From 1bafadf7cd5beb8c65ebbd2b3e70d4baa3b794b9 Mon Sep 17 00:00:00 2001
From: Clemens Barth <barth@root-1.de>
Date: Fri, 23 Mar 2012 20:34:45 +0000
Subject: [PATCH] - Option 'smooth' permits now a better 'polishing' of the
sticks.
- The default value for the precision of the sticks (unit length)
has been put from 0.2 onto 0.05. If the sticks are shown, they do not
overlapp anymore.
- Code cleaning
- Due to the recent large changes of the code the addon has been tested
with even more PDB files.
Blendphys
PS: see recent comment here: http://blenderartists.org/forum/showthread.php?235003-Atomic-Blender-for-loading-PDB-files-into-Blender-2.5&p=2079416&viewfull=1#post2079416
---
io_mesh_pdb/__init__.py | 36 +++---------
io_mesh_pdb/export_pdb.py | 7 +--
io_mesh_pdb/import_pdb.py | 114 +++++++++++++++++---------------------
3 files changed, 61 insertions(+), 96 deletions(-)
diff --git a/io_mesh_pdb/__init__.py b/io_mesh_pdb/__init__.py
index 14b556f5e..3a479dbd1 100644
--- a/io_mesh_pdb/__init__.py
+++ b/io_mesh_pdb/__init__.py
@@ -42,12 +42,9 @@ from bpy.props import (StringProperty,
IntProperty,
FloatProperty)
-
-# TODO, allow reload
from . import import_pdb
from . import export_pdb
-
ATOM_PDB_ERROR = ""
ATOM_PDB_PANEL = ""
@@ -230,7 +227,7 @@ class CLASS_atom_pdb_Properties(bpy.types.PropertyGroup):
name = "Radius", default=0.1, min=0.0001,
description ="Radius of a stick")
sticks_unit_length = FloatProperty(
- name = "Unit", default=0.2, min=0.0001,
+ 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,
@@ -303,22 +300,6 @@ class CLASS_atom_pdb_datafile_apply(Operator):
import_pdb.DEF_atom_pdb_custom_datafile(scn.datafile)
- # TODO, move this into 'import_pdb' and call the function
- 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 import_pdb.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 import_pdb.ATOM_PDB_ELEMENTS:
- if element.name in obj.name:
- obj.scale = (element.radii[0],) * 3
- obj.active_material.diffuse_color = element.color
-
return {'FINISHED'}
@@ -350,7 +331,7 @@ class CLASS_atom_pdb_separate_atom(Operator):
# ... delete the new mesh including the separated vertex
bpy.ops.object.select_all(action='DESELECT')
new_object.select = True
- bpy.ops.object.delete() # TODO, use scene.objects.unlink()
+ bpy.ops.object.delete()
# Create a new atom/vacancy at the position of the old atom
current_layers=bpy.context.scene.layers
@@ -426,8 +407,7 @@ class CLASS_atom_pdb_radius_all_bigger_button(Operator):
scn = bpy.context.scene.atom_pdb[0]
import_pdb.DEF_atom_pdb_radius_all(
scn.radius_all,
- scn.radius_how,
- )
+ scn.radius_how,)
return {'FINISHED'}
@@ -441,8 +421,7 @@ class CLASS_atom_pdb_radius_all_smaller_button(Operator):
scn = bpy.context.scene.atom_pdb[0]
import_pdb.DEF_atom_pdb_radius_all(
1.0/scn.radius_all,
- scn.radius_how,
- )
+ scn.radius_how,)
return {'FINISHED'}
@@ -458,9 +437,8 @@ class CLASS_atom_pdb_radius_sticks_button(Operator):
scn = bpy.context.scene.atom_pdb[0]
result = import_pdb.DEF_atom_pdb_radius_sticks(
- scn.sticks_radius * 0.9,
- scn.radius_how,)
-
+ 0.01,
+ scn.radius_how,)
if result == False:
ATOM_PDB_ERROR = "No sticks => no changes"
bpy.ops.atom_pdb.error_dialog('INVOKE_DEFAULT')
@@ -606,7 +584,7 @@ class CLASS_ImportPDB(Operator, ImportHelper):
name = "Radius", default=0.1, min=0.0001,
description ="Radius of a stick")
sticks_unit_length = FloatProperty(
- name = "Unit", default=0.2, min=0.0001,
+ 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,
diff --git a/io_mesh_pdb/export_pdb.py b/io_mesh_pdb/export_pdb.py
index 5e17e0bbf..e47003610 100644
--- a/io_mesh_pdb/export_pdb.py
+++ b/io_mesh_pdb/export_pdb.py
@@ -25,7 +25,7 @@
#
# Start of project : 2011-08-31 by Clemens Barth
# First publication in Blender : 2011-11-11
-# Last modified : 2012-03-22
+# Last modified : 2012-03-23
#
# Acknowledgements: Thanks to ideasman, meta_androcto, truman, kilon,
# dairin0d, PKHG, Valter, etc
@@ -50,8 +50,6 @@ ATOM_PDB_PDBTEXT = ( "REMARK This pdb file has been created with Blender "
+ "REMARK\n")
-
-
class CLASS_atom_pdb_atoms_export(object):
__slots__ = ('element', 'location')
def __init__(self, element, location):
@@ -59,8 +57,6 @@ class CLASS_atom_pdb_atoms_export(object):
self.location = location
-
-
def DEF_atom_pdb_export(obj_type):
list_atoms = []
@@ -117,3 +113,4 @@ def DEF_atom_pdb_export(obj_type):
pdb_file_p.close()
return True
+
diff --git a/io_mesh_pdb/import_pdb.py b/io_mesh_pdb/import_pdb.py
index fa8a92f51..b4f52af50 100644
--- a/io_mesh_pdb/import_pdb.py
+++ b/io_mesh_pdb/import_pdb.py
@@ -25,7 +25,7 @@
#
# Start of project : 2011-08-31 by Clemens Barth
# First publication in Blender : 2011-11-11
-# Last modified : 2012-03-22
+# Last modified : 2012-03-23
#
# Acknowledgements: Thanks to ideasman, meta_androcto, truman, kilon,
# dairin0d, PKHG, Valter, etc
@@ -216,22 +216,18 @@ 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):
- vertices = []
- faces = []
-
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 )
@@ -243,7 +239,16 @@ def DEF_atom_pdb_build_stick(radius, length, sectors):
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]
@@ -254,28 +259,27 @@ def DEF_atom_pdb_build_stick(radius, length, sectors):
for j in range(2):
face_top.append(i+j+1)
