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Commit 4a26b71a authored by Clemens Barth's avatar Clemens Barth
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As discussed a couple of times in the IRC chat, we decided to separate the 

panel from the import/export addons. This means that the panel has had to be 
removed also from the PDB importer/exporter. This is what I have done.

Attention, this is a major change of the Atomic Blender PDB importer/exporter!

A lot of test today have shown, that the new version of the PDB 
importer/exporter has not lost its stability. In the next days, I will perform 
other stability tests.

Blendphys
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io_mesh_pdb/__init__.py
+ 12
− 541
View file @ 4a26b71a
......@@ -21,23 +21,26 @@
# Authors : Clemens Barth (Blendphys@root-1.de), ...
#
# Homepage(Wiki) : http://development.root-1.de/Atomic_Blender.php
# Tracker : http://projects.blender.org/tracker/index.php?func=detail&aid=29226&group_id=153&atid=467
#
# Start of project : 2011-08-31 by Clemens Barth
# First publication in Blender : 2011-11-11
# Last modified : 2012-10-14
# Last modified : 2012-11-03
#
# Acknowledgements: Thanks to ideasman, meta_androcto, truman, kilon,
# dairin0d, PKHG, Valter, etc
# Acknowledgements
# ================
#
# Blender: ideasman, meta_androcto, truman, kilon, CoDEmanX, dairin0d, PKHG,
# Valter, ...
# Other: Frank Palmino
#
bl_info = {
"name": "PDB Atomic Blender",
"name": "Atomic Blender - PDB",
"description": "Loading and manipulating atoms from PDB files",
"author": "Clemens Barth",
"version": (1,3),
"version": (1,5),
"blender": (2,6),
"location": "File -> Import -> PDB (.pdb), Panel: View 3D - Tools",
"location": "File -> Import -> PDB (.pdb)",
"warning": "",
"wiki_url": "http://wiki.blender.org/index.php/Extensions:2.6/"
"Py/Scripts/Import-Export/PDB",
......@@ -61,501 +64,9 @@ from bpy.props import (StringProperty,
from . import import_pdb
from . import export_pdb
ATOM_PDB_ERROR = ""
ATOM_PDB_PANEL = ""
# -----------------------------------------------------------------------------
# GUI
# The panel, which is loaded after the file has been
# chosen via the menu 'File -> Import'
class CLASS_atom_pdb_panel(Panel):
bl_label = "PDB - Atomic Blender"
bl_space_type = "VIEW_3D"
bl_region_type = "TOOL_PROPS"
@classmethod
def poll(self, context):
global ATOM_PDB_PANEL
if ATOM_PDB_PANEL == "0" and import_pdb.ATOM_PDB_FILEPATH == "":
return False
if ATOM_PDB_PANEL == "0" and import_pdb.ATOM_PDB_FILEPATH != "":
return True
if ATOM_PDB_PANEL == "1":
return True
if ATOM_PDB_PANEL == "2":
return False
return True
def draw(self, context):
