From 4a26b71a377679c0f5ff0ed7e5ee01db71446454 Mon Sep 17 00:00:00 2001
From: Clemens Barth <barth@root-1.de>
Date: Sat, 3 Nov 2012 19:38:28 +0000
Subject: [PATCH] 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
---
io_mesh_pdb/__init__.py | 553 +----------------------------
io_mesh_pdb/import_pdb.py | 718 +++++++++++---------------------------
2 files changed, 223 insertions(+), 1048 deletions(-)
diff --git a/io_mesh_pdb/__init__.py b/io_mesh_pdb/__init__.py
index 580fffa08..22e4e7104 100644
--- a/io_mesh_pdb/__init__.py
+++ b/io_mesh_pdb/__init__.py
@@ -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__)
diff --git a/io_mesh_pdb/import_pdb.py b/io_mesh_pdb/import_pdb.py
index 70795f6c1..f033b531d 100644
--- a/io_mesh_pdb/import_pdb.py
+++ b/io_mesh_pdb/import_pdb.py
@@ -25,17 +25,6 @@ from math import pi, cos, sin
from mathutils import Vector, Matrix
from copy import copy
-# This variable contains the path of the PDB file.
-# It is used almost everywhere, which explains why it
-# should stay global. First, it is empty and gets 'filled' directly
-# after having chosen the PDB file (see 'class LoadPDB' further below).
-
-ATOM_PDB_FILEPATH = ""
-
-# Some string stuff for the console.
-ATOM_PDB_STRING = "Atomic Blender\n==================="
-
-
# -----------------------------------------------------------------------------
# Atom, stick and element data
@@ -200,393 +189,11 @@ class CLASS_atom_pdb_stick(object):
self.number = number
self.dist = dist
-# -----------------------------------------------------------------------------
-# Some small routines
-
-# Routine which produces a cylinder. All is somewhat easy to undertsand.
-def DEF_atom_pdb_build_stick(radius, length, sectors):
-
- 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("Sticks_Cylinder")
- cylinder.from_pydata(vertices, [], faces1)
- cylinder.update()
- new_cylinder = bpy.data.objects.new("Sticks_Cylinder", cylinder)
- bpy.context.scene.objects.link(new_cylinder)
-
- # Build the mesh, Cups
- cups = bpy.data.meshes.new("Sticks_Cups")
- cups.from_pydata(vertices, [], faces2)
- cups.update()
- new_cups = bpy.data.objects.new("Sticks_Cups", cups)
- bpy.context.scene.objects.link(new_cups)
-
- return (new_cylinder, new_cups)
-
-
-# This function measures the distance between two active objects (atoms).
-def DEF_atom_pdb_distance():
-
- if len(bpy.context.selected_bases) > 1:
- object_1 = bpy.context.selected_objects[0]
- object_2 = bpy.context.selected_objects[1]
- else:
- return "N.A."
-
- dv = object_2.location - object_1.location
- return str(dv.length)
-
-
-# Routine to modify the radii via the type: predefined, atomic or van der Waals
-# Explanations here are also valid for the next 3 DEFs.
-def DEF_atom_pdb_radius_type(rtype,how):
-
- if how == "ALL_IN_LAYER":
-
- # Note all layers that are active.
- layers = []
- for i in range(20):
- if bpy.context.scene.layers[i] == True:
- layers.append(i)
-
- # Put all objects, which are in the layers, into a list.
- change_objects = []
- for obj in bpy.context.scene.objects:
- for layer in layers:
- if obj.layers[layer] == True:
- change_objects.append(obj)
-
- # Consider all objects, which are in the list 'change_objects'.
