diff --git a/io_mesh_pdb/__init__.py b/io_mesh_pdb/__init__.py
index 19c7c4a474c09b936ca1ee9bce4d88d3274a033b..1d2a7cecc24399f01e33c26082a75d2ee0396af3 100644
--- a/io_mesh_pdb/__init__.py
+++ b/io_mesh_pdb/__init__.py
@@ -24,21 +24,23 @@
#
# Start of project : 2011-08-31 by Clemens Barth
# First publication in Blender : 2011-11-11
-# Last modified : 2013-03-22
+# Last modified : 2013-04-04
#
# Acknowledgements
# ================
-#
# Blender: ideasman, meta_androcto, truman, kilon, CoDEmanX, dairin0d, PKHG,
# Valter, ...
-# Other: Frank Palmino
+# Other : Frank Palmino
+#
+#
+# To do: 1. Sticks in normal representation: options bonds and colors
#
bl_info = {
"name": "Atomic Blender - PDB",
"description": "Loading and manipulating atoms from PDB files",
"author": "Clemens Barth",
- "version": (1, 6),
+ "version": (1, 7),
"blender": (2, 60, 0),
"location": "File -> Import -> PDB (.pdb)",
"warning": "",
@@ -73,6 +75,9 @@ class ImportPDB(Operator, ImportHelper):
filename_ext = ".pdb"
filter_glob = StringProperty(default="*.pdb", options={'HIDDEN'},)
+ use_center = BoolProperty(
+ name = "Object to origin", default=True,
+ description = "Put the object into the global origin")
use_camera = BoolProperty(
name="Camera", default=False,
description="Do you need a camera?")
@@ -99,7 +104,7 @@ class ImportPDB(Operator, ImportHelper):
name = "Distances", default=1.0, min=0.0001,
description = "Scale factor for all distances")
atomradius = EnumProperty(
- name="Type of radius",
+ name="Type",
description="Choose type of atom radius",
items=(('0', "Pre-defined", "Use pre-defined radius"),
('1', "Atomic", "Use atomic radius"),
@@ -107,10 +112,14 @@ class ImportPDB(Operator, ImportHelper):
default='0',)
use_sticks = BoolProperty(
name="Use sticks", default=True,
- description="Do you want to display the sticks?")
- use_sticks_skin = BoolProperty(
- name="Use skin modifier", default=False,
- description="Do you want to display the sticks with the skin modifier?")
+ description="Do you want to display the sticks?")
+ use_sticks_type = EnumProperty(
+ name="Type",
+ description="Choose type of stick",
+ items=(('0', "Dupliverts", "Use dupliverts structures"),
+ ('1', "Skin", "Use skin and subdivision modifier"),
+ ('2', "Normal", "Use simple cylinders")),
+ default='0',)
sticks_subdiv_view = IntProperty(
name = "SubDivV", default=2, min=1,
description="Number of subdivisions (view)")
@@ -136,11 +145,14 @@ class ImportPDB(Operator, ImportHelper):
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")
- use_center = BoolProperty(
- name = "Object to origin", default=True,
- description = "Put the object into the global origin")
+ name="", default = 1.1, min=1.0, max=3.0,
+ description="Distance between sticks measured in stick diameter")
+ use_sticks_one_object = BoolProperty(
+ name="One object", default=True,
+ description="All sticks are one object.")
