1, view_align=False, enter_editmode=False,
+ location=loc_vec+loc_obj_vec,
+ rotation=(0, 0, 0),
+ layers=current_layers)
+ else:
+ bpy.ops.mesh.primitive_cube_add(
+ view_align=False, enter_editmode=False,
+ location=loc_vec+loc_obj_vec,
+ rotation=(0.0, 0.0, 0.0),
+ layers=current_layers)
+
+ new_atom = bpy.context.scene.objects.active
+ # Scale, material and name it.
+ new_atom.scale = scale
+ new_atom.active_material = material
+ new_atom.name = name + "_sep"
+
+ # Switch back into the 'Edit mode' because we would like to seprate
+ # other atoms may be (more convinient)
+ new_atom.select = False
+ obj.select = True
+ bpy.context.scene.objects.active = obj
+ bpy.ops.object.select_all(action='DESELECT')
+ bpy.ops.object.mode_set(mode='EDIT', toggle=False)
+
+ return {'FINISHED'}
+
+
+# Button for measuring the distance of the active objects
+class CLASS_atom_pdb_distance_button(bpy.types.Operator):
+ bl_idname = "atom_pdb.button_distance"
+ bl_label = "Measure ..."
+ bl_description = "Measure the distance between two objects"
+
+ def execute(self, context):
+ scn = bpy.context.scene
+ dist = import_pdb.DEF_atom_pdb_distance()
+
+ if dist != "N.A.":
+ # The string length is cut, 3 digits after the first 3 digits
+ # after the '.'. Append also "Angstrom".
+ # Remember: 1 Angstrom = 10^(-10) m
+ pos = str.find(dist, ".")
+ dist = dist[:pos+4]
+ dist = dist + " A"
+
+ # Put the distance into the string of the output field.
+ scn.atom_pdb_distance = dist
+ return {'FINISHED'}
+
+
+# Button for increasing the radii of all atoms
+class CLASS_atom_pdb_radius_all_bigger_button(bpy.types.Operator):
+ bl_idname = "atom_pdb.radius_all_bigger"
+ bl_label = "Bigger ..."
+ bl_description = "Increase the radii of the atoms"
+
+ def execute(self, context):
+ scn = bpy.context.scene
+ import_pdb.DEF_atom_pdb_radius_all(
+ scn.atom_pdb_radius_all,
+ scn.atom_pdb_radius_how,
+ )
+ return {'FINISHED'}
+
+
+# Button for decreasing the radii of all atoms
+class CLASS_atom_pdb_radius_all_smaller_button(bpy.types.Operator):
+ bl_idname = "atom_pdb.radius_all_smaller"
+ bl_label = "Smaller ..."
+ bl_description = "Decrease the radii of the atoms"
+
+ def execute(self, context):
+ scn = bpy.context.scene
+ import_pdb.DEF_atom_pdb_radius_all(
+ 1.0/scn.atom_pdb_radius_all,
+ scn.atom_pdb_radius_how,
+ )
+ return {'FINISHED'}
+
+
+# The button for loading the atoms and creating the scene
+class CLASS_atom_pdb_load_button(bpy.types.Operator):
+ bl_idname = "atom_pdb.button_reload"
+ bl_label = "RELOAD"
+ 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
+ ssector = scn.atom_pdb_sticks_sectors
+ sradius = scn.atom_pdb_sticks_radius
+ 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 an other time ... from the panel
+ atom_number = import_pdb.DEF_atom_pdb_main(
+ mesh, azimuth, zenith, bradius,
+ radiustype, bdistance, sticks,
+ ssector, sradius, center, cam, lamp, datafile,
+ )
+ scn.atom_pdb_number_atoms = str(atom_number) + " atoms"
+
+ return {'FINISHED'}
+
+
+# This is the class for the file dialog.
+class CLASS_LoadPDB(bpy.types.Operator, ImportHelper):
+ bl_idname = "import_pdb.pdb"
+ bl_label = "Import PDB"
+
+ filename_ext = ".pdb"
+ filter_glob = StringProperty(default="*.pdb", options={'HIDDEN'},)
+
+ 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 = layout.row()
+ col = row.column()
+ col.prop(scn, "use_atom_pdb_mesh")
+ col = row.column(align=True)
+ col.prop(scn, "atom_pdb_mesh_azimuth")
+ col.prop(scn, "atom_pdb_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")
+ row = layout.row()
+ col = row.column()
+ col.prop(scn, "use_atom_pdb_sticks")
+ col = row.column(align=True)
+ col.prop(scn, "atom_pdb_sticks_sectors")
+ col.prop(scn, "atom_pdb_sticks_radius")
+
+ row = layout.row()
+ row.prop(scn, "use_atom_pdb_center")
+
+ row = layout.row()
+ row.prop(scn, "atom_pdb_atomradius")
+
+ def execute(self, context):
+ global ATOM_PDB_ELEMENTS_DEFAULT
+ global ATOM_PDB_ELEMENTS
+
+ 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
+ ssector = scn.atom_pdb_sticks_sectors
+ sradius = scn.atom_pdb_sticks_radius
+ 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
+ atom_number = import_pdb.DEF_atom_pdb_main(
+ mesh, azimuth, zenith, bradius,
+ radiustype, bdistance, sticks,
+ ssector, sradius, center, cam, lamp, datafile)
+
+ scn.atom_pdb_number_atoms = str(atom_number) + " atoms"
+
+ return {'FINISHED'}
+
+
+# The entry into the menu 'file -> import'
+def menu_func(self, context):
+ self.layout.operator(CLASS_LoadPDB.bl_idname, text="PDB (.pdb)")
+
+
+def register():
+ bpy.utils.register_class(CLASS_atom_pdb_panel)
+ bpy.utils.register_class(CLASS_atom_pdb_datafile_apply)
+ bpy.utils.register_class(CLASS_atom_pdb_IO)
+ bpy.utils.register_class(CLASS_atom_pdb_load_button)
+ bpy.utils.register_class(CLASS_atom_pdb_radius_all_bigger_button)
+ bpy.utils.register_class(CLASS_atom_pdb_radius_all_smaller_button)
+ bpy.utils.register_class(CLASS_atom_pdb_distance_button)
+ bpy.utils.register_class(CLASS_atom_pdb_separate_atom)
+ bpy.utils.register_module(__name__)
+ bpy.types.INFO_MT_file_import.append(menu_func)
+
+def unregister():
+ bpy.utils.unregister_class(CLASS_atom_pdb_panel)
+ bpy.utils.unregister_class(CLASS_atom_pdb_datafile_apply)
+ bpy.utils.unregister_class(CLASS_atom_pdb_IO)
+ bpy.utils.unregister_class(CLASS_atom_pdb_load_button)
+ bpy.utils.unregister_class(CLASS_atom_pdb_radius_all_bigger_button)
+ bpy.utils.unregister_class(CLASS_atom_pdb_radius_all_smaller_button)
+ bpy.utils.unregister_class(CLASS_atom_pdb_distance_button)
+ bpy.utils.unregister_class(CLASS_atom_pdb_separate_atom)
+ bpy.utils.unregister_module(__name__)
+ bpy.types.INFO_MT_file_import.remove(menu_func)
+
+if __name__ == "__main__":
+
+ register()
diff --git a/io_mesh_pdb/atom_info.dat b/io_mesh_pdb/atom_info.dat
new file mode 100644
index 0000000000000000000000000000000000000000..efd72f6f6b1ee34da88f4bddeb9ab8319b989ba2
--- /dev/null
+++ b/io_mesh_pdb/atom_info.dat
@@ -0,0 +1,1536 @@
+Atom
+====
+Number : 1
+Name : Hydrogen
+Short name : H
+Color : 0.0,0.0,1.0
+Radius used : 0.320000
+Radius, covalent : 0.320000
+Radius, atomic : 0.790000
+Charge state : -1
+Radius, ionic : 1.540000
+
+
+Atom
+====
+Number : 2
+Name : Helium
+Short name : He
+Color : 0.207843137255,0.56862745098,0.207843137255
+Radius used : 0.930000
+Radius, covalent : 0.930000
+Radius, atomic : 0.490000
+
+
+Atom
+====
+Number : 3
+Name : Lithium
+Short name : Li
+Color : 0.729411764706,0.278431372549,0.254901960784
+Radius used : 1.230000
+Radius, covalent : 1.230000
+Radius, atomic : 2.050000
+Charge state : 1
+Radius, ionic : 0.680000
+
+
+Atom
+====
+Number : 4
+Name : Beryllium
+Short name : Be
+Color : 0.447058823529,0.725490196078,0.309803921569
+Radius used : 0.900000
+Radius, covalent : 0.900000
+Radius, atomic : 1.400000
+Charge state : 1
+Radius, ionic : 0.440000
+Charge state : 2
+Radius, ionic : 0.350000
+
+
+Atom
+====
+Number : 5
+Name : Boron
+Short name : B
+Color : 1.0,1.0,1.0
+Radius used : 0.820000
+Radius, covalent : 0.820000
+Radius, atomic : 1.170000
+Charge state : 1
+Radius, ionic : 0.350000
+Charge state : 3
+Radius, ionic : 0.230000
+
+
+Atom
+====
+Number : 6
+Name : Carbon
+Short name : C
+Color : 0.0,0.0,0.0
+Radius used : 0.770000
+Radius, covalent : 0.770000
+Radius, atomic : 0.910000
+Charge state : -4
+Radius, ionic : 2.600000
+Charge state : 4
+Radius, ionic : 0.160000
+
+
+Atom
+====
+Number : 7
+Name : Nitrogen
+Short name : N
+Color : 0.0,0.0,1.0
+Radius used : 0.750000
+Radius, covalent : 0.750000
+Radius, atomic : 0.750000
+Charge state : -3
+Radius, ionic : 1.710000
+Charge state : 1
+Radius, ionic : 0.250000
+Charge state : 3
+Radius, ionic : 0.160000
+Charge state : 5
+Radius, ionic : 0.130000
+
+
+Atom
+====
+Number : 8
+Name : Oxygen
+Short name : O
+Color : 1.0,0.0,0.0
+Radius used : 0.730000
+Radius, covalent : 0.730000
+Radius, atomic : 0.650000
+Charge state : -2
+Radius, ionic : 1.320000
+Charge state : -1
+Radius, ionic : 1.760000
+Charge state : 1
+Radius, ionic : 0.220000
+Charge state : 6
+Radius, ionic : 0.090000
+
+
+Atom
+====
+Number : 9
+Name : Fluorine
+Short name : F
+Color : 0.0,1.0,0.0
+Radius used : 0.720000
+Radius, covalent : 0.720000
+Radius, atomic : 0.570000
+Charge state : -1
+Radius, ionic : 1.330000
+Charge state : 7
+Radius, ionic : 0.080000
+
+
+Atom
+====
+Number : 10
+Name : Neon
+Short name : Ne
+Color : 0.537254901961,0.607843137255,0.525490196078
