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authorClemens Barth <barth@root-1.de>2019-03-28 12:37:49 +0300
committerClemens Barth <barth@root-1.de>2019-03-28 12:37:49 +0300
commit9791bd3a2233ace2d8a588c4f8b7fe6cb4c8fa7e (patch)
treebfd9c54d67676a8b992dbf50fdfc3ef69c9a1997 /io_mesh_atomic
parent6ee42b89a9cf2fae3320d037c606646c73c66f0d (diff)
The new ‘Atomic Blender PDB/XYZ’ importer. T62804
Comments ======== This is the fusion of the 3 atomic blender addons from Blender 2.79: 1. PDB (I/O addon for .pdb files, was in trunk before) 2. XYZ (I/O addon for .xyz files, was in contrib before) 3. Utilities (panel for modifying atomic structures, was in contrib before), into one single addon called ‘Atomic Blender PDB/XYZ’.
Diffstat (limited to 'io_mesh_atomic')
-rw-r--r--io_mesh_atomic/__init__.py219
-rw-r--r--io_mesh_atomic/atom_info.dat2172
-rw-r--r--io_mesh_atomic/pdb_export.py81
-rw-r--r--io_mesh_atomic/pdb_gui.py270
-rw-r--r--io_mesh_atomic/pdb_import.py1549
-rw-r--r--io_mesh_atomic/utility_gui.py422
-rw-r--r--io_mesh_atomic/utility_panel.py1074
-rw-r--r--io_mesh_atomic/xyz_export.py83
-rw-r--r--io_mesh_atomic/xyz_gui.py210
-rw-r--r--io_mesh_atomic/xyz_import.py810
10 files changed, 6890 insertions, 0 deletions
diff --git a/io_mesh_atomic/__init__.py b/io_mesh_atomic/__init__.py
new file mode 100644
index 00000000..2b2d89d7
--- /dev/null
+++ b/io_mesh_atomic/__init__.py
@@ -0,0 +1,219 @@
+# ##### 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 #####
+#
+# Author : Clemens Barth (Blendphys@root-1.de)
+# Homepage(Wiki) : http://development.root-1.de/Atomic_Blender.php
+#
+# Start of project : 2011-08-31 by CB
+# First publication in Blender : 2011-11-11 by CB
+# Fusion of the PDB, XYZ and Panel : 2019-03-22 by CB
+# Last modified : 2019-03-28
+#
+# Contributing authors
+# ====================
+#
+# So far ... none ... .
+#
+#
+# Acknowledgements
+# ================
+#
+# A big thank you to all those people who I met in particular in the IRC and
+# who helped me a lot.
+#
+# Blender developers
+# ------------------
+# Campbell Barton (ideasman)
+# Brendon Murphy (meta_androcto)
+# Truman Melton (?) (truman)
+# Kilon Alios (kilon)
+# ?? (CoDEmanX)
+# Dima Glib (dairin0d)
+# Peter K.H. Gragert (PKHG)
+# Valter Battioli (?) (valter)
+# ? (atmind)
+# Ray Molenkamp (bzztploink)
+#
+# Other
+# -----
+# Frank Palmino (Femto-St institute, Belfort-Montbéliard, France)
+# ... for testing the addons and for feedback
+#
+
+bl_info = {
+ "name": "Atomic Blender PDB/XYZ",
+ "description": "Importing atoms listed in PDB or XYZ files as balls into Blender",
+ "author": "Clemens Barth",
+ "version": (1, 8),
+ "blender": (2, 80, 0),
+ "location": "File -> Import -> PDB (.pdb) and File -> Import -> XYZ (.xyz)",
+ "warning": "",
+ "wiki_url": "https://wiki.blender.org/",
+ "category": "Import-Export",
+}
+
+import bpy
+from bpy.types import Operator, AddonPreferences
+from bpy_extras.io_utils import ImportHelper, ExportHelper
+from bpy.props import (
+ StringProperty,
+ BoolProperty,
+ EnumProperty,
+ IntProperty,
+ FloatProperty,
+ )
+
+from . import (
+ pdb_gui,
+ xyz_gui,
+ utility_gui,
+ utility_panel
+ )
+
+# -----------------------------------------------------------------------------
+# Preferences
+
+class AddonPreferences(AddonPreferences):
+ # This must match the addon name, use '__package__'
+ # when defining this in a submodule of a python package.
+ bl_idname = __name__
+
+ bool_pdb = BoolProperty(
+ name="PDB import/export",
+ default=True,
+ description="Import/export PDB",
+ )
+ bool_xyz = BoolProperty(
+ name="XYZ import/export",
+ default=True,
+ description="Import/export XYZ",
+ )
+ # This boolean is checked in the poll function in PANEL_PT_prepare
+ # (see utility.py).
+ bool_utility = BoolProperty(
+ name="Utility panel",
+ default=False,
+ description=("Panel with functionalities for modifying " \
+ "atomic structures"),
+ )
+
+ def draw(self, context):
+ layout = self.layout
+ layout.label(text="Choose the importer(s) and a 'utility' panel")
+ layout.prop(self, "bool_pdb")
+ layout.prop(self, "bool_xyz")
+ layout.prop(self, "bool_utility")
+
+
+# -----------------------------------------------------------------------------
+# Menu
+
+
+# The entry into the menu 'file -> import'
+def menu_func_import_pdb(self, context):
+ lay = self.layout
+ lay.operator(pdb_gui.IMPORT_OT_pdb.bl_idname,text="Protein Data Bank (.pdb)")
+
+def menu_func_import_xyz(self, context):
+ lay = self.layout
+ lay.operator(xyz_gui.IMPORT_OT_xyz.bl_idname,text="XYZ (.xyz)")
+
+# The entry into the menu 'file -> export'
+def menu_func_export_pdb(self, context):
+ lay = self.layout
+ lay.operator(pdb_gui.EXPORT_OT_pdb.bl_idname,text="Protein Data Bank (.pdb)")
+
+def menu_func_export_xyz(self, context):
+ lay = self.layout
+ lay.operator(xyz_gui.EXPORT_OT_xyz.bl_idname,text="XYZ (.xyz)")
+
+
+# -----------------------------------------------------------------------------
+# Register
+
+def register():
+ from bpy.utils import register_class
+
+ register_class(AddonPreferences)
+
+ register_class(pdb_gui.IMPORT_OT_pdb)
+ register_class(pdb_gui.EXPORT_OT_pdb)
+ bpy.types.TOPBAR_MT_file_import.append(menu_func_import_pdb)
+ bpy.types.TOPBAR_MT_file_export.append(menu_func_export_pdb)
+
+ register_class(xyz_gui.IMPORT_OT_xyz)
+ register_class(xyz_gui.EXPORT_OT_xyz)
+ bpy.types.TOPBAR_MT_file_import.append(menu_func_import_xyz)
+ bpy.types.TOPBAR_MT_file_export.append(menu_func_export_xyz)
+
+ classes = (utility_gui.PANEL_PT_prepare,
+ utility_gui.PanelProperties,
+ utility_gui.DatafileApply,
+ utility_gui.DefaultAtom,
+ utility_gui.ReplaceAtom,
+ utility_gui.SeparateAtom,
+ utility_gui.DistanceButton,
+ utility_gui.RadiusAllBiggerButton,
+ utility_gui.RadiusAllSmallerButton,
+ utility_gui.SticksAllBiggerButton,
+ utility_gui.SticksAllSmallerButton)
+ from bpy.utils import register_class
+ utility_panel.read_elements()
+ for cls in classes:
+ register_class(cls)
+
+ scene = bpy.types.Scene
+ scene.atom_blend = bpy.props.PointerProperty(type=utility_gui.PanelProperties)
+
+
+def unregister():
+ from bpy.utils import unregister_class
+
+ unregister_class(AddonPreferences)
+
+ unregister_class(pdb_gui.IMPORT_OT_pdb)
+ unregister_class(pdb_gui.EXPORT_OT_pdb)
+ bpy.types.TOPBAR_MT_file_import.remove(menu_func_import_pdb)
+ bpy.types.TOPBAR_MT_file_export.remove(menu_func_export_pdb)
+
+ unregister_class(xyz_gui.IMPORT_OT_xyz)
+ unregister_class(xyz_gui.EXPORT_OT_xyz)
+ bpy.types.TOPBAR_MT_file_import.remove(menu_func_import_xyz)
+ bpy.types.TOPBAR_MT_file_export.remove(menu_func_export_xyz)
+
+ classes = (utility_gui.PANEL_PT_prepare,
+ utility_gui.PanelProperties,
+ utility_gui.DatafileApply,
+ utility_gui.DefaultAtom,
+ utility_gui.ReplaceAtom,
+ utility_gui.SeparateAtom,
+ utility_gui.DistanceButton,
+ utility_gui.RadiusAllBiggerButton,
+ utility_gui.RadiusAllSmallerButton,
+ utility_gui.SticksAllBiggerButton,
+ utility_gui.SticksAllSmallerButton)
+ for cls in classes:
+ unregister_class(cls)
+
+
+# -----------------------------------------------------------------------------
+# Main
+
+if __name__ == "__main__":
+
+ register()
diff --git a/io_mesh_atomic/atom_info.dat b/io_mesh_atomic/atom_info.dat
new file mode 100644
index 00000000..83dde4b8
--- /dev/null
+++ b/io_mesh_atomic/atom_info.dat
@@ -0,0 +1,2172 @@
+Atom
+====
+Number : 1
+Name : Hydrogen
+Short name : H
+Color : 1.0,1.0,1.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.850980392157,1.0,1.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+Radius used : 0.930000
+Radius, covalent : 0.930000
+Radius, atomic : 0.490000
+
+
+Atom
+====
+Number : 3
+Name : Lithium
+Short name : Li
+Color : 0.8,0.501960784314,1.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.760784313725,1.0,0.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 1.0,0.709803921569,0.709803921569,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.564705882353,0.564705882353,0.564705882353,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.188235294118,0.313725490196,0.972549019608,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 1.0,0.0509803921569,0.0509803921569,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.564705882353,0.878431372549,0.313725490196,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.701960784314,0.890196078431,0.960784313725,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.670588235294,0.360784313725,0.949019607843,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.541176470588,1.0,0.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.749019607843,0.650980392157,0.650980392157,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.941176470588,0.78431372549,0.627450980392,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 1.0,0.501960784314,0.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 1.0,1.0,0.188235294118,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.121568627451,0.941176470588,0.121568627451,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.501960784314,0.819607843137,0.890196078431,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.560784313725,0.250980392157,0.83137254902,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.239215686275,1.0,0.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.901960784314,0.901960784314,0.901960784314,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.749019607843,0.760784313725,0.780392156863,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.650980392157,0.650980392157,0.670588235294,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.541176470588,0.6,0.780392156863,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.611764705882,0.478431372549,0.780392156863,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.878431372549,0.4,0.2,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.941176470588,0.564705882353,0.627450980392,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.313725490196,0.81568627451,0.313725490196,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.78431372549,0.501960784314,0.2,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.490196078431,0.501960784314,0.690196078431,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.760784313725,0.560784313725,0.560784313725,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.4,0.560784313725,0.560784313725,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.741176470588,0.501960784314,0.890196078431,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 1.0,0.63137254902,0.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.650980392157,0.160784313725,0.160784313725,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.360784313725,0.721568627451,0.819607843137,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+Radius used : 1.310000
+Radius, covalent : 1.310000
+Radius, atomic : 1.240000
+
+
+Atom
+====
+Number : 37
+Name : Rubidium
+Short name : Rb
+Color : 0.439215686275,0.180392156863,0.690196078431,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0,1.0,0.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.580392156863,1.0,1.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.580392156863,0.878431372549,0.878431372549,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.450980392157,0.760784313725,0.788235294118,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.329411764706,0.709803921569,0.709803921569,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.23137254902,0.619607843137,0.619607843137,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.141176470588,0.560784313725,0.560784313725,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0392156862745,0.490196078431,0.549019607843,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0,0.411764705882,0.521568627451,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.752941176471,0.752941176471,0.752941176471,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 1.0,0.850980392157,0.560784313725,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.650980392157,0.458823529412,0.450980392157,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.4,0.501960784314,0.501960784314,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.619607843137,0.388235294118,0.709803921569,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.83137254902,0.478431372549,0.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.580392156863,0.0,0.580392156863,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.258823529412,0.619607843137,0.690196078431,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+Radius used : 1.310000
+Radius, covalent : 1.310000
+Radius, atomic : 1.240000
+
+
+Atom
+====
+Number : 55
+Name : Caesium
+Short name : Cs
+Color : 0.341176470588,0.0901960784314,0.560784313725,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0,0.788235294118,0.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.439215686275,0.83137254902,1.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 1.0,1.0,0.780392156863,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.850980392157,1.0,0.780392156863,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.780392156863,1.0,0.780392156863,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.639215686275,1.0,0.780392156863,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.560784313725,1.0,0.780392156863,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.380392156863,1.0,0.780392156863,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.270588235294,1.0,0.780392156863,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.188235294118,1.0,0.780392156863,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.121568627451,1.0,0.780392156863,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0,1.0,0.611764705882,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0,0.901960784314,0.458823529412,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0,0.83137254902,0.321568627451,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0,0.749019607843,0.219607843137,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0,0.670588235294,0.141176470588,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.301960784314,0.760784313725,1.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.301960784314,0.650980392157,1.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.129411764706,0.580392156863,0.839215686275,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.149019607843,0.490196078431,0.670588235294,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.149019607843,0.4,0.588235294118,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0901960784314,0.329411764706,0.529411764706,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.81568627451,0.81568627451,0.878431372549,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 1.0,0.819607843137,0.137254901961,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.721568627451,0.721568627451,0.81568627451,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.650980392157,0.329411764706,0.301960784314,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.341176470588,0.349019607843,0.380392156863,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.619607843137,0.309803921569,0.709803921569,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.670588235294,0.360784313725,0.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.458823529412,0.309803921569,0.270588235294,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.258823529412,0.509803921569,0.588235294118,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.340000
+
+
+Atom
+====
+Number : 87
+Name : Francium
+Short name : Fr
+Color : 0.258823529412,0.0,0.4,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0,0.490196078431,0.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.439215686275,0.670588235294,0.980392156863,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0,0.729411764706,1.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0,0.63137254902,1.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0,0.560784313725,1.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0,0.501960784314,1.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.0,0.419607843137,1.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.329411764706,0.360784313725,0.949019607843,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+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 : 0.470588235294,0.360784313725,0.890196078431,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 97
+Name : Berkelium
+Short name : Bk
+Color : 0.541176470588,0.309803921569,0.890196078431,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 98
+Name : Californium
+Short name : Cf
+Color : 0.63137254902,0.211764705882,0.83137254902,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 99
+Name : Einsteinium
+Short name : Es
+Color : 0.701960784314,0.121568627451,0.83137254902,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 100
+Name : Fermium
+Short name : Fm
+Color : 0.701960784314,0.121568627451,0.729411764706,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 101
+Name : Mendelevium
+Short name : Md
+Color : 0.701960784314,0.0509803921569,0.650980392157,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 102
+Name : Nobelium
+Short name : No
+Color : 0.741176470588,0.0509803921569,0.529411764706,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 103
+Name : Lawrencium
+Short name : Lr
+Color : 0.780392156863,0.0,0.4,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+Radius used : 1.000000
+Radius, covalent : 1.000000
+Radius, atomic : 1.000000
+
+
+Atom
+====
+Number : 104
+Name : Vacancy
+Short name : Vac
+Color : 0.5,0.5,0.5,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+Radius used : 1.0
+Radius, covalent : 1.0
+Radius, atomic : 1.0
+
+
+Atom
+====
+Number : 105
+Name : Default
+Short name : Default
+Color : 1.0,1.0,1.0,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+Radius used : 1.0
+Radius, covalent : 1.0
+Radius, atomic : 1.0
+
+
+Atom
+====
+Number : 106
+Name : Stick
+Short name : Stick
+Color : 0.5,0.5,0.5,1.0
+Diffuse itensity : 0.8
+Specular itensity: 0.5
+Specular hard : 50
+Traceable : 1
+Shadow receive : 1
+Shadow cast : 1
+Radius used : 1.0
+Radius, covalent : 1.0
+Radius, atomic : 1.0
diff --git a/io_mesh_atomic/pdb_export.py b/io_mesh_atomic/pdb_export.py
new file mode 100644
index 00000000..949ee5e2
--- /dev/null
+++ b/io_mesh_atomic/pdb_export.py
@@ -0,0 +1,81 @@
+# ##### 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 #####
+
+import bpy
+from io_mesh_atomic.pdb_import import ELEMENTS_DEFAULT
+
+class AtomPropExport(object):
+ __slots__ = ('element', 'location')
+ def __init__(self, element, location):
+ self.element = element
+ self.location = location
+
+
+def export_pdb(obj_type, filepath_pdb):
+
+ list_atoms = []
+ for obj in bpy.context.selected_objects:
+
+ if "STICK" in obj.name.upper():
+ continue
+
+ if obj.type not in {'MESH', 'SURFACE', 'META'}:
+ continue
+
+ name = ""
+ for element in ELEMENTS_DEFAULT:
+ if element[1] in obj.name:
+ if element[2] == "Vac":
+ name = "X"
+ else:
+ name = element[2]
+
+ if name == "":
+ if obj_type == "0":
+ name = "?"
+ else:
+ continue
+
+ if len(obj.children) != 0:
+ for vertex in obj.data.vertices:
+ location = obj.matrix_world @ vertex.co
+ list_atoms.append(AtomPropExport(name, location))
+ else:
+ if not obj.parent:
+ location = obj.location
+ list_atoms.append(AtomPropExport(name, location))
+
+ pdb_file_p = open(filepath_pdb, "w")
+ pdb_file_p.write("REMARK This pdb file has been created with Blender "
+ "and the addon Atomic Blender - PDB\n"
+ "REMARK For more details see the wiki pages of Blender.\n"
+ "REMARK\n"
+ "REMARK\n")
+
+ for i, atom in enumerate(list_atoms):
+ string = "ATOM %6d%3s%24.3f%8.3f%8.3f%6.2f%6.2f%12s\n" % (
+ i, atom.element,
+ atom.location[0],
+ atom.location[1],
+ atom.location[2],
+ 1.00, 1.00, atom.element)
+ pdb_file_p.write(string)
+
+ pdb_file_p.close()
+
+ return True
diff --git a/io_mesh_atomic/pdb_gui.py b/io_mesh_atomic/pdb_gui.py
new file mode 100644
index 00000000..76736eaa
--- /dev/null
+++ b/io_mesh_atomic/pdb_gui.py
@@ -0,0 +1,270 @@
+# ##### 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 #####
+
+import bpy
+from bpy.types import Operator, AddonPreferences
+from bpy_extras.io_utils import ImportHelper, ExportHelper
+from bpy.props import (
+ StringProperty,
+ BoolProperty,
+ EnumProperty,
+ IntProperty,
+ FloatProperty,
+ )
+
+from io_mesh_atomic.pdb_import import import_pdb
+from io_mesh_atomic.pdb_export import export_pdb
+
+# -----------------------------------------------------------------------------
+# Operators
+
+# This is the class for the file dialog of the importer.
+class IMPORT_OT_pdb(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_center: BoolProperty(
+ name = "Object to origin", default=True,
+ description = "Put the object into the global origin")
+ use_camera: BoolProperty(
+ name="Camera", default=False,
+ description="Do you need a camera?")
+ use_light: BoolProperty(
+ name="Lamp", default=False,
+ description = "Do you need a lamp?")
+ ball: EnumProperty(
+ name="Type of ball",
+ description="Choose ball",
+ items=(('0', "NURBS", "NURBS balls"),
+ ('1', "Mesh" , "Mesh balls"),
+ ('2', "Meta" , "Metaballs")),
+ default='0',)
+ 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")
+ atomradius: EnumProperty(
+ name="Type",
+ 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',)
+ use_sticks: BoolProperty(
+ name="Use sticks", default=True,
+ description="Do you want to display the sticks?")
+ use_sticks_type: EnumProperty(
+ name="Type",
+ description="Choose type of stick",
+ items=(('0', "Dupliverts", "Use dupliverts structures"),
+ ('1', "Skin", "Use skin and subdivision modifier"),
+ ('2', "Normal", "Use simple cylinders")),
+ default='0',)
+ sticks_subdiv_view: IntProperty(
+ name = "SubDivV", default=2, min=1,
+ description="Number of subdivisions (view)")
+ sticks_subdiv_render: IntProperty(
+ name = "SubDivR", default=2, min=1,
+ description="Number of subdivisions (render)")
+ sticks_sectors: IntProperty(
+ name = "Sector", default=20, min=1,
+ description="Number of sectors of a stick")
+ sticks_radius: FloatProperty(
+ name = "Radius", default=0.2, min=0.0001,
+ description ="Radius of a stick")
+ sticks_unit_length: FloatProperty(
+ name = "Unit", default=0.05, 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=True,
+ description="The sticks are round (sectors are not visible)")
+ use_sticks_bonds: BoolProperty(
+ name="Bonds", default=False,
+ description="Show double and triple bonds")
+ sticks_dist: FloatProperty(
+ name="", default = 1.1, min=1.0, max=3.0,
+ description="Distance between sticks measured in stick diameter")
+ use_sticks_one_object: BoolProperty(
+ name="One object", default=True,
+ description="All sticks are one object")
+ use_sticks_one_object_nr: IntProperty(
+ name = "No.", default=200, min=10,
+ description="Number of sticks to be grouped at once")
+ datafile: StringProperty(
+ name = "", description="Path to your custom data file",
+ maxlen = 256, default = "", subtype='FILE_PATH')
+
+ # This thing here just guarantees that the menu entry is not active when the
+ # check box in the addon preferences is not activated! See __init__.py
+ @classmethod
+ def poll(cls, context):
+ pref = context.preferences
+ return pref.addons[__package__].preferences.bool_pdb
+
+ def draw(self, context):
+ layout = self.layout
+ row = layout.row()
+ row.prop(self, "use_camera")
+ row.prop(self, "use_light")
+ row = layout.row()
+ row.prop(self, "use_center")
+ # Balls
+ box = layout.box()
+ row = box.row()
+ row.label(text="Balls / atoms")
+ row = box.row()
+ col = row.column()
+ col.prop(self, "ball")
+ row = box.row()
+ row.active = (self.ball == "1")
+ col = row.column(align=True)
+ col.prop(self, "mesh_azimuth")
+ col.prop(self, "mesh_zenith")
+ row = box.row()
+ col = row.column()
+ col.label(text="Scaling factors")
+ col = row.column(align=True)
+ col.prop(self, "scale_ballradius")
+ col.prop(self, "scale_distances")
+ row = box.row()
+ row.prop(self, "atomradius")
+ # Sticks
+ box = layout.box()
+ row = box.row()
+ row.label(text="Sticks / bonds")
+ row = box.row()
+ row.prop(self, "use_sticks")
+ row = box.row()
+ row.active = self.use_sticks
+ row.prop(self, "use_sticks_type")
+ row = box.row()
+ row.active = self.use_sticks
+ col = row.column()
+ if self.use_sticks_type == '0' or self.use_sticks_type == '2':
+ col.prop(self, "sticks_sectors")
+ col.prop(self, "sticks_radius")
+ if self.use_sticks_type == '1':
+ row = box.row()
+ row.active = self.use_sticks
+ row.prop(self, "sticks_subdiv_view")
+ row.prop(self, "sticks_subdiv_render")
+ row = box.row()
+ row.active = self.use_sticks
+ if self.use_sticks_type == '0':
+ col.prop(self, "sticks_unit_length")
+ col = row.column(align=True)
+ if self.use_sticks_type == '0':
+ col.prop(self, "use_sticks_color")
+ col.prop(self, "use_sticks_smooth")
+ if self.use_sticks_type == '0' or self.use_sticks_type == '2':
+ col.prop(self, "use_sticks_bonds")
+ row = box.row()
+ if self.use_sticks_type == '0':
+ row.active = self.use_sticks and self.use_sticks_bonds
+ row.label(text="Distance")
+ row.prop(self, "sticks_dist")
+ if self.use_sticks_type == '2':
+ row.active = self.use_sticks
+ col = row.column()
+ col.prop(self, "use_sticks_one_object")
+ col = row.column()
+ col.active = self.use_sticks_one_object
+ col.prop(self, "use_sticks_one_object_nr")
+
+
+ def execute(self, context):
+ # This is in order to solve this strange 'relative path' thing.
