diff --git a/io_mesh_pdb/__init__.py b/io_mesh_pdb/__init__.py
index e8ba7a074ac056af6617ef4ccb06bbadbda8fb66..252983935a09f13c7811bdf4ca928d21feaf5db2 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": (1,1),
+ "version": (1,2),
"blender": (2,6),
"api": 31236,
"location": "File -> Import -> PDB (.pdb), Panel: View 3D - Tools",
@@ -58,24 +58,9 @@ class CLASS_atom_pdb_panel(Panel):
#bl_context = "physics"
# This could be also an option ... :
bl_space_type = "VIEW_3D"
+ #bl_region_type = "TOOLS"
bl_region_type = "TOOL_PROPS"
- # This 'poll thing' has taken 3 hours of a hard search and understanding.
- # I explain it in the following from my point of view:
- #
- # Before this class is entirely treaten (here: drawing the panel) the
- # poll method is called first. Basically, some conditions are
- # checked before other things in the class are done afterwards. If a
- # condition is not valid, one returns 'False' such that nothing further
- # is done. 'True' means: 'Go on'
- #
- # In the case here, it is verified if the ATOM_PDB_FILEPATH variable contains
- # a name. If not - and this is the case directly after having started the
- # script - the panel does not appear because 'False' is returned. However,
- # as soon as a file has been chosen, the panel appears because
- # ATOM_PDB_FILEPATH contains a name.
- #
- # Please, correct me if I'm wrong.
@classmethod
def poll(self, context):
if import_pdb.ATOM_PDB_FILEPATH == "":
@@ -106,21 +91,36 @@ class CLASS_atom_pdb_panel(Panel):
box = layout.box()
row = box.row()
- col = row.column(align=True)
+ col = row.column()
col.prop(scn, "use_atom_pdb_mesh")
+ col = row.column()
+ col.label(text="Scaling factors")
+ row = box.row()
+ col = row.column(align=True)
+ col.active = scn.use_atom_pdb_mesh
col.prop(scn, "atom_pdb_mesh_azimuth")
col.prop(scn, "atom_pdb_mesh_zenith")
col = row.column(align=True)
- col.label(text="Scaling factors")
col.prop(scn, "atom_pdb_scale_ballradius")
col.prop(scn, "atom_pdb_scale_distances")
row = box.row()
- col = row.column()
+ col = row.column()
col.prop(scn, "use_atom_pdb_sticks")
+ row = box.row()
+ row.active = scn.use_atom_pdb_sticks
col = row.column(align=True)
col.prop(scn, "atom_pdb_sticks_sectors")
col.prop(scn, "atom_pdb_sticks_radius")
+ col = row.column(align=True)
col.prop(scn, "use_atom_pdb_sticks_color")
+ col.prop(scn, "use_atom_pdb_sticks_smooth")
+ col.prop(scn, "use_atom_pdb_sticks_bonds")
+ row = box.row()
+ row.active = scn.use_atom_pdb_sticks
+ col = row.column(align=True)
+ col = row.column(align=True)
+ col.active = scn.use_atom_pdb_sticks and scn.use_atom_pdb_sticks_bonds
+ col.prop(scn, "atom_pdb_sticks_dist")
row = box.row()
row.prop(scn, "use_atom_pdb_center")
row = box.row()
@@ -129,7 +129,6 @@ class CLASS_atom_pdb_panel(Panel):
col.prop(scn, "use_atom_pdb_lamp")
col = row.column()
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")
@@ -137,6 +136,7 @@ class CLASS_atom_pdb_panel(Panel):
row = layout.row()
row.label(text="Modify atom radii")
+
box = layout.box()
row = box.row()
row.label(text="All changes concern:")
@@ -219,7 +219,7 @@ class CLASS_atom_pdb_IO(bpy.types.PropertyGroup):
name = "Object to origin", default=True,
description = "Put the object into the global origin")
scn.use_atom_pdb_sticks = BoolProperty(
- name="Use sticks", default=False,
+ name="Use sticks", default=True,
description="Do you want to display the sticks?")
scn.atom_pdb_sticks_sectors = IntProperty(
name = "Sector", default=20, min=0,
@@ -228,8 +228,17 @@ class CLASS_atom_pdb_IO(bpy.types.PropertyGroup):
name = "Radius", default=0.1, min=0.0,
description ="Radius of a stick")
scn.use_atom_pdb_sticks_color = BoolProperty(
- name="Color", default=False,
+ name="Color", default=True,
description="The sticks appear in the color of the atoms")
+ scn.use_atom_pdb_sticks_smooth = BoolProperty(
+ name="Smooth", default=False,
+ description="The sticks are round (sectors are not visible)")
+ scn.use_atom_pdb_sticks_bonds = BoolProperty(
+ name="Bonds", default=False,
+ description="Show double and tripple bonds.")