+Radius used : 0.710000
+Radius, covalent : 0.710000
+Radius, atomic : 0.510000
+Charge state : 1
+Radius, ionic : 1.120000
+
+
+Atom
+====
+Number : 11
+Name : Sodium
+Short name : Na
+Color : 0.0,0.0,1.0
+Radius used : 1.540000
+Radius, covalent : 1.540000
+Radius, atomic : 2.230000
+Charge state : 1
+Radius, ionic : 0.970000
+
+
+Atom
+====
+Number : 12
+Name : Magnesium
+Short name : Mg
+Color : 1.0,1.0,1.0
+Radius used : 1.360000
+Radius, covalent : 1.360000
+Radius, atomic : 1.720000
+Charge state : 1
+Radius, ionic : 0.820000
+Charge state : 2
+Radius, ionic : 0.660000
+
+
+Atom
+====
+Number : 13
+Name : Aluminium
+Short name : Al
+Color : 0.701960784314,0.2,0.623529411765
+Radius used : 1.180000
+Radius, covalent : 1.180000
+Radius, atomic : 1.820000
+Charge state : 3
+Radius, ionic : 0.510000
+
+
+Atom
+====
+Number : 14
+Name : Silicon
+Short name : Si
+Color : 0.654901960784,0.647058823529,0.278431372549
+Radius used : 1.110000
+Radius, covalent : 1.110000
+Radius, atomic : 1.460000
+Charge state : -4
+Radius, ionic : 2.710000
+Charge state : -1
+Radius, ionic : 3.840000
+Charge state : 1
+Radius, ionic : 0.650000
+Charge state : 4
+Radius, ionic : 0.420000
+
+
+Atom
+====
+Number : 15
+Name : Phosphorus
+Short name : P
+Color : 1.0,1.0,0.0
+Radius used : 1.060000
+Radius, covalent : 1.060000
+Radius, atomic : 1.230000
+Charge state : -3
+Radius, ionic : 2.120000
+Charge state : 3
+Radius, ionic : 0.440000
+Charge state : 5
+Radius, ionic : 0.350000
+
+
+Atom
+====
+Number : 16
+Name : Sulfur
+Short name : S
+Color : 1.0,1.0,0.501960784314
+Radius used : 1.020000
+Radius, covalent : 1.020000
+Radius, atomic : 1.090000
+Charge state : -2
+Radius, ionic : 1.840000
+Charge state : 2
+Radius, ionic : 2.190000
+Charge state : 4
+Radius, ionic : 0.370000
+Charge state : 6
+Radius, ionic : 0.300000
+
+
+Atom
+====
+Number : 17
+Name : Chlorine
+Short name : Cl
+Color : 0.0,1.0,0.0
+Radius used : 0.990000
+Radius, covalent : 0.990000
+Radius, atomic : 0.970000
+Charge state : -1
+Radius, ionic : 1.810000
+Charge state : 5
+Radius, ionic : 0.340000
+Charge state : 7
+Radius, ionic : 0.270000
+
+
+Atom
+====
+Number : 18
+Name : Argon
+Short name : Ar
+Color : 0.317647058824,0.329411764706,0.749019607843
+Radius used : 0.980000
+Radius, covalent : 0.980000
+Radius, atomic : 0.880000
+Charge state : 1
+Radius, ionic : 1.540000
+
+
+Atom
+====
+Number : 19
+Name : Potassium
+Short name : K
+Color : 0.811764705882,0.239215686275,0.423529411765
+Radius used : 2.030000
+Radius, covalent : 2.030000
+Radius, atomic : 2.770000
+Charge state : 1
+Radius, ionic : 0.810000
+
+
+Atom
+====
+Number : 20
+Name : Calcium
+Short name : Ca
+Color : 1.0,1.0,1.0
+Radius used : 1.740000
+Radius, covalent : 1.740000
+Radius, atomic : 2.230000
+Charge state : 1
+Radius, ionic : 1.180000
+Charge state : 2
+Radius, ionic : 0.990000
+
+
+Atom
+====
+Number : 21
+Name : Scandium
+Short name : Sc
+Color : 0.662745098039,0.447058823529,0.313725490196
+Radius used : 1.440000
+Radius, covalent : 1.440000
+Radius, atomic : 2.090000
+Charge state : 3
+Radius, ionic : 0.732000
+
+
+Atom
+====
+Number : 22
+Name : Titanium
+Short name : Ti
+Color : 0.270588235294,0.533333333333,0.686274509804
+Radius used : 1.320000
+Radius, covalent : 1.320000
+Radius, atomic : 2.000000
+Charge state : 1
+Radius, ionic : 0.960000
+Charge state : 2
+Radius, ionic : 0.940000
+Charge state : 3
+Radius, ionic : 0.760000
+Charge state : 4
+Radius, ionic : 0.680000
+
+
+Atom
+====
+Number : 23
+Name : Vanadium
+Short name : V
+Color : 0.270588235294,0.243137254902,0.635294117647
+Radius used : 1.220000
+Radius, covalent : 1.220000
+Radius, atomic : 1.920000
+Charge state : 2
+Radius, ionic : 0.880000
+Charge state : 3
+Radius, ionic : 0.740000
+Charge state : 4
+Radius, ionic : 0.630000
+Charge state : 5
+Radius, ionic : 0.590000
+
+
+Atom
+====
+Number : 24
+Name : Chromium
+Short name : Cr
+Color : 0.807843137255,0.286274509804,0.819607843137
+Radius used : 1.180000
+Radius, covalent : 1.180000
+Radius, atomic : 1.850000
+Charge state : 1
+Radius, ionic : 0.810000
+Charge state : 2
+Radius, ionic : 0.890000
+Charge state : 3
+Radius, ionic : 0.630000
+Charge state : 6
+Radius, ionic : 0.520000
+
+
+Atom
+====
+Number : 25
+Name : Manganese
+Short name : Mn
+Color : 0.752941176471,0.352941176471,0.552941176471
+Radius used : 1.170000
+Radius, covalent : 1.170000
+Radius, atomic : 1.790000
+Charge state : 2
+Radius, ionic : 0.800000
+Charge state : 3
+Radius, ionic : 0.660000
+Charge state : 4
+Radius, ionic : 0.600000
+Charge state : 7
+Radius, ionic : 0.460000
+
+
+Atom
+====
+Number : 26
+Name : Iron
+Short name : Fe
+Color : 1.0,0.0,0.0
+Radius used : 1.170000
+Radius, covalent : 1.170000
+Radius, atomic : 1.720000
+Charge state : 2
+Radius, ionic : 0.740000
+Charge state : 3
+Radius, ionic : 0.640000
+
+
+Atom
+====
+Number : 27
+Name : Cobalt
+Short name : Co
+Color : 0.274509803922,0.219607843137,0.752941176471
+Radius used : 1.160000
+Radius, covalent : 1.160000
+Radius, atomic : 1.670000
+Charge state : 2
+Radius, ionic : 0.720000
+Charge state : 3
+Radius, ionic : 0.630000
+
+
+Atom
+====
+Number : 28
+Name : Nickel
+Short name : Ni
+Color : 0.439215686275,0.360784313725,0.862745098039
+Radius used : 1.150000
+Radius, covalent : 1.150000
+Radius, atomic : 1.620000
+Charge state : 2
+Radius, ionic : 0.690000
+
+
+Atom
+====
+Number : 29
+Name : Copper
+Short name : Cu
+Color : 0.607843137255,0.0,0.0
+Radius used : 1.170000
+Radius, covalent : 1.170000
+Radius, atomic : 1.570000
+Charge state : 1
+Radius, ionic : 0.960000
+Charge state : 2
+Radius, ionic : 0.720000
+
+
+Atom
+====
+Number : 30
+Name : Zinc
+Short name : Zn
+Color : 0.423529411765,0.36862745098,0.450980392157
+Radius used : 1.250000
+Radius, covalent : 1.250000
+Radius, atomic : 1.530000
+Charge state : 1
+Radius, ionic : 0.880000
+Charge state : 2
+Radius, ionic : 0.740000
+
+
+Atom
+====
+Number : 31
+Name : Gallium
+Short name : Ga
+Color : 0.635294117647,0.729411764706,0.337254901961
+Radius used : 1.260000
+Radius, covalent : 1.260000
+Radius, atomic : 1.810000
+Charge state : 1
+Radius, ionic : 0.810000
+Charge state : 3
+Radius, ionic : 0.620000
+
+
+Atom
+====
+Number : 32
+Name : Germanium
+Short name : Ge
+Color : 0.423529411765,0.756862745098,0.301960784314
+Radius used : 1.220000
+Radius, covalent : 1.220000
+Radius, atomic : 1.520000
+Charge state : -4
+Radius, ionic : 2.720000
+Charge state : 2
+Radius, ionic : 0.730000
+Charge state : 4
+Radius, ionic : 0.530000
+
+
+Atom
+====
+Number : 33
+Name : Arsenic
+Short name : As
+Color : 0.396078431373,0.776470588235,0.250980392157
+Radius used : 1.200000
+Radius, covalent : 1.200000
+Radius, atomic : 1.330000
+Charge state : -3
+Radius, ionic : 2.220000
+Charge state : 3
+Radius, ionic : 0.580000
+Charge state : 5
+Radius, ionic : 0.460000
+
+
+Atom
+====
+Number : 34
+Name : Selenium
+Short name : Se
+Color : 0.952941176471,0.270588235294,0.905882352941
+Radius used : 1.160000
+Radius, covalent : 1.160000
+Radius, atomic : 1.220000
+Charge state : -2
+Radius, ionic : 1.910000
+Charge state : -1
+Radius, ionic : 2.320000
+Charge state : 1
+Radius, ionic : 0.660000
+Charge state : 4
+Radius, ionic : 0.500000
+Charge state : 6
+Radius, ionic : 0.420000
+
+
+Atom
+====
+Number : 35
+Name : Bromine
+Short name : Br
+Color : 0.0,0.498039215686,0.0
+Radius used : 1.140000
+Radius, covalent : 1.140000
+Radius, atomic : 1.120000
+Charge state : -1
+Radius, ionic : 1.960000
+Charge state : 5
+Radius, ionic : 0.470000
+Charge state : 7
+Radius, ionic : 0.390000
+
+
+Atom
+====
+Number : 36
+Name : Krypton
+Short name : Kr
+Color : 0.227450980392,0.435294117647,0.192156862745
+Radius used : 1.310000
+Radius, covalent : 1.310000
+Radius, atomic : 1.240000
+
+
+Atom
+====
+Number : 37
+Name : Rubidium
+Short name : Rb
+Color : 1.0,1.0,1.0
+Radius used : 2.160000
+Radius, covalent : 2.160000
+Radius, atomic : 2.980000
+Charge state : 1
+Radius, ionic : 1.470000
+
+
+Atom
+====
+Number : 38
+Name : Strontium
+Short name : Sr
+Color : 1.0,1.0,1.0
+Radius used : 1.910000
+Radius, covalent : 1.910000
+Radius, atomic : 2.450000
+Charge state : 2
+Radius, ionic : 1.120000
+
+
+Atom
+====
+Number : 39
+Name : Yttrium
+Short name : Y
+Color : 1.0,1.0,1.0
+Radius used : 1.620000
+Radius, covalent : 1.620000
+Radius, atomic : 2.270000
+Charge state : 3
+Radius, ionic : 0.893000
+
+
+Atom
+====
+Number : 40
+Name : Zirconium
+Short name : Zr
