[6ee42b89] master: Merging of old PDB importer/exporter into new ‘Atomic Blender PDB/XYZ’ importer. T62804
Clemens Barth
noreply at git.blender.org
Thu Mar 28 10:12:14 CET 2019
Commit: 6ee42b89a9cf2fae3320d037c606646c73c66f0d
Author: Clemens Barth
Date: Thu Mar 28 10:11:21 2019 +0100
Branches: master
https://developer.blender.org/rBA6ee42b89a9cf2fae3320d037c606646c73c66f0d
Merging of old PDB importer/exporter into new ‘Atomic Blender PDB/XYZ’ importer. T62804
Comments
========
The ‘old’ PDB addon was deleted because of 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’, which I commit here, too.
===================================================================
D io_mesh_pdb/__init__.py
D io_mesh_pdb/atom_info.dat
D io_mesh_pdb/export_pdb.py
D io_mesh_pdb/import_pdb.py
===================================================================
diff --git a/io_mesh_pdb/__init__.py b/io_mesh_pdb/__init__.py
deleted file mode 100644
index 7af4d4a7..00000000
--- a/io_mesh_pdb/__init__.py
+++ /dev/null
@@ -1,334 +0,0 @@
-# ##### BEGIN GPL LICENSE BLOCK #####
-#
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-#
-# ##### END GPL LICENSE BLOCK #####
-
-#
-#
-# Authors : Clemens Barth (Blendphys at root-1.de), ...
-#
-# Homepage(Wiki) : http://development.root-1.de/Atomic_Blender.php
-#
-# Start of project : 2011-08-31 by Clemens Barth
-# First publication in Blender : 2011-11-11
-# Last modified : 2019-03-15
-#
-# Acknowledgements
-# ================
-#
-# 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)
-#
-# Other
-# -----
-# Frank Palmino
-#
-#
-
-bl_info = {
- "name": "Atomic Blender - PDB",
- "description": "Importing atoms described in PDB files as balls into Blender",
- "author": "Clemens Barth",
- "version": (1, 8),
- "blender": (2, 80, 0),
- "location": "File -> Import -> PDB (.pdb)",
- "warning": "",
- "wiki_url": "... will be updated asap ...",
- "category": "Import-Export",
-}
-
-
-import bpy
-from bpy.types import Operator
-from bpy_extras.io_utils import ImportHelper, ExportHelper
-from bpy.props import (
- StringProperty,
- BoolProperty,
- EnumProperty,
- IntProperty,
- FloatProperty,
- )
-
-from . import (
- import_pdb,
- export_pdb,
- )
-
-# -----------------------------------------------------------------------------
-# GUI
-
-# 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')
-
- 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.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,
-
@@ Diff output truncated at 10240 characters. @@
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