+ filepath_pdb = bpy.path.abspath(self.filepath)
+
+ # Execute main routine
+ import_pdb(self.ball,
+ self.mesh_azimuth,
+ self.mesh_zenith,
+ self.scale_ballradius,
+ self.atomradius,
+ self.scale_distances,
+ self.use_sticks,
+ self.use_sticks_type,
+ self.sticks_subdiv_view,
+ self.sticks_subdiv_render,
+ self.use_sticks_color,
+ self.use_sticks_smooth,
+ self.use_sticks_bonds,
+ self.use_sticks_one_object,
+ self.use_sticks_one_object_nr,
+ self.sticks_unit_length,
+ self.sticks_dist,
+ self.sticks_sectors,
+ self.sticks_radius,
+ self.use_center,
+ self.use_camera,
+ self.use_light,
+ filepath_pdb)
+
+ return {'FINISHED'}
+
+
+# This is the class for the file dialog of the exporter.
+class EXPORT_OT_pdb(Operator, ExportHelper):
+ bl_idname = "export_mesh.pdb"
+ bl_label = "Export Protein Data Bank(*.pdb)"
+ filename_ext = ".pdb"
+
+ 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',)
+
+ # This thing here just guarantees that the menu entry is not active when the
+ # check box in the addon preferences is not activated! See __init__.py
+ @classmethod
+ def poll(cls, context):
+ pref = context.preferences
+ return pref.addons[__package__].preferences.bool_pdb
+
+ def draw(self, context):
+ layout = self.layout
+ row = layout.row()
+ row.prop(self, "atom_pdb_export_type")
+
+ def execute(self, context):
+ export_pdb(self.atom_pdb_export_type,
+ bpy.path.abspath(self.filepath))
+
+ return {'FINISHED'}
diff --git a/io_mesh_atomic/pdb_import.py b/io_mesh_atomic/pdb_import.py
new file mode 100644
index 00000000..06a808c0
--- /dev/null
+++ b/io_mesh_atomic/pdb_import.py
@@ -0,0 +1,1549 @@
+# ##### 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 #####
+
+import os
+import bpy
+import bmesh
+from math import pi, cos, sin, sqrt, ceil
+from mathutils import Vector, Matrix
+from copy import copy
+
+# -----------------------------------------------------------------------------
+# 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)
+
+ELEMENTS_DEFAULT = (
+( 1, "Hydrogen", "H", ( 1.0, 1.0, 1.0, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ),
+( 2, "Helium", "He", ( 0.85, 1.0, 1.0, 1.0), 0.93, 0.93, 0.49 ),
+( 3, "Lithium", "Li", ( 0.8, 0.50, 1.0, 1.0), 1.23, 1.23, 2.05 , 1 , 0.68 ),
+( 4, "Beryllium", "Be", ( 0.76, 1.0, 0.0, 1.0), 0.90, 0.90, 1.40 , 1 , 0.44 , 2 , 0.35 ),
+( 5, "Boron", "B", ( 1.0, 0.70, 0.70, 1.0), 0.82, 0.82, 1.17 , 1 , 0.35 , 3 , 0.23 ),
+( 6, "Carbon", "C", ( 0.56, 0.56, 0.56, 1.0), 0.77, 0.77, 0.91 , -4 , 2.60 , 4 , 0.16 ),
+( 7, "Nitrogen", "N", ( 0.18, 0.31, 0.97, 1.0), 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, 1.0), 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, 1.0), 0.72, 0.72, 0.57 , -1 , 1.33 , 7 , 0.08 ),
+(10, "Neon", "Ne", ( 0.70, 0.89, 0.96, 1.0), 0.71, 0.71, 0.51 , 1 , 1.12 ),
+(11, "Sodium", "Na", ( 0.67, 0.36, 0.94, 1.0), 1.54, 1.54, 2.23 , 1 , 0.97 ),
+(12, "Magnesium", "Mg", ( 0.54, 1.0, 0.0, 1.0), 1.36, 1.36, 1.72 , 1 , 0.82 , 2 , 0.66 ),
+(13, "Aluminium", "Al", ( 0.74, 0.65, 0.65, 1.0), 1.18, 1.18, 1.82 , 3 , 0.51 ),
+(14, "Silicon", "Si", ( 0.94, 0.78, 0.62, 1.0), 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, 1.0), 1.06, 1.06, 1.23 , -3 , 2.12 , 3 , 0.44 , 5 , 0.35 ),
+(16, "Sulfur", "S", ( 1.0, 1.0, 0.18, 1.0), 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, 1.0), 0.99, 0.99, 0.97 , -1 , 1.81 , 5 , 0.34 , 7 , 0.27 ),
+(18, "Argon", "Ar", ( 0.50, 0.81, 0.89, 1.0), 0.98, 0.98, 0.88 , 1 , 1.54 ),
+(19, "Potassium", "K", ( 0.56, 0.25, 0.83, 1.0), 2.03, 2.03, 2.77 , 1 , 0.81 ),
+(20, "Calcium", "Ca", ( 0.23, 1.0, 0.0, 1.0), 1.74, 1.74, 2.23 , 1 , 1.18 , 2 , 0.99 ),
+(21, "Scandium", "Sc", ( 0.90, 0.90, 0.90, 1.0), 1.44, 1.44, 2.09 , 3 , 0.73 ),
+(22, "Titanium", "Ti", ( 0.74, 0.76, 0.78, 1.0), 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, 1.0), 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, 1.0), 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, 1.0), 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, 1.0), 1.17, 1.17, 1.72 , 2 , 0.74 , 3 , 0.64 ),
+(27, "Cobalt", "Co", ( 0.94, 0.56, 0.62, 1.0), 1.16, 1.16, 1.67 , 2 , 0.72 , 3 , 0.63 ),
+(28, "Nickel", "Ni", ( 0.31, 0.81, 0.31, 1.0), 1.15, 1.15, 1.62 , 2 , 0.69 ),
+(29, "Copper", "Cu", ( 0.78, 0.50, 0.2, 1.0), 1.17, 1.17, 1.57 , 1 , 0.96 , 2 , 0.72 ),
+(30, "Zinc", "Zn", ( 0.49, 0.50, 0.69, 1.0), 1.25, 1.25, 1.53 , 1 , 0.88 , 2 , 0.74 ),
+(31, "Gallium", "Ga", ( 0.76, 0.56, 0.56, 1.0), 1.26, 1.26, 1.81 , 1 , 0.81 , 3 , 0.62 ),
+(32, "Germanium", "Ge", ( 0.4, 0.56, 0.56, 1.0), 1.22, 1.22, 1.52 , -4 , 2.72 , 2 , 0.73 , 4 , 0.53 ),
+(33, "Arsenic", "As", ( 0.74, 0.50, 0.89, 1.0), 1.20, 1.20, 1.33 , -3 , 2.22 , 3 , 0.58 , 5 , 0.46 ),
+(34, "Selenium", "Se", ( 1.0, 0.63, 0.0, 1.0), 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, 1.0), 1.14, 1.14, 1.12 , -1 , 1.96 , 5 , 0.47 , 7 , 0.39 ),
+(36, "Krypton", "Kr", ( 0.36, 0.72, 0.81, 1.0), 1.31, 1.31, 1.24 ),
+(37, "Rubidium", "Rb", ( 0.43, 0.18, 0.69, 1.0), 2.16, 2.16, 2.98 , 1 , 1.47 ),
+(38, "Strontium", "Sr", ( 0.0, 1.0, 0.0, 1.0), 1.91, 1.91, 2.45 , 2 , 1.12 ),
+(39, "Yttrium", "Y", ( 0.58, 1.0, 1.0, 1.0), 1.62, 1.62, 2.27 , 3 , 0.89 ),
+(40, "Zirconium", "Zr", ( 0.58, 0.87, 0.87, 1.0), 1.45, 1.45, 2.16 , 1 , 1.09 , 4 , 0.79 ),
+(41, "Niobium", "Nb", ( 0.45, 0.76, 0.78, 1.0), 1.34, 1.34, 2.08 , 1 , 1.00 , 4 , 0.74 , 5 , 0.69 ),
+(42, "Molybdenum", "Mo", ( 0.32, 0.70, 0.70, 1.0), 1.30, 1.30, 2.01 , 1 , 0.93 , 4 , 0.70 , 6 , 0.62 ),
+(43, "Technetium", "Tc", ( 0.23, 0.61, 0.61, 1.0), 1.27, 1.27, 1.95 , 7 , 0.97 ),
+(44, "Ruthenium", "Ru", ( 0.14, 0.56, 0.56, 1.0), 1.25, 1.25, 1.89 , 4 , 0.67 ),
+(45, "Rhodium", "Rh", ( 0.03, 0.49, 0.54, 1.0), 1.25, 1.25, 1.83 , 3 , 0.68 ),
+(46, "Palladium", "Pd", ( 0.0, 0.41, 0.52, 1.0), 1.28, 1.28, 1.79 , 2 , 0.80 , 4 , 0.65 ),
+(47, "Silver", "Ag", ( 0.75, 0.75, 0.75, 1.0), 1.34, 1.34, 1.75 , 1 , 1.26 , 2 , 0.89 ),
+(48, "Cadmium", "Cd", ( 1.0, 0.85, 0.56, 1.0), 1.48, 1.48, 1.71 , 1 , 1.14 , 2 , 0.97 ),
+(49, "Indium", "In", ( 0.65, 0.45, 0.45, 1.0), 1.44, 1.44, 2.00 , 3 , 0.81 ),
+(50, "Tin", "Sn", ( 0.4, 0.50, 0.50, 1.0), 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, 1.0), 1.40, 1.40, 1.53 , -3 , 2.45 , 3 , 0.76 , 5 , 0.62 ),
+(52, "Tellurium", "Te", ( 0.83, 0.47, 0.0, 1.0), 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, 1.0), 1.33, 1.33, 1.32 , -1 , 2.20 , 5 , 0.62 , 7 , 0.50 ),
+(54, "Xenon", "Xe", ( 0.25, 0.61, 0.69, 1.0), 1.31, 1.31, 1.24 ),
+(55, "Caesium", "Cs", ( 0.34, 0.09, 0.56, 1.0), 2.35, 2.35, 3.35 , 1 , 1.67 ),
+(56, "Barium", "Ba", ( 0.0, 0.78, 0.0, 1.0), 1.98, 1.98, 2.78 , 1 , 1.53 , 2 , 1.34 ),
+(57, "Lanthanum", "La", ( 0.43, 0.83, 1.0, 1.0), 1.69, 1.69, 2.74 , 1 , 1.39 , 3 , 1.06 ),
+(58, "Cerium", "Ce", ( 1.0, 1.0, 0.78, 1.0), 1.65, 1.65, 2.70 , 1 , 1.27 , 3 , 1.03 , 4 , 0.92 ),
+(59, "Praseodymium", "Pr", ( 0.85, 1.0, 0.78, 1.0), 1.65, 1.65, 2.67 , 3 , 1.01 , 4 , 0.90 ),
+(60, "Neodymium", "Nd", ( 0.78, 1.0, 0.78, 1.0), 1.64, 1.64, 2.64 , 3 , 0.99 ),
+(61, "Promethium", "Pm", ( 0.63, 1.0, 0.78, 1.0), 1.63, 1.63, 2.62 , 3 , 0.97 ),
+(62, "Samarium", "Sm", ( 0.56, 1.0, 0.78, 1.0), 1.62, 1.62, 2.59 , 3 , 0.96 ),
+(63, "Europium", "Eu", ( 0.38, 1.0, 0.78, 1.0), 1.85, 1.85, 2.56 , 2 , 1.09 , 3 , 0.95 ),
+(64, "Gadolinium", "Gd", ( 0.27, 1.0, 0.78, 1.0), 1.61, 1.61, 2.54 , 3 , 0.93 ),
+(65, "Terbium", "Tb", ( 0.18, 1.0, 0.78, 1.0), 1.59, 1.59, 2.51 , 3 , 0.92 , 4 , 0.84 ),
+(66, "Dysprosium", "Dy", ( 0.12, 1.0, 0.78, 1.0), 1.59, 1.59, 2.49 , 3 , 0.90 ),
+(67, "Holmium", "Ho", ( 0.0, 1.0, 0.61, 1.0), 1.58, 1.58, 2.47 , 3 , 0.89 ),
+(68, "Erbium", "Er", ( 0.0, 0.90, 0.45, 1.0), 1.57, 1.57, 2.45 , 3 , 0.88 ),
+(69, "Thulium", "Tm", ( 0.0, 0.83, 0.32, 1.0), 1.56, 1.56, 2.42 , 3 , 0.87 ),
+(70, "Ytterbium", "Yb", ( 0.0, 0.74, 0.21, 1.0), 1.74, 1.74, 2.40 , 2 , 0.93 , 3 , 0.85 ),
+(71, "Lutetium", "Lu", ( 0.0, 0.67, 0.14, 1.0), 1.56, 1.56, 2.25 , 3 , 0.85 ),
+(72, "Hafnium", "Hf", ( 0.30, 0.76, 1.0, 1.0), 1.44, 1.44, 2.16 , 4 , 0.78 ),
+(73, "Tantalum", "Ta", ( 0.30, 0.65, 1.0, 1.0), 1.34, 1.34, 2.09 , 5 , 0.68 ),
+(74, "Tungsten", "W", ( 0.12, 0.58, 0.83, 1.0), 1.30, 1.30, 2.02 , 4 , 0.70 , 6 , 0.62 ),
+(75, "Rhenium", "Re", ( 0.14, 0.49, 0.67, 1.0), 1.28, 1.28, 1.97 , 4 , 0.72 , 7 , 0.56 ),
+(76, "Osmium", "Os", ( 0.14, 0.4, 0.58, 1.0), 1.26, 1.26, 1.92 , 4 , 0.88 , 6 , 0.69 ),
+(77, "Iridium", "Ir", ( 0.09, 0.32, 0.52, 1.0), 1.27, 1.27, 1.87 , 4 , 0.68 ),
+(78, "Platinum", "Pt", ( 0.81, 0.81, 0.87, 1.0), 1.30, 1.30, 1.83 , 2 , 0.80 , 4 , 0.65 ),
+(79, "Gold", "Au", ( 1.0, 0.81, 0.13, 1.0), 1.34, 1.34, 1.79 , 1 , 1.37 , 3 , 0.85 ),
+(80, "Mercury", "Hg", ( 0.72, 0.72, 0.81, 1.0), 1.49, 1.49, 1.76 , 1 , 1.27 , 2 , 1.10 ),
+(81, "Thallium", "Tl", ( 0.65, 0.32, 0.30, 1.0), 1.48, 1.48, 2.08 , 1 , 1.47 , 3 , 0.95 ),
+(82, "Lead", "Pb", ( 0.34, 0.34, 0.38, 1.0), 1.47, 1.47, 1.81 , 2 , 1.20 , 4 , 0.84 ),
+(83, "Bismuth", "Bi", ( 0.61, 0.30, 0.70, 1.0), 1.46, 1.46, 1.63 , 1 , 0.98 , 3 , 0.96 , 5 , 0.74 ),
+(84, "Polonium", "Po", ( 0.67, 0.36, 0.0, 1.0), 1.46, 1.46, 1.53 , 6 , 0.67 ),
+(85, "Astatine", "At", ( 0.45, 0.30, 0.27, 1.0), 1.45, 1.45, 1.43 , -3 , 2.22 , 3 , 0.85 , 5 , 0.46 ),
+(86, "Radon", "Rn", ( 0.25, 0.50, 0.58, 1.0), 1.00, 1.00, 1.34 ),
+(87, "Francium", "Fr", ( 0.25, 0.0, 0.4, 1.0), 1.00, 1.00, 1.00 , 1 , 1.80 ),
+(88, "Radium", "Ra", ( 0.0, 0.49, 0.0, 1.0), 1.00, 1.00, 1.00 , 2 , 1.43 ),
+(89, "Actinium", "Ac", ( 0.43, 0.67, 0.98, 1.0), 1.00, 1.00, 1.00 , 3 , 1.18 ),
+(90, "Thorium", "Th", ( 0.0, 0.72, 1.0, 1.0), 1.65, 1.65, 1.00 , 4 , 1.02 ),
+(91, "Protactinium", "Pa", ( 0.0, 0.63, 1.0, 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, 1.0), 1.42, 1.42, 1.00 , 4 , 0.97 , 6 , 0.80 ),
+(93, "Neptunium", "Np", ( 0.0, 0.50, 1.0, 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, 1.0), 1.00, 1.00, 1.00 , 3 , 1.08 , 4 , 0.93 ),
+(95, "Americium", "Am", ( 0.32, 0.36, 0.94, 1.0), 1.00, 1.00, 1.00 , 3 , 1.07 , 4 , 0.92 ),
+(96, "Curium", "Cm", ( 0.47, 0.36, 0.89, 1.0), 1.00, 1.00, 1.00 ),
+(97, "Berkelium", "Bk", ( 0.54, 0.30, 0.89, 1.0), 1.00, 1.00, 1.00 ),
+(98, "Californium", "Cf", ( 0.63, 0.21, 0.83, 1.0), 1.00, 1.00, 1.00 ),
+(99, "Einsteinium", "Es", ( 0.70, 0.12, 0.83, 1.0), 1.00, 1.00, 1.00 ),
+(100, "Fermium", "Fm", ( 0.70, 0.12, 0.72, 1.0), 1.00, 1.00, 1.00 ),
+(101, "Mendelevium", "Md", ( 0.70, 0.05, 0.65, 1.0), 1.00, 1.00, 1.00 ),
+(102, "Nobelium", "No", ( 0.74, 0.05, 0.52, 1.0), 1.00, 1.00, 1.00 ),
+(103, "Lawrencium", "Lr", ( 0.78, 0.0, 0.4, 1.0), 1.00, 1.00, 1.00 ),
+(104, "Vacancy", "Vac", ( 0.5, 0.5, 0.5, 1.0), 1.00, 1.00, 1.00),
+(105, "Default", "Default", ( 1.0, 1.0, 1.0, 1.0), 1.00, 1.00, 1.00),
+(106, "Stick", "Stick", ( 0.5, 0.5, 0.5, 1.0), 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 (ElementProp). 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.
+ELEMENTS = []
+
+# This is the class, which stores the properties for one element.
+class ElementProp(object):
+ __slots__ = ('number', 'name', 'short_name', 'color', 'radii', 'radii_ionic')
+ 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 AtomProp(object):
+ __slots__ = ('element', 'name', 'location', 'radius', 'color', 'material')
+ 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 StickProp(object):
+ __slots__ = ('atom1', 'atom2', 'number', 'dist')
+ def __init__(self, atom1, atom2, number, dist):
+ self.atom1 = atom1
+ self.atom2 = atom2
+ self.number = number
+ self.dist = dist
+
+# -----------------------------------------------------------------------------
+# Some basic routines
+
+
+# The function, which reads all necessary properties of the elements.
+def read_elements():
+
+ del ELEMENTS[:]
+
+ for item in 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 = ElementProp(item[0],item[1],item[2],item[3],
+ radii,radii_ionic)
+ ELEMENTS.append(li)
+
+
+# The function, which reads the x,y,z positions of all atoms in a PDB
+# file.
+#
+# filepath_pdb: path to pdb file
+# radiustype : '0' default
+# '1' atomic radii
+# '2' van der Waals
+def read_pdb_file(filepath_pdb, radiustype):
+
+ # The list of all atoms as read from the PDB file.
+ all_atoms = []
+
+ # Open the pdb file ...
+ filepath_pdb_p = open(filepath_pdb, "r")
+
+ #Go to the line, in which "ATOM" or "HETATM" appears.
+ for line in filepath_pdb_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
+ # 2019-03-14, New
+ color = [0,0,0, 0]
+ location = Vector((0,0,0))
+ # Append the TER into the list. Material remains empty so far.
+ all_atoms.append(AtomProp(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
+ if line[12:13] == " " or line[12:13].isdigit() == True:
+ short_name = line[13:14]
+ if line[14:15].islower() == True:
+ short_name = short_name + line[14:15]
+ elif line[12:13].isupper() == True:
+ short_name = line[12:13]
+ if line[13:14].isalpha() == True:
+ short_name = short_name + line[13:14]
+ else:
+ print("Atomic Blender: Strange error in PDB file.\n"
+ "Look for element names at positions 13-16 and 78-79.\n")
+ return -1
+
+ if len(line) >= 78:
+
+ if line[76:77] == " ":
+ short_name2 = line[76:77]
+ else:
+ short_name2 = line[76:78]
+
+ if short_name2.isalpha() == True:
+ FOUND = False
+ for element in ELEMENTS:
+ if str.upper(short_name2) == str.upper(element.short_name):
+ FOUND = True
+ break
+ if FOUND == False:
+ short_name = short_name2
+
+ # ....................................................... to here.
+
+ # Go through all elements and find the element of the current atom.
+ FLAG_FOUND = False
+ for element in 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(ELEMENTS[-3].radii[int(radiustype)])
+ color = 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(ELEMENTS[-2].radii[int(radiustype)])
+ color = 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(AtomProp(short_name,
+ name,
+ location,
+ radius,
+ color,[]))
+
+ line = filepath_pdb_p.readline()
+ line = line[:-1]
+
+ filepath_pdb_p.close()
+ # From above it can be clearly seen that j is now the number of all atoms.
+ Number_of_total_atoms = j
+
+ return (Number_of_total_atoms, all_atoms)
+
+
+# The function, which reads the sticks in a PDB file.
+def read_pdb_file_sticks(filepath_pdb, use_sticks_bonds, all_atoms):
+
+ # The list of all sticks.
+ all_sticks = []
+
+ # Open the PDB file.
+ filepath_pdb_p = open(filepath_pdb, "r")
+
+ line = filepath_pdb_p.readline()
+ split_list = line.split(' ')
+
+ # Go to the first entry
+ if "CONECT" not in split_list[0]:
+ for line in filepath_pdb_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
+
+ # Note 2019-03-16: in a PDB file the identifier for sticks is called
+ # 'CONECT' and NOT 'CONNECT'! Please leave this as is, otherwise the
+ # sticks are NOT correctly loaded.