- for obj in change_objects:
- if len(obj.children) != 0:
- if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
- for element in ATOM_PDB_ELEMENTS:
- if element.name in obj.name:
- obj.children[0].scale = (element.radii[int(rtype)],) * 3
- else:
- if obj.type == "SURFACE" or obj.type == "MESH":
- for element in ATOM_PDB_ELEMENTS:
- if element.name in obj.name:
- obj.scale = (element.radii[int(rtype)],) * 3
-
- if how == "ALL_ACTIVE":
- for obj in bpy.context.selected_objects:
- if len(obj.children) != 0:
- if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
- for element in ATOM_PDB_ELEMENTS:
- if element.name in obj.name:
- obj.children[0].scale = (element.radii[int(rtype)],) * 3
- else:
- if obj.type == "SURFACE" or obj.type == "MESH":
- for element in ATOM_PDB_ELEMENTS:
- if element.name in obj.name:
- obj.scale = (element.radii[int(rtype)],) * 3
-
-
-# Routine to modify the radii in picometer of a specific type of atom
-def DEF_atom_pdb_radius_pm(atomname, radius_pm, how):
-
- if how == "ALL_IN_LAYER":
-
- layers = []
- for i in range(20):
- if bpy.context.scene.layers[i] == True:
- layers.append(i)
-
- change_objects = []
- for obj in bpy.context.scene.objects:
- for layer in layers:
- if obj.layers[layer] == True:
- change_objects.append(obj)
-
- for obj in change_objects:
- if len(obj.children) != 0:
- if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
- if atomname in obj.name:
- if "Stick" not in obj.name:
- obj.children[0].scale = (radius_pm/100,) * 3
- else:
- if obj.type == "SURFACE" or obj.type == "MESH":
- if atomname in obj.name:
- if "Stick" not in obj.name:
- obj.scale = (radius_pm/100,) * 3
-
- if how == "ALL_ACTIVE":
- for obj in bpy.context.selected_objects:
- if len(obj.children) != 0:
- if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
- if atomname in obj.name:
- if "Stick" not in obj.name:
- obj.children[0].scale = (radius_pm/100,) * 3
- else:
- if obj.type == "SURFACE" or obj.type == "MESH":
- if atomname in obj.name:
- if "Stick" not in obj.name:
- obj.scale = (radius_pm/100,) * 3
-
-
-# Routine to scale the radii of all atoms
-def DEF_atom_pdb_radius_all(scale, how):
-
- if how == "ALL_IN_LAYER":
-
- layers = []
- for i in range(20):
- if bpy.context.scene.layers[i] == True:
- layers.append(i)
-
- change_objects = []
- for obj in bpy.context.scene.objects:
- for layer in layers:
- if obj.layers[layer] == True:
- change_objects.append(obj)
-
-
- for obj in change_objects:
- if len(obj.children) != 0:
- if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
- if "Stick" not in obj.name:
- obj.children[0].scale *= scale
- else:
- if obj.type == "SURFACE" or obj.type == "MESH":
- if "Stick" not in obj.name:
- obj.scale *= scale
-
- if how == "ALL_ACTIVE":
- for obj in bpy.context.selected_objects:
- if len(obj.children) != 0:
- if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
- if "Stick" not in obj.name:
- obj.children[0].scale *= scale
- else:
- if obj.type == "SURFACE" or obj.type == "MESH":
- if "Stick" not in obj.name:
- obj.scale *= scale
-
-
-# This routine downscales all atom radii onto the value of the stick radius
-# for showing the sticks.
-def DEF_atom_pdb_radius_sticks(radius, how):
-
- # Are there any sticks?