+Color : 1.0,1.0,1.0
+Radius used : 1.450000
+Radius, covalent : 1.450000
+Radius, atomic : 2.160000
+Charge state : 1
+Radius, ionic : 1.090000
+Charge state : 4
+Radius, ionic : 0.790000
+
+
+Atom
+====
+Number : 41
+Name : Niobium
+Short name : Nb
+Color : 1.0,1.0,1.0
+Radius used : 1.340000
+Radius, covalent : 1.340000
+Radius, atomic : 2.080000
+Charge state : 1
+Radius, ionic : 1.000000
+Charge state : 4
+Radius, ionic : 0.740000
+Charge state : 5
+Radius, ionic : 0.690000
+
+
+Atom
+====
+Number : 42
+Name : Molybdenum
+Short name : Mo
+Color : 1.0,1.0,1.0
+Radius used : 1.300000
+Radius, covalent : 1.300000
+Radius, atomic : 2.010000
+Charge state : 1
+Radius, ionic : 0.930000
+Charge state : 4
+Radius, ionic : 0.700000
+Charge state : 6
+Radius, ionic : 0.620000
+
+
+Atom
+====
+Number : 43
+Name : Technetium
+Short name : Tc
+Color : 1.0,1.0,1.0
+Radius used : 1.270000
+Radius, covalent : 1.270000
+Radius, atomic : 1.950000
+Charge state : 7
+Radius, ionic : 0.979000
+
+
+Atom
+====
+Number : 44
+Name : Ruthenium
+Short name : Ru
+Color : 1.0,1.0,1.0
+Radius used : 1.250000
+Radius, covalent : 1.250000
+Radius, atomic : 1.890000
+Charge state : 4
+Radius, ionic : 0.670000
+
+
+Atom
+====
+Number : 45
+Name : Rhodium
+Short name : Rh
+Color : 1.0,1.0,1.0
+Radius used : 1.250000
+Radius, covalent : 1.250000
+Radius, atomic : 1.830000
+Charge state : 3
+Radius, ionic : 0.680000
+
+
+Atom
+====
+Number : 46
+Name : Palladium
+Short name : Pd
+Color : 1.0,1.0,1.0
+Radius used : 1.280000
+Radius, covalent : 1.280000
+Radius, atomic : 1.790000
+Charge state : 2
+Radius, ionic : 0.800000
+Charge state : 4
+Radius, ionic : 0.650000
+
+
+Atom
+====
+Number : 47
+Name : Silver
+Short name : Ag
+Color : 1.0,1.0,1.0
+Radius used : 1.340000
+Radius, covalent : 1.340000
+Radius, atomic : 1.750000
+Charge state : 1
+Radius, ionic : 1.260000
+Charge state : 2
+Radius, ionic : 0.890000
+
+
+Atom
+====
+Number : 48
+Name : Cadmium
+Short name : Cd
+Color : 1.0,1.0,1.0
+Radius used : 1.480000
+Radius, covalent : 1.480000
+Radius, atomic : 1.710000
+Charge state : 1
+Radius, ionic : 1.140000
+Charge state : 2
+Radius, ionic : 0.970000
+
+
+Atom
+====
+Number : 49
+Name : Indium
+Short name : In
+Color : 1.0,1.0,1.0
+Radius used : 1.440000
+Radius, covalent : 1.440000
+Radius, atomic : 2.000000
+Charge state : 3
+Radius, ionic : 0.810000
+
+
+Atom
+====
+Number : 50
+Name : Tin
+Short name : Sn
+Color : 1.0,1.0,1.0
+Radius used : 1.410000
+Radius, covalent : 1.410000
+Radius, atomic : 1.720000
+Charge state : -4
+Radius, ionic : 2.940000
+Charge state : -1
+Radius, ionic : 3.700000
+Charge state : 2
+Radius, ionic : 0.930000
+Charge state : 4
+Radius, ionic : 0.710000
+
+
+Atom
+====
+Number : 51
+Name : Antimony
+Short name : Sb
+Color : 1.0,1.0,1.0
+Radius used : 1.400000
+Radius, covalent : 1.400000
+Radius, atomic : 1.530000
+Charge state : -3
+Radius, ionic : 2.450000
+Charge state : 3
+Radius, ionic : 0.760000
+Charge state : 5
+Radius, ionic : 0.620000
+
+
+Atom
+====
+Number : 52
+Name : Tellurium
+Short name : Te
+Color : 1.0,1.0,1.0
+Radius used : 1.360000
+Radius, covalent : 1.360000
+Radius, atomic : 1.420000
+Charge state : -2
+Radius, ionic : 2.110000
+Charge state : -1
+Radius, ionic : 2.500000
+Charge state : 1
+Radius, ionic : 0.820000
+Charge state : 4
+Radius, ionic : 0.700000
+Charge state : 6
+Radius, ionic : 0.560000
+
+
+Atom
+====
+Number : 53
+Name : Iodine
+Short name : I
+Color : 0.0,0.498039215686,0.498039215686
+Radius used : 1.330000
+Radius, covalent : 1.330000
+Radius, atomic : 1.320000
+Charge state : -1
+Radius, ionic : 2.200000
+Charge state : 5
+Radius, ionic : 0.620000
+Charge state : 7
+Radius, ionic : 0.500000
+
+
+Atom
+====
+Number : 54
+Name : Xenon
+Short name : Xe
+Color : 1.0,1.0,1.0
+Radius used : 1.310000
+Radius, covalent : 1.310000
+Radius, atomic : 1.240000
+
+
+Atom
+====
+Number : 55
+Name : Caesium
+Short name : Cs
+Color : 1.0,1.0,1.0
+Radius used : 2.350000
+Radius, covalent : 2.350000
+Radius, atomic : 3.350000
+Charge state : 1
+Radius, ionic : 1.670000
+
+
+Atom
+====
+Number : 56
+Name : Barium
+Short name : Ba
+Color : 1.0,1.0,1.0
+Radius used : 1.980000
+Radius, covalent : 1.980000
+Radius, atomic : 2.780000
+Charge state : 1
+Radius, ionic : 1.530000
+Charge state : 2
+Radius, ionic : 1.340000
+
+
+Atom
+====
+Number : 57
+Name : Lanthanum
+Short name : La
+Color : 1.0,1.0,1.0
+Radius used : 1.690000
+Radius, covalent : 1.690000
+Radius, atomic : 2.740000
+Charge state : 1
+Radius, ionic : 1.390000
+Charge state : 3
+Radius, ionic : 1.061000
+
+
+Atom
+====
+Number : 58
+Name : Cerium
+Short name : Ce
+Color : 1.0,1.0,1.0
+Radius used : 1.650000
+Radius, covalent : 1.650000
+Radius, atomic : 2.700000
+Charge state : 1
+Radius, ionic : 1.270000
+Charge state : 3
+Radius, ionic : 1.034000
+Charge state : 4
+Radius, ionic : 0.920000
+
+
+Atom
+====
+Number : 59
+Name : Praseodymium
+Short name : Pr
+Color : 1.0,1.0,1.0
+Radius used : 1.650000
+Radius, covalent : 1.650000
+Radius, atomic : 2.670000
+Charge state : 3
+Radius, ionic : 1.013000
+Charge state : 4
+Radius, ionic : 0.900000
+
+
+Atom
+====
+Number : 60
+Name : Neodymium
+Short name : Nd
+Color : 1.0,1.0,1.0
+Radius used : 1.640000
+Radius, covalent : 1.640000
+Radius, atomic : 2.640000
+Charge state : 3
+Radius, ionic : 0.995000
+
+
+Atom
+====
+Number : 61
+Name : Promethium
+Short name : Pm
+Color : 1.0,1.0,1.0
+Radius used : 1.630000
+Radius, covalent : 1.630000
+Radius, atomic : 2.620000
+Charge state : 3
+Radius, ionic : 0.979000
+
+
+Atom
+====
+Number : 62
+Name : Samarium
+Short name : Sm
+Color : 1.0,1.0,1.0
+Radius used : 1.620000
+Radius, covalent : 1.620000
+Radius, atomic : 2.590000
+Charge state : 3
+Radius, ionic : 0.964000
+
+
+Atom
+====
+Number : 63
+Name : Europium
+Short name : Eu
+Color : 1.0,1.0,1.0
+Radius used : 1.850000
+Radius, covalent : 1.850000
+Radius, atomic : 2.560000
+Charge state : 2
+Radius, ionic : 1.090000
+Charge state : 3
+Radius, ionic : 0.950000
+
+
+Atom
+====
+Number : 64
+Name : Gadolinium
+Short name : Gd
+Color : 1.0,1.0,1.0
+Radius used : 1.610000
+Radius, covalent : 1.610000
+Radius, atomic : 2.540000
+Charge state : 3
+Radius, ionic : 0.938000
+
+
+Atom
+====
+Number : 65
+Name : Terbium
+Short name : Tb
+Color : 1.0,1.0,1.0
+Radius used : 1.590000
+Radius, covalent : 1.590000
+Radius, atomic : 2.510000
+Charge state : 3
+Radius, ionic : 0.923000
+Charge state : 4
+Radius, ionic : 0.840000
+
+
+Atom
+====
+Number : 66
+Name : Dysprosium
+Short name : Dy
+Color : 1.0,1.0,1.0
+Radius used : 1.590000
+Radius, covalent : 1.590000
+Radius, atomic : 2.490000
+Charge state : 3
+Radius, ionic : 0.908000
+
+
+Atom
+====
+Number : 67
+Name : Holmium
+Short name : Ho
+Color : 1.0,1.0,1.0
+Radius used : 1.580000
+Radius, covalent : 1.580000
+Radius, atomic : 2.470000
+Charge state : 3
+Radius, ionic : 0.894000
+
+
+Atom
+====
+Number : 68
+Name : Erbium
+Short name : Er
+Color : 0.482352941176,0.482352941176,0.482352941176
+Radius used : 1.570000
+Radius, covalent : 1.570000
+Radius, atomic : 2.450000
+Charge state : 3
+Radius, ionic : 0.881000
+
+
+Atom
+====
+Number : 69
+Name : Thulium
+Short name : Tm
+Color : 1.0,1.0,1.0
+Radius used : 1.560000
+Radius, covalent : 1.560000
+Radius, atomic : 2.420000
+Charge state : 3
+Radius, ionic : 0.870000
+
+
+Atom
+====
+Number : 70
+Name : Ytterbium
+Short name : Yb
+Color : 1.0,1.0,1.0
+Radius used : 1.740000
+Radius, covalent : 1.740000
+Radius, atomic : 2.400000
+Charge state : 2
+Radius, ionic : 0.930000
+Charge state : 3
+Radius, ionic : 0.858000
+
+
+Atom
+====
+Number : 71
+Name : Lutetium
+Short name : Lu
+Color : 1.0,1.0,1.0
+Radius used : 1.560000
+Radius, covalent : 1.560000
+Radius, atomic : 2.250000
+Charge state : 3
+Radius, ionic : 0.850000
+
+
+Atom
+====
+Number : 72
+Name : Hafnium
+Short name : Hf
+Color : 1.0,1.0,1.0
+Radius used : 1.440000
+Radius, covalent : 1.440000
+Radius, atomic : 2.160000
+Charge state : 4
+Radius, ionic : 0.780000
+
+
+Atom
+====
+Number : 73
+Name : Tantalum
+Short name : Ta
+Color : 1.0,1.0,1.0
+Radius used : 1.340000
+Radius, covalent : 1.340000
+Radius, atomic : 2.090000
+Charge state : 5
+Radius, ionic : 0.680000
+
+
+Atom
+====
+Number : 74
+Name : Tungsten
+Short name : W
+Color : 1.0,1.0,1.0
+Radius used : 1.300000
+Radius, covalent : 1.300000
+Radius, atomic : 2.020000
+Charge state : 4
+Radius, ionic : 0.700000
+Charge state : 6
