diff --git a/io_mesh_pdb/import_pdb.py b/io_mesh_pdb/import_pdb.py
index 42efa3194b867eb1b1d7052ee2f27dd3b8969486..6692f9f3281fba67df1d0a7c5a44fca03522f346 100644
--- a/io_mesh_pdb/import_pdb.py
+++ b/io_mesh_pdb/import_pdb.py
@@ -689,6 +689,319 @@ 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
+
+ # 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,
+ all_sticks,
+ Stick_diameter,
+ Stick_sectors,
+ Stick_unit,
+ Stick_dist,
+ use_sticks_smooth,
+ use_sticks_color):
+
+ dl = Stick_unit
+
+ if use_sticks_color == False:
+ bpy.ops.object.material_slot_add()
+ stick_material = bpy.data.materials.new(ELEMENTS[-1].name)
+ stick_material.diffuse_color = ELEMENTS[-1].color
+
+ # Sort the sticks and put them into a new list such that ...
+ sticks_all_lists = []
+ if use_sticks_color == True:
+ for atom_type in atom_all_types_list:
+ if atom_type[0] == "TER":
+ continue
+ sticks_list = []
+ for stick in all_sticks:
+
+ for repeat in range(stick.number):
+
+ atom1 = copy(all_atoms[stick.atom1-1].location)
+ atom2 = copy(all_atoms[stick.atom2-1].location)
+
+ dist = Stick_diameter * Stick_dist
+
+ if stick.number == 2:
+ if repeat == 0:
+ atom1 += (stick.dist * dist)
+ atom2 += (stick.dist * dist)
+ if repeat == 1:
+ atom1 -= (stick.dist * dist)
+ atom2 -= (stick.dist * dist)
+
+ if stick.number == 3:
+ if repeat == 0:
+ atom1 += (stick.dist * dist)
+ atom2 += (stick.dist * dist)
+ if repeat == 2:
+ atom1 -= (stick.dist * dist)
+ atom2 -= (stick.dist * dist)
+
+ dv = atom1 - atom2
+ n = dv / dv.length
+ if atom_type[0] == all_atoms[stick.atom1-1].name:
+ location = atom1
+ name = "_" + all_atoms[stick.atom1-1].name
+ material = all_atoms[stick.atom1-1].material
+ sticks_list.append([name, location, dv, material])
+ if atom_type[0] == all_atoms[stick.atom2-1].name:
+ location = atom1 - n * dl * int(ceil(dv.length / (2.0 * dl)))
+ name = "_" + all_atoms[stick.atom2-1].name
+ material = all_atoms[stick.atom2-1].material
+ sticks_list.append([name, location, dv, material])
+
+ if sticks_list != []:
+ sticks_all_lists.append(sticks_list)
+ else:
+ sticks_list = []
+ for stick in all_sticks:
+
+ if stick.number > 3:
+ stick.number = 1
+
+ for repeat in range(stick.number):
+
+ atom1 = copy(all_atoms[stick.atom1-1].location)
+ atom2 = copy(all_atoms[stick.atom2-1].location)
+
+ dist = Stick_diameter * Stick_dist
+
+ if stick.number == 2:
+ if repeat == 0:
+ atom1 += (stick.dist * dist)
+ atom2 += (stick.dist * dist)
+ if repeat == 1:
+ atom1 -= (stick.dist * dist)
+ atom2 -= (stick.dist * dist)
+ if stick.number == 3:
+ if repeat == 0:
+ atom1 += (stick.dist * dist)
+ atom2 += (stick.dist * dist)
+ if repeat == 2:
+ atom1 -= (stick.dist * dist)
+ atom2 -= (stick.dist * dist)
+
+ dv = atom1 - atom2
+ n = dv / dv.length
+ location = atom1
+ material = stick_material
+ sticks_list.append(["", location, dv, material])
+
+ sticks_all_lists.append(sticks_list)
+
+ atom_object_list = []
+ # ... the sticks in the list can be drawn:
+ for stick_list in sticks_all_lists:
+ vertices = []
+ faces = []
+ i = 0
+
+ # What follows is school mathematics! :-)
+ for stick in stick_list:
+
+ dv = stick[2]
+ v1 = stick[1]
+ n = dv / dv.length
+ gamma = -n * v1
+ b = v1 + gamma * n
+ n_b = b / b.length
+
+ if use_sticks_color == True:
+ loops = int(ceil(dv.length / (2.0 * dl)))
+ else:
+ loops = int(ceil(dv.length / dl))
+
+ for j in range(loops):
+
+ g = v1 - n * dl / 2.0 - n * dl * j
+ p1 = g + n_b * Stick_diameter
+ p2 = g - n_b * Stick_diameter
+ p3 = g - n_b.cross(n) * Stick_diameter
+ p4 = g + n_b.cross(n) * Stick_diameter
+
+ vertices.append(p1)
+ vertices.append(p2)
+ vertices.append(p3)
+ vertices.append(p4)
+ faces.append((i*4+0,i*4+2,i*4+1,i*4+3))
+ i += 1
+
+ # Build the mesh.
