diff --git a/io_mesh_pdb/__init__.py b/io_mesh_pdb/__init__.py
index 7cd3d3e6b8f1c53a5e409a75a00a3a2b394aaa32..0a99e7ebfa903f73de5d687de98c3e8ea798d459 100644
--- a/io_mesh_pdb/__init__.py
+++ b/io_mesh_pdb/__init__.py
@@ -20,7 +20,7 @@ bl_info = {
"name": "PDB Atomic Blender",
"description": "Loading and manipulating atoms from PDB files",
"author": "Clemens Barth",
- "version": (1,0),
+ "version": (1,1),
"blender": (2,6),
"api": 31236,
"location": "File -> Import -> PDB (.pdb), Panel: View 3D - Tools",
@@ -119,6 +119,7 @@ class CLASS_atom_pdb_panel(Panel):
col = row.column(align=True)
col.prop(scn, "atom_pdb_sticks_sectors")
col.prop(scn, "atom_pdb_sticks_radius")
+ col.prop(scn, "use_atom_pdb_sticks_color")
row = box.row()
row.prop(scn, "use_atom_pdb_center")
row = box.row()
@@ -129,14 +130,14 @@ class CLASS_atom_pdb_panel(Panel):
col.operator("atom_pdb.button_reload")
# TODO, use lanel() instead
col.prop(scn, "atom_pdb_number_atoms")
+ row = box.row()
+ row.operator("atom_pdb.button_distance")
+ row.prop(scn, "atom_pdb_distance")
row = layout.row()
row.label(text="Modify atom radii")
box = layout.box()
row = box.row()
- row.operator("atom_pdb.button_distance")
- row.prop(scn, "atom_pdb_distance")
- row = box.row()
row.label(text="All changes concern:")
row = box.row()
row.prop(scn, "atom_pdb_radius_how")
@@ -158,6 +159,11 @@ class CLASS_atom_pdb_panel(Panel):
col = row.column(align=True)
col.operator( "atom_pdb.radius_all_bigger" )
col.operator( "atom_pdb.radius_all_smaller" )
+ row = box.row()
+ row.label(text="4. Show sticks only")
+ row = box.row()
+ col = row.column()
+ col.operator( "atom_pdb.radius_sticks" )
if bpy.context.mode == 'EDIT_MESH':
@@ -221,6 +227,9 @@ class CLASS_atom_pdb_IO(bpy.types.PropertyGroup):
scn.atom_pdb_sticks_radius = FloatProperty(
name = "Radius", default=0.1, min=0.0,
description ="Radius of a stick")
+ scn.use_atom_pdb_sticks_color = BoolProperty(
+ name="Color of atoms", default=False,
+ description="Shall the sticks appear in the color of the atoms?")
scn.atom_pdb_atomradius = EnumProperty(
name="Type of radius",
description="Choose type of atom radius",
@@ -301,7 +310,7 @@ class CLASS_atom_pdb_datafile_apply(Operator):
return {'FINISHED'}
-# Button for measuring the distance of the active objects
+# Button for separating single objects from a atom mesh
class CLASS_atom_pdb_separate_atom(Operator):
bl_idname = "atom_pdb.separate_atom"
bl_label = "Separate atom"
@@ -426,7 +435,23 @@ class CLASS_atom_pdb_radius_all_smaller_button(Operator):
return {'FINISHED'}
-# The button for loading the atoms and creating the scene
+# Button for showing the sticks only - the radii of the atoms have the radius
+# of the sticks
+class CLASS_atom_pdb_radius_sticks_button(Operator):
+ bl_idname = "atom_pdb.radius_sticks"
+ bl_label = "Show sticks"
+ bl_description = "Show only the sticks (atom radii = stick radii)"
+
+ def execute(self, context):
+ scn = bpy.context.scene
+ import_pdb.DEF_atom_pdb_radius_sticks(
+ scn.atom_pdb_sticks_radius,
+ scn.atom_pdb_radius_how,
+ )
+ return {'FINISHED'}
+
+
+# The button for reloading the atoms and creating the scene
class CLASS_atom_pdb_load_button(Operator):
bl_idname = "atom_pdb.button_reload"
bl_label = "RELOAD"
@@ -442,6 +467,7 @@ class CLASS_atom_pdb_load_button(Operator):
radiustype = scn.atom_pdb_atomradius
center = scn.use_atom_pdb_center
sticks = scn.use_atom_pdb_sticks
+ sticks_col = scn.use_atom_pdb_sticks_color