+
+ # 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 lots of 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 atom2 in atom_list[1:]:
+
+ if use_sticks_bonds == True:
+ number = atom_list[1:].count(atom2)
+
+ if number == 2 or number == 3:
+ basis_list = list(set(atom_list[1:]))
+
+ if len(basis_list) > 1:
+ basis1 = (all_atoms[atom1-1].location
+ - all_atoms[basis_list[0]-1].location)
+ basis2 = (all_atoms[atom1-1].location
+ - all_atoms[basis_list[1]-1].location)
+ plane_n = basis1.cross(basis2)
+
+ dist_n = (all_atoms[atom1-1].location
+ - all_atoms[atom2-1].location)
+ dist_n = dist_n.cross(plane_n)
+ dist_n = dist_n / dist_n.length
+ else:
+ dist_n = (all_atoms[atom1-1].location
+ - all_atoms[atom2-1].location)
+ dist_n = Vector((dist_n[1],-dist_n[0],0))
+ dist_n = dist_n / dist_n.length
+
+ elif number > 3:
+ number = 1
+ dist_n = None
+ else:
+ dist_n = None
+ else:
+ number = 1
+ dist_n = None
+
+ # 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(StickProp(atom1,atom2,number,dist_n))
+ Number_of_sticks += 1
+ j += 1
+
+ line = filepath_pdb_p.readline()
+ line = line.rstrip()
+
+ filepath_pdb_p.close()
+
+ return all_sticks
+
+
+# Function, which produces a cylinder. All is somewhat easy to understand.
+def build_stick(radius, length, sectors, element_name):
+
+ dphi = 2.0 * pi/(float(sectors)-1)
+
+ # Vertices
+ vertices_top = [Vector((0,0,length / 2.0))]
+ vertices_bottom = [Vector((0,0,-length / 2.0))]
+ vertices = []
+ 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
+
+ # Side facets (Cylinder)
+ faces1 = []
+ for i in range(sectors-1):
+ if i == sectors-2:
+ faces1.append( [i+1, 1, 1+sectors, i+1+sectors] )
+ else:
+ faces1.append( [i+1, i+2, i+2+sectors, i+1+sectors] )
+
+ # Top facets
+ faces2 = []
+ 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)
+ faces2.append(face_top)
+ faces2.append(face_bottom)
+
+ # Build the mesh, Cylinder
+ cylinder = bpy.data.meshes.new(element_name+"_sticks_cylinder")
+ cylinder.from_pydata(vertices, [], faces1)
+ cylinder.update()
+ new_cylinder = bpy.data.objects.new(element_name+"_sticks_cylinder", cylinder)
+ # Attention: the linking will be done a few moments later, after this
+ # is done definition.
+
+ # Build the mesh, Cups
+ cups = bpy.data.meshes.new(element_name+"_sticks_cup")
+ cups.from_pydata(vertices, [], faces2)
+ cups.update()
+ new_cups = bpy.data.objects.new(element_name+"_sticks_cup", cups)
+ # Attention: the linking will be done a few moments later, after this
+ # is done definition.
+
+ return (new_cylinder, new_cups)
+
+
+# Rotate an object.
+def rotate_object(rot_mat, obj):
+
+ bpy.ops.object.select_all(action='DESELECT')
+ obj.select_set(True)
+
+ # Decompose world_matrix's components, and from them assemble 4x4 matrices.
+ orig_loc, orig_rot, orig_scale = obj.matrix_world.decompose()
+
+ orig_loc_mat = Matrix.Translation(orig_loc)
+ orig_rot_mat = orig_rot.to_matrix().to_4x4()
+ orig_scale_mat = (Matrix.Scale(orig_scale[0],4,(1,0,0)) @
+ Matrix.Scale(orig_scale[1],4,(0,1,0)) @
+ Matrix.Scale(orig_scale[2],4,(0,0,1)))
+
+ # Assemble the new matrix.
+ obj.matrix_world = orig_loc_mat @ rot_mat @ orig_rot_mat @ orig_scale_mat
+
+
+# Function, which puts a camera and light source into the 3D scene
+def camera_light_source(use_camera,
+ use_light,
+ object_center_vec,
+ object_size):
+
+ 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 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((sqrt(object_size) * camera_factor,
+ 0.0,
+ sqrt(object_size) * camera_factor))
+ camera_xyz_vec = object_center_vec + object_camera_vec
+
+ # Create the camera
+ camera_data = bpy.data.cameras.new("A_camera")
+ camera_data.lens = 45
+ camera_data.clip_end = 500.0
+ camera = bpy.data.objects.new("A_camera", camera_data)
+ camera.location = camera_xyz_vec
+ bpy.context.collection.objects.link(camera)
+
+ # 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.
+ camera.rotation_euler = Matrix.Rotation(angle, 4, axis_vec).to_euler()
+
+ # Rotate the camera around its axis by 90° such that we have a nice
+ # camera position and view onto the object.
+ bpy.ops.object.select_all(action='DESELECT')
+ camera.select_set(True)
+
+ # Rotate the camera around its axis 'object_camera_vec' by 90° such
+ # that we have a nice camera view onto the object.
+ matrix_rotation = Matrix.Rotation(90/360*2*pi, 4, object_camera_vec)
+ rotate_object(matrix_rotation, camera)
+
+ # Here a lamp is put into the scene, if chosen.
+ if use_light == True:
+
+ # This is the distance from the object measured in terms of %
+ # of the camera distance. It is set onto 50% (1/2) distance.
+ light_dl = 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).
+ light_dy_right = light_dl * (3.0/4.0)
+
+ # Create x, y and z for the lamp.
+ object_light_vec = Vector((light_dl,light_dy_right,light_dl))
+ light_xyz_vec = object_center_vec + object_light_vec
+
+ # Create the lamp
+ light_data = bpy.data.lights.new(name="A_light", type="SUN")
+ light_data.distance = 500.0
+ light_data.energy = 3.0
+ lamp = bpy.data.objects.new("A_light", light_data)
+ lamp.location = light_xyz_vec
+ bpy.context.collection.objects.link(lamp)
+
+ # Some settings for the World: a bit ambient occlusion
+ bpy.context.scene.world.light_settings.use_ambient_occlusion = True
+ bpy.context.scene.world.light_settings.ao_factor = 0.1
+ # Some properties for cycles
+ lamp.data.use_nodes = True
+ lmp_P_BSDF = lamp.data.node_tree.nodes['Emission']
+ lmp_P_BSDF.inputs['Strength'].default_value = 5
+
+
+# Function, which draws the atoms of one type (balls). This is one
+# dupliverts structure then.
+# Return: the dupliverts structure
+def draw_atoms_one_type(draw_all_atoms_type,
+ Ball_type,
+ Ball_azimuth,
+ Ball_zenith,
+ Ball_radius_factor,
+ object_center_vec,
+ collection_molecule):
+
+ # Create 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 subtracted. At the end
+ # the whole object is translated back to 'object_center_vec'.
+ atom_vertices.append(atom[2] - object_center_vec)
+
+ # IMPORTANT: First, we create a collection of the element, which contains
+ # the atoms (balls + mesh) AND the sticks! The definition dealing with the
+ # sticks will put the sticks inside this collection later on.
+ coll_element_name = atom[0] # the element name
+ # Create the new collection and ...
+ coll_element = bpy.data.collections.new(coll_element_name)
+ # ... link it to the collection, which contains all parts of the
+ # molecule.
+ collection_molecule.children.link(coll_element)
+
+ # Now, create a collection for the atoms, which includes the representative
+ # ball and the mesh.
+ coll_atom_name = atom[0] + "_atom"
+ # Create the new collection and ...
+ coll_atom = bpy.data.collections.new(coll_atom_name)
+ # ... link it to the collection, which contains all parts of the
+ # element (ball and mesh).
+ coll_element.children.link(coll_atom)
+
+ # 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] + "_mesh", atom_mesh)
+
+ # Link active object to the new collection
+ coll_atom.objects.link(new_atom_mesh)
+
+ # Now, build a representative sphere (atom).
+ 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))
+ else:
+ # NURBS balls
+ if Ball_type == "0":
+ 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))
+ # UV balls
+ elif Ball_type == "1":
+ 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))
+ # Meta balls
+ elif Ball_type == "2":
+ bpy.ops.object.metaball_add(type='BALL', view_align=False,
+ enter_editmode=False, location=(0, 0, 0),
+ rotation=(0, 0, 0))
+
+ ball = bpy.context.view_layer.objects.active
+ # Hide this ball because its appearance has no meaning. It is just the
+ # representative ball. The ball is visible at the vertices of the mesh.
+ # Rememmber, this is a dupliverts construct!
+ ball.hide_set(True)
+ # Scale up/down the ball radius.
+ ball.scale = (atom[3]*Ball_radius_factor,) * 3
+
+ if atom[0] == "Vacancy":
+ ball.name = atom[0] + "_cube"
+ else:
+ ball.name = atom[0] + "_ball"
+
+ ball.active_material = atom[1]
+ ball.parent = new_atom_mesh
+ new_atom_mesh.instance_type = 'VERTS'
+ # The object is back translated to 'object_center_vec'.
+ new_atom_mesh.location = object_center_vec
+
+ # Note the collection where the ball was placed into.
+ coll_all = ball.users_collection
+ if len(coll_all) > 0:
+ coll_past = coll_all[0]
+ else:
+ coll_past = bpy.context.scene.collection
+
+ # Put the atom into the new collection 'atom' and ...
+ coll_atom.objects.link(ball)
+ # ... unlink the atom from the other collection.
+ coll_past.objects.unlink(ball)
+
+ return new_atom_mesh, coll_element
+
+
+# Function, which draws the sticks with help of the dupliverts technique.
+# Return: list of dupliverts structures.
+def draw_sticks_dupliverts(all_atoms,
+ atom_all_types_list,
+ center,
+ all_sticks,
+ Stick_diameter,
+ Stick_sectors,
+ Stick_unit,
+ Stick_dist,
+ use_sticks_smooth,
+ use_sticks_color,
+ list_coll_elements):
+
+ dl = Stick_unit
+
+ if use_sticks_color == False:
+ stick_material = bpy.data.materials.new(ELEMENTS[-1].name)
+ stick_material.diffuse_color = ELEMENTS[-1].color
+
+ # Sort the sticks and put them into a new list such that ...
+ sticks_all_lists = []
+ if use_sticks_color == True:
+ for atom_type in atom_all_types_list:
+ if atom_type[0] == "TER":
+ continue
+ sticks_list = []
+ for stick in all_sticks:
+ for repeat in range(stick.number):
+
+ atom1 = copy(all_atoms[stick.atom1-1].location)-center
+ atom2 = copy(all_atoms[stick.atom2-1].location)-center
+
+ dist = Stick_diameter * Stick_dist
+
+ if stick.number == 2:
+ if repeat == 0:
+ atom1 += (stick.dist * dist)
+ atom2 += (stick.dist * dist)
+ if repeat == 1:
+ atom1 -= (stick.dist * dist)
+ atom2 -= (stick.dist * dist)
+
+ if stick.number == 3:
+ if repeat == 0:
+ atom1 += (stick.dist * dist)
+ atom2 += (stick.dist * dist)
+ if repeat == 2:
+ atom1 -= (stick.dist * dist)
+ atom2 -= (stick.dist * dist)
+
+ dv = atom1 - atom2
+ n = dv / dv.length
+ if atom_type[0] == all_atoms[stick.atom1-1].name:
+ location = atom1
+ name = "_" + all_atoms[stick.atom1-1].name
+ material = all_atoms[stick.atom1-1].material
+ sticks_list.append([name, location, dv, material])
+ if atom_type[0] == all_atoms[stick.atom2-1].name:
+ location = atom1 - n * dl * int(ceil(dv.length / (2.0 * dl)))
+ name = "_" + all_atoms[stick.atom2-1].name
+ material = all_atoms[stick.atom2-1].material
+ sticks_list.append([name, location, dv, material])
+
+ if sticks_list != []:
+ sticks_all_lists.append(sticks_list)
+ else:
+ sticks_list = []
+ for stick in all_sticks:
+
+ if stick.number > 3:
+ stick.number = 1
+
+ for repeat in range(stick.number):
+
+ atom1 = copy(all_atoms[stick.atom1-1].location)-center
+ atom2 = copy(all_atoms[stick.atom2-1].location)-center
+
+ dist = Stick_diameter * Stick_dist
+
+ if stick.number == 2:
+ if repeat == 0:
+ atom1 += (stick.dist * dist)
+ atom2 += (stick.dist * dist)
+ if repeat == 1:
+ atom1 -= (stick.dist * dist)
+ atom2 -= (stick.dist * dist)
+ if stick.number == 3:
+ if repeat == 0:
+ atom1 += (stick.dist * dist)
+ atom2 += (stick.dist * dist)
+ if repeat == 2:
+ atom1 -= (stick.dist * dist)
+ atom2 -= (stick.dist * dist)
+
+ dv = atom1 - atom2
+ n = dv / dv.length
+ location = atom1
+ material = stick_material
+ sticks_list.append(["", location, dv, material])
+
+ sticks_all_lists.append(sticks_list)
+
+ atom_object_list = []
+ # ... the sticks in the list can be drawn:
+ for stick_list in sticks_all_lists:
+ vertices = []
+ faces = []
+ i = 0
+
+ # What follows is school mathematics! :-)
+ for stick in stick_list:
+
+ dv = stick[2]
+ v1 = stick[1]
+ n = dv / dv.length
+ gamma = -n.dot(v1)
+ b = v1 + gamma * n
+ n_b = b / b.length
+
+ if use_sticks_color == True:
+ loops = int(ceil(dv.length / (2.0 * dl)))
+ else:
+ loops = int(ceil(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
+
+ # Create a collection for the sticks, which includes the representative
+ # cylinders, cups and the mesh.
+ coll_name = stick[0][1:] + "_sticks"
+ # Create the collection and ...
+ coll = bpy.data.collections.new(coll_name)
+ # ... link it to the collection, which contains all parts of the
+ # element. 'stick[0][1:]' contains the name of the element!
+ for coll_element_from_list in list_coll_elements:
+ if stick[0][1:] in coll_element_from_list.name:
+ break
+ coll_element_from_list.children.link(coll)
+
+ # Build the mesh.
+ mesh = bpy.data.meshes.new("Sticks_"+stick[0][1:])
+ mesh.from_pydata(vertices, [], faces)
+ mesh.update()
+ new_mesh = bpy.data.objects.new(stick[0][1:]+"_sticks_mesh", mesh)
+ # Link active object to the new collection
+ coll.objects.link(new_mesh)
+
+ # Build the object.
+ # Get the cylinder from the 'build_stick' function.
+ object_stick = build_stick(Stick_diameter,
+ dl,
+ Stick_sectors,
+ stick[0][1:])
+ # Link active object to the new collection
+ coll.objects.link(object_stick[0])
+ coll.objects.link(object_stick[1])
+
+ # Hide these objects because their appearance has no meaning. They are
+ # just the representative objects. The cylinder and cups are visible at
+ # the vertices of the mesh. Rememmber, this is a dupliverts construct!
+ object_stick[0].hide_set(True)
+ object_stick[1].hide_set(True)
+
+ stick_cylinder = object_stick[0]
+ stick_cylinder.active_material = stick[3]
+ stick_cups = object_stick[1]
+ stick_cups.active_material = stick[3]
+
+ # Smooth the cylinders.
+ if use_sticks_smooth == True:
+ bpy.ops.object.select_all(action='DESELECT')
+ stick_cylinder.select_set(True)
+ stick_cups.select_set(True)
+ bpy.ops.object.shade_smooth()
+
+ # Parenting the mesh to the cylinder.
+ stick_cylinder.parent = new_mesh
+ stick_cups.parent = new_mesh
+ new_mesh.instance_type = 'FACES'
+ new_mesh.location = center
+ atom_object_list.append(new_mesh)
+
+ # Return the list of dupliverts structures.
+ return atom_object_list
+
+
+# Function, which draws the sticks with help of the skin and subdivision
+# modifiers.
+def draw_sticks_skin(all_atoms,
+ all_sticks,
+ Stick_diameter,
+ use_sticks_smooth,
+ sticks_subdiv_view,
+ sticks_subdiv_render,
+ coll_molecule):
+
+ # These counters are for the edges, in the shape [i,i+1].
+ i = 0
+
+ # This is the list of vertices, containing the atom position
+ # (vectors)).
+ stick_vertices = []
+ # This is the 'same' list, which contains not vector position of
+ # the atoms but their numbers. It is used to handle the edges.
+ stick_vertices_nr = []
+ # This is the list of edges.
+ stick_edges = []
+
+ # Go through the list of all sticks. For each stick do:
+ for stick in all_sticks:
+
+ # Each stick has two atoms = two vertices.
+
+ """
+ [ 0,1 , 3,4 , 0,8 , 7,3]
+ [[0,1], [2,3], [4,5], [6,7]]
+
+ [ 0,1 , 3,4 , x,8 , 7,x] x:deleted
+ [[0,1], [2,3], [0,5], [6,2]]
+ """
+
+ # Check, if the vertex (atom) is already in the vertex list.
+ # edge: [s1,s2]
+ FLAG_s1 = False
+ s1 = 0
+ for stick2 in stick_vertices_nr:
+ if stick2 == stick.atom1-1:
+ FLAG_s1 = True
+ break
+ s1 += 1
+ FLAG_s2 = False
+ s2 = 0
+ for stick2 in stick_vertices_nr:
+ if stick2 == stick.atom2-1:
+ FLAG_s2 = True
+ break
+ s2 += 1
+
+ # If the vertex (atom) is not yet in the vertex list:
+ # append the number of atom and the vertex to the two lists.
+ # For the first atom:
+ if FLAG_s1 == False:
+ atom1 = copy(all_atoms[stick.atom1-1].location)
+ stick_vertices.append(atom1)
+ stick_vertices_nr.append(stick.atom1-1)
+ # For the second atom:
+ if FLAG_s2 == False:
+ atom2 = copy(all_atoms[stick.atom2-1].location)
+ stick_vertices.append(atom2)
+ stick_vertices_nr.append(stick.atom2-1)
+
+ # Build the edges:
+
+ # If both vertices (atoms) were not in the lists, then
+ # the edge is simply [i,i+1]. These are two new vertices
+ # (atoms), so increase i by 2.
+ if FLAG_s1 == False and FLAG_s2 == False:
+ stick_edges.append([i,i+1])
+ i += 2
+ # Both vertices (atoms) were already in the list, so then
+ # use the vertices (atoms), which already exist. They are
+ # at positions s1 and s2.
+ if FLAG_s1 == True and FLAG_s2 == True:
+ stick_edges.append([s1,s2])
+ # The following two if cases describe the situation that
+ # only one vertex (atom) was in the list. Since only ONE
+ # new vertex was added, increase i by one.
+ if FLAG_s1 == True and FLAG_s2 == False:
+ stick_edges.append([s1,i])
+ i += 1
+ if FLAG_s1 == False and FLAG_s2 == True:
+ stick_edges.append([i,s2])
+ i += 1
+
+ # Build the mesh of the sticks
+ stick_mesh = bpy.data.meshes.new("Mesh_sticks")
+ stick_mesh.from_pydata(stick_vertices, stick_edges, [])
+ stick_mesh.update()
+ new_stick_mesh = bpy.data.objects.new("Sticks", stick_mesh)
+ # Link the active mesh to the molecule collection
+ coll_molecule.objects.link(new_stick_mesh)
+
+ # Apply the skin modifier.
+ new_stick_mesh.modifiers.new(name="Sticks_skin", type='SKIN')
+ # Smooth the skin surface if this option has been chosen.
+ new_stick_mesh.modifiers[0].use_smooth_shade = use_sticks_smooth
+ # Apply the Subdivision modifier.
+ new_stick_mesh.modifiers.new(name="Sticks_subsurf", type='SUBSURF')
+ # Options: choose the levels
+ new_stick_mesh.modifiers[1].levels = sticks_subdiv_view
+ new_stick_mesh.modifiers[1].render_levels = sticks_subdiv_render
+
+ stick_material = bpy.data.materials.new(ELEMENTS[-1].name)
+ stick_material.diffuse_color = ELEMENTS[-1].color
+ new_stick_mesh.active_material = stick_material
+
+ # This is for putting the radius of the sticks onto
+ # the desired value 'Stick_diameter'
+ bpy.context.view_layer.objects.active = new_stick_mesh
+ # EDIT mode
+ bpy.ops.object.mode_set(mode='EDIT', toggle=False)
+ bm = bmesh.from_edit_mesh(new_stick_mesh.data)
+ bpy.ops.mesh.select_all(action='DESELECT')
+
+ # Select all vertices
+ for v in bm.verts:
+ v.select = True
+
+ # This is somewhat a factor for the radius.
+ r_f = 4.0
+ # Apply operator 'skin_resize'.
+ bpy.ops.transform.skin_resize(value=(Stick_diameter*r_f,
+ Stick_diameter*r_f,
+ Stick_diameter*r_f),
+ constraint_axis=(False, False, False),
+ orient_type='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)
+ # Back to the OBJECT mode.
+ bpy.ops.object.mode_set(mode='OBJECT', toggle=False)
+
+ return new_stick_mesh
+
+
+# Draw the sticks the normal way: connect the atoms by simple cylinders.
+# Two options: 1. single cylinders parented to an empty
+# 2. one single mesh object
+def draw_sticks_normal(all_atoms,
+ all_sticks,
+ center,
+ Stick_diameter,
+ Stick_sectors,
+ use_sticks_smooth,
+ use_sticks_one_object,
+ use_sticks_one_object_nr,
+ coll_molecule):
+
+ stick_material = bpy.data.materials.new(ELEMENTS[-1].name)
+ stick_material.diffuse_color = ELEMENTS[-1].color
+
+ up_axis = Vector([0.0, 0.0, 1.0])
+
+ # For all sticks, do ...
+ list_group = []
+ list_group_sub = []
+ counter = 0
+ for stick in all_sticks:
+
+ # The vectors of the two atoms
+ atom1 = all_atoms[stick.atom1-1].location-center
+ atom2 = all_atoms[stick.atom2-1].location-center
+ # Location
+ location = (atom1 + atom2) * 0.5
+ # The difference of both vectors
+ v = (atom2 - atom1)
+ # Angle with respect to the z-axis
+ angle = v.angle(up_axis, 0)
+ # Cross-product between v and the z-axis vector. It is the
+ # vector of rotation.
+ axis = up_axis.cross(v)
+ # Calculate Euler angles
+ euler = Matrix.Rotation(angle, 4, axis).to_euler()
+ # Create stick
+ stick = bpy.ops.mesh.primitive_cylinder_add(vertices=Stick_sectors,
+ radius=Stick_diameter,
+ depth=v.length,
+ end_fill_type='NGON',
+ view_align=False,
+ enter_editmode=False,
+ location=location,
+ rotation=(0, 0, 0))
+ # Put the stick into the scene ...
+ stick = bpy.context.view_layer.objects.active
+ # ... and rotate the stick.