+Radius, ionic : 0.620000
+
+
+Atom
+====
+Number : 75
+Name : Rhenium
+Short name : Re
+Color : 1.0,1.0,1.0
+Radius used : 1.280000
+Radius, covalent : 1.280000
+Radius, atomic : 1.970000
+Charge state : 4
+Radius, ionic : 0.720000
+Charge state : 7
+Radius, ionic : 0.560000
+
+
+Atom
+====
+Number : 76
+Name : Osmium
+Short name : Os
+Color : 1.0,1.0,1.0
+Radius used : 1.260000
+Radius, covalent : 1.260000
+Radius, atomic : 1.920000
+Charge state : 4
+Radius, ionic : 0.880000
+Charge state : 6
+Radius, ionic : 0.690000
+
+
+Atom
+====
+Number : 77
+Name : Iridium
+Short name : Ir
+Color : 1.0,1.0,1.0
+Radius used : 1.270000
+Radius, covalent : 1.270000
+Radius, atomic : 1.870000
+Charge state : 4
+Radius, ionic : 0.680000
+
+
+Atom
+====
+Number : 78
+Name : Platinium
+Short name : Pt
+Color : 1.0,1.0,1.0
+Radius used : 1.300000
+Radius, covalent : 1.300000
+Radius, atomic : 1.830000
+Charge state : 2
+Radius, ionic : 0.800000
+Charge state : 4
+Radius, ionic : 0.650000
+
+
+Atom
+====
+Number : 79
+Name : Gold
+Short name : Au
+Color : 1.0,1.0,1.0
+Radius used : 1.340000
+Radius, covalent : 1.340000
+Radius, atomic : 1.790000
+Charge state : 1
+Radius, ionic : 1.370000
+Charge state : 3
+Radius, ionic : 0.850000
+
+
+Atom
+====
+Number : 80
+Name : Mercury
+Short name : Hg
+Color : 1.0,1.0,1.0
+Radius used : 1.490000
+Radius, covalent : 1.490000
+Radius, atomic : 1.760000
+Charge state : 1
+Radius, ionic : 1.270000
+Charge state : 2
+Radius, ionic : 1.100000
+
+
+Atom
+====
+Number : 81
+Name : Thallium
+Short name : Tl
+Color : 1.0,1.0,1.0
+Radius used : 1.480000
+Radius, covalent : 1.480000
+Radius, atomic : 2.080000
+Charge state : 1
+Radius, ionic : 1.470000
+Charge state : 3
+Radius, ionic : 0.950000
+
+
+Atom
+====
+Number : 82
+Name : Lead
+Short name : Pb
+Color : 0.498039215686,0.498039215686,0.498039215686
+Radius used : 1.470000
+Radius, covalent : 1.470000
+Radius, atomic : 1.810000
+Charge state : 2
+Radius, ionic : 1.200000
+Charge state : 4
+Radius, ionic : 0.840000
+
+
+Atom
+====
+Number : 83
+Name : Bismuth
+Short name : Bi
+Color : 1.0,1.0,1.0
+Radius used : 1.460000
+Radius, covalent : 1.460000
+Radius, atomic : 1.630000
+Charge state : 1
+Radius, ionic : 0.980000
+Charge state : 3
+Radius, ionic : 0.960000
+Charge state : 5
+Radius, ionic : 0.740000
+
+
+Atom
+====
+Number : 84
+Name : Polonium
+Short name : Po
+Color : 1.0,1.0,1.0
+Radius used : 1.460000
+Radius, covalent : 1.460000
+Radius, atomic : 1.530000
+Charge state : 6
+Radius, ionic : 0.670000
+
+
+Atom
+====
+Number : 85
+Name : Astatine
+Short name : At
+Color : 1.0,1.0,1.0
+Radius used : 1.450000
+Radius, covalent : 1.450000
+Radius, atomic : 1.430000
+Charge state : -3
+Radius, ionic : 2.220000
+Charge state : 3
+Radius, ionic : 0.850000
+Charge state : 5
+Radius, ionic : 0.460000
+
+
+Atom
+====
+Number : 86
+Name : Radon
+Short name : Rn
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.340000
+
+
+Atom
+====
+Number : 87
+Name : Francium
+Short name : Fr
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+Charge state : 1
+Radius, ionic : 1.800000
+
+
+Atom
+====
+Number : 88
+Name : Radium
+Short name : Ra
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+Charge state : 2
+Radius, ionic : 1.430000
+
+
+Atom
+====
+Number : 89
+Name : Actinium
+Short name : Ac
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+Charge state : 3
+Radius, ionic : 1.180000
+
+
+Atom
+====
+Number : 90
+Name : Thorium
+Short name : Th
+Color : 1.0,1.0,1.0
+Radius used : 1.650000
+Radius, covalent : 1.650000
+Radius, atomic : 1.000000
+Charge state : 4
+Radius, ionic : 1.020000
+
+
+Atom
+====
+Number : 91
+Name : Protactinium
+Short name : Pa
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+Charge state : 3
+Radius, ionic : 1.130000
+Charge state : 4
+Radius, ionic : 0.980000
+Charge state : 5
+Radius, ionic : 0.890000
+
+
+Atom
+====
+Number : 92
+Name : Uranium
+Short name : U
+Color : 1.0,1.0,1.0
+Radius used : 1.420000
+Radius, covalent : 1.420000
+Radius, atomic : 1.000000
+Charge state : 4
+Radius, ionic : 0.970000
+Charge state : 6
+Radius, ionic : 0.800000
+
+
+Atom
+====
+Number : 93
+Name : Neptunium
+Short name : Np
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+Charge state : 3
+Radius, ionic : 1.100000
+Charge state : 4
+Radius, ionic : 0.950000
+Charge state : 7
+Radius, ionic : 0.710000
+
+
+Atom
+====
+Number : 94
+Name : Plutonium
+Short name : Pu
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+Charge state : 3
+Radius, ionic : 1.080000
+Charge state : 4
+Radius, ionic : 0.930000
+
+
+Atom
+====
+Number : 95
+Name : Americium
+Short name : Am
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+Charge state : 3
+Radius, ionic : 1.070000
+Charge state : 4
+Radius, ionic : 0.920000
+
+
+Atom
+====
+Number : 96
+Name : Curium
+Short name : Cm
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 97
+Name : Berkelium
+Short name : Bk
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 98
+Name : Californium
+Short name : Cf
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 99
+Name : Einsteinium
+Short name : Es
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 100
+Name : Fermium
+Short name : Fm
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 101
+Name : Mendelevium
+Short name : Md
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 102
+Name : Nobelium
+Short name : No
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 103
+Name : Lawrencium
+Short name : Lr
+Color : 1.0,1.0,1.0
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 104
+Name : Vacancy
+Short name : Vac
+Color : 0.5,0.5,0.5
+Radius used : 1.0
+Radius, covalent : 1.0
+Radius, atomic : 1.0
+
+
+Atom
+====
+Number : 105
+Name : Default
+Short name : Default
+Color : 1.0,1.0,1.0
+Radius used : 1.0
+Radius, covalent : 1.0
+Radius, atomic : 1.0
+
+
+Atom
+====
+Number : 106
+Name : Stick
+Short name : Stick
+Color : 0.5,0.5,0.5
+Radius used : 1.0
+Radius, covalent : 1.0
+Radius, atomic : 1.0
diff --git a/io_mesh_pdb/import_pdb.py b/io_mesh_pdb/import_pdb.py
new file mode 100644
index 0000000000000000000000000000000000000000..eff89985a7dec062c353407747075d9496620258
--- /dev/null
+++ b/io_mesh_pdb/import_pdb.py
@@ -0,0 +1,1146 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+
+#
+#
+# Authors : Clemens Barth (Blendphys@root-1.de), ...
+#
+# Homepage(Wiki) : http://development.root-1.de/Atomic_Blender.php
+# Tracker : http://projects.blender.org/tracker/index.php?func=detail&aid=29226&group_id=153&atid=467
+#
+# Start of project : 2011-08-31 by Clemens Barth
+# First publication in Blender : 2011-11-11
+# Last modified : 2011-12-01
+#
+# Acknowledgements: Thanks to ideasman, meta_androcto, truman, kilon,
+# dairin0d, PKHG, Valter, etc
+#
+
+import bpy
+import io
+import sys
+import math
+import os
+from math import pi, cos, sin
+from mathutils import Vector, Matrix
+
+# These are variables, which contain the name of the PDB file and
+# the path of the PDB file.
+# They are used almost everywhere, which is the reason why they
+# should stay global. First, they are empty and get 'filled' directly
+# after having chosen the PDB file (see 'class LoadPDB' further below).
+
+ATOM_PDB_FILEPATH = ""
+
+# Some string stuff for the console.
+ATOM_PDB_STRING = "Atomic Blender\n==================="
+
+
+# -----------------------------------------------------------------------------
+# Atom, stick and element data
+
+
+# This is a list that contains some data of all possible elements. The structure
+# is as follows:
+#
+# 1, "Hydrogen", "H", [0.0,0.0,1.0], 0.32, 0.32, 0.32 , -1 , 1.54 means
+#
+# No., name, short name, color, radius (used), radius (covalent), radius (atomic),
+#
+# charge state 1, radius (ionic) 1, charge state 2, radius (ionic) 2, ... all
+# charge states for any atom are listed, if existing.
+# The list is fixed and cannot be changed ... (see below)
+
+ATOM_PDB_ELEMENTS_DEFAULT = (
+( 1, "Hydrogen", "H", ( 1.0, 1.0, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ),
+( 2, "Helium", "He", ( 0.85, 1.0, 1.0), 0.93, 0.93, 0.49 ),
+( 3, "Lithium", "Li", ( 0.8, 0.50, 1.0), 1.23, 1.23, 2.05 , 1 , 0.68 ),
+( 4, "Beryllium", "Be", ( 0.76, 1.0, 0.0), 0.90, 0.90, 1.40 , 1 , 0.44 , 2 , 0.35 ),
+( 5, "Boron", "B", ( 1.0, 0.70, 0.70), 0.82, 0.82, 1.17 , 1 , 0.35 , 3 , 0.23 ),
+( 6, "Carbon", "C", ( 0.56, 0.56, 0.56), 0.77, 0.77, 0.91 , -4 , 2.60 , 4 , 0.16 ),