+ use_sticks_one_object_nr = IntProperty(
+ name = "No.", default=200, min=10,
+ description="Number of sticks to be grouped at once")
datafile = StringProperty(
name = "", description="Path to your custom data file",
maxlen = 256, default = "", subtype='FILE_PATH')
@@ -151,58 +163,71 @@ class ImportPDB(Operator, ImportHelper):
row.prop(self, "use_camera")
row.prop(self, "use_lamp")
row = layout.row()
- row.prop(self, "use_center")
- row = layout.row()
+ row.prop(self, "use_center")
+ # Balls
+ box = layout.box()
+ row = box.row()
+ row.label(text="Balls / atoms")
+ row = box.row()
col = row.column()
col.prop(self, "ball")
- row = layout.row()
+ row = box.row()
row.active = (self.ball == "1")
col = row.column(align=True)
col.prop(self, "mesh_azimuth")
col.prop(self, "mesh_zenith")
- row = layout.row()
+ row = box.row()
col = row.column()
col.label(text="Scaling factors")
col = row.column(align=True)
col.prop(self, "scale_ballradius")
col.prop(self, "scale_distances")
- row = layout.row()
+ row = box.row()
row.prop(self, "atomradius")
- row = layout.row()
- # Sticks
+ # Sticks
+ box = layout.box()
+ row = box.row()
+ row.label(text="Sticks / bonds")
+ row = box.row()
row.prop(self, "use_sticks")
- row = layout.row()
+ row = box.row()
row.active = self.use_sticks
- row.prop(self, "use_sticks_skin")
- row = layout.row()
+ row.prop(self, "use_sticks_type")
+ row = box.row()
row.active = self.use_sticks
col = row.column()
- if not self.use_sticks_skin:
+ if self.use_sticks_type == '0' or self.use_sticks_type == '2':
col.prop(self, "sticks_sectors")
col.prop(self, "sticks_radius")
- if self.use_sticks_skin:
- row = layout.row()
+ if self.use_sticks_type == '1':
+ row = box.row()
row.active = self.use_sticks
row.prop(self, "sticks_subdiv_view")
row.prop(self, "sticks_subdiv_render")
- row = layout.row()
+ row = box.row()
row.active = self.use_sticks
- if not self.use_sticks_skin:
+ if self.use_sticks_type == '0':
col.prop(self, "sticks_unit_length")
col = row.column(align=True)
- if not self.use_sticks_skin:
+ if self.use_sticks_type == '0':
col.prop(self, "use_sticks_color")
col.prop(self, "use_sticks_smooth")
- if not self.use_sticks_skin:
+ if self.use_sticks_type == '0' or self.use_sticks_type == '2':
col.prop(self, "use_sticks_bonds")
- row = layout.row()
- row.active = self.use_sticks
- col = row.column(align=True)
- col = row.column(align=True)
- col.active = self.use_sticks
- if not self.use_sticks_skin:
- col.prop(self, "sticks_dist")
-
+ row = box.row()
+ if self.use_sticks_type == '0':
+ row.active = self.use_sticks and self.use_sticks_bonds
+ row.label(text="Distance")
+ row.prop(self, "sticks_dist")
+ if self.use_sticks_type == '2':
+ row.active = self.use_sticks
+ col = row.column()
+ col.prop(self, "use_sticks_one_object")
+ col = row.column()
+ col.active = self.use_sticks_one_object
+ col.prop(self, "use_sticks_one_object_nr")
+
+
def execute(self, context):
# This is in order to solve this strange 'relative path' thing.
filepath_pdb = bpy.path.abspath(self.filepath)
@@ -216,12 +241,14 @@ class ImportPDB(Operator, ImportHelper):
self.atomradius,
self.scale_distances,
self.use_sticks,
- self.use_sticks_skin,
+ self.use_sticks_type,
self.sticks_subdiv_view,
self.sticks_subdiv_render,
self.use_sticks_color,
self.use_sticks_smooth,
self.use_sticks_bonds,
+ self.use_sticks_one_object,
+ self.use_sticks_one_object_nr,
self.sticks_unit_length,
self.sticks_dist,
self.sticks_sectors,
diff --git a/io_mesh_pdb/import_pdb.py b/io_mesh_pdb/import_pdb.py
index d52a7e9fb1686b86dde912066943809b247d44ba..37109cacc0fc0b49604f3e266e94a713e6cfc450 100644
--- a/io_mesh_pdb/import_pdb.py
+++ b/io_mesh_pdb/import_pdb.py
@@ -690,154 +690,11 @@ def draw_atoms_one_type(draw_all_atoms_type,
return new_atom_mesh
-# Function, which draws the sticks with help of the skin and subdivision
-# modifiers.