+ stick.rotation_euler = euler
+ # ... and name
+ stick.name = "Stick_Cylinder"
+ counter += 1
+
+ # Smooth the cylinder.
+ if use_sticks_smooth == True:
+ bpy.ops.object.select_all(action='DESELECT')
+ stick.select_set(True)
+ bpy.ops.object.shade_smooth()
+
+ list_group_sub.append(stick)
+
+ if use_sticks_one_object == True:
+ if counter == use_sticks_one_object_nr:
+ bpy.ops.object.select_all(action='DESELECT')
+ for stick in list_group_sub:
+ stick.select_set(True)
+ bpy.ops.object.join()
+ list_group.append(bpy.context.view_layer.objects.active)
+ bpy.ops.object.select_all(action='DESELECT')
+ list_group_sub = []
+ counter = 0
+ else:
+ # Material ...
+ stick.active_material = stick_material
+
+ if use_sticks_one_object == True:
+ bpy.ops.object.select_all(action='DESELECT')
+ for stick in list_group_sub:
+ stick.select_set(True)
+ bpy.ops.object.join()
+ list_group.append(bpy.context.view_layer.objects.active)
+ bpy.ops.object.select_all(action='DESELECT')
+
+ for group in list_group:
+ group.select_set(True)
+ bpy.ops.object.join()
+ bpy.ops.object.origin_set(type='ORIGIN_GEOMETRY',
+ center='MEDIAN')
+ sticks = bpy.context.view_layer.objects.active
+ sticks.active_material = stick_material
+
+ sticks.location += center
+
+ # Collections
+ # ===========
+ # Note the collection where the sticks were placed into.
+ coll_all = sticks.users_collection
+ if len(coll_all) > 0:
+ coll_past = coll_all[0]
+ else:
+ coll_past = bpy.context.scene.collection
+
+ # Link the sticks with the collection of the molecule ...
+ coll_molecule.objects.link(sticks)
+ # ... and unlink them from the collection it has been before.
+ coll_past.objects.unlink(sticks)
+
+ return sticks
+ else:
+ # Here we use an empty ...
+ bpy.ops.object.empty_add(type='ARROWS',
+ view_align=False,
+ location=(0, 0, 0),
+ rotation=(0, 0, 0))
+ sticks_empty = bpy.context.view_layer.objects.active
+ sticks_empty.name = "A_sticks_empty"
+ # ... that is parent to all sticks. With this, we can better move
+ # all sticks if necessary.
+ for stick in list_group_sub:
+ stick.parent = sticks_empty
+
+ sticks_empty.location += center
+
+ # Collections
+ # ===========
+ # Create a collection that will contain all sticks + the empty and ...
+ coll = bpy.data.collections.new("Sticks")
+ # ... link it to the collection, which contains all parts of the
+ # molecule.
+ coll_molecule.children.link(coll)
+ # Now, create a collection that only contains the sticks and ...
+ coll_cylinder = bpy.data.collections.new("Sticks_cylinders")
+ # ... link it to the collection, which contains the sticks and empty.
+ coll.children.link(coll_cylinder)
+
+ # Note the collection where the empty was placed into, ...
+ coll_all = sticks_empty.users_collection
+ if len(coll_all) > 0:
+ coll_past = coll_all[0]
+ else:
+ coll_past = bpy.context.scene.collection
+ # ... link the empty with the new collection ...
+ coll.objects.link(sticks_empty)
+ # ... and unlink it from the old collection where it has been before.
+ coll_past.objects.unlink(sticks_empty)
+
+ # Note the collection where the cylinders were placed into, ...
+ coll_all = list_group_sub[0].users_collection
+ if len(coll_all) > 0:
+ coll_past = coll_all[0]
+ else:
+ coll_past = bpy.context.scene.collection
+
+ for stick in list_group_sub:
+ # ... link each stick with the new collection ...
+ coll_cylinder.objects.link(stick)
+ # ... and unlink it from the old collection.
+ coll_past.objects.unlink(stick)
+
+ return sticks_empty
+
+
+# -----------------------------------------------------------------------------
+# The main routine
+
+def import_pdb(Ball_type,
+ Ball_azimuth,
+ Ball_zenith,
+ Ball_radius_factor,
+ radiustype,
+ Ball_distance_factor,
+ use_sticks,
+ use_sticks_type,
+ sticks_subdiv_view,
+ sticks_subdiv_render,
+ use_sticks_color,
+ use_sticks_smooth,
+ use_sticks_bonds,
+ use_sticks_one_object,
+ use_sticks_one_object_nr,
+ Stick_unit, Stick_dist,
+ Stick_sectors,
+ Stick_diameter,
+ put_to_center,
+ use_camera,
+ use_light,
+ filepath_pdb):
+
+ # 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
+
+ read_elements()
+
+ # ------------------------------------------------------------------------
+ # READING DATA OF ATOMS
+
+ (Number_of_total_atoms, all_atoms) = read_pdb_file(filepath_pdb, radiustype)
+
+ # ------------------------------------------------------------------------
+ # 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.metallic = 0.8
+ material.specular_intensity = 0.5
+ material.roughness = 0.3
+ material.blend_method = 'ADD'
+ material.show_transparent_back = False
+ # Some properties for cycles
+ material.use_nodes = True
+ mat_P_BSDF = material.node_tree.nodes['Principled BSDF']
+ mat_P_BSDF.inputs['Metallic'].default_value = 0.1
+ mat_P_BSDF.inputs['Roughness'].default_value = 0.2
+ mat_P_BSDF.inputs['Transmission'].default_value = 0.97
+ mat_P_BSDF.inputs['IOR'].default_value = 0.8
+ # The atom gets its properties.
+ atom.material = material
+
+ # ------------------------------------------------------------------------
+ # READING DATA OF STICKS
+
+ all_sticks = read_pdb_file_sticks(filepath_pdb,
+ use_sticks_bonds,
+ all_atoms)
+ #
+ # So far, all atoms, sticks and materials 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 subtracted).
+
+ 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 subtracted
+ 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 farthest 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 = max(object_size_vec).length
+
+ # ------------------------------------------------------------------------
+ # 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], ...]
+
+ # 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", ...]
+ draw_all_atoms = []
+ 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)
+
+ # ------------------------------------------------------------------------
+ # COLLECTION
+
+ # Before we start to draw the atoms and sticks, we first create a
+ # collection for the molecule. All atoms (balls) and sticks (cylinders)
+ # are put into this collection.
+ coll_molecule_name = os.path.basename(filepath_pdb)
+ scene = bpy.context.scene
+ coll_molecule = bpy.data.collections.new(coll_molecule_name)
+ scene.collection.children.link(coll_molecule)
+
+ # ------------------------------------------------------------------------
+ # DRAWING THE ATOMS
+
+ bpy.ops.object.select_all(action='DESELECT')
+
+ list_coll_elements = []
+ # For each list of atoms of ONE type (e.g. Hydrogen)
+ for draw_all_atoms_type in draw_all_atoms:
+
+ atom_mesh, coll_element = draw_atoms_one_type(draw_all_atoms_type,
+ Ball_type,
+ Ball_azimuth,
+ Ball_zenith,
+ Ball_radius_factor,
+ object_center_vec,
+ coll_molecule)
+ atom_object_list.append(atom_mesh)
+ list_coll_elements.append(coll_element)
+
+ # ------------------------------------------------------------------------
+ # DRAWING THE STICKS: cylinders in a dupliverts structure
+
+ if use_sticks == True and use_sticks_type == '0' and all_sticks != []:
+
+ sticks = draw_sticks_dupliverts(all_atoms,
+ atom_all_types_list,
+ object_center_vec,
+ all_sticks,
+ Stick_diameter,
+ Stick_sectors,
+ Stick_unit,
+ Stick_dist,
+ use_sticks_smooth,
+ use_sticks_color,
+ list_coll_elements)
+ for stick in sticks:
+ atom_object_list.append(stick)
+
+ # ------------------------------------------------------------------------
+ # DRAWING THE STICKS: skin and subdivision modifier
+
+ if use_sticks == True and use_sticks_type == '1' and all_sticks != []:
+
+ sticks = draw_sticks_skin(all_atoms,
+ all_sticks,
+ Stick_diameter,
+ use_sticks_smooth,
+ sticks_subdiv_view,
+ sticks_subdiv_render,
+ coll_molecule)
+ atom_object_list.append(sticks)
+
+ # ------------------------------------------------------------------------
+ # DRAWING THE STICKS: normal cylinders
+
+ if use_sticks == True and use_sticks_type == '2' and all_sticks != []:
+
+ sticks = draw_sticks_normal(all_atoms,
+ all_sticks,
+ object_center_vec,
+ Stick_diameter,
+ Stick_sectors,
+ use_sticks_smooth,
+ use_sticks_one_object,
+ use_sticks_one_object_nr,
+ coll_molecule)
+ atom_object_list.append(sticks)
+
+ # ------------------------------------------------------------------------
+ # CAMERA and LIGHT SOURCES
+
+ camera_light_source(use_camera,
+ use_light,
+ object_center_vec,
+ object_size)
+
+ # ------------------------------------------------------------------------
+ # SELECT ALL LOADED OBJECTS
+ bpy.ops.object.select_all(action='DESELECT')
+ obj = None
+ for obj in atom_object_list:
+ obj.select_set(True)
+
+ # activate the last selected object
+ if obj:
+ bpy.context.view_layer.objects.active = obj
diff --git a/io_mesh_atomic/utility_gui.py b/io_mesh_atomic/utility_gui.py
new file mode 100644
index 00000000..a9f7cb6d
--- /dev/null
+++ b/io_mesh_atomic/utility_gui.py
@@ -0,0 +1,422 @@
+# ##### 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 #####
+
+import bpy
+from bpy.types import Operator, Panel
+from bpy.props import (StringProperty,
+ EnumProperty,
+ FloatProperty,
+ BoolProperty)
+
+from io_mesh_atomic.utility_panel import choose_objects
+from io_mesh_atomic.utility_panel import custom_datafile
+from io_mesh_atomic.utility_panel import custom_datafile_change_atom_props
+from io_mesh_atomic.utility_panel import separate_atoms
+from io_mesh_atomic.utility_panel import distance
+
+
+# -----------------------------------------------------------------------------
+# GUI
+
+# The panel.
+class PANEL_PT_prepare(Panel):
+ bl_label = "Atomic Blender Utilities"
+ bl_space_type = "VIEW_3D"
+ bl_region_type = "UI"
+ bl_options = {'DEFAULT_CLOSED'}
+ bl_context = "objectmode"
+ bl_category = "Tools"
+ bl_idname = "ATOMIC_PT_utilities"
+
+
+ # This thing here just guarantees that the panel is NOT opened when the
+ # check box in the addon preferences is not activated! See __init__.py
+ @classmethod
+ def poll(cls, context):
+ pref = context.preferences
+ return pref.addons[__package__].preferences.bool_utility
+
+ def draw(self, context):
+ layout = self.layout
+ scn = context.scene.atom_blend
+
+ box = layout.box()
+ col = box.column(align=True)
+ col.label(text="Custom data file")
+ col.prop(scn, "datafile")
+ col.operator("atom_blend.datafile_apply")
+
+ box = layout.box()
+ col = box.column(align=True)
+ col.label(text="Measure distances")
+ col.operator("atom_blend.button_distance")
+ col.prop(scn, "distance")
+
+ # This is from Blender 2.79 and does not work in 2.80. However, it
+ # might be useful later on if changed.
+ #
+ #box = layout.box()
+ #col = box.column(align=True)
+ #col.label(text="All changes concern:")
+ #col.prop(scn, "action_type")
+
+ box = layout.box()
+ col = box.column(align=True)
+ col.label(text="Change atom size")
+ col.label(text="1. Type of radii")
+ col.prop(scn, "radius_type")
+ col2 = col.column()
+ col2.active = (scn.radius_type == '3')
+ col2.prop(scn, "radius_type_ionic")
+ col = box.column(align=True)
+ col.label(text="2. Radii in pm")
+ col.prop(scn, "radius_pm_name")
+ col.prop(scn, "radius_pm")
+ col = box.column(align=True)
+ col.label(text="3. Radii by scale")
+ col.prop(scn, "radius_all")
+ row = col.row()
+ row.operator("atom_blend.radius_all_smaller")
+ row.operator("atom_blend.radius_all_bigger")
+
+ box = layout.box()
+ col = box.column(align=True)
+ col.label(text="Change stick size")
+ col.prop(scn, "sticks_all")
+ row = col.row()
+ row.operator("atom_blend.sticks_all_smaller")
+ row.operator("atom_blend.sticks_all_bigger")
+
+ box = layout.box()
+ col = box.column(align=True)
+ col.label(text="Change atom shape")
+ col2 = col.column()
+ col2.active = (scn.replace_objs_special == '0')
+ col2.prop(scn, "replace_objs")
+ col2.prop(scn, "replace_objs_material")
+ col.prop(scn, "replace_objs_special")
+ col.operator("atom_blend.replace_atom")
+ col.label(text="Default values")
+ col.operator("atom_blend.default_atoms")
+
+ box = layout.box()
+ col = box.column(align=True)
+ col.label(text="Separate atoms")
+ col3 = col.column()
+ col3.active = (bpy.context.mode == 'EDIT_MESH')
+ col3.operator("atom_blend.separate_atom")
+
+
+# The properties of buttons etc. in the panel.
+class PanelProperties(bpy.types.PropertyGroup):
+
+ def Callback_radius_type(self, context):
+ scn = bpy.context.scene.atom_blend
+ choose_objects("ATOM_RADIUS_TYPE",
+ scn.action_type,
+ None,
+ None,
+ scn.radius_type,
+ scn.radius_type_ionic,
+ None)
+ def Callback_radius_pm(self, context):
+ scn = bpy.context.scene.atom_blend
+ choose_objects("ATOM_RADIUS_PM",
+ scn.action_type,
+ None,
+ [scn.radius_pm_name,
+ scn.radius_pm],
+ None,
+ None,
+ None)
+
+ datafile: StringProperty(
+ name = "", description="Path to your custom data file",
+ maxlen = 256, default = "", subtype='FILE_PATH')
+ XYZ_file: StringProperty(
+ name = "Path to file", default="",
+ description = "Path of the XYZ file")
+ number_atoms: StringProperty(name="",
+ default="Number", description = "This output shows "
+ "the number of atoms which have been loaded")
+ distance: StringProperty(
+ name="", default="Distance (A)",
+ description="Distance of 2 objects in Angstrom")
+ replace_objs: EnumProperty(
+ name="Shape",
+ description="Choose a different atom shape.",
+ items=(('0',"Unchanged", "Do not change the shape"),
+ ('1a',"Sphere (Mesh)", "Replace with a sphere (Mesh)"),
+ ('1b',"Sphere (NURBS)", "Replace with a sphere (NURBS)"),
+ ('2',"Cube", "Replace with a cube"),
+ ('3',"Plane", "Replace with a plane"),
+ ('4a',"Circle (Mesh)", "Replace with a circle (Mesh)"),
+ ('4b',"Circle (NURBS)", "Replace with a circle (NURBS)"),
+ ('5a',"Icosphere 1", "Replace with a icosphere, subd=1"),
+ ('5b',"Icosphere 2", "Replace with a icosphere, subd=2"),
+ ('5c',"Icosphere 3", "Replace with a icosphere, subd=3"),
+ ('5d',"Icosphere 4", "Replace with a icosphere, subd=4"),
+ ('5e',"Icosphere 5", "Replace with a icosphere, subd=5"),
+ ('6a',"Cylinder (Mesh)", "Replace with a cylinder (Mesh)"),
+ ('6b',"Cylinder (NURBS)", "Replace with a cylinder (NURBS)"),
+ ('7',"Cone", "Replace with a cone"),
+ ('8a',"Torus (Mesh)", "Replace with a torus (Mesh)"),
+ ('8b',"Torus (NURBS)", "Replace with a torus (NURBS)")),
+ default='0',)
+ replace_objs_material: EnumProperty(
+ name="Material",
+ description="Choose a different material.",
+ items=(('0',"Unchanged", "Leave the material unchanged"),
+ ('1',"Normal", "Use normal material (no transparency and reflection)"),
+ ('2',"Transparent", "Use transparent material"),
+ ('3',"Reflecting", "Use reflecting material"),
+ ('4',"Transparent + reflecting", "Use transparent and reflecting material")),
+ default='0',)
+ replace_objs_special: EnumProperty(
+ name="Special",
+ description="Choose a special atom shape.",
+ items=(('0',"None", "Use no special shape."),
+ ('1',"F2+ center", "Replace with a F2+ center"),
+ ('2',"F+ center", "Replace with a F+ center"),
+ ('3',"F0 center", "Replace with a F0 center")),
+ default='0',)
+ action_type: EnumProperty(
+ name="",
+ description="Which objects shall be modified?",
+ items=(('ALL_ACTIVE',"all active objects", "in the current layer"),
+ ('ALL_IN_LAYER',"all in all selected layers",
+ "in selected layer(s)")),
+ default='ALL_ACTIVE',)
+ 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"),
+ ('3',"ionic radii", "Use ionic radii")),
+ default='0',update=Callback_radius_type)
+ radius_type_ionic: EnumProperty(
+ name="Charge",
+ description="Charge state of the ions if existing.",
+ items=(('0',"-4", "Charge state -4"),
+ ('1',"-3", "Charge state -3"),
+ ('2',"-2", "Charge state -2"),
+ ('3',"-1", "Charge state -1"),
+ ('4'," 0", "Charge state 0: nothing is done"),
+ ('5',"+1", "Charge state +1"),
+ ('6',"+2", "Charge state +2"),
+ ('7',"+3", "Charge state +3"),
+ ('8',"+4", "Charge state +4"),
+ ('9',"+5", "Charge state +5"),
+ ('10',"+6", "Charge state +6"),
+ ('11',"+7", "Charge state +7")),
+ default='4',update=Callback_radius_type)
+ radius_pm_name: StringProperty(
+ name="", default="Atom name",
+ description="Put in the name of the atom (e.g. Hydrogen)")
+ radius_pm: FloatProperty(
+ name="", default=100.0, min=0.0,
+ description="Put in the radius of the atom (in pm)",
+ update=Callback_radius_pm)
+ radius_all: FloatProperty(
+ name="Scale", default = 1.05, min=1.0, max=5.0,
+ description="Put in the scale factor")
+ sticks_all: FloatProperty(
+ name="Scale", default = 1.05, min=1.0, max=5.0,
+ description="Put in the scale factor")
+
+
+# Button loading a custom data file
+class DatafileApply(Operator):
+ bl_idname = "atom_blend.datafile_apply"
+ bl_label = "Apply"
+ bl_description = "Use color and radii values stored in the custom file"
+
+ def execute(self, context):
+ scn = bpy.context.scene.atom_blend
+
+ if scn.datafile == "":
+ return {'FINISHED'}
+
+ custom_datafile(scn.datafile)
+ custom_datafile_change_atom_props()
+
+ return {'FINISHED'}
+
+
+# Button for separating single atoms from a dupliverts structure
+class DefaultAtom(Operator):
+ bl_idname = "atom_blend.default_atoms"
+ bl_label = "Default"
+ bl_description = ("Use default shapes and colors for atoms.")
+
+ # Are we in the OBJECT mode?
+ @classmethod
+ def poll(self, context):
+ if bpy.context.mode == 'OBJECT':
+ return True
+ else:
+ return False
+
+ def execute(self, context):
+ scn = bpy.context.scene.atom_blend
+ choose_objects("ATOM_DEFAULT_OBJ",
+ scn.action_type,
+ None,
+ None,
+ None,
+ None,
+ None)
+ return {'FINISHED'}
+
+
+# Button for separating single atoms from a dupliverts structure
+class ReplaceAtom(Operator):
+ bl_idname = "atom_blend.replace_atom"
+ bl_label = "Replace"
+ bl_description = ("Replace selected atoms with atoms of different shape.")
+
+ # Are we in the OBJECT mode?
+ @classmethod
+ def poll(self, context):
+ if bpy.context.mode == 'OBJECT':
+ return True
+ else:
+ return False
+
+ def execute(self, context):
+ scn = bpy.context.scene.atom_blend
+ choose_objects("ATOM_REPLACE_OBJ",
+ scn.action_type,
+ None,
+ None,
+ None,
+ None,
+ None)
+ return {'FINISHED'}
+
+
+# Button for separating single atoms from a dupliverts structure
+class SeparateAtom(Operator):
+ bl_idname = "atom_blend.separate_atom"
+ bl_label = "Separate"
+ bl_description = ("Separate selected atoms in a dupliverts structure. "
+ "You have to be in the 'Edit Mode'")
+
+ # Are we in the EDIT mode?
+ @classmethod
+ def poll(self, context):
+ if bpy.context.mode == 'EDIT_MESH':
+ return True
+ else:
+ return False
+
+ def execute(self, context):
+ scn = bpy.context.scene.atom_blend
+
+ separate_atoms(scn)
+
+ return {'FINISHED'}
+
+
+# Button for measuring the distance of active objects
+class DistanceButton(Operator):
+ bl_idname = "atom_blend.button_distance"
+ bl_label = "Measure ..."
+ bl_description = "Measure the distance between two atoms (objects)."
+
+ def execute(self, context):
+ scn = bpy.context.scene.atom_blend
+ dist = distance()
+
+ # Put the distance into the string of the output field.
+ scn.distance = dist
+ return {'FINISHED'}
+
+
+# Button for increasing the radii of all selected atoms
+class RadiusAllBiggerButton(Operator):
+ bl_idname = "atom_blend.radius_all_bigger"
+ bl_label = "Bigger ..."
+ bl_description = "Increase the radii of selected atoms"
+
+ def execute(self, context):
+ scn = bpy.context.scene.atom_blend
+ choose_objects("ATOM_RADIUS_ALL",
+ scn.action_type,
+ scn.radius_all,
+ None,
+ None,
+ None,
+ None)
+ return {'FINISHED'}
+
+
+# Button for decreasing the radii of all selected atoms
+class RadiusAllSmallerButton(Operator):
+ bl_idname = "atom_blend.radius_all_smaller"
+ bl_label = "Smaller ..."
+ bl_description = "Decrease the radii of selected atoms"
+
+ def execute(self, context):
+ scn = bpy.context.scene.atom_blend
+ choose_objects("ATOM_RADIUS_ALL",
+ scn.action_type,
+ 1.0/scn.radius_all,
+ None,
+ None,
+ None,
+ None)
+ return {'FINISHED'}
+
+
+# Button for increasing the radii of all selected sticks
+class SticksAllBiggerButton(Operator):
+ bl_idname = "atom_blend.sticks_all_bigger"
+ bl_label = "Bigger ..."
+ bl_description = "Increase the radii of selected sticks"
+
+ def execute(self, context):
+ scn = bpy.context.scene.atom_blend
+ choose_objects("STICKS_RADIUS_ALL",
+ scn.action_type,
+ None,
+ None,
+ None,
+ None,
+ scn.sticks_all)
+ return {'FINISHED'}
+
+
+# Button for decreasing the radii of all selected sticks
+class SticksAllSmallerButton(Operator):
+ bl_idname = "atom_blend.sticks_all_smaller"
+ bl_label = "Smaller ..."