layout = self.layout
# This is for the case that a blend file is loaded.
if len(context.scene.atom_pdb) == 0:
bpy.context.scene.atom_pdb.add()
scn = context.scene.atom_pdb[0]
row = layout.row()
row.label(text="Outputs and custom data file")
box = layout.box()
row = box.row()
row.label(text="Custom data file")
row = box.row()
col = row.column()
col.prop(scn, "datafile")
col.operator("atom_pdb.datafile_apply")
row = box.row()
col = row.column(align=True)
col.prop(scn, "PDB_file")
row = layout.row()
row.label(text="Reload structure")
box = layout.box()
row = box.row()
col = row.column()
col.prop(scn, "use_mesh")
col = row.column()
col.label(text="Scaling factors")
row = box.row()
col = row.column(align=True)
col.active = scn.use_mesh
col.prop(scn, "mesh_azimuth")
col.prop(scn, "mesh_zenith")
col = row.column(align=True)
col.prop(scn, "scale_ballradius")
col.prop(scn, "scale_distances")
row = box.row()
col = row.column()
col.prop(scn, "use_sticks")
row = box.row()
row.active = scn.use_sticks
col = row.column(align=True)
col.prop(scn, "sticks_sectors")
col.prop(scn, "sticks_radius")
col.prop(scn, "sticks_unit_length")
col = row.column(align=True)
col.prop(scn, "use_sticks_color")
col.prop(scn, "use_sticks_smooth")
col.prop(scn, "use_sticks_bonds")
row = box.row()
row.active = scn.use_sticks
col = row.column(align=True)
col = row.column(align=True)
col.active = scn.use_sticks and scn.use_sticks_bonds
col.prop(scn, "sticks_dist")
row = box.row()
row.prop(scn, "use_center")
row = box.row()
col = row.column()
col.prop(scn, "use_camera")
col.prop(scn, "use_lamp")
col = row.column()
col.operator("atom_pdb.button_reload")
col.prop(scn, "number_atoms")
row = box.row()
row.operator("atom_pdb.button_distance")
row.prop(scn, "distance")
row = layout.row()
row.label(text="Modify atom radii")
box = layout.box()
row = box.row()
row.label(text="All changes concern:")
row = box.row()
row.prop(scn, "radius_how")
row = box.row()
row.label(text="1. Change type of radii")
row = box.row()
row.prop(scn, "radius_type")
row = box.row()
row.label(text="2. Change atom radii in pm")
row = box.row()
row.prop(scn, "radius_pm_name")
row = box.row()
row.prop(scn, "radius_pm")
row = box.row()
row.label(text="3. Change atom radii by scale")
row = box.row()
col = row.column()
col.prop(scn, "radius_all")
col = row.column(align=True)
col.operator( "atom_pdb.radius_all_bigger" )
col.operator( "atom_pdb.radius_all_smaller" )
row = box.row()
row.label(text="4. Show sticks only")
row = box.row()
col = row.column()
col.operator( "atom_pdb.radius_sticks" )
if bpy.context.mode == 'EDIT_MESH':
row = layout.row()
row.label(text="Separate atom")
box = layout.box()
row = box.row()
row.operator( "atom_pdb.separate_atom" )
# The properties (gadgets) in the panel. They all go to scene
# during initialization (see end)
class CLASS_atom_pdb_Properties(bpy.types.PropertyGroup):
def Callback_radius_type(self, context):
scn = bpy.context.scene.atom_pdb[0]
import_pdb.DEF_atom_pdb_radius_type(
scn.radius_type,
scn.radius_how,)
def Callback_radius_pm(self, context):
scn = bpy.context.scene.atom_pdb[0]
import_pdb.DEF_atom_pdb_radius_pm(
scn.radius_pm_name,
scn.radius_pm,
scn.radius_how,)
# In the file dialog window - Import
use_camera = BoolProperty(
name="Camera", default=False,
description="Do you need a camera?")
use_lamp = BoolProperty(
name="Lamp", default=False,
description = "Do you need a lamp?")
use_mesh = BoolProperty(
name = "Mesh balls", default=False,
description = "Use mesh balls instead of NURBS")
mesh_azimuth = IntProperty(
name = "Azimuth", default=32, min=1,
description = "Number of sectors (azimuth)")
mesh_zenith = IntProperty(
name = "Zenith", default=32, min=1,
description = "Number of sectors (zenith)")
scale_ballradius = FloatProperty(
name = "Balls", default=1.0, min=0.0001,
description = "Scale factor for all atom radii")
scale_distances = FloatProperty (
name = "Distances", default=1.0, min=0.0001,
description = "Scale factor for all distances")
use_center = BoolProperty(
name = "Object to origin", default=True,
description = "Put the object into the global origin")
use_sticks = BoolProperty(
name="Use sticks", default=True,
description="Do you want to display the sticks?")
sticks_sectors = IntProperty(
name = "Sector", default=20, min=1,
description="Number of sectors of a stick")
sticks_radius = FloatProperty(
name = "Radius", default=0.1, min=0.0001,
description ="Radius of a stick")
sticks_unit_length = FloatProperty(
name = "Unit", default=0.05, 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=False,
description="The sticks are round (sectors are not visible)")
use_sticks_bonds = BoolProperty(
name="Bonds", default=False,
description="Show double and tripple bonds.")