+ mesh = bpy.data.meshes.new("Sticks"+stick[0])
+ mesh.from_pydata(vertices, [], faces)
+ mesh.update()
+ new_mesh = bpy.data.objects.new("Sticks"+stick[0], mesh)
+ 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]
+ 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')
+ stick_cylinder.select = True
+ stick_cups.select = True
+ bpy.ops.object.shade_smooth()
+
+ # Parenting the mesh to the cylinder.
+ stick_cylinder.parent = new_mesh
+ stick_cups.parent = new_mesh
+ new_mesh.dupli_type = 'FACES'
+ atom_object_list.append(new_mesh)
+
+ # Return the list of dupliverts structures.
+ return atom_object_list
+
+
# -----------------------------------------------------------------------------
# The main routine
@@ -793,7 +1106,9 @@ def import_pdb(Ball_type,
use_sticks_bonds,
all_atoms)
+ #
# So far, all atoms, sticks and materials have been registered.
+ #
# ------------------------------------------------------------------------
# TRANSLATION OF THE STRUCTURE TO THE ORIGIN
@@ -803,15 +1118,11 @@ def import_pdb(Ball_type,
# (the offset is substracted).
if put_to_center == True:
-
sum_vec = Vector((0.0,0.0,0.0))
-
# Sum of all atom coordinates
sum_vec = sum([atom.location for atom in all_atoms], sum_vec)
-
# Then the average is taken
sum_vec = sum_vec / Number_of_total_atoms
-
# After, for each atom the center of gravity is substracted
for atom in all_atoms:
atom.location -= sum_vec
@@ -850,11 +1161,11 @@ def import_pdb(Ball_type,
# draw_all_atoms = [ data_hydrogen,data_carbon,data_nitrogen ]
# data_hydrogen = [["Hydrogen", Material_Hydrogen, Vector((x,y,z)), 109], ...]
- draw_all_atoms = []
# 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", ...]
+ draw_all_atoms = []
for atom_type in atom_all_types_list:
# Don't draw 'TER atoms'.
@@ -897,292 +1208,29 @@ def import_pdb(Ball_type,
if use_sticks == True and use_sticks_skin == True and all_sticks != []:
- # 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
-
- # 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)
-
-
+ draw_sticks_skin(all_atoms,
+ all_sticks,
+ Stick_diameter,
+ use_sticks_smooth,
+ sticks_subdiv_view,
+ sticks_subdiv_render)
# ------------------------------------------------------------------------
- # DRAWING THE STICKS: regular cylinders in a dupliverts structure
+ # DRAWING THE STICKS: cylinders in a dupliverts structure
if use_sticks == True and all_sticks != [] and use_sticks_skin == False:
- dl = Stick_unit
-
- if use_sticks_color == False:
- bpy.ops.object.material_slot_add()
- stick_material = bpy.data.materials.new(ELEMENTS[-1].name)
- stick_material.diffuse_color = ELEMENTS[-1].color
-
- # Sort the sticks and put them into a new list such that ...