+ bl_description = "Decrease the radii of selected sticks"
+
+ def execute(self, context):
+ scn = bpy.context.scene.atom_blend
+ choose_objects("STICKS_RADIUS_ALL",
+ scn.action_type,
+ None,
+ None,
+ None,
+ None,
+ 1.0/scn.sticks_all)
+ return {'FINISHED'}
+
diff --git a/io_mesh_atomic/utility_panel.py b/io_mesh_atomic/utility_panel.py
new file mode 100644
index 00000000..5e85c0c8
--- /dev/null
+++ b/io_mesh_atomic/utility_panel.py
@@ -0,0 +1,1074 @@
+# ##### 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 #####
+
+import os
+import bpy
+import bmesh
+from mathutils import Vector
+from math import sqrt
+from copy import copy
+
+# -----------------------------------------------------------------------------
+# Atom 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)
+
+ELEMENTS_DEFAULT = (
+( 1, "Hydrogen", "H", ( 1.0, 1.0, 1.0, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ),
+( 2, "Helium", "He", ( 0.85, 1.0, 1.0, 1.0), 0.93, 0.93, 0.49 ),
+( 3, "Lithium", "Li", ( 0.8, 0.50, 1.0, 1.0), 1.23, 1.23, 2.05 , 1 , 0.68 ),
+( 4, "Beryllium", "Be", ( 0.76, 1.0, 0.0, 1.0), 0.90, 0.90, 1.40 , 1 , 0.44 , 2 , 0.35 ),
+( 5, "Boron", "B", ( 1.0, 0.70, 0.70, 1.0), 0.82, 0.82, 1.17 , 1 , 0.35 , 3 , 0.23 ),
+( 6, "Carbon", "C", ( 0.56, 0.56, 0.56, 1.0), 0.77, 0.77, 0.91 , -4 , 2.60 , 4 , 0.16 ),
+( 7, "Nitrogen", "N", ( 0.18, 0.31, 0.97, 1.0), 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, 1.0), 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, 1.0), 0.72, 0.72, 0.57 , -1 , 1.33 , 7 , 0.08 ),
+(10, "Neon", "Ne", ( 0.70, 0.89, 0.96, 1.0), 0.71, 0.71, 0.51 , 1 , 1.12 ),
+(11, "Sodium", "Na", ( 0.67, 0.36, 0.94, 1.0), 1.54, 1.54, 2.23 , 1 , 0.97 ),
+(12, "Magnesium", "Mg", ( 0.54, 1.0, 0.0, 1.0), 1.36, 1.36, 1.72 , 1 , 0.82 , 2 , 0.66 ),
+(13, "Aluminium", "Al", ( 0.74, 0.65, 0.65, 1.0), 1.18, 1.18, 1.82 , 3 , 0.51 ),
+(14, "Silicon", "Si", ( 0.94, 0.78, 0.62, 1.0), 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, 1.0), 1.06, 1.06, 1.23 , -3 , 2.12 , 3 , 0.44 , 5 , 0.35 ),
+(16, "Sulfur", "S", ( 1.0, 1.0, 0.18, 1.0), 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, 1.0), 0.99, 0.99, 0.97 , -1 , 1.81 , 5 , 0.34 , 7 , 0.27 ),
+(18, "Argon", "Ar", ( 0.50, 0.81, 0.89, 1.0), 0.98, 0.98, 0.88 , 1 , 1.54 ),
+(19, "Potassium", "K", ( 0.56, 0.25, 0.83, 1.0), 2.03, 2.03, 2.77 , 1 , 0.81 ),
+(20, "Calcium", "Ca", ( 0.23, 1.0, 0.0, 1.0), 1.74, 1.74, 2.23 , 1 , 1.18 , 2 , 0.99 ),
+(21, "Scandium", "Sc", ( 0.90, 0.90, 0.90, 1.0), 1.44, 1.44, 2.09 , 3 , 0.73 ),
+(22, "Titanium", "Ti", ( 0.74, 0.76, 0.78, 1.0), 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, 1.0), 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, 1.0), 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, 1.0), 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, 1.0), 1.17, 1.17, 1.72 , 2 , 0.74 , 3 , 0.64 ),
+(27, "Cobalt", "Co", ( 0.94, 0.56, 0.62, 1.0), 1.16, 1.16, 1.67 , 2 , 0.72 , 3 , 0.63 ),
+(28, "Nickel", "Ni", ( 0.31, 0.81, 0.31, 1.0), 1.15, 1.15, 1.62 , 2 , 0.69 ),
+(29, "Copper", "Cu", ( 0.78, 0.50, 0.2, 1.0), 1.17, 1.17, 1.57 , 1 , 0.96 , 2 , 0.72 ),
+(30, "Zinc", "Zn", ( 0.49, 0.50, 0.69, 1.0), 1.25, 1.25, 1.53 , 1 , 0.88 , 2 , 0.74 ),
+(31, "Gallium", "Ga", ( 0.76, 0.56, 0.56, 1.0), 1.26, 1.26, 1.81 , 1 , 0.81 , 3 , 0.62 ),
+(32, "Germanium", "Ge", ( 0.4, 0.56, 0.56, 1.0), 1.22, 1.22, 1.52 , -4 , 2.72 , 2 , 0.73 , 4 , 0.53 ),
+(33, "Arsenic", "As", ( 0.74, 0.50, 0.89, 1.0), 1.20, 1.20, 1.33 , -3 , 2.22 , 3 , 0.58 , 5 , 0.46 ),
+(34, "Selenium", "Se", ( 1.0, 0.63, 0.0, 1.0), 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, 1.0), 1.14, 1.14, 1.12 , -1 , 1.96 , 5 , 0.47 , 7 , 0.39 ),
+(36, "Krypton", "Kr", ( 0.36, 0.72, 0.81, 1.0), 1.31, 1.31, 1.24 ),
+(37, "Rubidium", "Rb", ( 0.43, 0.18, 0.69, 1.0), 2.16, 2.16, 2.98 , 1 , 1.47 ),
+(38, "Strontium", "Sr", ( 0.0, 1.0, 0.0, 1.0), 1.91, 1.91, 2.45 , 2 , 1.12 ),
+(39, "Yttrium", "Y", ( 0.58, 1.0, 1.0, 1.0), 1.62, 1.62, 2.27 , 3 , 0.89 ),
+(40, "Zirconium", "Zr", ( 0.58, 0.87, 0.87, 1.0), 1.45, 1.45, 2.16 , 1 , 1.09 , 4 , 0.79 ),
+(41, "Niobium", "Nb", ( 0.45, 0.76, 0.78, 1.0), 1.34, 1.34, 2.08 , 1 , 1.00 , 4 , 0.74 , 5 , 0.69 ),
+(42, "Molybdenum", "Mo", ( 0.32, 0.70, 0.70, 1.0), 1.30, 1.30, 2.01 , 1 , 0.93 , 4 , 0.70 , 6 , 0.62 ),
+(43, "Technetium", "Tc", ( 0.23, 0.61, 0.61, 1.0), 1.27, 1.27, 1.95 , 7 , 0.97 ),
+(44, "Ruthenium", "Ru", ( 0.14, 0.56, 0.56, 1.0), 1.25, 1.25, 1.89 , 4 , 0.67 ),
+(45, "Rhodium", "Rh", ( 0.03, 0.49, 0.54, 1.0), 1.25, 1.25, 1.83 , 3 , 0.68 ),
+(46, "Palladium", "Pd", ( 0.0, 0.41, 0.52, 1.0), 1.28, 1.28, 1.79 , 2 , 0.80 , 4 , 0.65 ),
+(47, "Silver", "Ag", ( 0.75, 0.75, 0.75, 1.0), 1.34, 1.34, 1.75 , 1 , 1.26 , 2 , 0.89 ),
+(48, "Cadmium", "Cd", ( 1.0, 0.85, 0.56, 1.0), 1.48, 1.48, 1.71 , 1 , 1.14 , 2 , 0.97 ),
+(49, "Indium", "In", ( 0.65, 0.45, 0.45, 1.0), 1.44, 1.44, 2.00 , 3 , 0.81 ),
+(50, "Tin", "Sn", ( 0.4, 0.50, 0.50, 1.0), 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, 1.0), 1.40, 1.40, 1.53 , -3 , 2.45 , 3 , 0.76 , 5 , 0.62 ),
+(52, "Tellurium", "Te", ( 0.83, 0.47, 0.0, 1.0), 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, 1.0), 1.33, 1.33, 1.32 , -1 , 2.20 , 5 , 0.62 , 7 , 0.50 ),
+(54, "Xenon", "Xe", ( 0.25, 0.61, 0.69, 1.0), 1.31, 1.31, 1.24 ),
+(55, "Caesium", "Cs", ( 0.34, 0.09, 0.56, 1.0), 2.35, 2.35, 3.35 , 1 , 1.67 ),
+(56, "Barium", "Ba", ( 0.0, 0.78, 0.0, 1.0), 1.98, 1.98, 2.78 , 1 , 1.53 , 2 , 1.34 ),
+(57, "Lanthanum", "La", ( 0.43, 0.83, 1.0, 1.0), 1.69, 1.69, 2.74 , 1 , 1.39 , 3 , 1.06 ),
+(58, "Cerium", "Ce", ( 1.0, 1.0, 0.78, 1.0), 1.65, 1.65, 2.70 , 1 , 1.27 , 3 , 1.03 , 4 , 0.92 ),
+(59, "Praseodymium", "Pr", ( 0.85, 1.0, 0.78, 1.0), 1.65, 1.65, 2.67 , 3 , 1.01 , 4 , 0.90 ),
+(60, "Neodymium", "Nd", ( 0.78, 1.0, 0.78, 1.0), 1.64, 1.64, 2.64 , 3 , 0.99 ),
+(61, "Promethium", "Pm", ( 0.63, 1.0, 0.78, 1.0), 1.63, 1.63, 2.62 , 3 , 0.97 ),
+(62, "Samarium", "Sm", ( 0.56, 1.0, 0.78, 1.0), 1.62, 1.62, 2.59 , 3 , 0.96 ),
+(63, "Europium", "Eu", ( 0.38, 1.0, 0.78, 1.0), 1.85, 1.85, 2.56 , 2 , 1.09 , 3 , 0.95 ),
+(64, "Gadolinium", "Gd", ( 0.27, 1.0, 0.78, 1.0), 1.61, 1.61, 2.54 , 3 , 0.93 ),
+(65, "Terbium", "Tb", ( 0.18, 1.0, 0.78, 1.0), 1.59, 1.59, 2.51 , 3 , 0.92 , 4 , 0.84 ),
+(66, "Dysprosium", "Dy", ( 0.12, 1.0, 0.78, 1.0), 1.59, 1.59, 2.49 , 3 , 0.90 ),
+(67, "Holmium", "Ho", ( 0.0, 1.0, 0.61, 1.0), 1.58, 1.58, 2.47 , 3 , 0.89 ),
+(68, "Erbium", "Er", ( 0.0, 0.90, 0.45, 1.0), 1.57, 1.57, 2.45 , 3 , 0.88 ),
+(69, "Thulium", "Tm", ( 0.0, 0.83, 0.32, 1.0), 1.56, 1.56, 2.42 , 3 , 0.87 ),
+(70, "Ytterbium", "Yb", ( 0.0, 0.74, 0.21, 1.0), 1.74, 1.74, 2.40 , 2 , 0.93 , 3 , 0.85 ),
+(71, "Lutetium", "Lu", ( 0.0, 0.67, 0.14, 1.0), 1.56, 1.56, 2.25 , 3 , 0.85 ),
+(72, "Hafnium", "Hf", ( 0.30, 0.76, 1.0, 1.0), 1.44, 1.44, 2.16 , 4 , 0.78 ),
+(73, "Tantalum", "Ta", ( 0.30, 0.65, 1.0, 1.0), 1.34, 1.34, 2.09 , 5 , 0.68 ),
+(74, "Tungsten", "W", ( 0.12, 0.58, 0.83, 1.0), 1.30, 1.30, 2.02 , 4 , 0.70 , 6 , 0.62 ),
+(75, "Rhenium", "Re", ( 0.14, 0.49, 0.67, 1.0), 1.28, 1.28, 1.97 , 4 , 0.72 , 7 , 0.56 ),
+(76, "Osmium", "Os", ( 0.14, 0.4, 0.58, 1.0), 1.26, 1.26, 1.92 , 4 , 0.88 , 6 , 0.69 ),
+(77, "Iridium", "Ir", ( 0.09, 0.32, 0.52, 1.0), 1.27, 1.27, 1.87 , 4 , 0.68 ),
+(78, "Platinum", "Pt", ( 0.81, 0.81, 0.87, 1.0), 1.30, 1.30, 1.83 , 2 , 0.80 , 4 , 0.65 ),
+(79, "Gold", "Au", ( 1.0, 0.81, 0.13, 1.0), 1.34, 1.34, 1.79 , 1 , 1.37 , 3 , 0.85 ),
+(80, "Mercury", "Hg", ( 0.72, 0.72, 0.81, 1.0), 1.49, 1.49, 1.76 , 1 , 1.27 , 2 , 1.10 ),
+(81, "Thallium", "Tl", ( 0.65, 0.32, 0.30, 1.0), 1.48, 1.48, 2.08 , 1 , 1.47 , 3 , 0.95 ),
+(82, "Lead", "Pb", ( 0.34, 0.34, 0.38, 1.0), 1.47, 1.47, 1.81 , 2 , 1.20 , 4 , 0.84 ),
+(83, "Bismuth", "Bi", ( 0.61, 0.30, 0.70, 1.0), 1.46, 1.46, 1.63 , 1 , 0.98 , 3 , 0.96 , 5 , 0.74 ),
+(84, "Polonium", "Po", ( 0.67, 0.36, 0.0, 1.0), 1.46, 1.46, 1.53 , 6 , 0.67 ),
+(85, "Astatine", "At", ( 0.45, 0.30, 0.27, 1.0), 1.45, 1.45, 1.43 , -3 , 2.22 , 3 , 0.85 , 5 , 0.46 ),
+(86, "Radon", "Rn", ( 0.25, 0.50, 0.58, 1.0), 1.00, 1.00, 1.34 ),
+(87, "Francium", "Fr", ( 0.25, 0.0, 0.4, 1.0), 1.00, 1.00, 1.00 , 1 , 1.80 ),
+(88, "Radium", "Ra", ( 0.0, 0.49, 0.0, 1.0), 1.00, 1.00, 1.00 , 2 , 1.43 ),
+(89, "Actinium", "Ac", ( 0.43, 0.67, 0.98, 1.0), 1.00, 1.00, 1.00 , 3 , 1.18 ),
+(90, "Thorium", "Th", ( 0.0, 0.72, 1.0, 1.0), 1.65, 1.65, 1.00 , 4 , 1.02 ),
+(91, "Protactinium", "Pa", ( 0.0, 0.63, 1.0, 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, 1.0), 1.42, 1.42, 1.00 , 4 , 0.97 , 6 , 0.80 ),
+(93, "Neptunium", "Np", ( 0.0, 0.50, 1.0, 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, 1.0), 1.00, 1.00, 1.00 , 3 , 1.08 , 4 , 0.93 ),
+(95, "Americium", "Am", ( 0.32, 0.36, 0.94, 1.0), 1.00, 1.00, 1.00 , 3 , 1.07 , 4 , 0.92 ),
+(96, "Curium", "Cm", ( 0.47, 0.36, 0.89, 1.0), 1.00, 1.00, 1.00 ),
+(97, "Berkelium", "Bk", ( 0.54, 0.30, 0.89, 1.0), 1.00, 1.00, 1.00 ),
+(98, "Californium", "Cf", ( 0.63, 0.21, 0.83, 1.0), 1.00, 1.00, 1.00 ),
+(99, "Einsteinium", "Es", ( 0.70, 0.12, 0.83, 1.0), 1.00, 1.00, 1.00 ),
+(100, "Fermium", "Fm", ( 0.70, 0.12, 0.72, 1.0), 1.00, 1.00, 1.00 ),
+(101, "Mendelevium", "Md", ( 0.70, 0.05, 0.65, 1.0), 1.00, 1.00, 1.00 ),
+(102, "Nobelium", "No", ( 0.74, 0.05, 0.52, 1.0), 1.00, 1.00, 1.00 ),
+(103, "Lawrencium", "Lr", ( 0.78, 0.0, 0.4, 1.0), 1.00, 1.00, 1.00 ),
+(104, "Vacancy", "Vac", ( 0.5, 0.5, 0.5, 1.0), 1.00, 1.00, 1.00),
+(105, "Default", "Default", ( 1.0, 1.0, 1.0, 1.0), 1.00, 1.00, 1.00),
+(106, "Stick", "Stick", ( 0.5, 0.5, 0.5, 1.0), 1.00, 1.00, 1.00),
+)
+
+# The list 'ELEMENTS' contains all data of the elements and will be used during
+# runtime. The list will be initialized with the fixed
+# data from above via the class below (ElementProp). One fixed list (above),
+# which cannot be changed, and a list of classes with same data (ELEMENTS) exist.
+# The list 'ELEMENTS' can be modified by e.g. loading a separate custom
+# data file.
+ELEMENTS = []
+
+
+# This is the class, which stores the properties for one element.
+class ElementProp(object):
+ __slots__ = ('number', 'name', 'short_name', 'color', 'radii', 'radii_ionic')
+ 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 function measures the distance between two selected objects.
+def distance():
+
+ # In the 'EDIT' mode
+ if bpy.context.mode == 'EDIT_MESH':
+
+ atom = bpy.context.edit_object
+ bm = bmesh.from_edit_mesh(atom.data)
+ locations = []
+
+ for v in bm.verts:
+ if v.select:
+ locations.append(atom.matrix_world @ v.co)
+
+ if len(locations) > 1:
+ location1 = locations[0]
+ location2 = locations[1]
+ else:
+ return "N.A"
+ # In the 'OBJECT' mode
+ else:
+
+ if len(bpy.context.selected_bases) > 1:
+ location1 = bpy.context.selected_objects[0].location
+ location2 = bpy.context.selected_objects[1].location
+ else:
+ return "N.A."
+
+ dv = location2 - location1
+ dist = str(dv.length)
+ pos = str.find(dist, ".")
+ dist = dist[:pos+4]
+ dist = dist + " A"
+
+ return dist
+
+
+def choose_objects(action_type,
+ who,
+ radius_all,
+ radius_pm,
+ radius_type,
+ radius_type_ionic,
+ sticks_all):
+
+ # For selected objects of all selected layers
+ if who == "ALL_IN_LAYER":
+ # Determine all selected layers.
+ layers = []
+ for i, layer in enumerate(bpy.context.scene.layers):
+ if layer == True:
+ layers.append(i)
+
+ # Put all objects, which are in the layers, into a list.
+ change_objects_all = []
+ for atom in bpy.context.scene.objects:
+ for layer in layers:
+ if atom.layers[layer] == True:
+ change_objects_all.append(atom)
+ # For selected objects of the visible layer
+ elif who == "ALL_ACTIVE":
+ change_objects_all = []
+ # Note all selected objects first.
+ for atom in bpy.context.selected_objects:
+ change_objects_all.append(atom)
+
+ # This is very important now: If there are dupliverts structures, note
+ # only the parents and NOT the children! Otherwise the double work is
+ # done or the system can even crash if objects are deleted. - The
+ # chidlren are accessed anyways (see below).
+ change_objects = []
+ for atom in change_objects_all:
+ if atom.parent != None:
+ FLAG = False
+ for atom2 in change_objects:
+ if atom2 == atom.parent:
+ FLAG = True
+ if FLAG == False:
+ change_objects.append(atom)
+ else:
+ change_objects.append(atom)
+
+ # And now, consider all objects, which are in the list 'change_objects'.
+ for atom in change_objects:
+ if len(atom.children) != 0:
+ for atom_child in atom.children:
+ if atom_child.type in {'SURFACE', 'MESH', 'META'}:
+ modify_objects(action_type,
+ atom_child,
+ radius_all,
+ radius_pm,
+ radius_type,
+ radius_type_ionic,
+ sticks_all)
+ else:
+ if atom.type in {'SURFACE', 'MESH', 'META'}:
+ modify_objects(action_type,
+ atom,
+ radius_all,
+ radius_pm,
+ radius_type,
+ radius_type_ionic,
+ sticks_all)
+
+
+# Modifying the radius of a selected atom or stick
+def modify_objects(action_type,
+ atom,
+ radius_all,
+ radius_pm,
+ radius_type,
+ radius_type_ionic,
+ sticks_all):
+
+ # Modify atom radius (in pm)
+ if action_type == "ATOM_RADIUS_PM" and "STICK" not in atom.name.upper():
+ if radius_pm[0] in atom.name:
+ atom.scale = (radius_pm[1]/100,) * 3
+
+ # Modify atom radius (all selected)
+ if action_type == "ATOM_RADIUS_ALL" and "STICK" not in atom.name.upper():
+ atom.scale *= radius_all
+
+ # Modify atom radius (type, van der Waals, atomic or ionic)
+ if action_type == "ATOM_RADIUS_TYPE" and "STICK" not in atom.name.upper():
+ for element in ELEMENTS:
+ if element.name in atom.name:
+ # For ionic radii
+ if radius_type == '3':
+ charge_states = element.radii_ionic[::2]
+ charge_radii = element.radii_ionic[1::2]
+ charge_state_chosen = int(radius_type_ionic) - 4
+
+ find = (lambda searchList, elem:
+ [[i for i, x in enumerate(searchList) if x == e]
+ for e in elem])
+ index = find(charge_states,[charge_state_chosen])[0]
+
+ # Is there a charge state?
+ if index != []:
+ atom.scale = (charge_radii[index[0]],) * 3
+
+ # For atomic and van der Waals radii.
+ else:
+ atom.scale = (element.radii[int(radius_type)],) * 3
+
+ # Modify atom sticks
+ if (action_type == "STICKS_RADIUS_ALL" and 'STICK' in atom.name.upper() and
+ ('CUP' in atom.name.upper() or
+ 'CYLINDER' in atom.name.upper())):
+
+ # Make the cylinder or cup visible first, otherwise one cannot
+ # go into EDIT mode. Note that 'atom' here is in fact a 'stick'
+ # (cylinder or cup).
+ atom.hide_set(False)
+ bpy.context.view_layer.objects.active = atom
+ bpy.ops.object.mode_set(mode='EDIT', toggle=False)
+ bm = bmesh.from_edit_mesh(atom.data)
+
+ locations = []
+ for v in bm.verts:
+ locations.append(v.co)
+
+ center = Vector((0.0,0.0,0.0))
+ center = sum([location for location in locations], center)/len(locations)
+
+ radius = sum([(loc[0]-center[0])**2+(loc[1]-center[1])**2
+ for loc in locations], 0)
+ radius_new = radius * sticks_all
+
+ for v in bm.verts:
+ v.co[0] = ((v.co[0] - center[0]) / radius) * radius_new + center[0]
+ v.co[1] = ((v.co[1] - center[1]) / radius) * radius_new + center[1]
+
+ bpy.ops.object.mode_set(mode='OBJECT', toggle=False)
+ # Hide again the representative stick (cylinder or cup).