-def draw_sticks_skin(all_atoms,
- all_sticks,
- Stick_diameter,
- use_sticks_smooth,
- sticks_subdiv_view,
- sticks_subdiv_render):
-
- # These counters are for the edges, in the shape [i,i+1].
- i = 0
-
- # This is the list of vertices, containing the atom position
- # (vectors)).
- stick_vertices = []
- # This is the 'same' list, which contains not vector position of
- # the atoms but their numbers. It is used to handle the edges.
- stick_vertices_nr = []
- # This is the list of edges.
- stick_edges = []
-
- # Go through the list of all sticks. For each stick do:
- for stick in all_sticks:
-
- # Each stick has two atoms = two vertices.
-
- """
- [ 0,1 , 3,4 , 0,8 , 7,3]
- [[0,1], [2,3], [4,5], [6,7]]
-
- [ 0,1 , 3,4 , x,8 , 7,x] x:deleted
- [[0,1], [2,3], [0,5], [6,2]]
- """
-
- # Check, if the vertex (atom) is already in the vertex list.
- # edge: [s1,s2]
- FLAG_s1 = False
- s1 = 0
- for stick2 in stick_vertices_nr:
- if stick2 == stick.atom1-1:
- FLAG_s1 = True
- break
- s1 += 1
- FLAG_s2 = False
- s2 = 0
- for stick2 in stick_vertices_nr:
- if stick2 == stick.atom2-1:
- FLAG_s2 = True
- break
- s2 += 1
-
- # If the vertex (atom) is not yet in the vertex list:
- # append the number of atom and the vertex to the two lists.
- # For the first atom:
- if FLAG_s1 == False:
- atom1 = copy(all_atoms[stick.atom1-1].location)
- stick_vertices.append(atom1)
- stick_vertices_nr.append(stick.atom1-1)
- # For the second atom:
- if FLAG_s2 == False:
- atom2 = copy(all_atoms[stick.atom2-1].location)
- stick_vertices.append(atom2)
- stick_vertices_nr.append(stick.atom2-1)
-
- # Build the edges:
-
- # If both vertices (atoms) were not in the lists, then
- # the edge is simply [i,i+1]. These are two new vertices
- # (atoms), so increase i by 2.
- if FLAG_s1 == False and FLAG_s2 == False:
- stick_edges.append([i,i+1])
- i += 2
- # Both vertices (atoms) were already in the list, so then
- # use the vertices (atoms), which already exist. They are
- # at positions s1 and s2.
- if FLAG_s1 == True and FLAG_s2 == True:
- stick_edges.append([s1,s2])
- # The following two if cases describe the situation that
- # only one vertex (atom) was in the list. Since only ONE
- # new vertex was added, increase i by one.
- if FLAG_s1 == True and FLAG_s2 == False:
- stick_edges.append([s1,i])
- i += 1
- if FLAG_s1 == False and FLAG_s2 == True:
- stick_edges.append([i,s2])
- i += 1
-
- # Build the mesh of the sticks
- stick_mesh = bpy.data.meshes.new("Mesh_sticks")
- stick_mesh.from_pydata(stick_vertices, stick_edges, [])
- stick_mesh.update()
- new_stick_mesh = bpy.data.objects.new("Sticks", stick_mesh)
- bpy.context.scene.objects.link(new_stick_mesh)
-
- # Apply the skin modifier.
- new_stick_mesh.modifiers.new(name="Sticks_skin", type='SKIN')
- # Smooth the skin surface if this option has been chosen.
- new_stick_mesh.modifiers[0].use_smooth_shade = use_sticks_smooth
- # Apply the Subdivision modifier.
- new_stick_mesh.modifiers.new(name="Sticks_subsurf", type='SUBSURF')
- # Options: choose the levels
- new_stick_mesh.modifiers[1].levels = sticks_subdiv_view
- new_stick_mesh.modifiers[1].render_levels = sticks_subdiv_render
-
- bpy.ops.object.material_slot_add()
- stick_material = bpy.data.materials.new(ELEMENTS[-1].name)
- stick_material.diffuse_color = ELEMENTS[-1].color
- new_stick_mesh.active_material = stick_material
-
- # This is for putting the radiu of the sticks onto
- # the desired value 'Stick_diameter'
- bpy.context.scene.objects.active = new_stick_mesh
- # EDIT mode
- bpy.ops.object.mode_set(mode='EDIT', toggle=False)
- bm = bmesh.from_edit_mesh(new_stick_mesh.data)
- bpy.ops.mesh.select_all(action='DESELECT')
-
- # Select all vertices
- for v in bm.verts:
- v.select = True
-
- # This is somewhat a factor for the radius.
