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Commit 1bafadf7 authored by Clemens Barth's avatar Clemens Barth
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- 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
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io_mesh_pdb/__init__.py
+ 7
− 29
View file @ 1bafadf7
......@@ -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,
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,
......
io_mesh_pdb/export_pdb.py
+ 2
− 5
View file @ 1bafadf7
......@@ -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
io_mesh_pdb/import_pdb.py
+ 52
− 62
View file @ 1bafadf7
......@@ -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)
faces2.append(face_top)
faces2.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] )
# 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
......@@ -557,13 +560,26 @@ def DEF_atom_pdb_custom_datafile(path_datafile):
data_file_p.close()
return True
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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