sticks_dist = FloatProperty(
name="Distance", default = 1.1, min=1.0, max=3.0,
description="Distance between sticks measured in stick diameter")
atomradius = EnumProperty(
name="Type of radius",
description="Choose type of atom radius",
items=(('0', "Pre-defined", "Use pre-defined radius"),
('1', "Atomic", "Use atomic radius"),
('2', "van der Waals", "Use van der Waals radius")),
default='0',)
# In the panel
datafile = StringProperty(
name = "", description="Path to your custom data file",
maxlen = 256, default = "", subtype='FILE_PATH')
PDB_file = StringProperty(
name = "PDB file", default="",
description = "Path of the PDB 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")
radius_how = EnumProperty(
name="",
description="Which objects shall be modified?",
items=(('ALL_ACTIVE',"all active objects", "in the current layer"),
('ALL_IN_LAYER',"all"," in active layer(s)")),
default='ALL_ACTIVE',)
radius_type = EnumProperty(
name="Type",
description="Which type of atom radii?",
items=(('0',"predefined", "Use pre-defined radii"),
('1',"atomic", "Use atomic radii"),
('2',"van der Waals","Use van der Waals radii")),
default='0',update=Callback_radius_type)
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=0.01,
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")
# Button loading a custom data file
class CLASS_atom_pdb_datafile_apply(Operator):
bl_idname = "atom_pdb.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_pdb[0]
if scn.datafile == "":
return {'FINISHED'}
import_pdb.DEF_atom_pdb_custom_datafile(scn.datafile)
return {'FINISHED'}
# Button for separating single objects from a atom mesh
class CLASS_atom_pdb_separate_atom(Operator):
bl_idname = "atom_pdb.separate_atom"
bl_label = "Separate atom"
bl_description = "Separate the atom you have chosen"
def execute(self, context):
scn = bpy.context.scene.atom_pdb[0]
# Get first all important properties from the atoms, which the user
# has chosen: location, color, scale
obj = bpy.context.edit_object
bm = bmesh.from_edit_mesh(obj.data)
locations = []
for v in bm.verts:
if v.select:
locations.append(obj.matrix_world * v.co)
bm.free()
del(bm)
name = obj.name
scale = obj.children[0].scale
material = obj.children[0].active_material
# Separate the vertex from the main mesh and create a new mesh.
bpy.ops.mesh.separate()
new_object = bpy.context.scene.objects[0]
# And now, switch to the OBJECT mode such that we can ...
bpy.ops.object.mode_set(mode='OBJECT', toggle=False)
# ... delete the new mesh including the separated vertex
bpy.ops.object.select_all(action='DESELECT')
new_object.select = True
bpy.ops.object.delete()
# Create new atoms/vacancies at the position of the old atoms
current_layers=bpy.context.scene.layers
# For all selected positions do:
for location in locations:
if "Vacancy" not in name:
if scn.use_mesh == False:
bpy.ops.surface.primitive_nurbs_surface_sphere_add(
view_align=False, enter_editmode=False,
location=location,
rotation=(0.0, 0.0, 0.0),
layers=current_layers)
else:
bpy.ops.mesh.primitive_uv_sphere_add(
segments=scn.mesh_azimuth,
ring_count=scn.mesh_zenith,
size=1, view_align=False, enter_editmode=False,
location=location,
rotation=(0, 0, 0),
layers=current_layers)
else:
bpy.ops.mesh.primitive_cube_add(
view_align=False, enter_editmode=False,
location=location,
rotation=(0.0, 0.0, 0.0),
layers=current_layers)
new_atom = bpy.context.scene.objects.active
# Scale, material and name it.
new_atom.scale = scale
new_atom.active_material = material
new_atom.name = name + "_sep"
new_atom.select = False
bpy.context.scene.objects.active = obj
bpy.ops.object.select_all(action='DESELECT')
return {'FINISHED'}
# Button for measuring the distance of the active objects
class CLASS_atom_pdb_distance_button(Operator):
bl_idname = "atom_pdb.button_distance"
bl_label = "Measure ..."
bl_description = "Measure the distance between two objects (only in Object Mode)"
def execute(self, context):
scn = bpy.context.scene.atom_pdb[0]
dist = import_pdb.DEF_atom_pdb_distance()
if dist != "N.A.":
# The string length is cut, 3 digits after the first 3 digits
# after the '.'. Append also "Angstrom".
# Remember: 1 Angstrom = 10^(-10) m
pos = str.find(dist, ".")