- r_f = 4.0
- # Apply operator 'skin_resize'.
- bpy.ops.transform.skin_resize(value=(Stick_diameter*r_f,
- Stick_diameter*r_f,
- Stick_diameter*r_f),
- constraint_axis=(False, False, False),
- constraint_orientation='GLOBAL',
- mirror=False,
- proportional='DISABLED',
- proportional_edit_falloff='SMOOTH',
- proportional_size=1,
- snap=False,
- snap_target='CLOSEST',
- snap_point=(0, 0, 0),
- snap_align=False,
- snap_normal=(0, 0, 0),
- texture_space=False,
- release_confirm=False)
- # Back to the OBJECT mode.
- bpy.ops.object.mode_set(mode='OBJECT', toggle=False)
-
-
# Function, which draws the sticks with help of the dupliverts technique.
# Return: list of dupliverts structures.
def draw_sticks_dupliverts(all_atoms,
atom_all_types_list,
+ center,
all_sticks,
Stick_diameter,
Stick_sectors,
@@ -864,8 +721,8 @@ def draw_sticks_dupliverts(all_atoms,
for repeat in range(stick.number):
- atom1 = copy(all_atoms[stick.atom1-1].location)
- atom2 = copy(all_atoms[stick.atom2-1].location)
+ atom1 = copy(all_atoms[stick.atom1-1].location)-center
+ atom2 = copy(all_atoms[stick.atom2-1].location)-center
dist = Stick_diameter * Stick_dist
@@ -909,8 +766,8 @@ def draw_sticks_dupliverts(all_atoms,
for repeat in range(stick.number):
- atom1 = copy(all_atoms[stick.atom1-1].location)
- atom2 = copy(all_atoms[stick.atom2-1].location)
+ atom1 = copy(all_atoms[stick.atom1-1].location)-center
+ atom2 = copy(all_atoms[stick.atom2-1].location)-center
dist = Stick_diameter * Stick_dist
@@ -982,7 +839,6 @@ def draw_sticks_dupliverts(all_atoms,
bpy.context.scene.objects.link(new_mesh)
# Build the object.
- current_layers = bpy.context.scene.layers
# Get the cylinder from the 'build_stick' function.
object_stick = build_stick(Stick_diameter, dl, Stick_sectors)
stick_cylinder = object_stick[0]
@@ -1001,12 +857,269 @@ def draw_sticks_dupliverts(all_atoms,
stick_cylinder.parent = new_mesh
stick_cups.parent = new_mesh
new_mesh.dupli_type = 'FACES'
+ new_mesh.location = center
atom_object_list.append(new_mesh)
# Return the list of dupliverts structures.
return atom_object_list
+# Function, which draws the sticks with help of the skin and subdivision
+# modifiers.
+def draw_sticks_skin(all_atoms,
+ all_sticks,
+ Stick_diameter,
+ use_sticks_smooth,
+ sticks_subdiv_view,
+ sticks_subdiv_render):
+
+ # These counters are for the edges, in the shape [i,i+1].
+ i = 0
+
+ # This is the list of vertices, containing the atom position
+ # (vectors)).
+ stick_vertices = []
+ # This is the 'same' list, which contains not vector position of
+ # the atoms but their numbers. It is used to handle the edges.
+ stick_vertices_nr = []
+ # This is the list of edges.
+ stick_edges = []
+
+ # Go through the list of all sticks. For each stick do:
+ for stick in all_sticks:
+
+ # Each stick has two atoms = two vertices.
