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Concept change: massive use of the collection principle to well structure atoms and sticks of the molecule 

Thanks to the great concept of 'collections', which Blender 2.80 is proposing, all parts of
the molecule (atoms and sticks) can be organized in an hierarchical order in dependence
on the chemical elements. Atoms (balls) are further separated from sticks (cylinders). For
some molecules, I tested all possible properties one can chose during the import, and it
works very well.
This commit is contained in:
Clemens Barth 2019-03-17 17:12:29 +01:00
parent 72c03e3efe
commit 850dfa2aa0
1 changed files with 169 additions and 39 deletions
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208
io_mesh_pdb/import_pdb.py
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@ -16,6 +16,7 @@
#
# ##### END GPL LICENSE BLOCK #####
import os
import bpy
import bmesh
from math import pi, cos, sin, sqrt, ceil
@ -529,15 +530,17 @@ def build_stick(radius, length, sectors, element_name):
cylinder.from_pydata(vertices, [], faces1)
cylinder.update()
new_cylinder = bpy.data.objects.new(element_name+"_sticks_cylinder", cylinder)
bpy.context.collection.objects.link(new_cylinder)
# Attention: the linking will be done a few moments later, after this
# is done definition.
# Build the mesh, Cups
cups = bpy.data.meshes.new(element_name+"_sticks_cup")
cups.from_pydata(vertices, [], faces2)
cups.update()
new_cups = bpy.data.objects.new(element_name+"_sticks_cup", cups)
bpy.context.collection.objects.link(new_cups)
# Attention: the linking will be done a few moments later, after this
# is done definition.
return (new_cylinder, new_cups)
@ -635,10 +638,10 @@ def draw_atoms_one_type(draw_all_atoms_type,
Ball_azimuth,
Ball_zenith,
Ball_radius_factor,
object_center_vec):
object_center_vec,
collection_molecule):
# Create first the vertices composed of the coordinates of all
# atoms of one type
# Create the vertices composed of the coordinates of all atoms of one type
atom_vertices = []
for atom in draw_all_atoms_type:
# In fact, the object is created in the World's origin.
@ -646,15 +649,35 @@ def draw_atoms_one_type(draw_all_atoms_type,
# the whole object is translated back to 'object_center_vec'.
atom_vertices.append(atom[2] - object_center_vec)
# IMPORTANT: First, we create a collection of the element, which contains
# the atoms (balls + mesh) AND the sticks! The definition dealing with the
# sticks will put the sticks inside this collection later on.
coll_element_name = atom[0] # the element name
# Create the new collection and ...
coll_element = bpy.data.collections.new(coll_element_name)
# ... link it to the collection, which contains all parts of the
# molecule.
collection_molecule.children.link(coll_element)
# Now, create a collection for the atoms, which includes the representative
# ball and the mesh.
coll_atom_name = atom[0] + "_atom"
# Create the new collection and ...
coll_atom = bpy.data.collections.new(coll_atom_name)
# ... link it to the collection, which contains all parts of the
# element (ball and mesh).
coll_element.children.link(coll_atom)
# Build the mesh
atom_mesh = bpy.data.meshes.new("Mesh_"+atom[0])
atom_mesh.from_pydata(atom_vertices, [], [])
atom_mesh.update()
new_atom_mesh = bpy.data.objects.new(atom[0] + "_mesh", atom_mesh)
bpy.context.collection.objects.link(new_atom_mesh)
# Link active object to the new collection
coll_atom.objects.link(new_atom_mesh)
# Now, build a representative sphere (atom).
if atom[0] == "Vacancy":
bpy.ops.mesh.primitive_cube_add(
view_align=False, enter_editmode=False,
@ -685,13 +708,26 @@ def draw_atoms_one_type(draw_all_atoms_type,
ball.name = atom[0] + "_cube"
else:
ball.name = atom[0] + "_ball"
ball.active_material = atom[1]
ball.parent = new_atom_mesh
new_atom_mesh.instance_type = 'VERTS'
# The object is back translated to 'object_center_vec'.
new_atom_mesh.location = object_center_vec
return new_atom_mesh
# Note the collection where the ball was placed into.
coll_all = ball.users_collection
if len(coll_all) > 0:
coll_past = coll_all[0]
else:
coll_past = bpy.context.scene.collection
# Put the atom into the new collection 'atom' and ...
coll_atom.objects.link(ball)
# ... unlink the atom from the other collection.
coll_past.objects.unlink(ball)