+ atom.hide_set(True)
+ bpy.context.view_layer.objects.active = None
+
+ # Replace atom objects
+ if action_type == "ATOM_REPLACE_OBJ" and "STICK" not in atom.name.upper():
+
+ scn = bpy.context.scene.atom_blend
+
+ new_material = draw_obj_material(scn.replace_objs_material,
+ atom.active_material)
+
+ # Special object (like halo, etc.)
+ if scn.replace_objs_special != '0':
+ new_atom = draw_obj_special(scn.replace_objs_special, atom)
+ # Standard geometrical objects
+ else:
+ # If the atom shape shall not be changed, then:
+ if scn.replace_objs == '0':
+ atom.active_material = new_material
+ #return {'FINISHED'}
+ # If the atom shape shall change, then:
+ else:
+ new_atom = draw_obj(scn.replace_objs, atom, new_material)
+
+ # Default shapes and colors for atoms
+ if action_type == "ATOM_DEFAULT_OBJ" and "STICK" not in atom.name.upper():
+
+ scn = bpy.context.scene.atom_blend
+
+ # Create new material
+ new_material = bpy.data.materials.new("tmp")
+ # Create new object (NURBS sphere = '1b')
+ new_atom = draw_obj('1b', atom, new_material)
+ new_atom.active_material = new_material
+ new_material = draw_obj_material('0', new_material)
+
+ # Change size and color of the new object
+ for element in ELEMENTS:
+ if element.name in new_atom.name:
+ new_atom.scale = (element.radii[0],) * 3
+ new_atom.active_material.diffuse_color = element.color
+ new_atom.name = element.name + "_ball"
+ new_atom.active_material.name = element.name
+ break
+
+
+# Separating atoms from a dupliverts strucutre.
+def separate_atoms(scn):
+
+ # Get the mesh.
+ mesh = bpy.context.edit_object
+
+ # Do nothing if it is not a dupliverts structure.
+ if not mesh.instance_type == "VERTS":
+ return {'FINISHED'}
+
+ # This is the name of the mesh
+ mesh_name = mesh.name
+ # Get the collection
+ coll = mesh.users_collection[0]
+
+ # Get the coordinates of the selected vertices (atoms)
+ bm = bmesh.from_edit_mesh(mesh.data)
+ locations = []
+ for v in bm.verts:
+ if v.select:
+ locations.append(mesh.matrix_world @ v.co)
+
+ # Free memory
+ bm.free()
+ del(bm)
+
+ # Delete already the selected vertices
+ bpy.ops.mesh.delete(type='VERT')
+
+ # Find the representative ball within the collection.
+ for obj in coll.objects:
+ if obj.parent != None:
+ if obj.parent.name == mesh_name:
+ break
+
+ # Create balls and put them at the places where the vertices (atoms) have
+ # been before.
+ for location in locations:
+ obj_dupli = obj.copy()
+ obj_dupli.data = obj.data.copy()
+ obj_dupli.parent = None
+ coll.objects.link(obj_dupli)
+ obj_dupli.location = location
+ obj_dupli.name = obj.name + "_sep"
+
+ bpy.ops.object.mode_set(mode='OBJECT', toggle=False)
+ bpy.context.view_layer.objects.active = mesh
+
+
+# Prepare a new material
+def draw_obj_material(material_type, material):
+
+ if material_type == '0': # Unchanged
+ material_new = material
+ if material_type == '1': # Normal
+ material_new = bpy.data.materials.new(material.name + "_normal")
+ if material_type == '2': # Transparent
+ material_new = bpy.data.materials.new(material.name + "_transparent")
+ material_new.metallic = 0.8
+ material_new.specular_intensity = 0.5
+ material_new.roughness = 0.3
+ material_new.blend_method = 'ADD'
+ material_new.show_transparent_back = False
+ # Some properties for cycles
+ material_new.use_nodes = True
+ mat_P_BSDF = material_new.node_tree.nodes['Principled BSDF']
+ mat_P_BSDF.inputs['Metallic'].default_value = 0.1
+ mat_P_BSDF.inputs['Roughness'].default_value = 0.2
+ mat_P_BSDF.inputs['Transmission'].default_value = 0.9
+ mat_P_BSDF.inputs['IOR'].default_value = 0.8
+ if material_type == '3': # Reflecting
+ material_new = bpy.data.materials.new(material.name + "_reflecting")
+ material_new.metallic = 0.5
+ material_new.specular_intensity = 0.5
+ material_new.roughness = 0.0
+ material_new.blend_method = 'OPAQUE'
+ # Some properties for cycles
+ material_new.use_nodes = True
+ mat_P_BSDF = material_new.node_tree.nodes['Principled BSDF']
+ mat_P_BSDF.inputs['Metallic'].default_value = 0.95
+ mat_P_BSDF.inputs['Roughness'].default_value = 0.1
+ mat_P_BSDF.inputs['Transmission'].default_value = 0.0
+ mat_P_BSDF.inputs['IOR'].default_value = 1.0
+ if material_type == '4': # Transparent + reflecting
+ material_new = bpy.data.materials.new(material.name + "_trans+refl")
+ material_new.metallic = 0.3
+ material_new.specular_intensity = 0.5
+ material_new.roughness = 0.3
+ material_new.blend_method = 'ADD'
+ material_new.show_transparent_back = False
+ # Some properties for cycles
+ material_new.use_nodes = True
+ mat_P_BSDF = material_new.node_tree.nodes['Principled BSDF']
+ mat_P_BSDF.inputs['Metallic'].default_value = 0.5
+ mat_P_BSDF.inputs['Roughness'].default_value = 0.2
+ mat_P_BSDF.inputs['Transmission'].default_value = 0.5
+ mat_P_BSDF.inputs['IOR'].default_value = 0.8
+
+ # Always, when the material is changed, a new name is created. Note that
+ # this makes sense: Imagine, an other object uses the same material as the
+ # selected one. After changing the material of the selected object the old
+ # material should certainly not change and remain the same.
+ if material_type in {'1','2','3','4'}:
+ if "_repl" in material.name:
+ pos = material.name.rfind("_repl")
+ if material.name[pos+5:].isdigit():
+ counter = int(material.name[pos+5:])
+ material_new.name = material.name[:pos]+"_repl"+str(counter+1)
+ else:
+ material_new.name = material.name+"_repl1"
+ else:
+ material_new.name = material.name+"_repl1"
+ material_new.diffuse_color = material.diffuse_color
+
+ return material_new
+
+
+# Get the collection of an object.
+def get_collection_object(obj):
+
+ coll_all = obj.users_collection
+ if len(coll_all) > 0:
+ coll = coll_all[0]
+ else:
+ coll = bpy.context.scene.collection
+
+ return coll
+
+
+# Draw an object (e.g. cube, sphere, cylinder, ...)
+def draw_obj(atom_shape, atom, new_material):
+
+ # No change
+ if atom_shape == '0':
+ return None
+
+ if atom_shape == '1a': #Sphere mesh
+ bpy.ops.mesh.primitive_uv_sphere_add(
+ segments=32,
+ ring_count=32,
+ radius=1,
+ view_align=False,
+ enter_editmode=False,
+ location=atom.location,
+ rotation=(0, 0, 0))
+ if atom_shape == '1b': #Sphere NURBS
+ bpy.ops.surface.primitive_nurbs_surface_sphere_add(
+ view_align=False,
+ enter_editmode=False,
+ location=atom.location,
+ rotation=(0.0, 0.0, 0.0))
+ if atom_shape == '2': #Cube
+ bpy.ops.mesh.primitive_cube_add(
+ view_align=False,
+ enter_editmode=False,
+ location=atom.location,
+ rotation=(0.0, 0.0, 0.0))
+ if atom_shape == '3': #Plane
+ bpy.ops.mesh.primitive_plane_add(
+ view_align=False,
+ enter_editmode=False,
+ location=atom.location,
+ rotation=(0.0, 0.0, 0.0))
+ if atom_shape == '4a': #Circle
+ bpy.ops.mesh.primitive_circle_add(
+ vertices=32,
+ radius=1,
+ fill_type='NOTHING',
+ view_align=False,
+ enter_editmode=False,
+ location=atom.location,
+ rotation=(0, 0, 0))
+ if atom_shape == '4b': #Circle NURBS
+ bpy.ops.surface.primitive_nurbs_surface_circle_add(
+ view_align=False,
+ enter_editmode=False,
+ location=atom.location,
+ rotation=(0, 0, 0))
+ if atom_shape in {'5a','5b','5c','5d','5e'}: #Icosphere
+ index = {'5a':1,'5b':2,'5c':3,'5d':4,'5e':5}
+ bpy.ops.mesh.primitive_ico_sphere_add(
+ subdivisions=int(index[atom_shape]),
+ radius=1,
+ view_align=False,
+ enter_editmode=False,
+ location=atom.location,
+ rotation=(0, 0, 0))
+ if atom_shape == '6a': #Cylinder
+ bpy.ops.mesh.primitive_cylinder_add(
+ vertices=32,
+ radius=1,
+ depth=2,
+ end_fill_type='NGON',
+ view_align=False,
+ enter_editmode=False,
+ location=atom.location,
+ rotation=(0, 0, 0))
+ if atom_shape == '6b': #Cylinder NURBS
+ bpy.ops.surface.primitive_nurbs_surface_cylinder_add(
+ view_align=False,
+ enter_editmode=False,
+ location=atom.location,
+ rotation=(0, 0, 0))
+ if atom_shape == '7': #Cone
+ bpy.ops.mesh.primitive_cone_add(
+ vertices=32,
+ radius1=1,
+ radius2=0,
+ depth=2,
+ end_fill_type='NGON',
+ view_align=False,
+ enter_editmode=False,
+ location=atom.location,
+ rotation=(0, 0, 0))
+ if atom_shape == '8a': #Torus
+ bpy.ops.mesh.primitive_torus_add(
+ rotation=(0, 0, 0),
+ location=atom.location,
+ view_align=False,
+ major_radius=1,
+ minor_radius=0.25,
+ major_segments=48,
+ minor_segments=12,
+ abso_major_rad=1,
+ abso_minor_rad=0.5)
+ if atom_shape == '8b': #Torus NURBS
+ bpy.ops.surface.primitive_nurbs_surface_torus_add(
+ view_align=False,
+ enter_editmode=False,
+ location=atom.location,
+ rotation=(0, 0, 0))
+
+ new_atom = bpy.context.view_layer.objects.active
+ new_atom.scale = atom.scale + Vector((0.0,0.0,0.0))
+ new_atom.name = atom.name
+ new_atom.select_set(True)
+
+ new_atom.active_material = new_material
+
+ # If it is the representative object of a duplivert structure then
+ # transfer the parent and hide the new object.
+ if atom.parent != None:
+ new_atom.parent = atom.parent
+ new_atom.hide_set(True)
+
+ # Note the collection where the old object was placed into.
+ coll_old_atom = get_collection_object(atom)
+
+ # Note the collection where the new object was placed into.
+ coll_new_atom_past = get_collection_object(new_atom)
+
+ # If it is not the same collection then ...
+ if coll_new_atom_past != coll_old_atom:
+ # Put the new object into the collection of the old object and ...
+ coll_old_atom.objects.link(new_atom)
+ # ... unlink the new atom from its original collection.
+ coll_new_atom_past.objects.unlink(new_atom)
+
+ # If necessary, remove the childrens of the old object.
+ for child in atom.children:
+ bpy.ops.object.select_all(action='DESELECT')
+ child.hide_set(True)
+ child.select_set(True)
+ child.parent = None
+ coll_child = get_collection_object(child)
+ coll_child.objects.unlink(child)
+ bpy.ops.object.delete()
+ del(child)
+
+ # Deselect everything
+ bpy.ops.object.select_all(action='DESELECT')
+ # Make the old atom visible.
+ atom.hide_set(True)
+ # Select the old atom.
+ atom.select_set(True)
+ # Remove the parent if necessary.
+ atom.parent = None
+ # Unlink the old object from the collection.
+ coll_old_atom.objects.unlink(atom)
+ # Delete the old atom
+ bpy.ops.object.delete()
+ del(atom)
+
+ #if "_F2+_center" or "_F+_center" or "_F0_center" in coll_old_atom:
+ # print("Delete the collection")
+
+ return new_atom
+
+
+# Draw a special object (e.g. halo, etc. ...)
+def draw_obj_special(atom_shape, atom):
+
+ # Note the collection where 'atom' is placed into.
+ coll_atom = get_collection_object(atom)
+
+ # Now, create a collection for the new objects
+ coll_new = atom.name
+ # Create the new collection and ...
+ coll_new = bpy.data.collections.new(coll_new)
+ # ... link it to the collection, which contains 'atom'.
+ coll_atom.children.link(coll_new)
+
+
+ # F2+ center
+ if atom_shape == '1':
+ # Create first a cube
+ bpy.ops.mesh.primitive_cube_add(view_align=False,
+ enter_editmode=False,
+ location=atom.location,
+ rotation=(0.0, 0.0, 0.0))
+ cube = bpy.context.view_layer.objects.active
+ cube.scale = atom.scale + Vector((0.0,0.0,0.0))
+ cube.name = atom.name + "_F2+_vac"
+ cube.select_set(True)
+ # New material for this cube
+ material_cube = bpy.data.materials.new(atom.name + "_F2+_vac")
+ material_cube.diffuse_color = [0.8, 0.0, 0.0, 1.0]
+ material_cube.metallic = 0.8
+ material_cube.specular_intensity = 0.5
+ material_cube.roughness = 0.3
+ material_cube.blend_method = 'ADD'
+ material_cube.show_transparent_back = True
+ # Some properties for cycles
+ material_cube.use_nodes = True
+ mat_P_BSDF = material_cube.node_tree.nodes['Principled BSDF']
+ mat_P_BSDF.inputs['Metallic'].default_value = 0.1
+ mat_P_BSDF.inputs['Roughness'].default_value = 0.2
+ mat_P_BSDF.inputs['Transmission'].default_value = 0.9
+ mat_P_BSDF.inputs['IOR'].default_value = 0.8
+ cube.active_material = material_cube
+ # Put a nice point lamp inside the defect
+ lamp_data = bpy.data.lights.new(name=atom.name + "_F2+_lamp",
+ type="POINT")
+ lamp_data.distance = atom.scale[0] * 2.0
+ lamp_data.energy = 1.0
+ lamp_data.color = (0.8, 0.8, 0.8)
+ lamp = bpy.data.objects.new(atom.name + "_F2+_lamp", lamp_data)
+ lamp.location = Vector((0.0, 0.0, 0.0))
+ bpy.context.collection.objects.link(lamp)
+ lamp.parent = cube
+ # Some properties for cycles
+ lamp.data.use_nodes = True
+ lmp_P_BSDF = lamp.data.node_tree.nodes['Emission']
+ lmp_P_BSDF.inputs['Strength'].default_value = 2000
+ # The new 'atom' is the F2+ defect
+ new_atom = cube
+
+ # Note the collection where all the new objects were placed into.
+ # We use only one object, the cube
+ coll_ori = get_collection_object(cube)
+
+ # If it is not the same collection then ...
+ if coll_ori != coll_new:
+ # Put all new objects into the new collection and ...
+ coll_new.objects.link(cube)
+ coll_new.objects.link(lamp)
+ # ... unlink them from their original collection.
+ coll_ori.objects.unlink(cube)
+ coll_ori.objects.unlink(lamp)
+
+ coll_new.name = atom.name + "_F2+_center"
+
+ if atom.parent != None:
+ cube.parent = atom.parent
+ cube.hide_set(True)
+ lamp.hide_set(True)
+
+ # F+ center
+ if atom_shape == '2':
+ # Create first a cube
+ bpy.ops.mesh.primitive_cube_add(view_align=False,
+ enter_editmode=False,
+ location=atom.location,
+ rotation=(0.0, 0.0, 0.0))
+ cube = bpy.context.view_layer.objects.active
+ cube.scale = atom.scale + Vector((0.0,0.0,0.0))
+ cube.name = atom.name + "_F+_vac"
+ cube.select_set(True)
+ # New material for this cube
+ material_cube = bpy.data.materials.new(atom.name + "_F+_vac")
+ material_cube.diffuse_color = [0.0, 0.0, 0.8, 1.0]
+ material_cube.metallic = 0.8
+ material_cube.specular_intensity = 0.5
+ material_cube.roughness = 0.3
+ material_cube.blend_method = 'ADD'
+ material_cube.show_transparent_back = True
+ # Some properties for cycles
+ material_cube.use_nodes = True
+ mat_P_BSDF = material_cube.node_tree.nodes['Principled BSDF']
+ mat_P_BSDF.inputs['Metallic'].default_value = 0.1
+ mat_P_BSDF.inputs['Roughness'].default_value = 0.2
+ mat_P_BSDF.inputs['Transmission'].default_value = 0.9
+ mat_P_BSDF.inputs['IOR'].default_value = 0.8
+ cube.active_material = material_cube
+ # Create now an electron
+ scale = atom.scale / 10.0
+ bpy.ops.surface.primitive_nurbs_surface_sphere_add(
+ view_align=False,
+ enter_editmode=False,
+ location=(0.0, 0.0, 0.0),
+ rotation=(0.0, 0.0, 0.0))
+ electron = bpy.context.view_layer.objects.active
+ electron.scale = scale
+ electron.name = atom.name + "_F+_electron"
+ electron.parent = cube
+ # New material for the electron
+ material_electron = bpy.data.materials.new(atom.name + "_F+-center")
+ material_electron.diffuse_color = [0.0, 0.0, 0.8, 1.0]
+ material_electron.metallic = 0.8
+ material_electron.specular_intensity = 0.5
+ material_electron.roughness = 0.3
+ material_electron.blend_method = 'OPAQUE'
+ material_electron.show_transparent_back = False
+ electron.active_material = material_electron
+ # Put a nice point lamp inside the electron
+ lamp_data = bpy.data.lights.new(name=atom.name + "_F+_lamp",
+ type="POINT")
+ lamp_data.distance = atom.scale[0] * 2.0
+ lamp_data.energy = 1.0
+ lamp_data.color = (0.8, 0.8, 0.8)
+ lamp = bpy.data.objects.new(atom.name + "_F+_lamp", lamp_data)
+ lamp.location = Vector((scale[0]*1.5, 0.0, 0.0))
+ bpy.context.collection.objects.link(lamp)
+ lamp.parent = cube
+ # Some properties for cycles
+ lamp.data.use_nodes = True
+ lmp_P_BSDF = lamp.data.node_tree.nodes['Emission']
+ lmp_P_BSDF.inputs['Strength'].default_value = 2000
+ # The new 'atom' is the F+ defect complex + lamp
+ new_atom = cube
+
+ # Note the collection where all the new objects were placed into.
+ # We use only one object, the cube
+ coll_ori = get_collection_object(cube)
+
+ # If it is not the same collection then ...
+ if coll_ori != coll_new:
+ # Put all new objects into the new collection and ...
+ coll_new.objects.link(cube)
+ coll_new.objects.link(electron)
+ coll_new.objects.link(lamp)
+ # ... unlink them from their original collection.
+ coll_ori.objects.unlink(cube)
+ coll_ori.objects.unlink(electron)
+ coll_ori.objects.unlink(lamp)
+
+ coll_new.name = atom.name + "_F+_center"
+
+ if atom.parent != None:
+ cube.parent = atom.parent
+ cube.hide_set(True)
+ electron.hide_set(True)
+ lamp.hide_set(True)
+
+ # F0 center
+ if atom_shape == '3':
+ # Create first a cube
+ bpy.ops.mesh.primitive_cube_add(view_align=False,
+ enter_editmode=False,
+ location=atom.location,
+ rotation=(0.0, 0.0, 0.0))
+ cube = bpy.context.view_layer.objects.active
+ cube.scale = atom.scale + Vector((0.0,0.0,0.0))
+ cube.name = atom.name + "_F0_vac"
+ cube.select_set(True)
+ # New material for this cube
+ material_cube = bpy.data.materials.new(atom.name + "_F0_vac")
+ material_cube.diffuse_color = [0.8, 0.8, 0.8, 1.0]
+ material_cube.metallic = 0.8
+ material_cube.specular_intensity = 0.5
+ material_cube.roughness = 0.83
+ material_cube.blend_method = 'ADD'
+ material_cube.show_transparent_back = True
+ # Some properties for cycles
+ material_cube.use_nodes = True
+ mat_P_BSDF = material_cube.node_tree.nodes['Principled BSDF']
+ mat_P_BSDF.inputs['Metallic'].default_value = 0.1
+ mat_P_BSDF.inputs['Roughness'].default_value = 0.2
+ mat_P_BSDF.inputs['Transmission'].default_value = 0.9
+ mat_P_BSDF.inputs['IOR'].default_value = 0.8
+ cube.active_material = material_cube
+ # Create now two electrons
+ scale = atom.scale / 10.0
+ bpy.ops.surface.primitive_nurbs_surface_sphere_add(
+ view_align=False,
+ enter_editmode=False,
+ location=(scale[0]*1.5,0.0,0.0),
+ rotation=(0.0, 0.0, 0.0))
+ electron1 = bpy.context.view_layer.objects.active
+ electron1.scale = scale
+ electron1.name = atom.name + "_F0_electron1"
+ electron1.parent = cube
+ bpy.ops.surface.primitive_nurbs_surface_sphere_add(
+ view_align=False,
+ enter_editmode=False,
+ location=(-scale[0]*1.5,0.0,0.0),
+ rotation=(0.0, 0.0, 0.0))
+ electron2 = bpy.context.view_layer.objects.active
+ electron2.scale = scale
+ electron2.name = atom.name + "_F0_electron2"
+ electron2.parent = cube
+ # New material for the electrons
+ material_electron = bpy.data.materials.new(atom.name + "_F0-center")
+ material_electron.diffuse_color = [0.0, 0.0, 0.8, 1.0]
+ material_electron.metallic = 0.8
+ material_electron.specular_intensity = 0.5
+ material_electron.roughness = 0.3
+ material_electron.blend_method = 'OPAQUE'
+ material_electron.show_transparent_back = False
+ electron1.active_material = material_electron
+ electron2.active_material = material_electron
+ # Put two nice point lamps inside the electrons
+ lamp1_data = bpy.data.lights.new(name=atom.name + "_F0_lamp1",
+ type="POINT")
+ lamp1_data.distance = atom.scale[0] * 2.0
+ lamp1_data.energy = 1.0
+ lamp1_data.color = (0.8, 0.8, 0.8)
+ lamp1 = bpy.data.objects.new(atom.name + "_F0_lamp", lamp1_data)
+ lamp1.location = Vector((scale[0]*1.5, 0.0, 0.0))
+ bpy.context.collection.objects.link(lamp1)
+ lamp1.parent = cube
+ lamp2_data = bpy.data.lights.new(name=atom.name + "_F0_lamp2",
+ type="POINT")
+ lamp2_data.distance = atom.scale[0] * 2.0
+ lamp2_data.energy = 1.0
+ lamp2_data.color = (0.8, 0.8, 0.8)
+ lamp2 = bpy.data.objects.new(atom.name + "_F0_lamp", lamp2_data)
+ lamp2.location = Vector((-scale[0]*1.5, 0.0, 0.0))
+ bpy.context.collection.objects.link(lamp2)
+ lamp2.parent = cube
+ # Some properties for cycles
+ lamp1.data.use_nodes = True
+ lamp2.data.use_nodes = True
+ lmp1_P_BSDF = lamp1.data.node_tree.nodes['Emission']
+ lmp2_P_BSDF = lamp1.data.node_tree.nodes['Emission']
+ lmp1_P_BSDF.inputs['Strength'].default_value = 200
+ lmp2_P_BSDF.inputs['Strength'].default_value = 200
+ # The new 'atom' is the F0 defect complex + lamps
+ new_atom = cube
+
+ # Note the collection where all the new objects were placed into.