+
+ """
+ [ 0,1 , 3,4 , 0,8 , 7,3]
+ [[0,1], [2,3], [4,5], [6,7]]
+
+ [ 0,1 , 3,4 , x,8 , 7,x] x:deleted
+ [[0,1], [2,3], [0,5], [6,2]]
+ """
+
+ # Check, if the vertex (atom) is already in the vertex list.
+ # edge: [s1,s2]
+ FLAG_s1 = False
+ s1 = 0
+ for stick2 in stick_vertices_nr:
+ if stick2 == stick.atom1-1:
+ FLAG_s1 = True
+ break
+ s1 += 1
+ FLAG_s2 = False
+ s2 = 0
+ for stick2 in stick_vertices_nr:
+ if stick2 == stick.atom2-1:
+ FLAG_s2 = True
+ break
+ s2 += 1
+
+ # If the vertex (atom) is not yet in the vertex list:
+ # append the number of atom and the vertex to the two lists.
+ # For the first atom:
+ if FLAG_s1 == False:
+ atom1 = copy(all_atoms[stick.atom1-1].location)
+ stick_vertices.append(atom1)
+ stick_vertices_nr.append(stick.atom1-1)
+ # For the second atom:
+ if FLAG_s2 == False:
+ atom2 = copy(all_atoms[stick.atom2-1].location)
+ stick_vertices.append(atom2)
+ stick_vertices_nr.append(stick.atom2-1)
+
+ # Build the edges:
+
+ # If both vertices (atoms) were not in the lists, then
+ # the edge is simply [i,i+1]. These are two new vertices
+ # (atoms), so increase i by 2.
+ if FLAG_s1 == False and FLAG_s2 == False:
+ stick_edges.append([i,i+1])
+ i += 2
+ # Both vertices (atoms) were already in the list, so then
+ # use the vertices (atoms), which already exist. They are
+ # at positions s1 and s2.
+ if FLAG_s1 == True and FLAG_s2 == True:
+ stick_edges.append([s1,s2])
+ # The following two if cases describe the situation that
+ # only one vertex (atom) was in the list. Since only ONE
+ # new vertex was added, increase i by one.
+ if FLAG_s1 == True and FLAG_s2 == False:
+ stick_edges.append([s1,i])
+ i += 1
+ if FLAG_s1 == False and FLAG_s2 == True:
+ stick_edges.append([i,s2])
+ i += 1
+
+ # Build the mesh of the sticks
+ stick_mesh = bpy.data.meshes.new("Mesh_sticks")
+ stick_mesh.from_pydata(stick_vertices, stick_edges, [])
+ stick_mesh.update()
+ new_stick_mesh = bpy.data.objects.new("Sticks", stick_mesh)
+ bpy.context.scene.objects.link(new_stick_mesh)
+
+ # Apply the skin modifier.
+ new_stick_mesh.modifiers.new(name="Sticks_skin", type='SKIN')
+ # Smooth the skin surface if this option has been chosen.
+ new_stick_mesh.modifiers[0].use_smooth_shade = use_sticks_smooth
+ # Apply the Subdivision modifier.
+ new_stick_mesh.modifiers.new(name="Sticks_subsurf", type='SUBSURF')
+ # Options: choose the levels
+ new_stick_mesh.modifiers[1].levels = sticks_subdiv_view
+ new_stick_mesh.modifiers[1].render_levels = sticks_subdiv_render
+
+ bpy.ops.object.material_slot_add()
+ stick_material = bpy.data.materials.new(ELEMENTS[-1].name)
+ stick_material.diffuse_color = ELEMENTS[-1].color
+ new_stick_mesh.active_material = stick_material
+
+ # This is for putting the radiu of the sticks onto
+ # the desired value 'Stick_diameter'
+ bpy.context.scene.objects.active = new_stick_mesh
+ # EDIT mode
+ bpy.ops.object.mode_set(mode='EDIT', toggle=False)
+ bm = bmesh.from_edit_mesh(new_stick_mesh.data)
+ bpy.ops.mesh.select_all(action='DESELECT')
+
+ # Select all vertices
+ for v in bm.verts:
+ v.select = True
+
+ # This is somewhat a factor for the radius.