ssector = scn.atom_pdb_sticks_sectors
sradius = scn.atom_pdb_sticks_radius
cam = scn.use_atom_pdb_cam
@@ -452,7 +478,7 @@ class CLASS_atom_pdb_load_button(Operator):
# Execute main routine an other time ... from the panel
atom_number = import_pdb.DEF_atom_pdb_main(
mesh, azimuth, zenith, bradius,
- radiustype, bdistance, sticks,
+ radiustype, bdistance, sticks, sticks_col,
ssector, sradius, center, cam, lamp, datafile,
)
scn.atom_pdb_number_atoms = str(atom_number) + " atoms"
@@ -494,6 +520,7 @@ class ImportPDB(Operator, ImportHelper):
col = row.column(align=True)
col.prop(scn, "atom_pdb_sticks_sectors")
col.prop(scn, "atom_pdb_sticks_radius")
+ col.prop(scn, "use_atom_pdb_sticks_color")
row = layout.row()
row.prop(scn, "use_atom_pdb_center")
@@ -516,6 +543,7 @@ class ImportPDB(Operator, ImportHelper):
radiustype = scn.atom_pdb_atomradius
center = scn.use_atom_pdb_center
sticks = scn.use_atom_pdb_sticks
+ sticks_col = scn.use_atom_pdb_sticks_color
ssector = scn.atom_pdb_sticks_sectors
sradius = scn.atom_pdb_sticks_radius
cam = scn.use_atom_pdb_cam
@@ -526,7 +554,7 @@ class ImportPDB(Operator, ImportHelper):
# Execute main routine
atom_number = import_pdb.DEF_atom_pdb_main(
mesh, azimuth, zenith, bradius,
- radiustype, bdistance, sticks,
+ radiustype, bdistance, sticks, sticks_col,
ssector, sradius, center, cam, lamp, datafile)
scn.atom_pdb_number_atoms = str(atom_number) + " atoms"
diff --git a/io_mesh_pdb/import_pdb.py b/io_mesh_pdb/import_pdb.py
index b8da5051166eb4d65b92a55daf45e352da5ef764..78ec2f740b50cb2c01c4e6df7f4ea6dd785a9d6a 100644
--- a/io_mesh_pdb/import_pdb.py
+++ b/io_mesh_pdb/import_pdb.py
@@ -25,7 +25,7 @@
#
# Start of project : 2011-08-31 by Clemens Barth
# First publication in Blender : 2011-11-11
-# Last modified : 2011-12-22
+# Last modified : 2011-12-26
#
# Acknowledgements: Thanks to ideasman, meta_androcto, truman, kilon,
# dairin0d, PKHG, Valter, etc
@@ -284,8 +284,7 @@ def DEF_atom_pdb_distance():
return str(dv.length)
-# Routine to modify the radii via the type:
-# pre-defined, atomic or van der Waals
+# Routine to modify the radii via the type: predefined, atomic or van der Waals
# Explanations here are also valid for the next 3 DEFs.
def DEF_atom_pdb_radius_type(rtype,how):
@@ -351,22 +350,26 @@ def DEF_atom_pdb_radius_pm(atomname, radius_pm, how):
if len(obj.children) != 0:
if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
if atomname in obj.name:
- obj.children[0].scale = (radius_pm/100,) * 3
+ if "Stick" not in obj.name:
+ obj.children[0].scale = (radius_pm/100,) * 3
else:
if obj.type == "SURFACE" or obj.type == "MESH":
if atomname in obj.name:
- obj.scale = (radius_pm/100,) * 3
+ if "Stick" not in obj.name:
+ obj.scale = (radius_pm/100,) * 3
if how == "ALL_ACTIVE":
for obj in bpy.context.selected_objects:
if len(obj.children) != 0:
if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
if atomname in obj.name:
- obj.children[0].scale = (radius_pm/100,) * 3
+ if "Stick" not in obj.name:
+ obj.children[0].scale = (radius_pm/100,) * 3
else:
if obj.type == "SURFACE" or obj.type == "MESH":
if atomname in obj.name:
- obj.scale = (radius_pm/100,) * 3
+ if "Stick" not in obj.name:
+ obj.scale = (radius_pm/100,) * 3
# Routine to scale the radii of all atoms
@@ -408,6 +411,47 @@ def DEF_atom_pdb_radius_all(scale, how):
obj.scale *= scale
+# This routine downscales all atom radii onto the value of the stick radius
+# for showing the sticks.