+ # We use only one object, the cube
+ coll_ori = get_collection_object(cube)
+
+ # If it is not the same collection then ...
+ if coll_ori != coll_new:
+ # Put all new objects into the collection of 'atom' and ...
+ coll_new.objects.link(cube)
+ coll_new.objects.link(electron1)
+ coll_new.objects.link(electron2)
+ coll_new.objects.link(lamp1)
+ coll_new.objects.link(lamp2)
+ # ... unlink them from their original collection.
+ coll_ori.objects.unlink(cube)
+ coll_ori.objects.unlink(electron1)
+ coll_ori.objects.unlink(electron2)
+ coll_ori.objects.unlink(lamp1)
+ coll_ori.objects.unlink(lamp2)
+
+ coll_new.name = atom.name + "_F0_center"
+
+ if atom.parent != None:
+ cube.parent = atom.parent
+ cube.hide_set(True)
+ electron1.hide_set(True)
+ electron2.hide_set(True)
+ lamp1.hide_set(True)
+ lamp2.hide_set(True)
+
+ # Deselect everything
+ bpy.ops.object.select_all(action='DESELECT')
+ # Make the old atom visible.
+ atom.hide_set(True)
+ # Select the old atom.
+ atom.select_set(True)
+ # Remove the parent if necessary.
+ atom.parent = None
+ # Unlink the old object from the collection.
+ coll_atom.objects.unlink(atom)
+ # Delete the old atom
+ bpy.ops.object.delete()
+ del(atom)
+
+ return new_atom
+
+
+# Initialization of the list 'ELEMENTS'.
+def read_elements():
+
+ del ELEMENTS[:]
+
+ for item in 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 = item[7:]
+
+ li = ElementProp(item[0],item[1],item[2],item[3],
+ radii,radii_ionic)
+ ELEMENTS.append(li)
+
+
+# Custom data file: changing color and radii by using the list 'ELEMENTS'.
+def custom_datafile_change_atom_props():
+
+ for atom in bpy.context.selected_objects:
+ if len(atom.children) != 0:
+ child = atom.children[0]
+ if child.type in {'SURFACE', 'MESH', 'META'}:
+ for element in ELEMENTS:
+ if element.name in atom.name:
+ child.scale = (element.radii[0],) * 3
+ child.active_material.diffuse_color = element.color
+ else:
+ if atom.type in {'SURFACE', 'MESH', 'META'}:
+ for element in ELEMENTS:
+ if element.name in atom.name:
+ atom.scale = (element.radii[0],) * 3
+ atom.active_material.diffuse_color = element.color
+
+
+# Reading a custom data file and modifying the list 'ELEMENTS'.
+def 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.
+ del ELEMENTS[:]
+
+ # Read the data file, which contains all data
+ # (atom name, radii, colors, etc.)
+ data_file_p = 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]),
+ float(color_value[3])]
+ # 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 = ElementProp(number,name,short_name,color,
+ radii, radii_ionic)
+
+ ELEMENTS.append(element)
+
+ data_file_p.close()
+
+ return True
diff --git a/io_mesh_atomic/xyz_export.py b/io_mesh_atomic/xyz_export.py
new file mode 100644
index 00000000..79e99736
--- /dev/null
+++ b/io_mesh_atomic/xyz_export.py
@@ -0,0 +1,83 @@
+# ##### 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 #####
+
+import bpy
+from io_mesh_atomic.xyz_import import ELEMENTS_DEFAULT
+
+
+class AtomsExport(object):
+ __slots__ = ('element', 'location')
+ def __init__(self, element, location):
+ self.element = element
+ self.location = location
+
+
+def export_xyz(obj_type, filepath_xyz):
+
+ list_atoms = []
+ counter = 0
+ for obj in bpy.context.selected_objects:
+
+ if "STICK" in obj.name.upper():
+ continue
+
+ if obj.type not in {'MESH', 'SURFACE', 'META'}:
+ continue
+
+ name = ""
+ for element in ELEMENTS_DEFAULT:
+ if element[1] in obj.name:
+ if element[2] == "Vac":
+ name = "X"
+ else:
+ name = element[2]
+
+ if name == "":
+ if obj_type == "0":
+ name = "?"
+ else:
+ continue
+
+ if len(obj.children) != 0:
+ for vertex in obj.data.vertices:
+ location = obj.matrix_world @ vertex.co
+ list_atoms.append(AtomsExport(name, location))
+ counter += 1
+ else:
+ if not obj.parent:
+ location = obj.location
+ list_atoms.append(AtomsExport(name, location))
+ counter += 1
+
+ xyz_file_p = open(filepath_xyz, "w")
+ xyz_file_p.write("%d\n" % counter)
+ xyz_file_p.write("This XYZ file has been created with Blender "
+ "and the addon Atomic Blender - XYZ. "
+ "For more details see the wiki pages of Blender.\n")
+
+ for i, atom in enumerate(list_atoms):
+ string = "%3s%15.5f%15.5f%15.5f\n" % (
+ atom.element,
+ atom.location[0],
+ atom.location[1],
+ atom.location[2])
+ xyz_file_p.write(string)
+
+ xyz_file_p.close()
+
+ return True
diff --git a/io_mesh_atomic/xyz_gui.py b/io_mesh_atomic/xyz_gui.py
new file mode 100644
index 00000000..79b08f21
--- /dev/null
+++ b/io_mesh_atomic/xyz_gui.py
@@ -0,0 +1,210 @@
+# ##### 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 #####
+
+import bpy
+from bpy.types import Operator, AddonPreferences
+from bpy_extras.io_utils import ImportHelper, ExportHelper
+from bpy.props import (
+ StringProperty,
+ BoolProperty,
+ EnumProperty,
+ IntProperty,
+ FloatProperty,
+ )
+
+from io_mesh_atomic.xyz_import import import_xyz
+from io_mesh_atomic.xyz_import import ALL_FRAMES
+from io_mesh_atomic.xyz_import import ELEMENTS
+from io_mesh_atomic.xyz_import import STRUCTURE
+from io_mesh_atomic.xyz_import import build_frames
+from io_mesh_atomic.xyz_export import export_xyz
+
+# -----------------------------------------------------------------------------
+# Operators
+
+# This is the class for the file dialog.
+class IMPORT_OT_xyz(Operator, ImportHelper):
+ bl_idname = "import_mesh.xyz"
+ bl_label = "Import XYZ (*.xyz)"
+ bl_options = {'PRESET', 'UNDO'}
+
+ filename_ext = ".xyz"
+ filter_glob: StringProperty(default="*.xyz", 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?")
+ ball: EnumProperty(
+ name="Type of ball",
+ description="Choose ball",
+ items=(('0', "NURBS", "NURBS balls"),
+ ('1', "Mesh" , "Mesh balls"),
+ ('2', "Meta" , "Metaballs")),
+ default='0',)
+ 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")
+ 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',)
+ use_center: BoolProperty(
+ name = "Object to origin (first frames)", default=False,
+ description = "Put the object into the global origin, the first frame only")
+ use_center_all: BoolProperty(
+ name = "Object to origin (all frames)", default=True,
+ description = "Put the object into the global origin, all frames")
+ datafile: StringProperty(
+ name = "", description="Path to your custom data file",
+ maxlen = 256, default = "", subtype='FILE_PATH')
+ use_frames: BoolProperty(
+ name = "Load all frames?", default=False,
+ description = "Do you want to load all frames?")
+ skip_frames: IntProperty(
+ name="", default=0, min=0,
+ description="Number of frames you want to skip.")
+ images_per_key: IntProperty(
+ name="", default=1, min=1,
+ description="Choose the number of images between 2 keys.")
+
+ # This thing here just guarantees that the menu entry is not active when the
+ # check box in the addon preferences is not activated! See __init__.py
+ @classmethod
+ def poll(cls, context):
+ pref = context.preferences
+ return pref.addons[__package__].preferences.bool_xyz
+
+ def draw(self, context):
+ layout = self.layout
+ row = layout.row()
+ row.prop(self, "use_camera")
+ row.prop(self, "use_lamp")
+ row = layout.row()
+ col = row.column()
+ col.prop(self, "ball")
+ row = layout.row()
+ row.active = (self.ball == "1")
+ col = row.column(align=True)
+ 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(self, "scale_ballradius")
+ col.prop(self, "scale_distances")
+ row = layout.row()
+ row.prop(self, "use_center")
+ row = layout.row()
+ row.prop(self, "use_center_all")
+ row = layout.row()
+ row.prop(self, "atomradius")
+
+ row = layout.row()
+ row.prop(self, "use_frames")
+ row = layout.row()
+ row.active = self.use_frames
+ col = row.column()
+ col.label(text="Skip frames")
+ col = row.column()
+ col.prop(self, "skip_frames")
+ row = layout.row()
+ row.active = self.use_frames
+ col = row.column()
+ col.label(text="Frames/key")
+ col = row.column()
+ col.prop(self, "images_per_key")
+
+ def execute(self, context):
+
+ del ALL_FRAMES[:]
+ del ELEMENTS[:]
+ del STRUCTURE[:]
+
+ # This is to determine the path.
+ filepath_xyz = bpy.path.abspath(self.filepath)
+
+ # Execute main routine
+ import_xyz(self.ball,
+ self.mesh_azimuth,
+ self.mesh_zenith,
+ self.scale_ballradius,
+ self.atomradius,
+ self.scale_distances,
+ self.use_center,
+ self.use_center_all,
+ self.use_camera,
+ self.use_lamp,
+ filepath_xyz)
+
+ # Load frames
+ if len(ALL_FRAMES) > 1 and self.use_frames:
+
+ build_frames(self.images_per_key, self.skip_frames)
+
+ return {'FINISHED'}
+
+
+# This is the class for the file dialog of the exporter.
+class EXPORT_OT_xyz(Operator, ExportHelper):
+ bl_idname = "export_mesh.xyz"
+ bl_label = "Export XYZ (*.xyz)"
+ filename_ext = ".xyz"
+
+ filter_glob: StringProperty(
+ default="*.xyz", options={'HIDDEN'},)
+
+ atom_xyz_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',)
+
+ # This thing here just guarantees that the menu entry is not active when the
+ # check box in the addon preferences is not activated! See __init__.py
+ @classmethod
+ def poll(cls, context):
+ pref = context.preferences
+ return pref.addons[__package__].preferences.bool_xyz
+
+ def draw(self, context):
+ layout = self.layout
+ row = layout.row()
+ row.prop(self, "atom_xyz_export_type")
+
+ def execute(self, context):
+ export_xyz(self.atom_xyz_export_type, bpy.path.abspath(self.filepath))
+
+ return {'FINISHED'}
diff --git a/io_mesh_atomic/xyz_import.py b/io_mesh_atomic/xyz_import.py
new file mode 100644
index 00000000..fe903f4e
--- /dev/null
+++ b/io_mesh_atomic/xyz_import.py
@@ -0,0 +1,810 @@
+# ##### 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 #####
+
+import os
+import bpy
+from math import pi, sqrt
+from mathutils import Vector, Matrix
+
+# -----------------------------------------------------------------------------
+# Atom 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)
+
+ELEMENTS_DEFAULT = (
+( 1, "Hydrogen", "H", ( 1.0, 1.0, 1.0, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ),
+( 2, "Helium", "He", ( 0.85, 1.0, 1.0, 1.0), 0.93, 0.93, 0.49 ),
+( 3, "Lithium", "Li", ( 0.8, 0.50, 1.0, 1.0), 1.23, 1.23, 2.05 , 1 , 0.68 ),
+( 4, "Beryllium", "Be", ( 0.76, 1.0, 0.0, 1.0), 0.90, 0.90, 1.40 , 1 , 0.44 , 2 , 0.35 ),
+( 5, "Boron", "B", ( 1.0, 0.70, 0.70, 1.0), 0.82, 0.82, 1.17 , 1 , 0.35 , 3 , 0.23 ),
+( 6, "Carbon", "C", ( 0.56, 0.56, 0.56, 1.0), 0.77, 0.77, 0.91 , -4 , 2.60 , 4 , 0.16 ),
+( 7, "Nitrogen", "N", ( 0.18, 0.31, 0.97, 1.0), 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, 1.0), 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, 1.0), 0.72, 0.72, 0.57 , -1 , 1.33 , 7 , 0.08 ),
+(10, "Neon", "Ne", ( 0.70, 0.89, 0.96, 1.0), 0.71, 0.71, 0.51 , 1 , 1.12 ),
+(11, "Sodium", "Na", ( 0.67, 0.36, 0.94, 1.0), 1.54, 1.54, 2.23 , 1 , 0.97 ),
+(12, "Magnesium", "Mg", ( 0.54, 1.0, 0.0, 1.0), 1.36, 1.36, 1.72 , 1 , 0.82 , 2 , 0.66 ),
+(13, "Aluminium", "Al", ( 0.74, 0.65, 0.65, 1.0), 1.18, 1.18, 1.82 , 3 , 0.51 ),
+(14, "Silicon", "Si", ( 0.94, 0.78, 0.62, 1.0), 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, 1.0), 1.06, 1.06, 1.23 , -3 , 2.12 , 3 , 0.44 , 5 , 0.35 ),
+(16, "Sulfur", "S", ( 1.0, 1.0, 0.18, 1.0), 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, 1.0), 0.99, 0.99, 0.97 , -1 , 1.81 , 5 , 0.34 , 7 , 0.27 ),
+(18, "Argon", "Ar", ( 0.50, 0.81, 0.89, 1.0), 0.98, 0.98, 0.88 , 1 , 1.54 ),
+(19, "Potassium", "K", ( 0.56, 0.25, 0.83, 1.0), 2.03, 2.03, 2.77 , 1 , 0.81 ),
+(20, "Calcium", "Ca", ( 0.23, 1.0, 0.0, 1.0), 1.74, 1.74, 2.23 , 1 , 1.18 , 2 , 0.99 ),
+(21, "Scandium", "Sc", ( 0.90, 0.90, 0.90, 1.0), 1.44, 1.44, 2.09 , 3 , 0.73 ),
+(22, "Titanium", "Ti", ( 0.74, 0.76, 0.78, 1.0), 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, 1.0), 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, 1.0), 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, 1.0), 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, 1.0), 1.17, 1.17, 1.72 , 2 , 0.74 , 3 , 0.64 ),
+(27, "Cobalt", "Co", ( 0.94, 0.56, 0.62, 1.0), 1.16, 1.16, 1.67 , 2 , 0.72 , 3 , 0.63 ),
+(28, "Nickel", "Ni", ( 0.31, 0.81, 0.31, 1.0), 1.15, 1.15, 1.62 , 2 , 0.69 ),
+(29, "Copper", "Cu", ( 0.78, 0.50, 0.2, 1.0), 1.17, 1.17, 1.57 , 1 , 0.96 , 2 , 0.72 ),
+(30, "Zinc", "Zn", ( 0.49, 0.50, 0.69, 1.0), 1.25, 1.25, 1.53 , 1 , 0.88 , 2 , 0.74 ),
+(31, "Gallium", "Ga", ( 0.76, 0.56, 0.56, 1.0), 1.26, 1.26, 1.81 , 1 , 0.81 , 3 , 0.62 ),
+(32, "Germanium", "Ge", ( 0.4, 0.56, 0.56, 1.0), 1.22, 1.22, 1.52 , -4 , 2.72 , 2 , 0.73 , 4 , 0.53 ),
+(33, "Arsenic", "As", ( 0.74, 0.50, 0.89, 1.0), 1.20, 1.20, 1.33 , -3 , 2.22 , 3 , 0.58 , 5 , 0.46 ),
+(34, "Selenium", "Se", ( 1.0, 0.63, 0.0, 1.0), 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, 1.0), 1.14, 1.14, 1.12 , -1 , 1.96 , 5 , 0.47 , 7 , 0.39 ),
+(36, "Krypton", "Kr", ( 0.36, 0.72, 0.81, 1.0), 1.31, 1.31, 1.24 ),
+(37, "Rubidium", "Rb", ( 0.43, 0.18, 0.69, 1.0), 2.16, 2.16, 2.98 , 1 , 1.47 ),
+(38, "Strontium", "Sr", ( 0.0, 1.0, 0.0, 1.0), 1.91, 1.91, 2.45 , 2 , 1.12 ),
+(39, "Yttrium", "Y", ( 0.58, 1.0, 1.0, 1.0), 1.62, 1.62, 2.27 , 3 , 0.89 ),
+(40, "Zirconium", "Zr", ( 0.58, 0.87, 0.87, 1.0), 1.45, 1.45, 2.16 , 1 , 1.09 , 4 , 0.79 ),
+(41, "Niobium", "Nb", ( 0.45, 0.76, 0.78, 1.0), 1.34, 1.34, 2.08 , 1 , 1.00 , 4 , 0.74 , 5 , 0.69 ),
+(42, "Molybdenum", "Mo", ( 0.32, 0.70, 0.70, 1.0), 1.30, 1.30, 2.01 , 1 , 0.93 , 4 , 0.70 , 6 , 0.62 ),
+(43, "Technetium", "Tc", ( 0.23, 0.61, 0.61, 1.0), 1.27, 1.27, 1.95 , 7 , 0.97 ),
+(44, "Ruthenium", "Ru", ( 0.14, 0.56, 0.56, 1.0), 1.25, 1.25, 1.89 , 4 , 0.67 ),
+(45, "Rhodium", "Rh", ( 0.03, 0.49, 0.54, 1.0), 1.25, 1.25, 1.83 , 3 , 0.68 ),
+(46, "Palladium", "Pd", ( 0.0, 0.41, 0.52, 1.0), 1.28, 1.28, 1.79 , 2 , 0.80 , 4 , 0.65 ),
+(47, "Silver", "Ag", ( 0.75, 0.75, 0.75, 1.0), 1.34, 1.34, 1.75 , 1 , 1.26 , 2 , 0.89 ),
+(48, "Cadmium", "Cd", ( 1.0, 0.85, 0.56, 1.0), 1.48, 1.48, 1.71 , 1 , 1.14 , 2 , 0.97 ),
+(49, "Indium", "In", ( 0.65, 0.45, 0.45, 1.0), 1.44, 1.44, 2.00 , 3 , 0.81 ),
+(50, "Tin", "Sn", ( 0.4, 0.50, 0.50, 1.0), 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, 1.0), 1.40, 1.40, 1.53 , -3 , 2.45 , 3 , 0.76 , 5 , 0.62 ),
+(52, "Tellurium", "Te", ( 0.83, 0.47, 0.0, 1.0), 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, 1.0), 1.33, 1.33, 1.32 , -1 , 2.20 , 5 , 0.62 , 7 , 0.50 ),
+(54, "Xenon", "Xe", ( 0.25, 0.61, 0.69, 1.0), 1.31, 1.31, 1.24 ),
+(55, "Caesium", "Cs", ( 0.34, 0.09, 0.56, 1.0), 2.35, 2.35, 3.35 , 1 , 1.67 ),
+(56, "Barium", "Ba", ( 0.0, 0.78, 0.0, 1.0), 1.98, 1.98, 2.78 , 1 , 1.53 , 2 , 1.34 ),
+(57, "Lanthanum", "La", ( 0.43, 0.83, 1.0, 1.0), 1.69, 1.69, 2.74 , 1 , 1.39 , 3 , 1.06 ),
+(58, "Cerium", "Ce", ( 1.0, 1.0, 0.78, 1.0), 1.65, 1.65, 2.70 , 1 , 1.27 , 3 , 1.03 , 4 , 0.92 ),
+(59, "Praseodymium", "Pr", ( 0.85, 1.0, 0.78, 1.0), 1.65, 1.65, 2.67 , 3 , 1.01 , 4 , 0.90 ),
+(60, "Neodymium", "Nd", ( 0.78, 1.0, 0.78, 1.0), 1.64, 1.64, 2.64 , 3 , 0.99 ),
+(61, "Promethium", "Pm", ( 0.63, 1.0, 0.78, 1.0), 1.63, 1.63, 2.62 , 3 , 0.97 ),
+(62, "Samarium", "Sm", ( 0.56, 1.0, 0.78, 1.0), 1.62, 1.62, 2.59 , 3 , 0.96 ),
+(63, "Europium", "Eu", ( 0.38, 1.0, 0.78, 1.0), 1.85, 1.85, 2.56 , 2 , 1.09 , 3 , 0.95 ),
+(64, "Gadolinium", "Gd", ( 0.27, 1.0, 0.78, 1.0), 1.61, 1.61, 2.54 , 3 , 0.93 ),
+(65, "Terbium", "Tb", ( 0.18, 1.0, 0.78, 1.0), 1.59, 1.59, 2.51 , 3 , 0.92 , 4 , 0.84 ),
+(66, "Dysprosium", "Dy", ( 0.12, 1.0, 0.78, 1.0), 1.59, 1.59, 2.49 , 3 , 0.90 ),
+(67, "Holmium", "Ho", ( 0.0, 1.0, 0.61, 1.0), 1.58, 1.58, 2.47 , 3 , 0.89 ),
+(68, "Erbium", "Er", ( 0.0, 0.90, 0.45, 1.0), 1.57, 1.57, 2.45 , 3 , 0.88 ),
+(69, "Thulium", "Tm", ( 0.0, 0.83, 0.32, 1.0), 1.56, 1.56, 2.42 , 3 , 0.87 ),
+(70, "Ytterbium", "Yb", ( 0.0, 0.74, 0.21, 1.0), 1.74, 1.74, 2.40 , 2 , 0.93 , 3 , 0.85 ),
+(71, "Lutetium", "Lu", ( 0.0, 0.67, 0.14, 1.0), 1.56, 1.56, 2.25 , 3 , 0.85 ),
+(72, "Hafnium", "Hf", ( 0.30, 0.76, 1.0, 1.0), 1.44, 1.44, 2.16 , 4 , 0.78 ),
+(73, "Tantalum", "Ta", ( 0.30, 0.65, 1.0, 1.0), 1.34, 1.34, 2.09 , 5 , 0.68 ),
+(74, "Tungsten", "W", ( 0.12, 0.58, 0.83, 1.0), 1.30, 1.30, 2.02 , 4 , 0.70 , 6 , 0.62 ),
+(75, "Rhenium", "Re", ( 0.14, 0.49, 0.67, 1.0), 1.28, 1.28, 1.97 , 4 , 0.72 , 7 , 0.56 ),
+(76, "Osmium", "Os", ( 0.14, 0.4, 0.58, 1.0), 1.26, 1.26, 1.92 , 4 , 0.88 , 6 , 0.69 ),
+(77, "Iridium", "Ir", ( 0.09, 0.32, 0.52, 1.0), 1.27, 1.27, 1.87 , 4 , 0.68 ),
+(78, "Platinum", "Pt", ( 0.81, 0.81, 0.87, 1.0), 1.30, 1.30, 1.83 , 2 , 0.80 , 4 , 0.65 ),
+(79, "Gold", "Au", ( 1.0, 0.81, 0.13, 1.0), 1.34, 1.34, 1.79 , 1 , 1.37 , 3 , 0.85 ),
+(80, "Mercury", "Hg", ( 0.72, 0.72, 0.81, 1.0), 1.49, 1.49, 1.76 , 1 , 1.27 , 2 , 1.10 ),
+(81, "Thallium", "Tl", ( 0.65, 0.32, 0.30, 1.0), 1.48, 1.48, 2.08 , 1 , 1.47 , 3 , 0.95 ),
+(82, "Lead", "Pb", ( 0.34, 0.34, 0.38, 1.0), 1.47, 1.47, 1.81 , 2 , 1.20 , 4 , 0.84 ),
+(83, "Bismuth", "Bi", ( 0.61, 0.30, 0.70, 1.0), 1.46, 1.46, 1.63 , 1 , 0.98 , 3 , 0.96 , 5 , 0.74 ),
+(84, "Polonium", "Po", ( 0.67, 0.36, 0.0, 1.0), 1.46, 1.46, 1.53 , 6 , 0.67 ),
+(85, "Astatine", "At", ( 0.45, 0.30, 0.27, 1.0), 1.45, 1.45, 1.43 , -3 , 2.22 , 3 , 0.85 , 5 , 0.46 ),
+(86, "Radon", "Rn", ( 0.25, 0.50, 0.58, 1.0), 1.00, 1.00, 1.34 ),
+(87, "Francium", "Fr", ( 0.25, 0.0, 0.4, 1.0), 1.00, 1.00, 1.00 , 1 , 1.80 ),
+(88, "Radium", "Ra", ( 0.0, 0.49, 0.0, 1.0), 1.00, 1.00, 1.00 , 2 , 1.43 ),
+(89, "Actinium", "Ac", ( 0.43, 0.67, 0.98, 1.0), 1.00, 1.00, 1.00 , 3 , 1.18 ),
+(90, "Thorium", "Th", ( 0.0, 0.72, 1.0, 1.0), 1.65, 1.65, 1.00 , 4 , 1.02 ),
+(91, "Protactinium", "Pa", ( 0.0, 0.63, 1.0, 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, 1.0), 1.42, 1.42, 1.00 , 4 , 0.97 , 6 , 0.80 ),
+(93, "Neptunium", "Np", ( 0.0, 0.50, 1.0, 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, 1.0), 1.00, 1.00, 1.00 , 3 , 1.08 , 4 , 0.93 ),
+(95, "Americium", "Am", ( 0.32, 0.36, 0.94, 1.0), 1.00, 1.00, 1.00 , 3 , 1.07 , 4 , 0.92 ),
+(96, "Curium", "Cm", ( 0.47, 0.36, 0.89, 1.0), 1.00, 1.00, 1.00 ),
+(97, "Berkelium", "Bk", ( 0.54, 0.30, 0.89, 1.0), 1.00, 1.00, 1.00 ),
+(98, "Californium", "Cf", ( 0.63, 0.21, 0.83, 1.0), 1.00, 1.00, 1.00 ),
+(99, "Einsteinium", "Es", ( 0.70, 0.12, 0.83, 1.0), 1.00, 1.00, 1.00 ),
+(100, "Fermium", "Fm", ( 0.70, 0.12, 0.72, 1.0), 1.00, 1.00, 1.00 ),
+(101, "Mendelevium", "Md", ( 0.70, 0.05, 0.65, 1.0), 1.00, 1.00, 1.00 ),
+(102, "Nobelium", "No", ( 0.74, 0.05, 0.52, 1.0), 1.00, 1.00, 1.00 ),
+(103, "Lawrencium", "Lr", ( 0.78, 0.0, 0.4, 1.0), 1.00, 1.00, 1.00 ),
+(104, "Vacancy", "Vac", ( 0.5, 0.5, 0.5, 1.0), 1.00, 1.00, 1.00),
+(105, "Default", "Default", ( 1.0, 1.0, 1.0, 1.0), 1.00, 1.00, 1.00),
+(106, "Stick", "Stick", ( 0.5, 0.5, 0.5, 1.0), 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 (ElementProp). 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 for instance.
