From 57f376e9465c6b79ebd4409bc30e0b5930dd4140 Mon Sep 17 00:00:00 2001 From: Campbell Barton Date: Sun, 19 Mar 2017 12:49:03 +1100 Subject: Cleanup: trailing space --- io_mesh_pdb/export_pdb.py | 12 +- io_mesh_pdb/import_pdb.py | 342 +++++++++++++++++++++++----------------------- 2 files changed, 177 insertions(+), 177 deletions(-) (limited to 'io_mesh_pdb') diff --git a/io_mesh_pdb/export_pdb.py b/io_mesh_pdb/export_pdb.py index 81b60cb9..d0eb07eb 100644 --- a/io_mesh_pdb/export_pdb.py +++ b/io_mesh_pdb/export_pdb.py @@ -20,7 +20,7 @@ import bpy from . import import_pdb -class AtomPropExport(object): +class AtomPropExport(object): __slots__ = ('element', 'location') def __init__(self, element, location): self.element = element @@ -31,13 +31,13 @@ def export_pdb(obj_type, filepath_pdb): list_atoms = [] for obj in bpy.context.selected_objects: - + if "Stick" in obj.name: continue - + if obj.type not in {'MESH', 'SURFACE', 'META'}: - continue - + continue + name = "" for element in import_pdb.ELEMENTS_DEFAULT: if element[1] in obj.name: @@ -45,7 +45,7 @@ def export_pdb(obj_type, filepath_pdb): name = "X" else: name = element[2] - + if name == "": if obj_type == "0": name = "?" diff --git a/io_mesh_pdb/import_pdb.py b/io_mesh_pdb/import_pdb.py index 3ca3b51f..a7a0be7d 100644 --- a/io_mesh_pdb/import_pdb.py +++ b/io_mesh_pdb/import_pdb.py @@ -167,7 +167,7 @@ class ElementProp(object): self.radii_ionic = radii_ionic # This is the class, which stores the properties of one atom. -class AtomProp(object): +class AtomProp(object): __slots__ = ('element', 'name', 'location', 'radius', 'color', 'material') def __init__(self, element, name, location, radius, color, material): self.element = element @@ -187,10 +187,10 @@ class StickProp(object): self.dist = dist # ----------------------------------------------------------------------------- -# Some basic routines +# Some basic routines -# The function, which reads all necessary properties of the elements. +# The function, which reads all necessary properties of the elements. def read_elements(): del ELEMENTS[:] @@ -208,7 +208,7 @@ def read_elements(): ELEMENTS.append(li) -# The function, which reads the x,y,z positions of all atoms in a PDB +# The function, which reads the x,y,z positions of all atoms in a PDB # file. # # filepath_pdb: path to pdb file @@ -250,39 +250,39 @@ def read_pdb_file(filepath_pdb, radiustype): color = [0,0,0] location = Vector((0,0,0)) # Append the TER into the list. Material remains empty so far. - all_atoms.append(AtomProp(short_name, - name, - location, + all_atoms.append(AtomProp(short_name, + name, + location, radius, color,[])) - + # If 'ATOM or 'HETATM' appears in the line then do ... elif "ATOM" in line or "HETATM" in line: # What follows is due to deviations which appear from PDB to # PDB file. It is very special! - # + # # PLEASE, DO NOT CHANGE! ............................... from here if line[12:13] == " " or line[12:13].isdigit() == True: short_name = line[13:14] if line[14:15].islower() == True: - short_name = short_name + line[14:15] + short_name = short_name + line[14:15] elif line[12:13].isupper() == True: short_name = line[12:13] if line[13:14].isalpha() == True: short_name = short_name + line[13:14] else: - print("Atomic Blender: Strange error in PDB file.\n" + print("Atomic Blender: Strange error in PDB file.\n" "Look for element names at positions 13-16 and 78-79.\n") return -1 - + if len(line) >= 78: - + if line[76:77] == " ": short_name2 = line[76:77] else: short_name2 = line[76:78] - + if short_name2.isalpha() == True: FOUND = False for element in ELEMENTS: @@ -292,7 +292,7 @@ def read_pdb_file(filepath_pdb, radiustype): if FOUND == False: short_name = short_name2 # ....................................................... to here. - + # Go through all elements and find the element of the current atom. FLAG_FOUND = False for element in ELEMENTS: @@ -415,29 +415,29 @@ def read_pdb_file_sticks(filepath_pdb, use_sticks_bonds, all_atoms): # For all the other atoms in the list do: for atom2 in atom_list[1:]: - + if