+ r_f = 4.0
+ # Apply operator 'skin_resize'.
+ bpy.ops.transform.skin_resize(value=(Stick_diameter*r_f,
+ Stick_diameter*r_f,
+ Stick_diameter*r_f),
+ constraint_axis=(False, False, False),
+ constraint_orientation='GLOBAL',
+ mirror=False,
+ proportional='DISABLED',
+ proportional_edit_falloff='SMOOTH',
+ proportional_size=1,
+ snap=False,
+ snap_target='CLOSEST',
+ snap_point=(0, 0, 0),
+ snap_align=False,
+ snap_normal=(0, 0, 0),
+ texture_space=False,
+ release_confirm=False)
+ # Back to the OBJECT mode.
+ bpy.ops.object.mode_set(mode='OBJECT', toggle=False)
+
+ return new_stick_mesh
+
+
+# Draw the sticks the normal way: connect the atoms by simple cylinders.
+# Two options: 1. single cylinders parented to an empty
+# 2. one single mesh object
+def draw_sticks_normal(all_atoms,
+ all_sticks,
+ center,
+ Stick_diameter,
+ Stick_sectors,
+ use_sticks_smooth,
+ use_sticks_one_object,
+ use_sticks_one_object_nr):
+
+ bpy.ops.object.material_slot_add()
+ stick_material = bpy.data.materials.new(ELEMENTS[-1].name)
+ stick_material.diffuse_color = ELEMENTS[-1].color
+
+ up_axis = Vector([0.0, 0.0, 1.0])
+ current_layers = bpy.context.scene.layers
+
+ # For all sticks, do ...
+ list_group = []
+ list_group_sub = []
+ counter = 0
+ for stick in all_sticks:
+
+ # The vectors of the two atoms
+ atom1 = all_atoms[stick.atom1-1].location-center
+ atom2 = all_atoms[stick.atom2-1].location-center
+ # Location
+ location = (atom1 + atom2) * 0.5
+ # The difference of both vectors
+ v = (atom2 - atom1)
+ # Angle with respect to the z-axis
+ angle = v.angle(up_axis, 0)
+ # Cross-product between v and the z-axis vector. It is the
+ # vector of rotation.
+ axis = up_axis.cross(v)
+ # 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),
+ layers=current_layers)
+ # Put the stick into the scene ...
+ stick = bpy.context.scene.objects.active
+ # ... and rotate the stick.
+ stick.rotation_euler = euler
+ # ... and name
+ stick.name = "Stick_Cylinder"
+ counter += 1
+
+ # Smooth the cylinder.
+ if use_sticks_smooth == True:
+ bpy.ops.object.select_all(action='DESELECT')
+ stick.select = True
+ bpy.ops.object.shade_smooth()
+
+ list_group_sub.append(stick)
+
+ if use_sticks_one_object == True:
+ if counter == use_sticks_one_object_nr:
+ bpy.ops.object.select_all(action='DESELECT')
+ for stick in list_group_sub:
+ stick.select = True
+ bpy.ops.object.join()
+ list_group.append(bpy.context.scene.objects.active)
+ bpy.ops.object.select_all(action='DESELECT')
+ list_group_sub = []
+ counter = 0
+ else:
+ # Material ...