face_bottom.append(i+j+1+sectors)
- faces.append(face_top)
- faces.append(face_bottom)
-
- # Side facets
- for i in range(sectors-1):
- if i == sectors-2:
- faces.append( [i+1, 1, 1+sectors, i+1+sectors] )
- else:
- faces.append( [i+1, i+2, i+2+sectors, i+1+sectors] )
+ faces2.append(face_top)
+ faces2.append(face_bottom)
- # Build the mesh
+ # Build the mesh, Cylinder
cylinder = bpy.data.meshes.new("Sticks_Cylinder")
- cylinder.from_pydata(vertices, [], faces)
+ cylinder.from_pydata(vertices, [], faces1)
cylinder.update()
new_cylinder = bpy.data.objects.new("Sticks_Cylinder", cylinder)
bpy.context.scene.objects.link(new_cylinder)
- return 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 objects (atoms),
-# which are active.
+
+# This function measures the distance between two active objects (atoms).
def DEF_atom_pdb_distance():
if len(bpy.context.selected_bases) > 1:
@@ -495,7 +499,6 @@ def DEF_atom_pdb_radius_sticks(radius, how):
return True
-
# -----------------------------------------------------------------------------
# The custom data file
@@ -556,14 +559,27 @@ def DEF_atom_pdb_custom_datafile(path_datafile):
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,
@@ -602,11 +618,9 @@ 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.")
@@ -738,11 +752,9 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
# 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).
@@ -795,11 +807,9 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
# The atom gets its properties.
atom.material = material
-
# ------------------------------------------------------------------------
# READING DATA OF 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")
@@ -829,8 +839,8 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
# 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 many atoms: For instance, it may happen that one
- # has
+ # 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
@@ -914,11 +924,9 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
ATOM_PDB_FILEPATH_p.close()
# So far, all atoms and sticks 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 substracted).
@@ -937,20 +945,16 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
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))
@@ -968,7 +972,6 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
object_size = 0.0
object_size = max(object_size_vec).length
-
# ------------------------------------------------------------------------
# CAMERA AND LAMP
@@ -1024,14 +1027,6 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
snap_align=False, snap_normal=(0, 0, 0),
release_confirm=False)
-
- # This does not work, I don't know why.
- #
- #for area in bpy.context.screen.areas:
- # if area.type == 'VIEW_3D':
- # area.spaces[0].region_3d.view_perspective = 'CAMERA'
-
-
# Here a lamp is put into the scene, if chosen.
if use_lamp == True:
@@ -1063,11 +1058,9 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
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()
@@ -1079,11 +1072,9 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
print("Size of object (Angstrom) : ", object_size)
print()
-
# ------------------------------------------------------------------------
# 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], ...]
@@ -1116,11 +1107,9 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
# Now append the atom list to the list of all types of atoms
draw_all_atoms.append(draw_all_atoms_type)
-
# ------------------------------------------------------------------------
# DRAWING THE ATOMS
-
# This is the number of all atoms which are put into the scene.
bpy.ops.object.select_all(action='DESELECT')
@@ -1183,7 +1172,6 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
print()
-
# ------------------------------------------------------------------------
# DRAWING THE STICKS
@@ -1280,7 +1268,6 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
sticks_all_lists.append(sticks_list)
-
# ... the sticks in the list can be drawn:
for stick_list in sticks_all_lists:
vertices = []
@@ -1324,19 +1311,23 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
bpy.context.scene.objects.link(new_mesh)
current_layers = bpy.context.scene.layers
- stick_cylinder = DEF_atom_pdb_build_stick(Stick_diameter, dl, Stick_sectors)
+ object_stick = DEF_atom_pdb_build_stick(Stick_diameter, dl, Stick_sectors)
+ stick_cylinder = object_stick[0]
stick_cylinder.active_material = stick[3]
-
+ stick_cups = object_stick[1]
+ stick_cups.active_material = stick[3]
+
if use_sticks_smooth == True:
- for face in stick_cylinder.data.faces:
- face.use_smooth = True
+ bpy.ops.object.select_all(action='DESELECT')
+ stick_cylinder.select = True
+ stick_cups.select = True
+ bpy.ops.object.shade_smooth()
stick_cylinder.parent = new_mesh
+ stick_cups.parent = new_mesh
new_mesh.dupli_type = 'FACES'
atom_object_list.append(new_mesh)
-
-
# ------------------------------------------------------------------------
# SELECT ALL LOADED OBJECTS
bpy.ops.object.select_all(action='DESELECT')
@@ -1351,5 +1342,4 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
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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