- Found = False
- if how == "ALL_IN_LAYER":
-
- layers = []
- for i in range(20):
- if bpy.context.scene.layers[i] == True:
- layers.append(i)
-
- change_objects = []
- for obj in bpy.context.scene.objects:
- for layer in layers:
- if obj.layers[layer] == True:
- change_objects.append(obj)
-
- for obj in change_objects:
- if len(obj.children) != 0:
- if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
- if "Stick" in obj.name:
- Found = True
- else:
- if obj.type == "SURFACE" or obj.type == "MESH":
- if "Stick" in obj.name:
- Found = True
-
- if how == "ALL_ACTIVE":
- for obj in bpy.context.selected_objects:
- if len(obj.children) != 0:
- if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
- if "Stick" in obj.name:
- Found = True
- else:
- if obj.type == "SURFACE" or obj.type == "MESH":
- if "Stick" in obj.name:
- Found = True
-
- if Found == False:
- return False
-
- if how == "ALL_IN_LAYER":
-
- layers = []
- for i in range(20):
- if bpy.context.scene.layers[i] == True:
- layers.append(i)
-
- change_objects = []
- for obj in bpy.context.scene.objects:
- for layer in layers:
- if obj.layers[layer] == True:
- change_objects.append(obj)
-
-
- for obj in change_objects:
- if len(obj.children) != 0:
- if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
- if "Stick" not in obj.name:
- obj.children[0].scale = (radius,) * 3
- else:
- if obj.type == "SURFACE" or obj.type == "MESH":
- if "Stick" not in obj.name:
- obj.scale = (radius,) * 3
-
- if how == "ALL_ACTIVE":
- for obj in bpy.context.selected_objects:
- if len(obj.children) != 0:
- if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
- if "Stick" not in obj.name:
- obj.children[0].scale = (radius,) * 3
- else:
- if obj.type == "SURFACE" or obj.type == "MESH":
- if "Stick" not in obj.name:
- obj.scale = (radius,) * 3
-
- return True
-
-# -----------------------------------------------------------------------------
-# The custom data file
-
-def DEF_atom_pdb_custom_datafile(path_datafile):
-
- if path_datafile == "":
- return False
-
- path_datafile = bpy.path.abspath(path_datafile)
-
- if os.path.isfile(path_datafile) == False:
- return False
-
- # The whole list gets deleted! We build it new.
- ATOM_PDB_ELEMENTS[:] = []
-
- # Read the data file, which contains all data
- # (atom name, radii, colors, etc.)
- data_file_p = io.open(path_datafile, "r")
-
- for line in data_file_p:
-
- if "Atom" in line:
-
- line = data_file_p.readline()
-
- # Number
- line = data_file_p.readline()
- number = line[19:-1]
- # Name
- line = data_file_p.readline()
- name = line[19:-1]
- # Short name
- line = data_file_p.readline()
- short_name = line[19:-1]
- # Color
- line = data_file_p.readline()
- color_value = line[19:-1].split(',')
- color = [float(color_value[0]),
- float(color_value[1]),
- float(color_value[2])]
- # Used radius
- line = data_file_p.readline()
- radius_used = float(line[19:-1])
- # Atomic radius
- line = data_file_p.readline()
- radius_atomic = float(line[19:-1])
- # Van der Waals radius
- line = data_file_p.readline()
- radius_vdW = float(line[19:-1])
-
- radii = [radius_used,radius_atomic,radius_vdW]
- radii_ionic = []
-
- element = CLASS_atom_pdb_Elements(number,name,short_name,color,
- radii, radii_ionic)
-
- ATOM_PDB_ELEMENTS.append(element)
-
- data_file_p.close()
-
- for obj in bpy.context.selected_objects:
- if len(obj.children) != 0:
- child = obj.children[0]
- if child.type == "SURFACE" or child.type == "MESH":
- for element in ATOM_PDB_ELEMENTS:
- if element.name in obj.name:
- child.scale = (element.radii[0],) * 3
- child.active_material.diffuse_color = element.color
- else:
- if obj.type == "SURFACE" or obj.type == "MESH":
- for element in ATOM_PDB_ELEMENTS:
- if element.name in obj.name:
- obj.scale = (element.radii[0],) * 3
- obj.active_material.diffuse_color = element.color
-
- return True
# -----------------------------------------------------------------------------
-# The main routine
-
-def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
- Ball_radius_factor,radiustype,Ball_distance_factor,
- use_sticks,use_sticks_color,use_sticks_smooth,
- use_sticks_bonds, Stick_unit, Stick_dist,
- Stick_sectors,Stick_diameter,put_to_center,
- use_camera,use_lamp,path_datafile):
-
- # The list of all atoms as read from the PDB file.
- all_atoms = []
-
- # The list of all sticks.
- all_sticks = []
-
- # List of materials
- atom_material_list = []
+# Some basic routines
- # A list of ALL objects which are loaded (needed for selecting the loaded
- # structure.
- atom_object_list = []
-
-
- # ------------------------------------------------------------------------
- # INITIALIZE THE ELEMENT LIST
+def DEF_atom_pdb_read_elements():
ATOM_PDB_ELEMENTS[:] = []
@@ -602,17 +209,21 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
radii,radii_ionic)
ATOM_PDB_ELEMENTS.append(li)
- # ------------------------------------------------------------------------
- # READING DATA OF ATOMS
- if DEF_atom_pdb_custom_datafile(path_datafile):
- print("Custom data file is loaded.")