+( 7, "Nitrogen", "N", ( 0.18, 0.31, 0.97), 0.75, 0.75, 0.75 , -3 , 1.71 , 1 , 0.25 , 3 , 0.16 , 5 , 0.13 ),
+( 8, "Oxygen", "O", ( 1.0, 0.05, 0.05), 0.73, 0.73, 0.65 , -2 , 1.32 , -1 , 1.76 , 1 , 0.22 , 6 , 0.09 ),
+( 9, "Fluorine", "F", ( 0.56, 0.87, 0.31), 0.72, 0.72, 0.57 , -1 , 1.33 , 7 , 0.08 ),
+(10, "Neon", "Ne", ( 0.70, 0.89, 0.96), 0.71, 0.71, 0.51 , 1 , 1.12 ),
+(11, "Sodium", "Na", ( 0.67, 0.36, 0.94), 1.54, 1.54, 2.23 , 1 , 0.97 ),
+(12, "Magnesium", "Mg", ( 0.54, 1.0, 0.0), 1.36, 1.36, 1.72 , 1 , 0.82 , 2 , 0.66 ),
+(13, "Aluminium", "Al", ( 0.74, 0.65, 0.65), 1.18, 1.18, 1.82 , 3 , 0.51 ),
+(14, "Silicon", "Si", ( 0.94, 0.78, 0.62), 1.11, 1.11, 1.46 , -4 , 2.71 , -1 , 3.84 , 1 , 0.65 , 4 , 0.42 ),
+(15, "Phosphorus", "P", ( 1.0, 0.50, 0.0), 1.06, 1.06, 1.23 , -3 , 2.12 , 3 , 0.44 , 5 , 0.35 ),
+(16, "Sulfur", "S", ( 1.0, 1.0, 0.18), 1.02, 1.02, 1.09 , -2 , 1.84 , 2 , 2.19 , 4 , 0.37 , 6 , 0.30 ),
+(17, "Chlorine", "Cl", ( 0.12, 0.94, 0.12), 0.99, 0.99, 0.97 , -1 , 1.81 , 5 , 0.34 , 7 , 0.27 ),
+(18, "Argon", "Ar", ( 0.50, 0.81, 0.89), 0.98, 0.98, 0.88 , 1 , 1.54 ),
+(19, "Potassium", "K", ( 0.56, 0.25, 0.83), 2.03, 2.03, 2.77 , 1 , 0.81 ),
+(20, "Calcium", "Ca", ( 0.23, 1.0, 0.0), 1.74, 1.74, 2.23 , 1 , 1.18 , 2 , 0.99 ),
+(21, "Scandium", "Sc", ( 0.90, 0.90, 0.90), 1.44, 1.44, 2.09 , 3 , 0.73 ),
+(22, "Titanium", "Ti", ( 0.74, 0.76, 0.78), 1.32, 1.32, 2.00 , 1 , 0.96 , 2 , 0.94 , 3 , 0.76 , 4 , 0.68 ),
+(23, "Vanadium", "V", ( 0.65, 0.65, 0.67), 1.22, 1.22, 1.92 , 2 , 0.88 , 3 , 0.74 , 4 , 0.63 , 5 , 0.59 ),
+(24, "Chromium", "Cr", ( 0.54, 0.6, 0.78), 1.18, 1.18, 1.85 , 1 , 0.81 , 2 , 0.89 , 3 , 0.63 , 6 , 0.52 ),
+(25, "Manganese", "Mn", ( 0.61, 0.47, 0.78), 1.17, 1.17, 1.79 , 2 , 0.80 , 3 , 0.66 , 4 , 0.60 , 7 , 0.46 ),
+(26, "Iron", "Fe", ( 0.87, 0.4, 0.2), 1.17, 1.17, 1.72 , 2 , 0.74 , 3 , 0.64 ),
+(27, "Cobalt", "Co", ( 0.94, 0.56, 0.62), 1.16, 1.16, 1.67 , 2 , 0.72 , 3 , 0.63 ),
+(28, "Nickel", "Ni", ( 0.31, 0.81, 0.31), 1.15, 1.15, 1.62 , 2 , 0.69 ),
+(29, "Copper", "Cu", ( 0.78, 0.50, 0.2), 1.17, 1.17, 1.57 , 1 , 0.96 , 2 , 0.72 ),
+(30, "Zinc", "Zn", ( 0.49, 0.50, 0.69), 1.25, 1.25, 1.53 , 1 , 0.88 , 2 , 0.74 ),
+(31, "Gallium", "Ga", ( 0.76, 0.56, 0.56), 1.26, 1.26, 1.81 , 1 , 0.81 , 3 , 0.62 ),
+(32, "Germanium", "Ge", ( 0.4, 0.56, 0.56), 1.22, 1.22, 1.52 , -4 , 2.72 , 2 , 0.73 , 4 , 0.53 ),
+(33, "Arsenic", "As", ( 0.74, 0.50, 0.89), 1.20, 1.20, 1.33 , -3 , 2.22 , 3 , 0.58 , 5 , 0.46 ),
+(34, "Selenium", "Se", ( 1.0, 0.63, 0.0), 1.16, 1.16, 1.22 , -2 , 1.91 , -1 , 2.32 , 1 , 0.66 , 4 , 0.50 , 6 , 0.42 ),
+(35, "Bromine", "Br", ( 0.65, 0.16, 0.16), 1.14, 1.14, 1.12 , -1 , 1.96 , 5 , 0.47 , 7 , 0.39 ),
+(36, "Krypton", "Kr", ( 0.36, 0.72, 0.81), 1.31, 1.31, 1.24 ),
+(37, "Rubidium", "Rb", ( 0.43, 0.18, 0.69), 2.16, 2.16, 2.98 , 1 , 1.47 ),
+(38, "Strontium", "Sr", ( 0.0, 1.0, 0.0), 1.91, 1.91, 2.45 , 2 , 1.12 ),
+(39, "Yttrium", "Y", ( 0.58, 1.0, 1.0), 1.62, 1.62, 2.27 , 3 , 0.89 ),
+(40, "Zirconium", "Zr", ( 0.58, 0.87, 0.87), 1.45, 1.45, 2.16 , 1 , 1.09 , 4 , 0.79 ),
+(41, "Niobium", "Nb", ( 0.45, 0.76, 0.78), 1.34, 1.34, 2.08 , 1 , 1.00 , 4 , 0.74 , 5 , 0.69 ),
+(42, "Molybdenum", "Mo", ( 0.32, 0.70, 0.70), 1.30, 1.30, 2.01 , 1 , 0.93 , 4 , 0.70 , 6 , 0.62 ),
+(43, "Technetium", "Tc", ( 0.23, 0.61, 0.61), 1.27, 1.27, 1.95 , 7 , 0.97 ),
+(44, "Ruthenium", "Ru", ( 0.14, 0.56, 0.56), 1.25, 1.25, 1.89 , 4 , 0.67 ),
+(45, "Rhodium", "Rh", ( 0.03, 0.49, 0.54), 1.25, 1.25, 1.83 , 3 , 0.68 ),
+(46, "Palladium", "Pd", ( 0.0, 0.41, 0.52), 1.28, 1.28, 1.79 , 2 , 0.80 , 4 , 0.65 ),
+(47, "Silver", "Ag", ( 0.75, 0.75, 0.75), 1.34, 1.34, 1.75 , 1 , 1.26 , 2 , 0.89 ),
+(48, "Cadmium", "Cd", ( 1.0, 0.85, 0.56), 1.48, 1.48, 1.71 , 1 , 1.14 , 2 , 0.97 ),
+(49, "Indium", "In", ( 0.65, 0.45, 0.45), 1.44, 1.44, 2.00 , 3 , 0.81 ),
+(50, "Tin", "Sn", ( 0.4, 0.50, 0.50), 1.41, 1.41, 1.72 , -4 , 2.94 , -1 , 3.70 , 2 , 0.93 , 4 , 0.71 ),
+(51, "Antimony", "Sb", ( 0.61, 0.38, 0.70), 1.40, 1.40, 1.53 , -3 , 2.45 , 3 , 0.76 , 5 , 0.62 ),
+(52, "Tellurium", "Te", ( 0.83, 0.47, 0.0), 1.36, 1.36, 1.42 , -2 , 2.11 , -1 , 2.50 , 1 , 0.82 , 4 , 0.70 , 6 , 0.56 ),
+(53, "Iodine", "I", ( 0.58, 0.0, 0.58), 1.33, 1.33, 1.32 , -1 , 2.20 , 5 , 0.62 , 7 , 0.50 ),
+(54, "Xenon", "Xe", ( 0.25, 0.61, 0.69), 1.31, 1.31, 1.24 ),
+(55, "Caesium", "Cs", ( 0.34, 0.09, 0.56), 2.35, 2.35, 3.35 , 1 , 1.67 ),
+(56, "Barium", "Ba", ( 0.0, 0.78, 0.0), 1.98, 1.98, 2.78 , 1 , 1.53 , 2 , 1.34 ),
+(57, "Lanthanum", "La", ( 0.43, 0.83, 1.0), 1.69, 1.69, 2.74 , 1 , 1.39 , 3 , 1.06 ),
+(58, "Cerium", "Ce", ( 1.0, 1.0, 0.78), 1.65, 1.65, 2.70 , 1 , 1.27 , 3 , 1.03 , 4 , 0.92 ),
+(59, "Praseodymium", "Pr", ( 0.85, 1.0, 0.78), 1.65, 1.65, 2.67 , 3 , 1.01 , 4 , 0.90 ),
+(60, "Neodymium", "Nd", ( 0.78, 1.0, 0.78), 1.64, 1.64, 2.64 , 3 , 0.99 ),
+(61, "Promethium", "Pm", ( 0.63, 1.0, 0.78), 1.63, 1.63, 2.62 , 3 , 0.97 ),
+(62, "Samarium", "Sm", ( 0.56, 1.0, 0.78), 1.62, 1.62, 2.59 , 3 , 0.96 ),
+(63, "Europium", "Eu", ( 0.38, 1.0, 0.78), 1.85, 1.85, 2.56 , 2 , 1.09 , 3 , 0.95 ),
+(64, "Gadolinium", "Gd", ( 0.27, 1.0, 0.78), 1.61, 1.61, 2.54 , 3 , 0.93 ),
+(65, "Terbium", "Tb", ( 0.18, 1.0, 0.78), 1.59, 1.59, 2.51 , 3 , 0.92 , 4 , 0.84 ),
+(66, "Dysprosium", "Dy", ( 0.12, 1.0, 0.78), 1.59, 1.59, 2.49 , 3 , 0.90 ),
+(67, "Holmium", "Ho", ( 0.0, 1.0, 0.61), 1.58, 1.58, 2.47 , 3 , 0.89 ),
+(68, "Erbium", "Er", ( 0.0, 0.90, 0.45), 1.57, 1.57, 2.45 , 3 , 0.88 ),
+(69, "Thulium", "Tm", ( 0.0, 0.83, 0.32), 1.56, 1.56, 2.42 , 3 , 0.87 ),
+(70, "Ytterbium", "Yb", ( 0.0, 0.74, 0.21), 1.74, 1.74, 2.40 , 2 , 0.93 , 3 , 0.85 ),
+(71, "Lutetium", "Lu", ( 0.0, 0.67, 0.14), 1.56, 1.56, 2.25 , 3 , 0.85 ),
+(72, "Hafnium", "Hf", ( 0.30, 0.76, 1.0), 1.44, 1.44, 2.16 , 4 , 0.78 ),
+(73, "Tantalum", "Ta", ( 0.30, 0.65, 1.0), 1.34, 1.34, 2.09 , 5 , 0.68 ),
+(74, "Tungsten", "W", ( 0.12, 0.58, 0.83), 1.30, 1.30, 2.02 , 4 , 0.70 , 6 , 0.62 ),
+(75, "Rhenium", "Re", ( 0.14, 0.49, 0.67), 1.28, 1.28, 1.97 , 4 , 0.72 , 7 , 0.56 ),
+(76, "Osmium", "Os", ( 0.14, 0.4, 0.58), 1.26, 1.26, 1.92 , 4 , 0.88 , 6 , 0.69 ),
+(77, "Iridium", "Ir", ( 0.09, 0.32, 0.52), 1.27, 1.27, 1.87 , 4 , 0.68 ),
+(78, "Platinium", "Pt", ( 0.81, 0.81, 0.87), 1.30, 1.30, 1.83 , 2 , 0.80 , 4 , 0.65 ),
+(79, "Gold", "Au", ( 1.0, 0.81, 0.13), 1.34, 1.34, 1.79 , 1 , 1.37 , 3 , 0.85 ),
+(80, "Mercury", "Hg", ( 0.72, 0.72, 0.81), 1.49, 1.49, 1.76 , 1 , 1.27 , 2 , 1.10 ),
+(81, "Thallium", "Tl", ( 0.65, 0.32, 0.30), 1.48, 1.48, 2.08 , 1 , 1.47 , 3 , 0.95 ),
+(82, "Lead", "Pb", ( 0.34, 0.34, 0.38), 1.47, 1.47, 1.81 , 2 , 1.20 , 4 , 0.84 ),
+(83, "Bismuth", "Bi", ( 0.61, 0.30, 0.70), 1.46, 1.46, 1.63 , 1 , 0.98 , 3 , 0.96 , 5 , 0.74 ),
+(84, "Polonium", "Po", ( 0.67, 0.36, 0.0), 1.46, 1.46, 1.53 , 6 , 0.67 ),
+(85, "Astatine", "At", ( 0.45, 0.30, 0.27), 1.45, 1.45, 1.43 , -3 , 2.22 , 3 , 0.85 , 5 , 0.46 ),
+(86, "Radon", "Rn", ( 0.25, 0.50, 0.58), 1.00, 1.00, 1.34 ),
+(87, "Francium", "Fr", ( 0.25, 0.0, 0.4), 1.00, 1.00, 1.00 , 1 , 1.80 ),
+(88, "Radium", "Ra", ( 0.0, 0.49, 0.0), 1.00, 1.00, 1.00 , 2 , 1.43 ),
+(89, "Actinium", "Ac", ( 0.43, 0.67, 0.98), 1.00, 1.00, 1.00 , 3 , 1.18 ),
+(90, "Thorium", "Th", ( 0.0, 0.72, 1.0), 1.65, 1.65, 1.00 , 4 , 1.02 ),
+(91, "Protactinium", "Pa", ( 0.0, 0.63, 1.0), 1.00, 1.00, 1.00 , 3 , 1.13 , 4 , 0.98 , 5 , 0.89 ),
+(92, "Uranium", "U", ( 0.0, 0.56, 1.0), 1.42, 1.42, 1.00 , 4 , 0.97 , 6 , 0.80 ),
+(93, "Neptunium", "Np", ( 0.0, 0.50, 1.0), 1.00, 1.00, 1.00 , 3 , 1.10 , 4 , 0.95 , 7 , 0.71 ),
+(94, "Plutonium", "Pu", ( 0.0, 0.41, 1.0), 1.00, 1.00, 1.00 , 3 , 1.08 , 4 , 0.93 ),
+(95, "Americium", "Am", ( 0.32, 0.36, 0.94), 1.00, 1.00, 1.00 , 3 , 1.07 , 4 , 0.92 ),
+(96, "Curium", "Cm", ( 0.47, 0.36, 0.89), 1.00, 1.00, 1.00 ),
+(97, "Berkelium", "Bk", ( 0.54, 0.30, 0.89), 1.00, 1.00, 1.00 ),
+(98, "Californium", "Cf", ( 0.63, 0.21, 0.83), 1.00, 1.00, 1.00 ),
+(99, "Einsteinium", "Es", ( 0.70, 0.12, 0.83), 1.00, 1.00, 1.00 ),
+(100, "Fermium", "Fm", ( 0.70, 0.12, 0.72), 1.00, 1.00, 1.00 ),
+(101, "Mendelevium", "Md", ( 0.70, 0.05, 0.65), 1.00, 1.00, 1.00 ),
+(102, "Nobelium", "No", ( 0.74, 0.05, 0.52), 1.00, 1.00, 1.00 ),
+(103, "Lawrencium", "Lr", ( 0.78, 0.0, 0.4), 1.00, 1.00, 1.00 ),
+(104, "Vacancy", "Vac", ( 0.5, 0.5, 0.5), 1.00, 1.00, 1.00),
+(105, "Default", "Default", ( 1.0, 1.0, 1.0), 1.00, 1.00, 1.00),
+(106, "Stick", "Stick", ( 0.5, 0.5, 0.5), 1.00, 1.00, 1.00),
+)
+
+# This list here contains all data of the elements and will be used during
+# runtime. It is a list of classes.