+def DEF_atom_pdb_radius_sticks(radius, how):
+
+ if how == "ALL_IN_LAYER":
+
+ layers = []
+ for i in range(20):
+ if bpy.context.scene.layers[i] == True:
+ layers.append(i)
+
+ change_objects = []
+ for obj in bpy.context.scene.objects:
+ for layer in layers:
+ if obj.layers[layer] == True:
+ change_objects.append(obj)
+
+
+ for obj in change_objects:
+ if len(obj.children) != 0:
+ if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
+ if "Stick" not in obj.name:
+ obj.children[0].scale = (radius,) * 3
+ else:
+ if obj.type == "SURFACE" or obj.type == "MESH":
+ if "Stick" not in obj.name:
+ obj.scale = (radius,) * 3
+
+ if how == "ALL_ACTIVE":
+ for obj in bpy.context.selected_objects:
+ if len(obj.children) != 0:
+ if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
+ if "Stick" not in obj.name:
+ obj.children[0].scale = (radius,) * 3
+ else:
+ if obj.type == "SURFACE" or obj.type == "MESH":
+ if "Stick" not in obj.name:
+ obj.scale = (radius,) * 3
+
+
+
# This reads a custom data file.
def DEF_atom_pdb_custom_datafile(path_datafile):
@@ -476,7 +520,7 @@ def DEF_atom_pdb_custom_datafile(path_datafile):
def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
Ball_radius_factor,radiustype,Ball_distance_factor,
- use_stick,Stick_sectors,Stick_diameter,put_to_center,
+ use_sticks,use_sticks_color,Stick_sectors,Stick_diameter,put_to_center,
use_camera,use_lamp,path_datafile):
# The list of all atoms as read from the PDB file.
@@ -1068,69 +1112,97 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
# ------------------------------------------------------------------------
# DRAWING THE STICKS
-
- if use_stick == True and all_sticks != []:
-
- # Create a new material with the corresponding color. The
- # color is taken from the all_atom list, it is the last entry
- # in the data file (index -1).
- bpy.ops.object.material_slot_add()
- stick_material = bpy.data.materials.new(ATOM_PDB_ELEMENTS[-1].name)
- stick_material.diffuse_color = ATOM_PDB_ELEMENTS[-1].color
-
- vertices = []
- faces = []
- dl = 0.1
-
- i = 0
- # For all sticks, do ...
- for stick in all_sticks:
-
+ if use_sticks == True and all_sticks != []:
+
+ dl = 0.05
+
+ if use_sticks_color == False:
+ bpy.ops.object.material_slot_add()
+ stick_material = bpy.data.materials.new(ATOM_PDB_ELEMENTS[-1].name)
+ stick_material.diffuse_color = ATOM_PDB_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:
+ dv = all_atoms[stick.atom1-1].location - all_atoms[stick.atom2-1].location
+ n = dv / dv.length
+ if atom_type[0] == all_atoms[stick.atom1-1].name:
+ location = all_atoms[stick.atom1-1].location
+ 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 = all_atoms[stick.atom1-1].location - n * dl * int(math.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])
+ sticks_all_lists.append(sticks_list)
+ else:
+ sticks_list = []
+ for stick in all_sticks:
+ dv = all_atoms[stick.atom1-1].location - all_atoms[stick.atom2-1].location
+ n = dv / dv.length
+ location = all_atoms[stick.atom1-1].location
+ 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! :-)
- v1 = all_atoms[stick.atom2-1].location
- v2 = all_atoms[stick.atom1-1].location
-
- dv = (v1 - v2)
-
- n = dv / dv.length
- # m = v1 - dv / 2.0 # UNUSED
-
- gamma = -n * v1
- b = v1 + gamma * n
- n_b = b / b.length
-
- loops = int(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")
- mesh.from_pydata(vertices, [], faces)
- mesh.update()
- new_mesh = bpy.data.objects.new("Sticks", mesh)
- bpy.context.scene.objects.link(new_mesh)
+ 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(math.ceil(dv.length / (2.0 * dl)))
+ else:
+ loops = int(math.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
- stick_cylinder = DEF_atom_pdb_build_stick(Stick_diameter, dl, Stick_sectors)
+ current_layers = bpy.context.scene.layers
+ stick_cylinder = DEF_atom_pdb_build_stick(Stick_diameter, dl, Stick_sectors)
+ stick_cylinder.active_material = stick[3]
+ stick_cylinder.parent = new_mesh
+ new_mesh.dupli_type = 'FACES'
+ atom_object_list.append(new_mesh)
- stick_cylinder.active_material = stick_material
- stick_cylinder.parent = new_mesh
- new_mesh.dupli_type = 'FACES'
- atom_object_list.append(new_mesh)
# ------------------------------------------------------------------------