+# filepath_pdb: path to pdb file
+# radiustype : '0' default
+# '1' atomic radii
+# '2' van der Waals
+def DEF_atom_pdb_read_pdb_file(filepath_pdb,radiustype):
+
+ # The list of all atoms as read from the PDB file.
+ all_atoms = []
- # Open the file ...
- ATOM_PDB_FILEPATH_p = io.open(ATOM_PDB_FILEPATH, "r")
+ # Open the pdb file ...
+ filepath_pdb_p = io.open(filepath_pdb, "r")
#Go to the line, in which "ATOM" or "HETATM" appears.
- for line in ATOM_PDB_FILEPATH_p:
+ for line in filepath_pdb_p:
split_list = line.split(' ')
if "ATOM" in split_list[0]:
break
@@ -729,80 +340,31 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
radius,
color,[]))
- line = ATOM_PDB_FILEPATH_p.readline()
+ line = filepath_pdb_p.readline()
line = line[:-1]
- ATOM_PDB_FILEPATH_p.close()
+ 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
- # ------------------------------------------------------------------------
- # 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)
+ return (Number_of_total_atoms, all_atoms)
+
- # Now, we go through all atoms and give them a material. For all atoms ...
- for atom in all_atoms:
- # ... and all materials ...
- for material in atom_material_list:
- # ... select the correct material for the current atom via
- # comparison of names ...
- if atom.name in material.name:
- # ... and give the atom its material properties.
- # However, before we check, if it is a vacancy, because then it
- # gets some additional preparation. The vacancy is represented
- # by a transparent cube.
- if atom.name == "Vacancy":
- material.transparency_method = 'Z_TRANSPARENCY'
- material.alpha = 1.3
- material.raytrace_transparency.fresnel = 1.6
- material.raytrace_transparency.fresnel_factor = 1.6
- material.use_transparency = True
- # The atom gets its properties.
- atom.material = material
+def DEF_atom_pdb_read_pdb_file_sticks(filepath_pdb,
+ use_sticks_bonds):
- # ------------------------------------------------------------------------
- # READING DATA OF STICKS
+ # The list of all sticks.
+ all_sticks = []
- # Open the PDB file again such that the file pointer is in the first
- # line ... . Stupid, I know ... ;-)
- ATOM_PDB_FILEPATH_p = io.open(ATOM_PDB_FILEPATH, "r")
+ # Open the PDB file again.
+ filepath_pdb_p = io.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 ATOM_PDB_FILEPATH_p:
+ for line in filepath_pdb_p:
split_list = line.split(' ')
if "CONECT" in split_list[0]:
break
@@ -902,11 +464,178 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
Number_of_sticks += 1
j += 1
- line = ATOM_PDB_FILEPATH_p.readline()
+ line = filepath_pdb_p.readline()
line = line.rstrip()
- ATOM_PDB_FILEPATH_p.close()
- # So far, all atoms and sticks have been registered.
+ filepath_pdb_p.close()
+
+ return all_sticks
+
+
+# Routine which produces a cylinder. All is somewhat easy to undertsand.
+def DEF_atom_pdb_build_stick(radius, length, sectors):
+
+ 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("Sticks_Cylinder")
+ cylinder.from_pydata(vertices, [], faces1)
+ cylinder.update()
+ new_cylinder = bpy.data.objects.new("Sticks_Cylinder", cylinder)
+ bpy.context.scene.objects.link(new_cylinder)
+
+ # Build the mesh, Cups
+ cups = bpy.data.meshes.new("Sticks_Cups")
+ cups.from_pydata(vertices, [], faces2)
+ cups.update()
+ new_cups = bpy.data.objects.new("Sticks_Cups", cups)
+ bpy.context.scene.objects.link(new_cups)
+
+ return (new_cylinder, new_cups)
+
+
+# -----------------------------------------------------------------------------
+# The main routine
+
+def DEF_atom_pdb_main(use_mesh,
+ Ball_azimuth,
+ Ball_zenith,
+ Ball_radius_factor,
+ radiustype,
+ Ball_distance_factor,
+ use_sticks,
+ use_sticks_color,
+ use_sticks_smooth,
+ use_sticks_bonds,
+ Stick_unit, Stick_dist,
+ Stick_sectors,
+ Stick_diameter,
+ put_to_center,
+ use_camera,
+ use_lamp,
+ 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
+
+ DEF_atom_pdb_read_elements()
+
+ # ------------------------------------------------------------------------
+ # READING DATA OF ATOMS
+
+ (Number_of_total_atoms, all_atoms) = DEF_atom_pdb_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.transparency_method = 'Z_TRANSPARENCY'
+ material.alpha = 1.3
+ material.raytrace_transparency.fresnel = 1.6
+ material.raytrace_transparency.fresnel_factor = 1.6
+ material.use_transparency = True
+ # The atom gets its properties.