+# During executing Atomic Blender, the list will be initialized with the fixed
+# data from above via the class structure below (CLASS_atom_pdb_Elements). We
+# have then one fixed list (above), which will never be changed, and a list of
+# classes with same data. The latter can be modified via loading a separate
+# custom data file.
+ATOM_PDB_ELEMENTS = []
+
+# This is the class, which stores the properties for one element.
+class CLASS_atom_pdb_Elements:
+ def __init__(self, number, name,short_name, color, radii, radii_ionic):
+ self.number = number
+ self.name = name
+ self.short_name = short_name
+ self.color = color
+ self.radii = radii
+ self.radii_ionic = radii_ionic
+
+# This is the class, which stores the properties of one atom.
+class CLASS_atom_pdb_atom:
+ def __init__(self, element, name, location, radius, color, material):
+ self.element = element
+ self.name = name
+ self.location = location
+ self.radius = radius
+ self.color = color
+ self.material = material
+
+# This is the class, which stores the two atoms of one stick.
+class CLASS_atom_pdb_stick:
+ def __init__(self, atom1, atom2):
+ self.atom1 = atom1
+ self.atom2 = atom2
+
+
+# -----------------------------------------------------------------------------
+# Some small routines
+
+
+# Routine which produces a cylinder. All is somewhat easy to undertsand.
+def DEF_atom_pdb_build_stick(radius, length, sectors):
+
+ vertices = []
+ faces = []
+
+ dphi = 2.0 * pi/(float(sectors)-1)
+
+ # Vertices
+ vertices_top = [Vector((0,0,length / 2.0))]
+ vertices_bottom = [Vector((0,0,-length / 2.0))]
+ for i in range(sectors-1):
+ x = radius * cos( dphi * i )
+ y = radius * sin( dphi * i )
+ z = length / 2.0
+ vertex = Vector((x,y,z))
+ vertices_top.append(vertex)
+ z = -length / 2.0
+ vertex = Vector((x,y,z))
+ vertices_bottom.append(vertex)
+ vertices = vertices_top + vertices_bottom
+
+ # Top facets
+ for i in range(sectors-1):
+ if i == sectors-2:
+ face_top = [0,sectors-1,1]
+ face_bottom = [sectors,2*sectors-1,sectors+1]
+ else:
+ face_top = [0]
+ face_bottom = [sectors]
+ for j in range(2):
+ face_top.append(i+j+1)
+ face_bottom.append(i+j+1+sectors)
+ faces.append(face_top)
+ faces.append(face_bottom)
+
+ # Side facets
+ for i in range(sectors-1):
+ if i == sectors-2:
+ faces.append( [i+1, 1, 1+sectors, i+1+sectors] )
+ else:
+ faces.append( [i+1, i+2, i+2+sectors, i+1+sectors] )
+
+ # Build the mesh
+ cylinder = bpy.data.meshes.new("Sticks_Cylinder")
+ cylinder.from_pydata(vertices, [], faces)
+ cylinder.update()
+ new_cylinder = bpy.data.objects.new("Sticks_Cylinder", cylinder)
+ bpy.context.scene.objects.link(new_cylinder)
+
+ return new_cylinder
+
+
+# This function measures the distance between two objects (atoms),
+# which are active.
+def DEF_atom_pdb_distance():
+
+ if len(bpy.context.selected_bases) > 1:
+ object_1 = bpy.context.selected_objects[0]
+ object_2 = bpy.context.selected_objects[1]
+ else:
+ return "N.A."
+
+ dv = object_2.location - object_1.location
+ return str(dv.length)
+
+
+# Routine to modify the radii via the type:
+# pre-defined, atomic or van der Waals
+# Explanations here are also valid for the next 3 DEFs.
+def DEF_atom_pdb_radius_type(rtype,how):
+
+ if how == "ALL_IN_LAYER":
+
+ # Note all layers that are active.
+ layers = []
+ for i in range(20):
+ if bpy.context.scene.layers[i] == True:
+ layers.append(i)
+
+ # Put all objects, which are in the layers, into a list.
+ change_objects = []
+ for obj in bpy.context.scene.objects:
+ for layer in layers:
+ if obj.layers[layer] == True:
+ change_objects.append(obj)
+
+ # Consider all objects, which are in the list 'change_objects'.
+ for obj in change_objects:
+ if len(obj.children) != 0:
+ if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
+ for element in ATOM_PDB_ELEMENTS:
+ if element.name in obj.name:
+ obj.children[0].scale = (element.radii[int(rtype)],
+ element.radii[int(rtype)],
+ element.radii[int(rtype)])
+ else:
+ if obj.type == "SURFACE" or obj.type == "MESH":
+ for element in ATOM_PDB_ELEMENTS:
+ if element.name in obj.name:
+ obj.scale = (element.radii[int(rtype)],
+ element.radii[int(rtype)],
+ element.radii[int(rtype)])
+
+ if how == "ALL_ACTIVE":
+ for obj in bpy.context.selected_objects:
+ if len(obj.children) != 0:
+ if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
+ for element in ATOM_PDB_ELEMENTS:
+ if element.name in obj.name:
+ obj.children[0].scale = (element.radii[int(rtype)],
+ element.radii[int(rtype)],
+ element.radii[int(rtype)])
+ else:
+ if obj.type == "SURFACE" or obj.type == "MESH":
+ for element in ATOM_PDB_ELEMENTS:
+ if element.name in obj.name:
+ obj.scale = (element.radii[int(rtype)],
+ element.radii[int(rtype)],
+ element.radii[int(rtype)])
+
+
+# Routine to modify the radii in picometer of a specific type of atom
+def DEF_atom_pdb_radius_pm(atomname, radius_pm, how):
+
+ if how == "ALL_IN_LAYER":
+
+ layers = []
+ for i in range(20):
+ if bpy.context.scene.layers[i] == True:
+ layers.append(i)
+
+ change_objects = []
+ for obj in bpy.context.scene.objects:
+ for layer in layers:
+ if obj.layers[layer] == True:
+ change_objects.append(obj)
+
+ for obj in change_objects:
+ if len(obj.children) != 0:
+ if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
+ if atomname in obj.name:
+ obj.children[0].scale = (radius_pm/100,
+ radius_pm/100,
+ radius_pm/100)
+ else:
+ if obj.type == "SURFACE" or obj.type == "MESH":
+ if atomname in obj.name:
+ obj.scale = (radius_pm/100,
+ radius_pm/100,
+ radius_pm/100)
+
+ if how == "ALL_ACTIVE":
+ for obj in bpy.context.selected_objects:
+ if len(obj.children) != 0:
+ if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
+ if atomname in obj.name:
+ obj.children[0].scale = (radius_pm/100,
+ radius_pm/100,
+ radius_pm/100)
+ else:
+ if obj.type == "SURFACE" or obj.type == "MESH":
+ if atomname in obj.name:
+ obj.scale = (radius_pm/100,
+ radius_pm/100,
+ radius_pm/100)
+
+
+# Routine to scale the radii of all atoms
+def DEF_atom_pdb_radius_all(scale, how):
+
+ if how == "ALL_IN_LAYER":
+
+ layers = []
+ for i in range(20):
+ if bpy.context.scene.layers[i] == True:
+ layers.append(i)
+
+ change_objects = []
+ for obj in bpy.context.scene.objects:
+ for layer in layers:
+ if obj.layers[layer] == True:
+ change_objects.append(obj)
+
+
+ for obj in change_objects:
+ if len(obj.children) != 0:
+ if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
+ if "Stick" not in obj.name:
+ obj.children[0].scale *= scale
+ else:
+ if obj.type == "SURFACE" or obj.type == "MESH":
+ if "Stick" not in obj.name:
+ obj.scale *= scale
+
+ if how == "ALL_ACTIVE":
+ for obj in bpy.context.selected_objects:
+ if len(obj.children) != 0:
+ if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
+ if "Stick" not in obj.name:
+ obj.children[0].scale *= scale
+ else:
+ if obj.type == "SURFACE" or obj.type == "MESH":
+ if "Stick" not in obj.name:
+ obj.scale *= scale
+
+
+# This reads a custom data file.
+def DEF_atom_pdb_custom_datafile(path_datafile):
+
+ if path_datafile == "":
+ return False
+
+ path_datafile = bpy.path.abspath(path_datafile)
+
+ if os.path.isfile(path_datafile) == False:
+ return False
+
+ # The whole list gets deleted! We build it new.
+ ATOM_PDB_ELEMENTS[:] = []
+
+ # Read the data file, which contains all data
+ # (atom name, radii, colors, etc.)
+ data_file_p = io.open(path_datafile, "r")
+
+ for line in data_file_p:
+
+ if "Atom" in line:
+
+ line = data_file_p.readline()
+
+ # Number
+ line = data_file_p.readline()
+ number = line[19:-1]
+ # Name
+ line = data_file_p.readline()
+ name = line[19:-1]
+ # Short name
+ line = data_file_p.readline()
+ short_name = line[19:-1]
+ # Color
+ line = data_file_p.readline()
+ color_value = line[19:-1].split(',')
+ color = [float(color_value[0]),
+ float(color_value[1]),
+ float(color_value[2])]
+ # Used radius
+ line = data_file_p.readline()
+ radius_used = float(line[19:-1])
+ # Atomic radius
+ line = data_file_p.readline()
+ radius_atomic = float(line[19:-1])
+ # Van der Waals radius
+ line = data_file_p.readline()
+ radius_vdW = float(line[19:-1])
+
+ radii = [radius_used,radius_atomic,radius_vdW]
+ radii_ionic = []
+
+ element = CLASS_atom_pdb_Elements(number,name,short_name,color,
+ radii, radii_ionic)
+
+ ATOM_PDB_ELEMENTS.append(element)
+
+ data_file_p.close()
+
+ return True
+
+
+# -----------------------------------------------------------------------------
+# The main routine
+
+
+def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
+ Ball_radius_factor,radiustype,Ball_distance_factor,
+ use_stick,Stick_sectors,Stick_diameter,put_to_center,
+ use_camera,use_lamp,path_datafile):
+
+ # The list of all atoms as read from the PDB file.