return new_atom_mesh, coll_element
# Function, which draws the sticks with help of the dupliverts technique.
@ -705,7 +741,8 @@ def draw_sticks_dupliverts(all_atoms,
Stick_unit,
Stick_dist,
use_sticks_smooth,
use_sticks_color):
use_sticks_color,
list_coll_elements):
dl = Stick_unit
@ -834,12 +871,25 @@ def draw_sticks_dupliverts(all_atoms,
faces.append((i*4+0,i*4+2,i*4+1,i*4+3))
i += 1
# Create a collection for the sticks, which includes the representative
# cylinders, cups and the mesh.
coll_name = stick[0][1:] + "_sticks"
# Create the collection and ...
coll = bpy.data.collections.new(coll_name)
# ... link it to the collection, which contains all parts of the
# element. 'stick[0][1:]' contains the name of the element!
for coll_element_from_list in list_coll_elements:
if stick[0][1:] in coll_element_from_list.name:
break
coll_element_from_list.children.link(coll)
# Build the mesh.
mesh = bpy.data.meshes.new("Sticks_"+stick[0][1:])
mesh.from_pydata(vertices, [], faces)
mesh.update()
new_mesh = bpy.data.objects.new(stick[0][1:]+"_sticks_mesh", mesh)
bpy.context.collection.objects.link(new_mesh)
# Link active object to the new collection
coll.objects.link(new_mesh)
# Build the object.
# Get the cylinder from the 'build_stick' function.
@ -847,11 +897,15 @@ def draw_sticks_dupliverts(all_atoms,
dl,
Stick_sectors,
stick[0][1:])
# Link active object to the new collection
coll.objects.link(object_stick[0])
coll.objects.link(object_stick[1])
stick_cylinder = object_stick[0]
stick_cylinder.active_material = stick[3]
stick_cups = object_stick[1]
stick_cups.active_material = stick[3]
# Smooth the cylinders.
if use_sticks_smooth == True:
bpy.ops.object.select_all(action='DESELECT')
@ -877,7 +931,8 @@ def draw_sticks_skin(all_atoms,
Stick_diameter,
use_sticks_smooth,
sticks_subdiv_view,
sticks_subdiv_render):
sticks_subdiv_render,
coll_molecule):
# These counters are for the edges, in the shape [i,i+1].
i = 0
@ -962,7 +1017,8 @@ def draw_sticks_skin(all_atoms,
stick_mesh.from_pydata(stick_vertices, stick_edges, [])
stick_mesh.update()
new_stick_mesh = bpy.data.objects.new("Sticks", stick_mesh)
bpy.context.collection.objects.link(new_stick_mesh)
# Link the active mesh to the molecule collection
coll_molecule.objects.link(new_stick_mesh)
# Apply the skin modifier.
new_stick_mesh.modifiers.new(name="Sticks_skin", type='SKIN')
@ -979,7 +1035,7 @@ def draw_sticks_skin(all_atoms,
stick_material.diffuse_color = ELEMENTS[-1].color
new_stick_mesh.active_material = stick_material
# This is for putting the radiu of the sticks onto
# This is for putting the radius of the sticks onto
# the desired value 'Stick_diameter'
bpy.context.view_layer.objects.active = new_stick_mesh
# EDIT mode
@ -1025,7 +1081,8 @@ def draw_sticks_normal(all_atoms,
Stick_sectors,
use_sticks_smooth,
use_sticks_one_object,
use_sticks_one_object_nr):
use_sticks_one_object_nr,
coll_molecule):
bpy.ops.object.material_slot_add()
stick_material = bpy.data.materials.new(ELEMENTS[-1].name)
@ -1054,14 +1111,14 @@ def draw_sticks_normal(all_atoms,
# Calculate Euler angles
euler = Matrix.Rotation(angle, 4, axis).to_euler()
# Create stick
bpy.ops.mesh.primitive_cylinder_add(vertices=Stick_sectors,
radius=Stick_diameter,
depth=v.length,
end_fill_type='NGON',
view_align=False,
enter_editmode=False,
location=location,
rotation=(0, 0, 0))
stick = bpy.ops.mesh.primitive_cylinder_add(vertices=Stick_sectors,
radius=Stick_diameter,
depth=v.length,
end_fill_type='NGON',
view_align=False,
enter_editmode=False,
location=location,
rotation=(0, 0, 0))
