From e333e19bed04fce92eb60fc4ca16d501c754c16b Mon Sep 17 00:00:00 2001
From: Clemens Barth <barth@root-1.de>
Date: Fri, 22 Mar 2013 17:09:36 +0000
Subject: [PATCH] New feature: Somebody asked me to make use of the skin and
subdivision modifier in Blender, which both can be used to draw the sticks.
This is what I have done and implemented.
The code has become a bit 'unreadable' there will be after some other commitments
including some code cleanups.
Blendphys.
---
io_mesh_pdb/__init__.py | 57 ++++++++++----
io_mesh_pdb/import_pdb.py | 155 +++++++++++++++++++++++++++++++++++++-
2 files changed, 193 insertions(+), 19 deletions(-)
diff --git a/io_mesh_pdb/__init__.py b/io_mesh_pdb/__init__.py
index be787ca1e..19c7c4a47 100644
--- a/io_mesh_pdb/__init__.py
+++ b/io_mesh_pdb/__init__.py
@@ -24,7 +24,7 @@
#
# Start of project : 2011-08-31 by Clemens Barth
# First publication in Blender : 2011-11-11
-# Last modified : 2013-01-16
+# Last modified : 2013-03-22
#
# Acknowledgements
# ================
@@ -38,7 +38,7 @@ bl_info = {
"name": "Atomic Blender - PDB",
"description": "Loading and manipulating atoms from PDB files",
"author": "Clemens Barth",
- "version": (1, 5),
+ "version": (1, 6),
"blender": (2, 60, 0),
"location": "File -> Import -> PDB (.pdb)",
"warning": "",
@@ -107,12 +107,21 @@ class ImportPDB(Operator, ImportHelper):
default='0',)
use_sticks = BoolProperty(
name="Use sticks", default=True,
- description="Do you want to display the sticks?")
+ 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?")
+ sticks_subdiv_view = IntProperty(
+ name = "SubDivV", default=2, min=1,
+ description="Number of subdivisions (view)")
+ sticks_subdiv_render = IntProperty(
+ name = "SubDivR", default=2, min=1,
+ description="Number of subdivisions (render)")
sticks_sectors = IntProperty(
name = "Sector", default=20, min=1,
description="Number of sectors of a stick")
sticks_radius = FloatProperty(
- name = "Radius", default=0.1, min=0.0001,
+ name = "Radius", default=0.2, min=0.0001,
description ="Radius of a stick")
sticks_unit_length = FloatProperty(
name = "Unit", default=0.05, min=0.0001,
@@ -142,6 +151,8 @@ 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()
col = row.column()
col.prop(self, "ball")
row = layout.row()
@@ -158,26 +169,39 @@ class ImportPDB(Operator, ImportHelper):
row = layout.row()
row.prop(self, "atomradius")
row = layout.row()
- col = row.column()
- col.prop(self, "use_sticks")
+ # Sticks
+ row.prop(self, "use_sticks")
+ row = layout.row()
+ row.active = self.use_sticks
+ row.prop(self, "use_sticks_skin")
row = layout.row()
row.active = self.use_sticks
col = row.column()
- col.prop(self, "sticks_sectors")
+ if not self.use_sticks_skin:
+ col.prop(self, "sticks_sectors")
col.prop(self, "sticks_radius")
- col.prop(self, "sticks_unit_length")
- col = row.column(align=True)
- col.prop(self, "use_sticks_color")
+ if self.use_sticks_skin:
+ row = layout.row()
+ row.active = self.use_sticks
+ row.prop(self, "sticks_subdiv_view")
+ row.prop(self, "sticks_subdiv_render")
+ row = layout.row()
+ row.active = self.use_sticks
+ if not self.use_sticks_skin:
+ col.prop(self, "sticks_unit_length")
+ col = row.column(align=True)
+ if not self.use_sticks_skin:
+ col.prop(self, "use_sticks_color")
col.prop(self, "use_sticks_smooth")
- col.prop(self, "use_sticks_bonds")
+ if not self.use_sticks_skin:
+ 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 and self.use_sticks_bonds
- col.prop(self, "sticks_dist")
- row = layout.row()
- row.prop(self, "use_center")
+ col.active = self.use_sticks
+ if not self.use_sticks_skin:
+ col.prop(self, "sticks_dist")
def execute(self, context):
# This is in order to solve this strange 'relative path' thing.
@@ -192,6 +216,9 @@ class ImportPDB(Operator, ImportHelper):
self.atomradius,
self.scale_distances,
self.use_sticks,
+ self.use_sticks_skin,
+ self.sticks_subdiv_view,
+ self.sticks_subdiv_render,
self.use_sticks_color,
self.use_sticks_smooth,
self.use_sticks_bonds,
diff --git a/io_mesh_pdb/import_pdb.py b/io_mesh_pdb/import_pdb.py
index 546398057..f669b3a21 100644
--- a/io_mesh_pdb/import_pdb.py
+++ b/io_mesh_pdb/import_pdb.py
@@ -17,6 +17,7 @@
# ##### END GPL LICENSE BLOCK #####
import bpy
+import bmesh
from math import pi, cos, sin, sqrt, ceil
from mathutils import Vector, Matrix
from copy import copy
@@ -188,6 +189,8 @@ class StickProp(object):
# -----------------------------------------------------------------------------
# Some basic routines
+
+# The function, which reads all necessary properties of the elements.
def read_elements():
del ELEMENTS[:]
@@ -205,6 +208,9 @@ def read_elements():
ELEMENTS.append(li)
+# The function, which reads the x,y,z positions of all atoms in a PDB
+# file.
+#
# filepath_pdb: path to pdb file
# radiustype : '0' default
# '1' atomic radii
@@ -343,14 +349,15 @@ def read_pdb_file(filepath_pdb, radiustype):
Number_of_total_atoms = j
return (Number_of_total_atoms, all_atoms)
-
+
+# The function, which reads the sticks in a PDB file.
def read_pdb_file_sticks(filepath_pdb, use_sticks_bonds, all_atoms):
# The list of all sticks.
all_sticks = []
- # Open the PDB file again.
+ # Open the PDB file.
filepath_pdb_p = open(filepath_pdb, "r")
line = filepath_pdb_p.readline()
@@ -411,6 +418,7 @@ def read_pdb_file_sticks(filepath_pdb, use_sticks_bonds, all_atoms):
if use_sticks_bonds == True:
number = atom_list[1:].count(atom2)
+
if number == 2 or number == 3:
basis_list = list(set(atom_list[1:]))
@@ -536,6 +544,9 @@ def import_pdb(Ball_type,
radiustype,
Ball_distance_factor,
use_sticks,
+ use_sticks_skin,
+ sticks_subdiv_view,
+ sticks_subdiv_render,
use_sticks_color,
use_sticks_smooth,
use_sticks_bonds,
@@ -863,9 +874,145 @@ def import_pdb(Ball_type,
atom_object_list.append(new_atom_mesh)
# ------------------------------------------------------------------------
- # DRAWING THE STICKS
+ # DRAWING THE STICKS: skin and subdivision modifier
+
+ 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)
+
+
+
+ # ------------------------------------------------------------------------
+ # DRAWING THE STICKS: regular cylinders in a dupliverts structure
- if use_sticks == True and all_sticks != []:
+ if use_sticks == True and all_sticks != [] and use_sticks_skin == False:
dl = Stick_unit
--
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