+ scn.atom_pdb_sticks_dist = FloatProperty(
+ name="Distance", default = 1.1, min=1.0, max=3.0,
+ description="Distance between sticks measured in stick diameter")
scn.atom_pdb_atomradius = EnumProperty(
name="Type of radius",
description="Choose type of atom radius",
@@ -243,9 +252,8 @@ class CLASS_atom_pdb_IO(bpy.types.PropertyGroup):
name = "", description="Path to your custom data file",
maxlen = 256, default = "", subtype='FILE_PATH')
scn.atom_pdb_PDB_file = StringProperty(
- name = "Path to file", default="",
+ name = "PDB file", default="",
description = "Path of the PDB file")
- # TODO, remove this property, its used for display only!
scn.atom_pdb_number_atoms = StringProperty(name="",
default="Number", description = "This output shows "
"the number of atoms which have been loaded")
@@ -435,8 +443,8 @@ class CLASS_atom_pdb_radius_all_smaller_button(Operator):
return {'FINISHED'}
-# Button for showing the sticks only - the radii of the atoms have the radius
-# of the sticks
+# Button for showing the sticks only - the radii of the atoms downscaled onto
+# 90% of the stick radius
class CLASS_atom_pdb_radius_sticks_button(Operator):
bl_idname = "atom_pdb.radius_sticks"
bl_label = "Show sticks"
@@ -448,7 +456,7 @@ class CLASS_atom_pdb_radius_sticks_button(Operator):
scn = bpy.context.scene
result = import_pdb.DEF_atom_pdb_radius_sticks(
- scn.atom_pdb_sticks_radius,
+ scn.atom_pdb_sticks_radius * 0.9,
scn.atom_pdb_radius_how,
)
@@ -476,19 +484,22 @@ class CLASS_atom_pdb_load_button(Operator):
center = scn.use_atom_pdb_center
sticks = scn.use_atom_pdb_sticks
sticks_col = scn.use_atom_pdb_sticks_color
+ sticks_sm = scn.use_atom_pdb_sticks_smooth
ssector = scn.atom_pdb_sticks_sectors
sradius = scn.atom_pdb_sticks_radius
+ stick_bond = scn.use_atom_pdb_sticks_bonds
+ stick_dist = scn.atom_pdb_sticks_dist
+
cam = scn.use_atom_pdb_cam
lamp = scn.use_atom_pdb_lamp
mesh = scn.use_atom_pdb_mesh
datafile = scn.atom_pdb_datafile
-
+
# Execute main routine an other time ... from the panel
atom_number = import_pdb.DEF_atom_pdb_main(
- mesh, azimuth, zenith, bradius,
- radiustype, bdistance, sticks, sticks_col,
- ssector, sradius, center, cam, lamp, datafile,
- )
+ mesh, azimuth, zenith, bradius, radiustype, bdistance,
+ sticks, sticks_col, sticks_sm, stick_bond,
+ stick_dist, ssector, sradius, center, cam, lamp, datafile)
scn.atom_pdb_number_atoms = str(atom_number) + " atoms"
return {'FINISHED'}
@@ -513,6 +524,7 @@ class ImportPDB(Operator, ImportHelper):
col = row.column()
col.prop(scn, "use_atom_pdb_mesh")
col = row.column(align=True)
+ col.active = scn.use_atom_pdb_mesh
col.prop(scn, "atom_pdb_mesh_azimuth")
col.prop(scn, "atom_pdb_mesh_zenith")
@@ -525,10 +537,21 @@ class ImportPDB(Operator, ImportHelper):
row = layout.row()
col = row.column()
col.prop(scn, "use_atom_pdb_sticks")
+ row = layout.row()
+ row.active = scn.use_atom_pdb_sticks
col = row.column(align=True)
col.prop(scn, "atom_pdb_sticks_sectors")
col.prop(scn, "atom_pdb_sticks_radius")
+ col = row.column(align=True)
col.prop(scn, "use_atom_pdb_sticks_color")
+ col.prop(scn, "use_atom_pdb_sticks_smooth")
+ col.prop(scn, "use_atom_pdb_sticks_bonds")
+ row = layout.row()
+ row.active = scn.use_atom_pdb_sticks
+ col = row.column(align=True)
+ col = row.column(align=True)
+ col.active = scn.use_atom_pdb_sticks and scn.use_atom_pdb_sticks_bonds
+ col.prop(scn, "atom_pdb_sticks_dist")
row = layout.row()
row.prop(scn, "use_atom_pdb_center")
@@ -552,18 +575,22 @@ class ImportPDB(Operator, ImportHelper):
center = scn.use_atom_pdb_center
sticks = scn.use_atom_pdb_sticks
sticks_col = scn.use_atom_pdb_sticks_color
+ sticks_sm = scn.use_atom_pdb_sticks_smooth
ssector = scn.atom_pdb_sticks_sectors
sradius = scn.atom_pdb_sticks_radius
+ stick_bond = scn.use_atom_pdb_sticks_bonds
+ stick_dist = scn.atom_pdb_sticks_dist
+