+ all_atoms = []
+
+ # The list of all sticks.
+ all_sticks = []
+
+ # List of materials
+ atom_material_list = []
+
+ # A list of ALL objects which are loaded (needed for selecting the loaded
+ # structure.
+ atom_object_list = []
+
+
+ # ------------------------------------------------------------------------
+ # INITIALIZE THE ELEMENT LIST
+
+ ATOM_PDB_ELEMENTS[:] = []
+
+ for item in ATOM_PDB_ELEMENTS_DEFAULT:
+
+ # All three radii into a list
+ radii = [item[4],item[5],item[6]]
+ # The handling of the ionic radii will be done later. So far, it is an
+ # empty list.
+ radii_ionic = []
+
+ li = CLASS_atom_pdb_Elements(item[0],item[1],item[2],item[3],
+ radii,radii_ionic)
+ ATOM_PDB_ELEMENTS.append(li)
+
+
+ # ------------------------------------------------------------------------
+ # READING DATA OF ATOMS
+
+
+ if DEF_atom_pdb_custom_datafile(path_datafile):
+ print("Custom data file is loaded.")
+
+ # Open the file ...
+ ATOM_PDB_FILEPATH_p = io.open(ATOM_PDB_FILEPATH, "r")
+
+ #Go to the line, in which "ATOM" or "HETATM" appears.
+ for line in ATOM_PDB_FILEPATH_p:
+ split_list = line.split(' ')
+ if "ATOM" in split_list[0]:
+ break
+ if "HETATM" in split_list[0]:
+ break
+
+ j = 0
+ # This is in fact an endless 'while loop', ...
+ while j > -1:
+
+ # ... the loop is broken here (EOF) ...
+ if line == "":
+ break
+
+ # If there is a "TER" we need to put empty entries into the lists
+ # in order to not destroy the order of atom numbers and same numbers
+ # used for sticks. "TER? What is that?" TER indicates the end of a
+ # list of ATOM/HETATM records for a chain.
+ if "TER" in line:
+ short_name = "TER"
+ name = "TER"
+ radius = 0.0
+ color = [0,0,0]
+ location = Vector((0,0,0))
+ # Append the TER into the list. Material remains empty so far.
+ all_atoms.append(CLASS_atom_pdb_atom(short_name,
+ name,
+ location,
+ radius,
+ color,[]))
+ # If 'ATOM or 'HETATM' appears in the line then do ...
+ elif "ATOM" in line or "HETATM" in line:
+
+ # What follows is due to deviations which appear from PDB to
+ # PDB file. It is very special. PLEASE, DO NOT CHANGE! From here ...
+ short_name = line[13:14]
+ if short_name.isupper() == True:
+ if line[14:15].islower() == True:
+ short_name = short_name + line[14:15]
+ else:
+ short_name = line[12:13]
+ if short_name.isupper() == True:
+ if line[13:14].islower() == True:
+ short_name = short_name + line[13:14]
+ # ... to here.
+
+ # Go through all elements and find the element of the current atom.
+ FLAG_FOUND = False
+ for element in ATOM_PDB_ELEMENTS:
+ if str.upper(short_name) == str.upper(element.short_name):
+ # Give the atom its proper names, color and radius:
+ short_name = str.upper(element.short_name)
+ name = element.name
+ # int(radiustype) => type of radius:
+ # pre-defined (0), atomic (1) or van der Waals (2)
+ radius = float(element.radii[int(radiustype)])
+ color = element.color
+ FLAG_FOUND = True
+ break
+
+ # Is it a vacancy or an 'unknown atom' ?
+ if FLAG_FOUND == False:
+ # Give this atom also a name. If it is an 'X' then it is a
+ # vacancy. Otherwise ...
+ if "X" in short_name:
+ short_name = "VAC"
+ name = "Vacancy"
+ radius = float(ATOM_PDB_ELEMENTS[-3].radii[int(radiustype)])
+ color = ATOM_PDB_ELEMENTS[-3].color
+ # ... take what is written in the PDB file. These are somewhat
+ # unknown atoms. This should never happen, the element list is
+ # almost complete. However, we do this due to security reasons.
+ else:
+ short_name = str.upper(short_name)
+ name = str.upper(short_name)
+ radius = float(ATOM_PDB_ELEMENTS[-2].radii[int(radiustype)])
+ color = ATOM_PDB_ELEMENTS[-2].color
+
+ # x,y and z are at fixed positions in the PDB file.
+ x = float(line[30:38].rsplit()[0])
+ y = float(line[38:46].rsplit()[0])
+ z = float(line[46:55].rsplit()[0])
+
+ location = Vector((x,y,z))
+
+ j += 1
+
+ # Append the atom to the list. Material remains empty so far.
+ all_atoms.append(CLASS_atom_pdb_atom(short_name,
+ name,
+ location,
+ radius,
+ color,[]))
+
+ line = ATOM_PDB_FILEPATH_p.readline()
+ line = line[:-1]
+
+ ATOM_PDB_FILEPATH_p.close()
+ # From above it can be clearly seen that j is now the number of all atoms.
+ Number_of_total_atoms = j
+
+
+ # ------------------------------------------------------------------------
+ # MATERIAL PROPERTIES FOR ATOMS
+
+
+ # The list that contains info about all types of atoms is created
+ # here. It is used for building the material properties for
+ # instance (see below).
+ atom_all_types_list = []
+
+ for atom in all_atoms:
+ FLAG_FOUND = False
+ for atom_type in atom_all_types_list:
+ # If the atom name is already in the list, FLAG on 'True'.
+ if atom_type[0] == atom.name:
+ FLAG_FOUND = True
+ break
+ # No name in the current list has been found? => New entry.
+ if FLAG_FOUND == False:
+ # Stored are: Atom label (e.g. 'Na'), the corresponding atom
+ # name (e.g. 'Sodium') and its color.
+ atom_all_types_list.append([atom.name, atom.element, atom.color])
+
+ # The list of materials is built.
+ # Note that all atoms of one type (e.g. all hydrogens) get only ONE
+ # material! This is good because then, by activating one atom in the
+ # Blender scene and changing the color of this atom, one changes the color
+ # of ALL atoms of the same type at the same time.
+
+ # Create first a new list of materials for each type of atom
+ # (e.g. hydrogen)
+ for atom_type in atom_all_types_list:
+ material = bpy.data.materials.new(atom_type[1])
+ material.name = atom_type[0]
+ material.diffuse_color = atom_type[2]
+ atom_material_list.append(material)
+
+ # Now, we go through all atoms and give them a material. For all atoms ...
+ for atom in all_atoms:
+ # ... and all materials ...
+ for material in atom_material_list:
+ # ... select the correct material for the current atom via
+ # comparison of names ...
+ if atom.name in material.name:
+ # ... and give the atom its material properties.
+ # However, before we check, if it is a vacancy, because then it
+ # gets some additional preparation. The vacancy is represented
+ # by a transparent cube.
+ if atom.name == "Vacancy":
+ material.transparency_method = 'Z_TRANSPARENCY'
+ material.alpha = 1.3
+ material.raytrace_transparency.fresnel = 1.6
+ material.raytrace_transparency.fresnel_factor = 1.6
+ material.use_transparency = True
+ # The atom gets its properties.
+ atom.material = material
+
+
+ # ------------------------------------------------------------------------
+ # READING DATA OF STICKS
+
+
+ # Open the PDB file again such that the file pointer is in the first
+ # line ... . Stupid, I know ... ;-)
+ ATOM_PDB_FILEPATH_p = io.open(ATOM_PDB_FILEPATH, "r")
+
+ split_list = line.split(' ')
+
+ # Go to the first entry
+ if "CONECT" not in split_list[0]:
+ for line in ATOM_PDB_FILEPATH_p:
+ split_list = line.split(' ')
+ if "CONECT" in split_list[0]:
+ break
+
+ Number_of_sticks = 0
+ sticks_double = 0
+ j = 0
+ # This is in fact an endless while loop, ...
+ while j > -1:
+
+ # ... which is broken here (EOF) ...
+ if line == "":
+ break
+ # ... or here, when no 'CONECT' appears anymore.
+ if "CONECT" not in line:
+ break
+
+ # The strings of the atom numbers do have a clear position in the file
+ # (From 7 to 12, from 13 to 18 and so on.) and one needs to consider
+ # this. One could also use the split function but then one gets into
+ # trouble if there are many atoms: For instance, it may happen that one
+ # has
+ # CONECT 11111 22244444
+ #
+ # In Fact it means that atom No. 11111 has a connection with atom
+ # No. 222 but also with atom No. 44444. The split function would give
+ # me only two numbers (11111 and 22244444), which is wrong.
+
+ # Cut spaces from the right and 'CONECT' at the beginning
+ line = line.rstrip()
+ line = line[6:]
+ # Amount of loops
+ length = len(line)
+ loops = int(length/5)
+
+ # List of atoms
+ atom_list = []
+ for i in range(loops):
+ number = line[5*i:5*(i+1)].rsplit()
+ if number != []:
+ if number[0].isdigit() == True:
+ atom_number = int(number[0])
+ atom_list.append(atom_number)
+
+ # The first atom is connected with all the others in the list.
+ atom1 = atom_list[0]
+
+ # For all the other atoms in the list do:
+ for each_atom in atom_list[1:]:
+
+ # The second, third, ... partner atom
+ atom2 = each_atom
+
+ # Note that in a PDB file, sticks of one atom pair can appear a
+ # couple of times. (Only god knows why ...)
+ # So, does a stick between the considered atoms already exist?
+ FLAG_BAR = False
+ for k in range(Number_of_sticks):
+ if ((all_sticks[k].atom1 == atom1 and all_sticks[k].atom2 == atom2) or
+ (all_sticks[k].atom2 == atom1 and all_sticks[k].atom1 == atom2)):
+ sticks_double += 1
+ # If yes, then FLAG on 'True'.
+ FLAG_BAR = True
+ break
+
+ # If the stick is not yet registered (FLAG_BAR == False), then
+ # register it!
+ if FLAG_BAR == False:
+ all_sticks.append(CLASS_atom_pdb_stick(atom1,atom2))
+ Number_of_sticks += 1
+ j += 1
+
+ line = ATOM_PDB_FILEPATH_p.readline()
+ line = line.rstrip()
+
+ ATOM_PDB_FILEPATH_p.close()
+ # So far, all atoms and sticks have been registered.
+
+
+ # ------------------------------------------------------------------------
+ # TRANSLATION OF THE STRUCTURE TO THE ORIGIN
+
+
+ # It may happen that the structure in a PDB file already has an offset
+ # If chosen, the structure is first put into the center of the scene
+ # (the offset is substracted).
+
+ if put_to_center == True:
+
+ sum_vec = Vector((0.0,0.0,0.0))
+
+ # Sum of all atom coordinates
+ sum_vec = sum([atom.location for atom in all_atoms], sum_vec)
+
+ # Then the average is taken
+ sum_vec = sum_vec / Number_of_total_atoms
+
+ # After, for each atom the center of gravity is substracted
+ for atom in all_atoms:
+ atom.location -= sum_vec
+
+
+ # ------------------------------------------------------------------------
+ # SCALING
+
+
+ # Take all atoms and adjust their radii and scale the distances.
+ for atom in all_atoms:
+ atom.location *= Ball_distance_factor
+
+
+ # ------------------------------------------------------------------------
+ # DETERMINATION OF SOME GEOMETRIC PROPERTIES
+
+
+ # In the following, some geometric properties of the whole object are
+ # determined: center, size, etc.
+ sum_vec = Vector((0.0,0.0,0.0))
+
+ # First the center is determined. All coordinates are summed up ...
+ sum_vec = sum([atom.location for atom in all_atoms], sum_vec)
+
+ # ... and the average is taken. This gives the center of the object.