+ELEMENTS = []
+
+# This is the list, which contains all atoms of all frames! Each item is a
+# list which contains the atoms of a single frame. It is a list of
+# 'AtomProp'.
+ALL_FRAMES = []
+
+# A list of ALL balls which are put into the scene
+STRUCTURE = []
+
+
+# This is the class, which stores the properties for one element.
+class ElementProp(object):
+ __slots__ = ('number', 'name', 'short_name', 'color', 'radii', 'radii_ionic')
+ 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 AtomProp(object):
+ __slots__ = ('element', 'name', 'location', 'radius', 'color', 'material')
+ 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
+
+
+# -----------------------------------------------------------------------------
+# Some basic routines
+
+def read_elements():
+
+ del ELEMENTS[:]
+
+ for item in 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 = ElementProp(item[0],item[1],item[2],item[3],
+ radii,radii_ionic)
+ ELEMENTS.append(li)
+
+
+# filepath_pdb: path to pdb file
+# radiustype : '0' default
+# '1' atomic radii
+# '2' van der Waals
+def read_xyz_file(filepath_xyz,radiustype):
+
+ number_frames = 0
+ total_number_atoms = 0
+
+ # Open the file ...
+ filepath_xyz_p = open(filepath_xyz, "r")
+
+ #Go through the whole file.
+ FLAG = False
+ for line in filepath_xyz_p:
+
+ # ... the loop is broken here (EOF) ...
+ if line == "":
+ continue
+
+ split_list = line.rsplit()
+
+ if len(split_list) == 1:
+ number_atoms = int(split_list[0])
+ FLAG = True
+
+ if FLAG == True:
+
+ line = filepath_xyz_p.readline()
+ line = line.rstrip()
+
+ all_atoms= []
+ for i in range(number_atoms):
+
+
+ # This is a guarantee that only the total number of atoms of the
+ # first frame is used. Condition is, so far, that the number of
+ # atoms in a xyz file is constant. However, sometimes the number
+ # may increase (or decrease). If it decreases, the addon crashes.
+ # If it increases, only the tot number of atoms of the first frame
+ # is used.
+ # By time, I will allow varying atom numbers ... but this takes
+ # some time ...
+ if number_frames != 0:
+ if i >= total_number_atoms:
+ break
+
+
+ line = filepath_xyz_p.readline()
+ line = line.rstrip()
+ split_list = line.rsplit()
+ short_name = str(split_list[0])
+
+ # Go through all elements and find the element of the current atom.
+ FLAG_FOUND = False
+ for element in ELEMENTS:
+ if str.upper(short_name) == str.upper(element.short_name):
+ # Give the atom its proper name, color and radius:
+ 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(ELEMENTS[-3].radii[int(radiustype)])
+ color = ELEMENTS[-3].color
+ # ... take what is written in the xyz 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:
+ name = str.upper(short_name)
+ radius = float(ELEMENTS[-2].radii[int(radiustype)])
+ color = ELEMENTS[-2].color
+
+ x = float(split_list[1])
+ y = float(split_list[2])
+ z = float(split_list[3])
+
+ location = Vector((x,y,z))
+
+ all_atoms.append([short_name, name, location, radius, color])
+
+ # We note here all elements. This needs to be done only once.
+ if number_frames == 0:
+
+ # This is a guarantee that only the total number of atoms of the
+ # first frame is used. Condition is, so far, that the number of
+ # atoms in a xyz file is constant. However, sometimes the number
+ # may increase (or decrease). If it decreases, the addon crashes.
+ # If it increases, only the tot number of atoms of the first frame
+ # is used.
+ # By time, I will allow varying atom numbers ... but this takes
+ # some time ...
+ total_number_atoms = number_atoms
+
+
+ elements = []
+ for atom in all_atoms:
+ FLAG_FOUND = False
+ for element in elements:
+ # If the atom name is already in the list,
+ # FLAG on 'True'.
+ if element == atom[1]:
+ 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.
+ elements.append(atom[1])
+
+ # Sort the atoms: create lists of atoms of one type
+ structure = []
+ for element in elements:
+ atoms_one_type = []
+ for atom in all_atoms:
+ if atom[1] == element:
+ atoms_one_type.append(AtomProp(atom[0],
+ atom[1],
+ atom[2],
+ atom[3],
+ atom[4],[]))
+ structure.append(atoms_one_type)
+
+ ALL_FRAMES.append(structure)
+ number_frames += 1
+ FLAG = False
+
+ filepath_xyz_p.close()
+
+ return total_number_atoms
+
+
+# Rotate an object.
+def rotate_object(rot_mat, obj):
+
+ bpy.ops.object.select_all(action='DESELECT')
+ obj.select_set(True)
+
+ # Decompose world_matrix's components, and from them assemble 4x4 matrices.
+ orig_loc, orig_rot, orig_scale = obj.matrix_world.decompose()
+
+ orig_loc_mat = Matrix.Translation(orig_loc)
+ orig_rot_mat = orig_rot.to_matrix().to_4x4()
+ orig_scale_mat = (Matrix.Scale(orig_scale[0],4,(1,0,0)) @
+ Matrix.Scale(orig_scale[1],4,(0,1,0)) @
+ Matrix.Scale(orig_scale[2],4,(0,0,1)))
+
+ # Assemble the new matrix.
+ obj.matrix_world = orig_loc_mat @ rot_mat @ orig_rot_mat @ orig_scale_mat
+
+
+# Function, which puts a camera and light source into the 3D scene
+def camera_light_source(use_camera,
+ use_light,
+ object_center_vec,
+ object_size):
+
+ 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 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((sqrt(object_size) * camera_factor,
+ 0.0,
+ sqrt(object_size) * camera_factor))
+ camera_xyz_vec = object_center_vec + object_camera_vec
+
+ # Create the camera
+ camera_data = bpy.data.cameras.new("A_camera")
+ camera_data.lens = 45
+ camera_data.clip_end = 500.0
+ camera = bpy.data.objects.new("A_camera", camera_data)
+ camera.location = camera_xyz_vec
+ bpy.context.collection.objects.link(camera)
+
+ # 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.
+ camera.rotation_euler = Matrix.Rotation(angle, 4, axis_vec).to_euler()
+
+ # Rotate the camera around its axis by 90° such that we have a nice
+ # camera position and view onto the object.
+ bpy.ops.object.select_all(action='DESELECT')
+ camera.select_set(True)
+
+ # Rotate the camera around its axis 'object_camera_vec' by 90° such
+ # that we have a nice camera view onto the object.
+ matrix_rotation = Matrix.Rotation(90/360*2*pi, 4, object_camera_vec)
+ rotate_object(matrix_rotation, camera)
+
+ # Here a lamp is put into the scene, if chosen.
+ if use_light == True:
+
+ # This is the distance from the object measured in terms of %
+ # of the camera distance. It is set onto 50% (1/2) distance.
+ light_dl = 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).
+ light_dy_right = light_dl * (3.0/4.0)
+
+ # Create x, y and z for the lamp.
+ object_light_vec = Vector((light_dl,light_dy_right,light_dl))
+ light_xyz_vec = object_center_vec + object_light_vec
+
+ # Create the lamp
+ light_data = bpy.data.lights.new(name="A_light", type="SUN")
+ light_data.distance = 500.0
+ light_data.energy = 3.0
+ lamp = bpy.data.objects.new("A_light", light_data)
+ lamp.location = light_xyz_vec
+ bpy.context.collection.objects.link(lamp)
+
+ # Some settings for the World: a bit ambient occlusion
+ bpy.context.scene.world.light_settings.use_ambient_occlusion = True
+ bpy.context.scene.world.light_settings.ao_factor = 0.2
+ # Some properties for cycles
+ lamp.data.use_nodes = True
+ lmp_P_BSDF = lamp.data.node_tree.nodes['Emission']
+ lmp_P_BSDF.inputs['Strength'].default_value = 5
+
+# -----------------------------------------------------------------------------
+# The main routine
+
+def import_xyz(Ball_type,
+ Ball_azimuth,
+ Ball_zenith,
+ Ball_radius_factor,
+ radiustype,
+ Ball_distance_factor,
+ put_to_center,
+ put_to_center_all,
+ use_camera,
+ use_light,
+ filepath_xyz):
+
+ # List of materials
+ atom_material_list = []
+
+ # ------------------------------------------------------------------------
+ # INITIALIZE THE ELEMENT LIST
+
+ read_elements()
+
+ # ------------------------------------------------------------------------
+ # READING DATA OF ATOMS
+
+ Number_of_total_atoms = read_xyz_file(filepath_xyz, radiustype)
+
+ # We show the atoms of the first frame.
+ first_frame = ALL_FRAMES[0]
+
+ # ------------------------------------------------------------------------
+ # MATERIAL PROPERTIES FOR ATOMS
+
+ # Create first a new list of materials for each type of atom
+ # (e.g. hydrogen)
+ for atoms_of_one_type in first_frame:
+ # Take the first atom
+ atom = atoms_of_one_type[0]
+ material = bpy.data.materials.new(atom.name)
+ material.name = atom.name
+ material.diffuse_color = atom.color
+ atom_material_list.append(material)
+
+ # Now, we go through all atoms and give them a material. For all atoms ...
+ for atoms_of_one_type in first_frame:
+ for atom in atoms_of_one_type:
+ # ... 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
+ # The vacancy is represented by a transparent cube.
+ if atom.name == "Vacancy":
+ material.metallic = 0.8
+ material.specular_intensity = 0.5
+ material.roughness = 0.3
+ material.blend_method = 'ADD'
+ material.show_transparent_back = False
+ # Some properties for cycles
+ material.use_nodes = True
+ mat_P_BSDF = material.node_tree.nodes['Principled BSDF']
+ mat_P_BSDF.inputs['Metallic'].default_value = 0.1
+ mat_P_BSDF.inputs['Roughness'].default_value = 0.2
+ mat_P_BSDF.inputs['Transmission'].default_value = 0.97
+ mat_P_BSDF.inputs['IOR'].default_value = 0.8
+ # The atom gets its properties.
+ atom.material = material
+
+ # ------------------------------------------------------------------------
+ # TRANSLATION OF THE STRUCTURE TO THE ORIGIN
+
+ # It may happen that the structure in a XYZ file already has an offset
+
+
+ # If chosen, the structure is put into the center of the scene
+ # (only the first frame).
+ if put_to_center == True and put_to_center_all == False:
+
+ sum_vec = Vector((0.0,0.0,0.0))
+
+ # Sum of all atom coordinates
+ for atoms_of_one_type in first_frame:
+ sum_vec = sum([atom.location for atom in atoms_of_one_type], 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 atoms_of_one_type in first_frame:
+ for atom in atoms_of_one_type:
+ atom.location -= sum_vec
+
+ # If chosen, the structure is put into the center of the scene
+ # (all frames).
+ if put_to_center_all == True:
+
+ # For all frames
+ for frame in ALL_FRAMES:
+
+ sum_vec = Vector((0.0,0.0,0.0))
+
+ # Sum of all atom coordinates
+ for (i, atoms_of_one_type) in enumerate(frame):
+
+ # This is a guarantee that only the total number of atoms of the
+ # first frame is used. Condition is, so far, that the number of
+ # atoms in a xyz file is constant. However, sometimes the number
+ # may increase (or decrease). If it decreases, the addon crashes.
+ # If it increases, only the tot number of atoms of the first frame
+ # is used.
+ # By time, I will allow varying atom numbers ... but this takes
+ # some time ...
+ if i >= Number_of_total_atoms:
+ break
+
+ sum_vec = sum([atom.location for atom in atoms_of_one_type], 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 atoms_of_one_type in frame:
+ for atom in atoms_of_one_type:
+ atom.location -= sum_vec
+
+
+ # ------------------------------------------------------------------------
+ # SCALING
+
+ # Take all atoms and adjust their radii and scale the distances.
+ for atoms_of_one_type in first_frame:
+ for atom in atoms_of_one_type:
+ 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 ...
+ for atoms_of_one_type in first_frame:
+ sum_vec = sum([atom.location for atom in atoms_of_one_type], 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 farthest 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 = []
+ for atoms_of_one_type in first_frame:
+ object_size_vec += [atom.location - object_center_vec for atom in atoms_of_one_type]
+
+ object_size = 0.0
+ object_size = max(object_size_vec).length
+
+ # ------------------------------------------------------------------------
+ # COLLECTION
+
+ # Before we start to draw the atoms, we first create a collection for the
+ # atomic structure. All atoms (balls) are put into this collection.
+ coll_structure_name = os.path.basename(filepath_xyz)
+ scene = bpy.context.scene
+ coll_structure = bpy.data.collections.new(coll_structure_name)
+ scene.collection.children.link(coll_structure)
+
+ # ------------------------------------------------------------------------
+ # DRAWING THE ATOMS
+
+ bpy.ops.object.select_all(action='DESELECT')
+
+ # For each list of atoms of ONE type (e.g. Hydrogen)
+ for atoms_of_one_type in first_frame:
+
+ # Create first the vertices composed of the coordinates of all
+ # atoms of one type
+ atom_vertices = []
+ for atom in atoms_of_one_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.location - object_center_vec )
+
+ # First, we create a collection of the element, which
+ # contains the atoms (balls + mesh)!
+ coll_element_name = atom.name # the element name
+ # Create the new collection and ...
+ coll_element = bpy.data.collections.new(coll_element_name)
+ # ... link it to the collection, which contains all parts of the
+ # structure.
+ coll_structure.children.link(coll_element)
+
+ # Now, create a collection for the atoms, which includes the
+ # representative ball and the mesh.
+ coll_atom_name = atom.name + "_atom"
+ # Create the new collection and ...
+ coll_atom = bpy.data.collections.new(coll_atom_name)
+ # ... link it to the collection, which contains all parts of the
+ # element (ball and mesh).
+ coll_element.children.link(coll_atom)
+
+ # Build the mesh
+ atom_mesh = bpy.data.meshes.new("Mesh_"+atom.name)
+ atom_mesh.from_pydata(atom_vertices, [], [])
+ atom_mesh.update()
+ new_atom_mesh = bpy.data.objects.new(atom.name + "_mesh", atom_mesh)
+
+ # Link active object to the new collection
+ coll_atom.objects.link(new_atom_mesh)
+
+ # Now, build a representative sphere (atom)
+ if atom.name == "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))
+ else:
+ # NURBS balls
+ if Ball_type == "0":
+ 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))
+ # UV balls
+ elif Ball_type == "1":
+ 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))
+ # Meta balls
+ elif Ball_type == "2":
+ bpy.ops.object.metaball_add(type='BALL', view_align=False,
+ enter_editmode=False, location=(0, 0, 0),
+ rotation=(0, 0, 0))
+
+ ball = bpy.context.view_layer.objects.active
+ # Hide this ball because its appearance has no meaning. It is just the
+ # representative ball. The ball is visible at the vertices of the mesh.
+ # Rememmber, this is a dupliverts construct!
+ ball.hide_set(True)
+ # Scale up/down the ball radius.
+ ball.scale = (atom.radius*Ball_radius_factor,) * 3
+
+ if atom.name == "Vacancy":
+ ball.name = atom.name + "_cube"
+ else:
+ ball.name = atom.name + "_ball"
+ ball.active_material = atom.material
+ ball.parent = new_atom_mesh
+ new_atom_mesh.instance_type = 'VERTS'
+ # The object is back translated to 'object_center_vec'.
+ new_atom_mesh.location = object_center_vec
+ STRUCTURE.append(new_atom_mesh)
+
+ # Note the collection where the ball was placed into.
+ coll_all = ball.users_collection
+ if len(coll_all) > 0:
+ coll_past = coll_all[0]
+ else:
+ coll_past = bpy.context.scene.collection
+
+ # Put the atom into the new collection 'atom' and ...
+ coll_atom.objects.link(ball)
+ # ... unlink the atom from the other collection.
+ coll_past.objects.unlink(ball)
+
+ # ------------------------------------------------------------------------
+ # CAMERA and LIGHT SOURCES
+
+ camera_light_source(use_camera,
+ use_light,
+ object_center_vec,
+ object_size)
+
+ # ------------------------------------------------------------------------
+ # SELECT ALL LOADED OBJECTS
+
+ bpy.ops.object.select_all(action='DESELECT')
+ obj = None
+ for obj in STRUCTURE:
+ obj.select_set(True)
+ # activate the last selected object (perhaps another should be active?)
+ if obj:
+ bpy.context.view_layer.objects.active = obj
+
+
+
+def build_frames(frame_delta, frame_skip):
+
+ scn = bpy.context.scene
+
+ # Introduce the basis for all elements that appear in the structure.
+ for element in STRUCTURE:
+
+ bpy.ops.object.select_all(action='DESELECT')
+ bpy.context.view_layer.objects.active = element
+ element.select_set(True)
+ bpy.ops.object.shape_key_add(True)
+
+ frame_skip += 1
+
+ # Introduce the keys and reference the atom positions for each key.
+ i = 0
+ for j, frame in enumerate(ALL_FRAMES):
+
+ if j % frame_skip == 0:
+
+ for elements_frame, elements_structure in zip(frame,STRUCTURE):
+
+ key = elements_structure.shape_key_add()
+
+ for atom_frame, atom_structure in zip(elements_frame, key.data):
+
+ atom_structure.co = (atom_frame.location
+ - elements_structure.location)
+
+ key.name = atom_frame.name + "_frame_" + str(i)
+
+ i += 1
+
+ num_frames = i
+
+ scn.frame_start = 0
+ scn.frame_end = frame_delta * num_frames
+
+ # Manage the values of the keys
+ for element in STRUCTURE:
+
+ scn.frame_current = 0
+
+ element.data.shape_keys.key_blocks[1].value = 1.0
+ element.data.shape_keys.key_blocks[2].value = 0.0
+ element.data.shape_keys.key_blocks[1].keyframe_insert("value")
+ element.data.shape_keys.key_blocks[2].keyframe_insert("value")
+
+ scn.frame_current += frame_delta
+
+ number = 0
+
+ for number in range(num_frames)[2:]:#-1]:
+
+ element.data.shape_keys.key_blocks[number-1].value = 0.0
+ element.data.shape_keys.key_blocks[number].value = 1.0
+ element.data.shape_keys.key_blocks[number+1].value = 0.0
+ element.data.shape_keys.key_blocks[number-1].keyframe_insert("value")
+ element.data.shape_keys.key_blocks[number].keyframe_insert("value")
+ element.data.shape_keys.key_blocks[number+1].keyframe_insert("value")
+
+ scn.frame_current += frame_delta
+
+ number += 1
+
+ element.data.shape_keys.key_blocks[number].value = 1.0
+ element.data.shape_keys.key_blocks[number-1].value = 0.0
+ element.data.shape_keys.key_blocks[number].keyframe_insert("value")
+ element.data.shape_keys.key_blocks[number-1].keyframe_insert("value")
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-26 16:00:15 +0300