use_sticks_bonds == True: number = atom_list[1:].count(atom2) - + if number == 2 or number == 3: basis_list = list(set(atom_list[1:])) - + if len(basis_list) > 1: - basis1 = (all_atoms[atom1-1].location + basis1 = (all_atoms[atom1-1].location - all_atoms[basis_list[0]-1].location) - basis2 = (all_atoms[atom1-1].location - - all_atoms[basis_list[1]-1].location) + basis2 = (all_atoms[atom1-1].location + - all_atoms[basis_list[1]-1].location) plane_n = basis1.cross(basis2) - - dist_n = (all_atoms[atom1-1].location + + dist_n = (all_atoms[atom1-1].location - all_atoms[atom2-1].location) dist_n = dist_n.cross(plane_n) - dist_n = dist_n / dist_n.length + dist_n = dist_n / dist_n.length else: - dist_n = (all_atoms[atom1-1].location + dist_n = (all_atoms[atom1-1].location - all_atoms[atom2-1].location) - dist_n = Vector((dist_n[1],-dist_n[0],0)) - dist_n = dist_n / dist_n.length + dist_n = Vector((dist_n[1],-dist_n[0],0)) + dist_n = dist_n / dist_n.length elif number > 3: number = 1 dist_n = None @@ -470,7 +470,7 @@ def read_pdb_file_sticks(filepath_pdb, use_sticks_bonds, all_atoms): line = line.rstrip() filepath_pdb_p.close() - + return all_sticks @@ -495,7 +495,7 @@ def build_stick(radius, length, sectors): vertices = vertices_top + vertices_bottom # Side facets (Cylinder) - faces1 = [] + faces1 = [] for i in range(sectors-1): if i == sectors-2: faces1.append( [i+1, 1, 1+sectors, i+1+sectors] ) @@ -503,7 +503,7 @@ def build_stick(radius, length, sectors): faces1.append( [i+1, i+2, i+2+sectors, i+1+sectors] ) # Top facets - faces2 = [] + faces2 = [] for i in range(sectors-1): if i == sectors-2: face_top = [0,sectors-1,1] @@ -535,9 +535,9 @@ def build_stick(radius, length, sectors): # Function, which puts a camera and light source into the 3D scene -def camera_light_source(use_camera, - use_lamp, - object_center_vec, +def camera_light_source(use_camera, + use_lamp, + object_center_vec, object_size): camera_factor = 15.0 @@ -556,7 +556,7 @@ def camera_light_source(use_camera, camera_xyz_vec = object_center_vec + object_camera_vec # Create the camera - current_layers=bpy.context.scene.layers + current_layers=bpy.context.scene.layers camera_data = bpy.data.cameras.new("A_camera") camera_data.lens = 45 camera_data.clip_end = 500.0 @@ -578,8 +578,8 @@ def camera_light_source(use_camera, # Rotate the camera around its axis by 90° such that we have a nice # camera position and view onto the object. - bpy.ops.object.select_all(action='DESELECT') - camera.select = True + bpy.ops.object.select_all(action='DESELECT') + camera.select = True bpy.ops.transform.rotate(value=(90.0*2*pi/360.0), axis=object_camera_vec, constraint_axis=(False, False, False), @@ -610,11 +610,11 @@ def camera_light_source(use_camera, lamp_data = bpy.data.lamps.new(name="A_lamp", type="POINT") lamp_data.distance = 500.0 lamp_data.energy = 3.0 - lamp_data.shadow_method = 'RAY_SHADOW' + lamp_data.shadow_method = 'RAY_SHADOW' lamp = bpy.data.objects.new("A_lamp", lamp_data) lamp.location = lamp_xyz_vec lamp.layers = current_layers - bpy.context.scene.objects.link(lamp) + bpy.context.scene.objects.link(lamp) # Some settings for the World: a bit ambient occlusion bpy.context.scene.world.light_settings.use_ambient_occlusion = True @@ -622,9 +622,9 @@ def camera_light_source(use_camera, # Function, which draws the atoms of one type (balls). This is one -# dupliverts structure then. +# dupliverts structure then. # Return: the dupliverts structure -def draw_atoms_one_type(draw_all_atoms_type, +def draw_atoms_one_type(draw_all_atoms_type, Ball_type, Ball_azimuth, Ball_zenith, @@ -672,8 +672,8 @@ def draw_atoms_one_type(draw_all_atoms_type, layers=current_layers) # Meta balls elif Ball_type == "2": - bpy.ops.object.metaball_add(type='BALL', view_align=False, - enter_editmode=False, location=(0, 0, 0), + bpy.ops.object.metaball_add(type='BALL', view_align=False, + enter_editmode=False, location=(0, 0, 0), rotation=(0, 0, 0), layers=current_layers) ball = bpy.context.scene.objects.active @@ -688,13 +688,13 @@ def draw_atoms_one_type(draw_all_atoms_type, new_atom_mesh.dupli_type = 'VERTS' # The object is back translated to 'object_center_vec'. new_atom_mesh.location = object_center_vec - + return new_atom_mesh # Function, which draws the sticks with help of the dupliverts technique. # Return: list of dupliverts structures. -def draw_sticks_dupliverts(all_atoms, +def draw_sticks_dupliverts(all_atoms, atom_all_types_list, center, all_sticks, @@ -706,89 +706,89 @@ def draw_sticks_dupliverts(all_atoms, use_sticks_color): dl = Stick_unit - - if use_sticks_color == False: + + 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 + stick_material.diffuse_color = ELEMENTS[-1].color - # Sort the sticks and put them into a new list such that ... + # 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 + continue sticks_list = [] for stick in all_sticks: - + for repeat in range(stick.number): - + atom1 = copy(all_atoms[stick.atom1-1].location)-center - atom2 = copy(all_atoms[stick.atom2-1].location)-center - + atom2 = copy(all_atoms[stick.atom2-1].location)-center + dist = Stick_diameter * Stick_dist - - if stick.number == 2: + + 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) + atom1 -= (stick.dist * dist) + atom2 -= (stick.dist * dist) - if stick.number == 3: + 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) + atom1 -= (stick.dist * dist) + atom2 -= (stick.dist * dist) - dv = atom1 - atom2 + 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: + 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 != []: + + 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): - + + for repeat in range(stick.number): + atom1 = copy(all_atoms[stick.atom1-1].location)-center atom2 = copy(all_atoms[stick.atom2-1].location)-center - + dist = Stick_diameter * Stick_dist - - if stick.number == 2: + + 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: + 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 + atom1 -= (stick.dist * dist) + atom2 -= (stick.dist * dist) + + dv = atom1 - atom2 n = dv / dv.length location = atom1 material = stick_material @@ -802,22 +802,22 @@ def draw_sticks_dupliverts(all_atoms, 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 @@ -846,10 +846,10 @@ def draw_sticks_dupliverts(all_atoms, stick_cylinder = object_stick[0] stick_cylinder.active_material = stick[3] stick_cups = object_stick[1] - stick_cups.active_material = stick[3] - + stick_cups.active_material = stick[3] + # Smooth the cylinders. - if use_sticks_smooth == True: + if use_sticks_smooth == True: bpy.ops.object.select_all(action='DESELECT') stick_cylinder.select = True stick_cups.select = True @@ -868,17 +868,17 @@ def draw_sticks_dupliverts(all_atoms, # Function, which draws the sticks with help of the skin and subdivision # modifiers. -def draw_sticks_skin(all_atoms, +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]. + # These counters are for the edges, in the shape [i,i+1]. i = 0 - - # This is the list of vertices, containing the atom position + + # This is the list of vertices, containing the atom position # (vectors)). stick_vertices = [] # This is the 'same' list, which contains not vector position of @@ -886,34 +886,34 @@ def draw_sticks_skin(all_atoms, 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. - + + # 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 + FLAG_s1 = False s1 = 0 - for stick2 in stick_vertices_nr: - if stick2 == stick.atom1-1: + 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: + for stick2 in stick_vertices_nr: if stick2 == stick.atom2-1: - FLAG_s2 = True + FLAG_s2 = True break s2 += 1 @@ -924,14 +924,14 @@ def draw_sticks_skin(all_atoms, 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: + # 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) + 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. @@ -940,15 +940,15 @@ def draw_sticks_skin(all_atoms, 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. + # 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 + # 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 + i += 1 if FLAG_s1 == False and FLAG_s2 == True: stick_edges.append([i,s2]) i += 1 @@ -959,8 +959,8 @@ def draw_sticks_skin(all_atoms, 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. + + # 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 @@ -969,20 +969,20 @@ def draw_sticks_skin(all_atoms, # 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 + 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) + 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 @@ -990,32 +990,32 @@ def draw_sticks_skin(all_atoms, # 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, + 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, +def draw_sticks_normal(all_atoms, all_sticks, center, Stick_diameter, @@ -1023,11 +1023,11 @@ def draw_sticks_normal(all_atoms, 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 @@ -1046,20 +1046,20 @@ def draw_sticks_normal(all_atoms, 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 + # 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), + 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 @@ -1068,15 +1068,15 @@ def draw_sticks_normal(all_atoms, # ... and name stick.name = "Stick_Cylinder" counter += 1 - + # Smooth the cylinder. - if use_sticks_smooth == True: + if use_sticks_smooth == True: bpy.ops.object.select_all(action='DESELECT') stick.select = True - bpy.ops.object.shade_smooth() - + 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') @@ -1088,8 +1088,8 @@ def draw_sticks_normal(all_atoms, list_group_sub = [] counter = 0 else: - # Material ... - stick.active_material = stick_material + # Material ... + stick.active_material = stick_material if use_sticks_one_object == True: bpy.ops.object.select_all(action='DESELECT') @@ -1101,21 +1101,21 @@ def draw_sticks_normal(all_atoms, for group in list_group: group.select = True - bpy.ops.object.join() - bpy.ops.object.origin_set(type='ORIGIN_GEOMETRY', + 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), + 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 @@ -1224,8 +1224,8 @@ def import_pdb(Ball_type, # ------------------------------------------------------------------------ # READING DATA OF STICKS - all_sticks = read_pdb_file_sticks(filepath_pdb, - use_sticks_bonds, + all_sticks = read_pdb_file_sticks(filepath_pdb, + use_sticks_bonds, all_atoms) # @@ -1318,7 +1318,7 @@ def import_pdb(Ball_type, # 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, + atom_mesh = draw_atoms_one_type(draw_all_atoms_type, Ball_type, Ball_azimuth, Ball_zenith, @@ -1327,11 +1327,11 @@ def import_pdb(Ball_type, atom_object_list.append(atom_mesh) # ------------------------------------------------------------------------ - # DRAWING THE STICKS: cylinders in a dupliverts structure + # 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, + + sticks = draw_sticks_dupliverts(all_atoms, atom_all_types_list, object_center_vec, all_sticks, @@ -1341,15 +1341,15 @@ def import_pdb(Ball_type, Stick_dist, use_sticks_smooth, use_sticks_color) - for stick in sticks: + for stick in sticks: atom_object_list.append(stick) # ------------------------------------------------------------------------ # DRAWING THE STICKS: skin and subdivision modifier - + if use_sticks == True and use_sticks_type == '1' and all_sticks != []: - sticks = draw_sticks_skin(all_atoms, + sticks = draw_sticks_skin(all_atoms, all_sticks, Stick_diameter, use_sticks_smooth, @@ -1359,10 +1359,10 @@ def import_pdb(Ball_type, # ------------------------------------------------------------------------ # DRAWING THE STICKS: normal cylinders - + if use_sticks == True and use_sticks_type == '2' and all_sticks != []: - - sticks = draw_sticks_normal(all_atoms, + + sticks = draw_sticks_normal(all_atoms, all_sticks, object_center_vec, Stick_diameter, @@ -1375,9 +1375,9 @@ def import_pdb(Ball_type, # ------------------------------------------------------------------------ # CAMERA and LIGHT SOURCES - camera_light_source(use_camera, - use_lamp, - object_center_vec, + camera_light_source(use_camera, + use_lamp, + object_center_vec, object_size) # ------------------------------------------------------------------------ -- cgit v1.2.3