+ object_center_vec = sum_vec / Number_of_total_atoms
+
+ # Now, we determine the size.The farest atom from the object center is
+ # taken as a measure. The size is used to place well the camera and light
+ # into the scene.
+ object_size_vec = [atom.location - object_center_vec for atom in all_atoms]
+ object_size = 0.0
+ object_size = max(object_size_vec).length
+
+
+ # ------------------------------------------------------------------------
+ # CAMERA AND LAMP
+
+ camera_factor = 15.0
+
+ # If chosen a camera is put into the scene.
+ if use_camera == True:
+
+ # Assume that the object is put into the global origin. Then, the
+ # camera is moved in x and z direction, not in y. The object has its
+ # size at distance math.sqrt(object_size) from the origin. So, move the
+ # camera by this distance times a factor of camera_factor in x and z.
+ # Then add x, y and z of the origin of the object.
+ object_camera_vec = Vector((math.sqrt(object_size) * camera_factor,
+ 0.0,
+ math.sqrt(object_size) * camera_factor))
+ camera_xyz_vec = object_center_vec + object_camera_vec
+
+ # Create the camera
+ current_layers=bpy.context.scene.layers
+ bpy.ops.object.camera_add(view_align=False, enter_editmode=False,
+ location=camera_xyz_vec,
+ rotation=(0.0, 0.0, 0.0), layers=current_layers)
+ # Some properties of the camera are changed.
+ camera = bpy.context.scene.objects.active
+ camera.name = "A_camera"
+ camera.data.name = "A_camera"
+ camera.data.lens = 45
+ camera.data.clip_end = 500.0
+
+ # Here the camera is rotated such it looks towards the center of
+ # the object. The [0.0, 0.0, 1.0] vector along the z axis
+ z_axis_vec = Vector((0.0, 0.0, 1.0))
+ # The angle between the last two vectors
+ angle = object_camera_vec.angle(z_axis_vec, 0)
+ # The cross-product of z_axis_vec and object_camera_vec
+ axis_vec = z_axis_vec.cross(object_camera_vec)
+ # Rotate 'axis_vec' by 'angle' and convert this to euler parameters.
+ # 4 is the size of the matrix.
+ euler = Matrix.Rotation(angle, 4, axis_vec).to_euler()
+ camera.rotation_euler = euler
+
+ # Rotate the camera around its axis by 90° such that we have a nice
+ # camera position and view onto the object.
+ bpy.ops.transform.rotate(value=(90.0*2*math.pi/360.0,),
+ axis=object_camera_vec,
+ constraint_axis=(False, False, False),
+ constraint_orientation='GLOBAL',
+ mirror=False, proportional='DISABLED',
+ proportional_edit_falloff='SMOOTH',
+ proportional_size=1, snap=False,
+ snap_target='CLOSEST', snap_point=(0, 0, 0),
+ snap_align=False, snap_normal=(0, 0, 0),
+ release_confirm=False)
+
+
+ # This does not work, I don't know why.
+ #
+ #for area in bpy.context.screen.areas:
+ # if area.type == 'VIEW_3D':
+ # area.spaces[0].region_3d.view_perspective = 'CAMERA'
+
+
+ # Here a lamp is put into the scene, if chosen.
+ if use_lamp == True:
+
+ # This is the distance from the object measured in terms of %
+ # of the camera distance. It is set onto 50% (1/2) distance.
+ lamp_dl = math.sqrt(object_size) * 15 * 0.5
+ # This is a factor to which extend the lamp shall go to the right
+ # (from the camera point of view).
+ lamp_dy_right = lamp_dl * (3.0/4.0)
+
+ # Create x, y and z for the lamp.
+ object_lamp_vec = Vector((lamp_dl,lamp_dy_right,lamp_dl))
+ lamp_xyz_vec = object_center_vec + object_lamp_vec
+
+ # Create the lamp
+ current_layers=bpy.context.scene.layers
+ bpy.ops.object.lamp_add (type = 'POINT', view_align=False,
+ location=lamp_xyz_vec,
+ rotation=(0.0, 0.0, 0.0),
+ layers=current_layers)
+ # Some properties of the lamp are changed.
+ lamp = bpy.context.scene.objects.active
+ lamp.data.name = "A_lamp"
+ lamp.name = "A_lamp"
+ lamp.data.distance = 500.0
+ lamp.data.energy = 3.0
+ lamp.data.shadow_method = 'RAY_SHADOW'
+
+ bpy.context.scene.world.light_settings.use_ambient_occlusion = True
+ bpy.context.scene.world.light_settings.ao_factor = 0.2
+
+
+ # ------------------------------------------------------------------------
+ # SOME OUTPUT ON THE CONSOLE
+
+
+ print()
+ print()
+ print()
+ print(ATOM_PDB_STRING)
+ print()
+ print("Total number of atoms : " + str(Number_of_total_atoms))
+ print("Total number of sticks : " + str(Number_of_sticks))
+ print("Center of object : ", object_center_vec)
+ print("Size of object : ", object_size)
+ print()
+
+
+ # ------------------------------------------------------------------------
+ # SORTING THE ATOMS
+
+
+ # Lists of atoms of one type are created. Example:
+ # draw_all_atoms = [ data_hydrogen,data_carbon,data_nitrogen ]
+ # data_hydrogen = [["Hydrogen", Material_Hydrogen, Vector((x,y,z)), 109], ...]
+
+ draw_all_atoms = []
+
+ # Go through the list which contains all types of atoms. It is the list,
+ # which has been created on the top during reading the PDB file.
+ # Example: atom_all_types_list = ["hydrogen", "carbon", ...]
+ for atom_type in atom_all_types_list:
+
+ # Don't draw 'TER atoms'.
+ if atom_type[0] == "TER":
+ continue
+
+ # This is the draw list, which contains all atoms of one type (e.g.
+ # all hydrogens) ...
+ draw_all_atoms_type = []
+
+ # Go through all atoms ...
+ for atom in all_atoms:
+ # ... select the atoms of the considered type via comparison ...
+ if atom.name == atom_type[0]:
+ # ... and append them to the list 'draw_all_atoms_type'.
+ draw_all_atoms_type.append([atom.name,
+ atom.material,
+ atom.location,
+ atom.radius])
+
+ # Now append the atom list to the list of all types of atoms
+ draw_all_atoms.append(draw_all_atoms_type)
+
+
+ # ------------------------------------------------------------------------
+ # DRAWING THE ATOMS
+
+
+ # This is the number of all atoms which are put into the scene.
+ number_loaded_atoms = 0
+ bpy.ops.object.select_all(action='DESELECT')
+
+ # For each list of atoms of ONE type (e.g. Hydrogen)
+ for draw_all_atoms_type in draw_all_atoms:
+
+ # Create first the vertices composed of the coordinates of all
+ # atoms of one type
+ atom_vertices = []
+ for atom in draw_all_atoms_type:
+ # In fact, the object is created in the World's origin.
+ # This is why 'object_center_vec' is substracted. At the end
+ # the whole object is translated back to 'object_center_vec'.
+ atom_vertices.append( atom[2] - object_center_vec )
+
+ # Build the mesh
+ atom_mesh = bpy.data.meshes.new("Mesh_"+atom[0])
+ atom_mesh.from_pydata(atom_vertices, [], [])
+ atom_mesh.update()
+ new_atom_mesh = bpy.data.objects.new(atom[0], atom_mesh)
+ bpy.context.scene.objects.link(new_atom_mesh)
+
+ # Now, build a representative sphere (atom)
+ current_layers=bpy.context.scene.layers
+
+ if atom[0] == "Vacancy":
+ bpy.ops.mesh.primitive_cube_add(
+ view_align=False, enter_editmode=False,
+ location=(0.0, 0.0, 0.0),
+ rotation=(0.0, 0.0, 0.0),
+ layers=current_layers)
+ else:
+ # NURBS balls
+ if use_mesh == False:
+ bpy.ops.surface.primitive_nurbs_surface_sphere_add(
+ view_align=False, enter_editmode=False,
+ location=(0,0,0), rotation=(0.0, 0.0, 0.0),
+ layers=current_layers)
+ # UV balls
+ else:
+ bpy.ops.mesh.primitive_uv_sphere_add(
+ segments=Ball_azimuth, ring_count=Ball_zenith,
+ size=1, view_align=False, enter_editmode=False,
+ location=(0,0,0), rotation=(0, 0, 0),
+ layers=current_layers)
+
+ ball = bpy.context.scene.objects.active
+ ball.scale = (atom[3]*Ball_radius_factor,
+ atom[3]*Ball_radius_factor,
+ atom[3]*Ball_radius_factor)
+
+ if atom[0] == "Vacancy":
+ ball.name = "Cube_"+atom[0]
+ else:
+ ball.name = "Ball (NURBS)_"+atom[0]
+ ball.active_material = atom[1]
+ ball.parent = new_atom_mesh
+ new_atom_mesh.dupli_type = 'VERTS'
+ # The object is back translated to 'object_center_vec'.
+ new_atom_mesh.location = object_center_vec
+ atom_object_list.append(new_atom_mesh)
+
+ print()
+
+
+ # ------------------------------------------------------------------------
+ # DRAWING THE STICKS
+
+
+ if use_stick == True and all_sticks != []:
+
+ # Create a new material with the corresponding color. The
+ # color is taken from the all_atom list, it is the last entry
+ # in the data file (index -1).
+ bpy.ops.object.material_slot_add()
+ stick_material = bpy.data.materials.new(ATOM_PDB_ELEMENTS[-1].name)
+ stick_material.diffuse_color = ATOM_PDB_ELEMENTS[-1].color
+
+ vertices = []
+ faces = []
+ dl = 0.2
+
+ i = 0
+ # For all sticks, do ...
+ for stick in all_sticks:
+
+ # What follows is school mathematics! :-)
+ v1 = all_atoms[stick.atom2-1].location
+ v2 = all_atoms[stick.atom1-1].location
+
+ dv = (v1 - v2)
+
+ n = dv / dv.length
+ m = v1 - dv / 2.0
+
+ gamma = -n * v1
+ b = v1 + gamma * n
+ n_b = b / b.length
+
+ loops = int(dv.length / dl)
+
+ for j in range(loops):
+
+ g = v1 - n * dl / 2.0 - n * dl * j
+
+ p1 = g + n_b * Stick_diameter
+ p2 = g - n_b * Stick_diameter
+ p3 = g - n_b.cross(n) * Stick_diameter
+ p4 = g + n_b.cross(n) * Stick_diameter
+
+ vertices.append(p1)
+ vertices.append(p2)
+ vertices.append(p3)
+ vertices.append(p4)
+ faces.append((i*4+0,i*4+2,i*4+1,i*4+3))
+ i += 1
+
+ mesh = bpy.data.meshes.new("Sticks")
+ mesh.from_pydata(vertices, [], faces)
+ mesh.update()
+ new_mesh = bpy.data.objects.new("Sticks", mesh)
+ bpy.context.scene.objects.link(new_mesh)
+
+ current_layers = bpy.context.scene.layers
+ stick_cylinder = DEF_atom_pdb_build_stick(Stick_diameter, dl, Stick_sectors)
+
+
+ stick_cylinder.active_material = stick_material
+ stick_cylinder.parent = new_mesh
+ new_mesh.dupli_type = 'FACES'
+ atom_object_list.append(new_mesh)
+
+
+ # ------------------------------------------------------------------------
+ # SELECT ALL LOADED OBJECTS
+ bpy.ops.object.select_all(action='DESELECT')
+ obj = None
+ for obj in atom_object_list:
+ obj.select = True
+
+ # activate the last selected object (perhaps another should be active?)
+ if obj:
+ bpy.context.scene.objects.active = obj
+
+ print("\n\nAll atoms (%d) and sticks (%d) have been drawn - finished.\n\n"
+ % (Number_of_total_atoms,Number_of_sticks))
+
+
+ return Number_of_total_atoms