+ stick.active_material = stick_material
+
+ if use_sticks_one_object == True:
+ bpy.ops.object.select_all(action='DESELECT')
+ for stick in list_group_sub:
+ stick.select = True
+ bpy.ops.object.join()
+ list_group.append(bpy.context.scene.objects.active)
+ bpy.ops.object.select_all(action='DESELECT')
+
+ for group in list_group:
+ group.select = True
+ bpy.ops.object.join()
+ bpy.ops.object.origin_set(type='ORIGIN_GEOMETRY',
+ center='MEDIAN')
+ sticks = bpy.context.scene.objects.active
+ sticks.active_material = stick_material
+ else:
+ bpy.ops.object.empty_add(type='ARROWS',
+ view_align=False,
+ location=(0, 0, 0),
+ rotation=(0, 0, 0),
+ layers=current_layers)
+ sticks = bpy.context.scene.objects.active
+ for stick in list_group_sub:
+ stick.parent = sticks
+
+ sticks.name = "Sticks"
+ sticks.location += center
+
+ return sticks
+
+
# -----------------------------------------------------------------------------
# The main routine
@@ -1017,12 +1130,14 @@ def import_pdb(Ball_type,
radiustype,
Ball_distance_factor,
use_sticks,
- use_sticks_skin,
+ use_sticks_type,
sticks_subdiv_view,
sticks_subdiv_render,
use_sticks_color,
use_sticks_smooth,
- use_sticks_bonds,
+ use_sticks_bonds,
+ use_sticks_one_object,
+ use_sticks_one_object_nr,
Stick_unit, Stick_dist,
Stick_sectors,
Stick_diameter,
@@ -1156,7 +1271,6 @@ def import_pdb(Ball_type,
# taken as a measure. The size is used to place well the camera and light
# into the scene.
object_size_vec = [atom.location - object_center_vec for atom in all_atoms]
- object_size = 0.0
object_size = max(object_size_vec).length
# ------------------------------------------------------------------------
@@ -1187,9 +1301,9 @@ def import_pdb(Ball_type,
if atom.name == atom_type[0]:
# ... and append them to the list 'draw_all_atoms_type'.
draw_all_atoms_type.append([atom.name,
- atom.material,
- atom.location,
- atom.radius])
+ atom.material,
+ atom.location,
+ atom.radius])
# Now append the atom list to the list of all types of atoms
draw_all_atoms.append(draw_all_atoms_type)
@@ -1208,34 +1322,51 @@ def import_pdb(Ball_type,
object_center_vec)
atom_object_list.append(atom_mesh)
+ # ------------------------------------------------------------------------
+ # DRAWING THE STICKS: cylinders in a dupliverts structure
+
+ if use_sticks == True and use_sticks_type == '0' and all_sticks != []:
+
+ sticks = draw_sticks_dupliverts(all_atoms,
+ atom_all_types_list,
+ object_center_vec,
+ all_sticks,
+ Stick_diameter,
+ Stick_sectors,
+ Stick_unit,
+ Stick_dist,
+ use_sticks_smooth,
+ use_sticks_color)
+ for stick in sticks:
+ atom_object_list.append(stick)
+
# ------------------------------------------------------------------------
# DRAWING THE STICKS: skin and subdivision modifier
- if use_sticks == True and use_sticks_skin == True and all_sticks != []:
+ if use_sticks == True and use_sticks_type == '1' and all_sticks != []:
- draw_sticks_skin(all_atoms,
- all_sticks,
- Stick_diameter,
- use_sticks_smooth,
- sticks_subdiv_view,
- sticks_subdiv_render)
+ sticks = draw_sticks_skin(all_atoms,
+ all_sticks,
+ Stick_diameter,
+ use_sticks_smooth,
+ sticks_subdiv_view,
+ sticks_subdiv_render)
+ atom_object_list.append(sticks)
# ------------------------------------------------------------------------
- # DRAWING THE STICKS: cylinders in a dupliverts structure
-
- if use_sticks == True and all_sticks != [] and use_sticks_skin == False:
-
- stick_meshes = draw_sticks_dupliverts(all_atoms,
- atom_all_types_list,
- all_sticks,
- Stick_diameter,
- Stick_sectors,
- Stick_unit,
- Stick_dist,
- use_sticks_smooth,
- use_sticks_color)
- for stick_mesh in stick_meshes:
- atom_object_list.append(stick_mesh)
+ # DRAWING THE STICKS: normal cylinders
+
+ if use_sticks == True and use_sticks_type == '2' and all_sticks != []:
+
+ sticks = draw_sticks_normal(all_atoms,
+ all_sticks,
+ object_center_vec,
+ Stick_diameter,
+ Stick_sectors,
+ use_sticks_smooth,
+ use_sticks_one_object,
+ use_sticks_one_object_nr)
+ atom_object_list.append(sticks)
# ------------------------------------------------------------------------
# CAMERA and LIGHT SOURCES