dist = dist[:pos+4]
dist = dist + " A"
# Put the distance into the string of the output field.
scn.distance = dist
return {'FINISHED'}
# Button for increasing the radii of all atoms
class CLASS_atom_pdb_radius_all_bigger_button(Operator):
bl_idname = "atom_pdb.radius_all_bigger"
bl_label = "Bigger ..."
bl_description = "Increase the radii of the atoms"
def execute(self, context):
scn = bpy.context.scene.atom_pdb[0]
import_pdb.DEF_atom_pdb_radius_all(
scn.radius_all,
scn.radius_how,)
return {'FINISHED'}
# Button for decreasing the radii of all atoms
class CLASS_atom_pdb_radius_all_smaller_button(Operator):
bl_idname = "atom_pdb.radius_all_smaller"
bl_label = "Smaller ..."
bl_description = "Decrease the radii of the atoms"
def execute(self, context):
scn = bpy.context.scene.atom_pdb[0]
import_pdb.DEF_atom_pdb_radius_all(
1.0/scn.radius_all,
scn.radius_how,)
return {'FINISHED'}
# Button for showing the sticks only - the radii of the atoms downscaled onto
# 90% of the stick radius
class CLASS_atom_pdb_radius_sticks_button(Operator):
bl_idname = "atom_pdb.radius_sticks"
bl_label = "Show sticks"
bl_description = "Show only the sticks (atom radii = stick radii)"
def execute(self, context):
global ATOM_PDB_ERROR
scn = bpy.context.scene.atom_pdb[0]
result = import_pdb.DEF_atom_pdb_radius_sticks(
0.01,
scn.radius_how,)
if result == False:
ATOM_PDB_ERROR = "No sticks => no changes"
bpy.ops.atom_pdb.error_dialog('INVOKE_DEFAULT')
return {'FINISHED'}
# The button for reloading the atoms and creating the scene
class CLASS_atom_pdb_load_button(Operator):
bl_idname = "atom_pdb.button_reload"
bl_label = "RELOAD"
bl_description = "Load the structure again"
def execute(self, context):
scn = context.scene.atom_pdb[0]
atom_number = import_pdb.DEF_atom_pdb_main(
scn.use_mesh,
scn.mesh_azimuth,
scn.mesh_zenith,
scn.scale_ballradius,
scn.atomradius,
scn.scale_distances,
scn.use_sticks,
scn.use_sticks_color,
scn.use_sticks_smooth,
scn.use_sticks_bonds,
scn.sticks_unit_length,
scn.sticks_dist,
scn.sticks_sectors,
scn.sticks_radius,
scn.use_center,
scn.use_camera,
scn.use_lamp,
scn.datafile)
scn.number_atoms = str(atom_number) + " atoms"
return {'FINISHED'}
def DEF_panel_yes_no():
global ATOM_PDB_PANEL
datafile_path = bpy.utils.user_resource('SCRIPTS', path='', create=False)
if os.path.isdir(datafile_path) == False:
bpy.utils.user_resource('SCRIPTS', path='', create=True)
datafile_path = os.path.join(datafile_path, "presets")
if os.path.isdir(datafile_path) == False:
os.mkdir(datafile_path)
datafile = os.path.join(datafile_path, "io_mesh_pdb.pref")
if os.path.isfile(datafile):
datafile_fp = io.open(datafile, "r")
for line in datafile_fp:
if "Panel" in line:
ATOM_PDB_PANEL = line[-2:]
ATOM_PDB_PANEL = ATOM_PDB_PANEL[0:1]
bpy.context.scene.use_panel = ATOM_PDB_PANEL
break
datafile_fp.close()
else:
DEF_panel_write_pref("0")
def DEF_panel_write_pref(value):
datafile_path = bpy.utils.user_resource('SCRIPTS', path='', create=False)
datafile_path = os.path.join(datafile_path, "presets")
datafile = os.path.join(datafile_path, "io_mesh_pdb.pref")
datafile_fp = io.open(datafile, "w")
datafile_fp.write("Atomic Blender PDB - Import/Export - Preferences\n")
datafile_fp.write("================================================\n")
datafile_fp.write("\n")
datafile_fp.write("Panel: "+value+"\n\n\n")
datafile_fp.close()
class CLASS_atom_pdb_error_dialog(bpy.types.Operator):
bl_idname = "atom_pdb.error_dialog"
bl_label = "Attention !"