# Put the stick into the scene ...
stick = bpy.context.view_layer.objects.active
# ... and rotate the stick.
@ -1107,19 +1164,76 @@ def draw_sticks_normal(all_atoms,
center='MEDIAN')
sticks = bpy.context.view_layer.objects.active
sticks.active_material = stick_material
sticks.location += center
# Collections
# ===========
# Note the collection where the sticks were placed into.
coll_all = sticks.users_collection
if len(coll_all) > 0:
coll_past = coll_all[0]
else:
coll_past = bpy.context.scene.collection
# Link the sticks with the collection of the molecule ...
coll_molecule.objects.link(sticks)
# ... and unlink them from the collection it has been before.
coll_past.objects.unlink(sticks)
return sticks
else:
# Here we use an empty ...
bpy.ops.object.empty_add(type='ARROWS',
view_align=False,
location=(0, 0, 0),
rotation=(0, 0, 0))
sticks = bpy.context.view_layer.objects.active
sticks_empty = bpy.context.view_layer.objects.active
sticks_empty.name = "A_sticks_empty"
# ... that is parent to all sticks. With this, we can better move
# all sticks if necessary.
for stick in list_group_sub:
stick.parent = sticks
stick.parent = sticks_empty
sticks.name = "Sticks"
sticks.location += center
sticks_empty.location += center
return sticks
# Collections
# ===========
# Create a collection that will contain all sticks + the empty and ...
coll = bpy.data.collections.new("Sticks")
# ... link it to the collection, which contains all parts of the
# molecule.
coll_molecule.children.link(coll)
# Now, create a collection that only contains the sticks and ...
coll_cylinder = bpy.data.collections.new("Sticks_cylinders")
# ... link it to the collection, which contains the sticks and empty.
coll.children.link(coll_cylinder)
# Note the collection where the empty was placed into, ...
coll_all = sticks_empty.users_collection
if len(coll_all) > 0:
coll_past = coll_all[0]
else:
coll_past = bpy.context.scene.collection
# ... link the empty with the new collection ...
coll.objects.link(sticks_empty)
# ... and unlink it from the old collection where it has been before.
coll_past.objects.unlink(sticks_empty)
# Note the collection where the cylinders were placed into, ...
coll_all = list_group_sub[0].users_collection
if len(coll_all) > 0:
coll_past = coll_all[0]
else:
coll_past = bpy.context.scene.collection
for stick in list_group_sub:
# ... link each stick with the new collection ...
coll_cylinder.objects.link(stick)
# ... and unlink it from the old collection.
coll_past.objects.unlink(stick)
return sticks_empty
# -----------------------------------------------------------------------------
@ -1280,7 +1394,6 @@ def import_pdb(Ball_type,
# draw_all_atoms = [ data_hydrogen,data_carbon,data_nitrogen ]
# data_hydrogen = [["Hydrogen", Material_Hydrogen, Vector((x,y,z)), 109], ...]
# Go through the list which contains all types of atoms. It is the list,
# which has been created on the top during reading the PDB file.
# Example: atom_all_types_list = ["hydrogen", "carbon", ...]
@ -1308,21 +1421,35 @@ def import_pdb(Ball_type,
# Now append the atom list to the list of all types of atoms
draw_all_atoms.append(draw_all_atoms_type)
# ------------------------------------------------------------------------
# COLLECTION
# Before we start to draw the atoms and sticks, we first create a
# collection for the molecule. All atoms (balls) and sticks (cylinders)
# are put into this collection.
coll_molecule_name = os.path.basename(filepath_pdb)
scene = bpy.context.scene
coll_molecule = bpy.data.collections.new(coll_molecule_name)
scene.collection.children.link(coll_molecule)
# ------------------------------------------------------------------------
# DRAWING THE ATOMS
bpy.ops.object.select_all(action='DESELECT')
list_coll_elements = []
# For each list of atoms of ONE type (e.g. Hydrogen)
for draw_all_atoms_type in draw_all_atoms:
atom_mesh = draw_atoms_one_type(draw_all_atoms_type,
Ball_type,
Ball_azimuth,
Ball_zenith,
Ball_radius_factor,
object_center_vec)
atom_mesh, coll_element = draw_atoms_one_type(draw_all_atoms_type,
Ball_type,
Ball_azimuth,
Ball_zenith,
Ball_radius_factor,
object_center_vec,
coll_molecule)
atom_object_list.append(atom_mesh)
list_coll_elements.append(coll_element)
# ------------------------------------------------------------------------
# DRAWING THE STICKS: cylinders in a dupliverts structure
@ -1338,7 +1465,8 @@ def import_pdb(Ball_type,
Stick_unit,
Stick_dist,
use_sticks_smooth,
use_sticks_color)
use_sticks_color,
list_coll_elements)
for stick in sticks:
atom_object_list.append(stick)
@ -1352,7 +1480,8 @@ def import_pdb(Ball_type,
Stick_diameter,
use_sticks_smooth,
sticks_subdiv_view,
sticks_subdiv_render)
sticks_subdiv_render,
coll_molecule)
atom_object_list.append(sticks)
# ------------------------------------------------------------------------
@ -1367,7 +1496,8 @@ def import_pdb(Ball_type,
Stick_sectors,
use_sticks_smooth,
use_sticks_one_object,
use_sticks_one_object_nr)
use_sticks_one_object_nr,
coll_molecule)
atom_object_list.append(sticks)
# ------------------------------------------------------------------------