- sticks_all_lists = []
- if use_sticks_color == True:
- for atom_type in atom_all_types_list:
- if atom_type[0] == "TER":
- continue
- sticks_list = []
- for stick in all_sticks:
-
- for repeat in range(stick.number):
-
- atom1 = copy(all_atoms[stick.atom1-1].location)
- atom2 = copy(all_atoms[stick.atom2-1].location)
-
- dist = Stick_diameter * Stick_dist
-
- if stick.number == 2:
- if repeat == 0:
- atom1 += (stick.dist * dist)
- atom2 += (stick.dist * dist)
- if repeat == 1:
- atom1 -= (stick.dist * dist)
- atom2 -= (stick.dist * dist)
-
- if stick.number == 3:
- if repeat == 0:
- atom1 += (stick.dist * dist)
- atom2 += (stick.dist * dist)
- if repeat == 2:
- atom1 -= (stick.dist * dist)
- atom2 -= (stick.dist * dist)
-
- dv = atom1 - atom2
- n = dv / dv.length
- if atom_type[0] == all_atoms[stick.atom1-1].name:
- location = atom1
- name = "_" + all_atoms[stick.atom1-1].name
- material = all_atoms[stick.atom1-1].material
- sticks_list.append([name, location, dv, material])
- if atom_type[0] == all_atoms[stick.atom2-1].name:
- location = atom1 - n * dl * int(ceil(dv.length / (2.0 * dl)))
- name = "_" + all_atoms[stick.atom2-1].name
- material = all_atoms[stick.atom2-1].material
- sticks_list.append([name, location, dv, material])
-
- if sticks_list != []:
- sticks_all_lists.append(sticks_list)
- else:
- sticks_list = []
- for stick in all_sticks:
-
- if stick.number > 3:
- stick.number = 1
-
- for repeat in range(stick.number):
-
- atom1 = copy(all_atoms[stick.atom1-1].location)
- atom2 = copy(all_atoms[stick.atom2-1].location)
-
- dist = Stick_diameter * Stick_dist
-
- if stick.number == 2:
- if repeat == 0:
- atom1 += (stick.dist * dist)
- atom2 += (stick.dist * dist)
- if repeat == 1:
- atom1 -= (stick.dist * dist)
- atom2 -= (stick.dist * dist)
- if stick.number == 3:
- if repeat == 0:
- atom1 += (stick.dist * dist)
- atom2 += (stick.dist * dist)
- if repeat == 2:
- atom1 -= (stick.dist * dist)
- atom2 -= (stick.dist * dist)
-
- dv = atom1 - atom2
- n = dv / dv.length
- location = atom1
- material = stick_material
- sticks_list.append(["", location, dv, material])
-
- sticks_all_lists.append(sticks_list)
-
- # ... the sticks in the list can be drawn:
- for stick_list in sticks_all_lists:
- vertices = []
- faces = []
- i = 0
-
- # What follows is school mathematics! :-)
- for stick in stick_list:
-
- dv = stick[2]
- v1 = stick[1]
- n = dv / dv.length
- gamma = -n * v1
- b = v1 + gamma * n
- n_b = b / b.length
-
- if use_sticks_color == True:
- loops = int(ceil(dv.length / (2.0 * dl)))
- else:
- loops = int(ceil(dv.length / dl))
-
- for j in range(loops):
-
- g = v1 - n * dl / 2.0 - n * dl * j
- p1 = g + n_b * Stick_diameter
- p2 = g - n_b * Stick_diameter
- p3 = g - n_b.cross(n) * Stick_diameter
- p4 = g + n_b.cross(n) * Stick_diameter
-
- vertices.append(p1)
- vertices.append(p2)
- vertices.append(p3)
- vertices.append(p4)
- faces.append((i*4+0,i*4+2,i*4+1,i*4+3))
- i += 1
-
- mesh = bpy.data.meshes.new("Sticks"+stick[0])
- mesh.from_pydata(vertices, [], faces)
- mesh.update()
- new_mesh = bpy.data.objects.new("Sticks"+stick[0], mesh)
- bpy.context.scene.objects.link(new_mesh)
-
- current_layers = bpy.context.scene.layers
- object_stick = 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:
- 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)
+ 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)
# ------------------------------------------------------------------------
# CAMERA and LIGHT SOURCES