[9791bd3a] master: The new ‘Atomic Blender PDB/XYZ’ importer. T62804
Clemens Barth
noreply at git.blender.org
Thu Mar 28 10:39:24 CET 2019
Commit: 9791bd3a2233ace2d8a588c4f8b7fe6cb4c8fa7e
Author: Clemens Barth
Date: Thu Mar 28 10:37:49 2019 +0100
Branches: master
https://developer.blender.org/rBA9791bd3a2233ace2d8a588c4f8b7fe6cb4c8fa7e
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’.
===================================================================
A io_mesh_atomic/__init__.py
A io_mesh_atomic/atom_info.dat
A io_mesh_atomic/pdb_export.py
A io_mesh_atomic/pdb_gui.py
A io_mesh_atomic/pdb_import.py
A io_mesh_atomic/utility_gui.py
A io_mesh_atomic/utility_panel.py
A io_mesh_atomic/xyz_export.py
A io_mesh_atomic/xyz_gui.py
A io_mesh_atomic/xyz_import.py
===================================================================
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 at 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
+
+
+Ato
@@ Diff output truncated at 10240 characters. @@
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