+ atom.material = material
+
+ # ------------------------------------------------------------------------
+ # READING DATA OF STICKS
+
+ all_sticks = DEF_atom_pdb_read_pdb_file_sticks(filepath_pdb,
+ use_sticks_bonds)
+
+
+ # So far, all atoms, sticks and materials have been registered.
# ------------------------------------------------------------------------
# TRANSLATION OF THE STRUCTURE TO THE ORIGIN
@@ -975,16 +704,14 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
camera_xyz_vec = object_center_vec + object_camera_vec
# Create the camera
- current_layers=bpy.context.scene.layers
- bpy.ops.object.camera_add(view_align=False, enter_editmode=False,
- location=camera_xyz_vec,
- rotation=(0.0, 0.0, 0.0), layers=current_layers)
- # Some properties of the camera are changed.
- camera = bpy.context.scene.objects.active
- camera.name = "A_camera"
- camera.data.name = "A_camera"
- camera.data.lens = 45
- camera.data.clip_end = 500.0
+ current_layers=bpy.context.scene.layers
+ 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
+ camera.layers = current_layers
+ bpy.context.scene.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
@@ -1027,35 +754,18 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
# Create the lamp
current_layers=bpy.context.scene.layers
- bpy.ops.object.lamp_add (type = 'POINT', view_align=False,
- location=lamp_xyz_vec,
- rotation=(0.0, 0.0, 0.0),
- layers=current_layers)
- # Some properties of the lamp are changed.
- lamp = bpy.context.scene.objects.active
- lamp.data.name = "A_lamp"
- lamp.name = "A_lamp"
- lamp.data.distance = 500.0
- lamp.data.energy = 3.0
- lamp.data.shadow_method = 'RAY_SHADOW'
+ lamp_data = bpy.data.lamps.new(name="A_lamp", type="POINT")
+ lamp_data.distance = 500.0
+ lamp_data.energy = 3.0
+ lamp_data.shadow_method = 'RAY_SHADOW'
+ lamp = bpy.data.objects.new("A_lamp", lamp_data)
+ lamp.location = lamp_xyz_vec
+ lamp.layers = current_layers
+ bpy.context.scene.objects.link(lamp)
bpy.context.scene.world.light_settings.use_ambient_occlusion = True
bpy.context.scene.world.light_settings.ao_factor = 0.2
- # ------------------------------------------------------------------------
- # SOME OUTPUT ON THE CONSOLE
-
- print()
- print()
- print()
- print(ATOM_PDB_STRING)
- print()
- print("Total number of atoms : " + str(Number_of_total_atoms))
- print("Total number of sticks : " + str(Number_of_sticks))
- print("Center of object (Angstrom) : ", object_center_vec)
- print("Size of object (Angstrom) : ", object_size)
- print()
-
# ------------------------------------------------------------------------
# SORTING THE ATOMS
@@ -1154,8 +864,6 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
new_atom_mesh.location = object_center_vec
atom_object_list.append(new_atom_mesh)
- print()
-
# ------------------------------------------------------------------------
# DRAWING THE STICKS
@@ -1323,7 +1031,3 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
if obj:
bpy.context.scene.objects.active = obj
- print("\n\nAll atoms (%d) and sticks (%d) have been drawn - finished.\n\n"
- % (Number_of_total_atoms,Number_of_sticks))
-
- return Number_of_total_atoms
--
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