cam = scn.use_atom_pdb_cam
lamp = scn.use_atom_pdb_lamp
mesh = scn.use_atom_pdb_mesh
datafile = scn.atom_pdb_datafile
-
+
# Execute main routine
atom_number = import_pdb.DEF_atom_pdb_main(
- mesh, azimuth, zenith, bradius,
- radiustype, bdistance, sticks, sticks_col,
- ssector, sradius, center, cam, lamp, datafile)
+ mesh, azimuth, zenith, bradius, radiustype, bdistance,
+ sticks, sticks_col, sticks_sm, stick_bond,
+ stick_dist, 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 d007603f88f713c6ed81b8ad8e66f5ae948883b5..cf559d9187b287a058760f95c8570244b39b2e8f 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 : 2011-12-26
+# Last modified : 2011-12-30
#
# Acknowledgements: Thanks to ideasman, meta_androcto, truman, kilon,
# dairin0d, PKHG, Valter, etc
@@ -35,8 +35,10 @@ import bpy
import io
import math
import os
+import copy
from math import pi, cos, sin
from mathutils import Vector, Matrix
+from copy import copy
# These are variables, which contain the name of the PDB file and
# the path of the PDB file.
@@ -207,10 +209,12 @@ class CLASS_atom_pdb_atom(object):
# This is the class, which stores the two atoms of one stick.
class CLASS_atom_pdb_stick(object):
- __slots__ = ('atom1', 'atom2')
- def __init__(self, atom1, atom2):
+ __slots__ = ('atom1', 'atom2', 'number', 'dist')
+ def __init__(self, atom1, atom2, number, dist):
self.atom1 = atom1
self.atom2 = atom2
+ self.number = number
+ self.dist = dist
# -----------------------------------------------------------------------------
@@ -492,7 +496,9 @@ def DEF_atom_pdb_radius_sticks(radius, how):
return True
-# This reads a custom data file.
+# -----------------------------------------------------------------------------
+# The custom data file
+
def DEF_atom_pdb_custom_datafile(path_datafile):
if path_datafile == "":
@@ -560,7 +566,9 @@ 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_sticks,use_sticks_color,Stick_sectors,Stick_diameter,put_to_center,
+ use_sticks,use_sticks_color,use_sticks_smooth,
+ use_sticks_bonds,Stick_dist,
+ Stick_sectors,Stick_diameter,put_to_center,
use_camera,use_lamp,path_datafile):
# The list of all atoms as read from the PDB file.
@@ -849,10 +857,34 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
atom1 = atom_list[0]
# For all the other atoms in the list do:
- for each_atom in atom_list[1:]:
-
- # The second, third, ... partner atom
- atom2 = each_atom
+ 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
+ - all_atoms[basis_list[0]-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
+ - all_atoms[atom2-1].location)
+ dist_n = dist_n.cross(plane_n)
+ dist_n = dist_n / dist_n.length
+ else:
+ dist_n = Vector((0,0,0))
+ elif number > 3:
+ number = 1
+ dist_n = None
+ else:
+ dist_n = None
+ else:
+ number = 1
+ dist_n = None
# Note that in a PDB file, sticks of one atom pair can appear a
# couple of times. (Only god knows why ...)
@@ -869,7 +901,7 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
# If the stick is not yet registered (FLAG_BAR == False), then
# register it!
if FLAG_BAR == False:
- all_sticks.append(CLASS_atom_pdb_stick(atom1,atom2))
+ all_sticks.append(CLASS_atom_pdb_stick(atom1,atom2,number,dist_n))
Number_of_sticks += 1
j += 1
@@ -1169,27 +1201,79 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
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])
+
+ 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(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])
+
+ 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)
@@ -1238,8 +1322,12 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith,
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
+
+ if use_sticks_smooth == True:
+ for face in stick_cylinder.data.faces:
+ face.use_smooth = True
+ stick_cylinder.parent = new_mesh
new_mesh.dupli_type = 'FACES'
atom_object_list.append(new_mesh)