def draw(self, context):
layout = self.layout
row = layout.row()
row.label(text=" "+ATOM_PDB_ERROR)
def execute(self, context):
print("Atomic Blender - Error: "+ATOM_PDB_ERROR+"\n")
return {'FINISHED'}
def invoke(self, context, event):
return context.window_manager.invoke_props_dialog(self)
# This is the class for the file dialog of the importer.
class CLASS_ImportPDB(Operator, ImportHelper):
......@@ -566,13 +77,6 @@ class CLASS_ImportPDB(Operator, ImportHelper):
filename_ext = ".pdb"
filter_glob = StringProperty(default="*.pdb", options={'HIDDEN'},)
bpy.types.Scene.use_panel = EnumProperty(
name="Panel",
description="Choose whether the panel shall appear or not in the View 3D.",
items=(('0', "Once", "The panel appears only in this session"),
('1', "Always", "The panel always appears when Blender is started"),
('2', "Never", "The panel never appears")),
default='0')
use_camera = BoolProperty(
name="Camera", default=False,
description="Do you need a camera?")
......@@ -673,12 +177,10 @@ class CLASS_ImportPDB(Operator, ImportHelper):
col.prop(self, "sticks_dist")
row = layout.row()
row.prop(self, "use_center")
row = layout.row()
row.prop(bpy.context.scene, "use_panel")
def execute(self, context):
# This is in order to solve this strange 'relative path' thing.
import_pdb.ATOM_PDB_FILEPATH = bpy.path.abspath(self.filepath)
filepath_pdb = bpy.path.abspath(self.filepath)
# Execute main routine
atom_number = import_pdb.DEF_atom_pdb_main(
......@@ -699,35 +201,7 @@ class CLASS_ImportPDB(Operator, ImportHelper):
self.use_center,
self.use_camera,
self.use_lamp,
self.datafile)
# Copy the whole bunch of values into the property collection.
scn = context.scene.atom_pdb[0]
scn.use_mesh = self.use_mesh
scn.mesh_azimuth = self.mesh_azimuth
scn.mesh_zenith = self.mesh_zenith
scn.scale_ballradius = self.scale_ballradius
scn.atomradius = self.atomradius
scn.scale_distances = self.scale_distances
scn.use_sticks = self.use_sticks
scn.use_sticks_color = self.use_sticks_color
scn.use_sticks_smooth = self.use_sticks_smooth
scn.use_sticks_bonds = self.use_sticks_bonds
scn.sticks_unit_length = self.sticks_unit_length
scn.sticks_dist = self.sticks_dist
scn.sticks_sectors = self.sticks_sectors
scn.sticks_radius = self.sticks_radius
scn.use_center = self.use_center
scn.use_camera = self.use_camera
scn.use_lamp = self.use_lamp
scn.datafile = self.datafile
scn.number_atoms = str(atom_number) + " atoms"
scn.PDB_file = import_pdb.ATOM_PDB_FILEPATH
global ATOM_PDB_PANEL
ATOM_PDB_PANEL = bpy.context.scene.use_panel
DEF_panel_write_pref(bpy.context.scene.use_panel)
filepath_pdb)
return {'FINISHED'}
......@@ -773,12 +247,9 @@ def DEF_menu_func_export(self, context):
def register():
DEF_panel_yes_no()
bpy.utils.register_module(__name__)
bpy.types.INFO_MT_file_import.append(DEF_menu_func_import)
bpy.types.INFO_MT_file_export.append(DEF_menu_func_export)
bpy.types.Scene.atom_pdb = bpy.props.CollectionProperty(type=CLASS_atom_pdb_Properties)
bpy.context.scene.atom_pdb.add()
def unregister():
bpy.utils.unregister_module(__name__)
......
io_mesh_pdb/import_pdb.py
+ 211
− 507
View file @ 4a26b71a
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