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Commit cdab4a56 authored by Clemens Barth's avatar Clemens Barth
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As in the case of the XYZ IE, names of classes and functions were changed, 

according to the "Style Guide for Python Code" 
(http://www.python.org/dev/peps/pep-0008/) and the recent review
(http://codereview.appspot.com/6815052). Some slight changes were done, too. 
Extensive tests have shown that the code is still well working.

Blendphys
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io_mesh_pdb/__init__.py
+ 14
− 21
View file @ cdab4a56
......@@ -24,7 +24,7 @@
#
# Start of project : 2011-08-31 by Clemens Barth
# First publication in Blender : 2011-11-11
# Last modified : 2012-11-03
# Last modified : 2012-11-09
#
# Acknowledgements
# ================
......@@ -49,10 +49,7 @@ bl_info = {
"category": "Import-Export"
}
import os
import io
import bpy
import bmesh
from bpy.types import Operator, Panel
from bpy_extras.io_utils import ImportHelper, ExportHelper
from bpy.props import (StringProperty,
......@@ -67,9 +64,8 @@ from . import export_pdb
# -----------------------------------------------------------------------------
# GUI
# This is the class for the file dialog of the importer.
class CLASS_ImportPDB(Operator, ImportHelper):
class ImportPDB(Operator, ImportHelper):
bl_idname = "import_mesh.pdb"
bl_label = "Import Protein Data Bank(*.pdb)"
bl_options = {'PRESET', 'UNDO'}
......@@ -183,7 +179,7 @@ class CLASS_ImportPDB(Operator, ImportHelper):
filepath_pdb = bpy.path.abspath(self.filepath)
# Execute main routine
atom_number = import_pdb.DEF_atom_pdb_main(
atom_number = import_pdb.import_pdb(
self.use_mesh,
self.mesh_azimuth,
self.mesh_zenith,
......@@ -206,9 +202,8 @@ class CLASS_ImportPDB(Operator, ImportHelper):
return {'FINISHED'}
# This is the class for the file dialog of the exporter.
class CLASS_ExportPDB(Operator, ExportHelper):
class ExportPDB(Operator, ExportHelper):
bl_idname = "export_mesh.pdb"
bl_label = "Export Protein Data Bank(*.pdb)"
filename_ext = ".pdb"
......@@ -230,31 +225,29 @@ class CLASS_ExportPDB(Operator, ExportHelper):
row.prop(self, "atom_pdb_export_type")
def execute(self, context):
# This is in order to solve this strange 'relative path' thing.
export_pdb.ATOM_PDB_FILEPATH = bpy.path.abspath(self.filepath)
export_pdb.DEF_atom_pdb_export(self.atom_pdb_export_type)
export_pdb.export_pdb(self.atom_pdb_export_type,
bpy.path.abspath(self.filepath))
return {'FINISHED'}
# The entry into the menu 'file -> import'
def DEF_menu_func_import(self, context):
self.layout.operator(CLASS_ImportPDB.bl_idname, text="Protein Data Bank (.pdb)")
def menu_func_import(self, context):
self.layout.operator(ImportPDB.bl_idname, text="Protein Data Bank (.pdb)")
# The entry into the menu 'file -> export'
def DEF_menu_func_export(self, context):
self.layout.operator(CLASS_ExportPDB.bl_idname, text="Protein Data Bank (.pdb)")
def menu_func_export(self, context):
self.layout.operator(ExportPDB.bl_idname, text="Protein Data Bank (.pdb)")
def register():
bpy.utils.register_module(__name__)
bpy.types.INFO_MT_file_import.append(DEF_menu_func_import)
bpy.types.INFO_MT_file_export.append(DEF_menu_func_export)
bpy.types.INFO_MT_file_import.append(menu_func_import)
bpy.types.INFO_MT_file_export.append(menu_func_export)
def unregister():
bpy.utils.unregister_module(__name__)
bpy.types.INFO_MT_file_import.remove(DEF_menu_func_import)
bpy.types.INFO_MT_file_export.remove(DEF_menu_func_export)
bpy.types.INFO_MT_file_import.remove(menu_func_import)
bpy.types.INFO_MT_file_export.remove(menu_func_export)
if __name__ == "__main__":
......
io_mesh_pdb/export_pdb.py
+ 12
− 26
View file @ cdab4a56
......@@ -17,32 +17,17 @@
# ##### END GPL LICENSE BLOCK #####
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
from . import import_pdb
ATOM_PDB_FILEPATH = ""
ATOM_PDB_PDBTEXT = ( "REMARK This pdb file has been created with Blender "
+ "and the addon Atomic Blender - PDB\n"
+ "REMARK For more details see wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/Import-Export/PDB\n"
+ "REMARK\n"
+ "REMARK\n")
class CLASS_atom_pdb_atoms_export(object):
class AtomPropExport(object):
__slots__ = ('element', 'location')
def __init__(self, element, location):
self.element = element
self.location = location
def DEF_atom_pdb_export(obj_type):
def export_pdb(obj_type, filepath_pdb):
list_atoms = []
for obj in bpy.context.selected_objects:
......@@ -54,7 +39,7 @@ def DEF_atom_pdb_export(obj_type):
continue
name = ""
for element in import_pdb.ATOM_PDB_ELEMENTS_DEFAULT:
for element in import_pdb.ELEMENTS_DEFAULT:
if element[1] in obj.name:
if element[2] == "Vac":
name = "X"
......@@ -70,18 +55,19 @@ def DEF_atom_pdb_export(obj_type):
if len(obj.children) != 0:
for vertex in obj.data.vertices:
location = obj.matrix_world*vertex.co
list_atoms.append(CLASS_atom_pdb_atoms_export(
name,
location))
list_atoms.append(AtomPropExport(name, location))
else:
if not obj.parent:
location = obj.location
list_atoms.append(CLASS_atom_pdb_atoms_export(
name,
location))
list_atoms.append(AtomPropExport(name, location))
pdb_file_p = open(ATOM_PDB_FILEPATH, "w")
pdb_file_p.write(ATOM_PDB_PDBTEXT)
pdb_file_p = open(filepath_pdb, "w")
pdb_file_p.write("REMARK This pdb file has been created with Blender "
"and the addon Atomic Blender - PDB\n"
"REMARK For more details see wiki.blender.org/index.php/"
"Extensions:2.6/Py/Scripts/Import-Export/PDB\n"
"REMARK\n"
"REMARK\n")
for i, atom in enumerate(list_atoms):
string = "ATOM %6d%3s%24.3f%8.3f%8.3f%6.2f%6.2f%12s\n" % (
......
io_mesh_pdb/import_pdb.py
+ 61
− 71
View file @ cdab4a56
......@@ -17,11 +17,8 @@
# ##### END GPL LICENSE BLOCK #####
import bpy
import io
import math
import os
import copy
from math import pi, cos, sin
from math import pi, cos, sin, sqrt, ceil
from mathutils import Vector, Matrix
from copy import copy
......@@ -40,7 +37,7 @@ from copy import copy
# charge states for any atom are listed, if existing.
# The list is fixed and cannot be changed ... (see below)
ATOM_PDB_ELEMENTS_DEFAULT = (
ELEMENTS_DEFAULT = (
( 1, "Hydrogen", "H", ( 1.0, 1.0, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ),
( 2, "Helium", "He", ( 0.85, 1.0, 1.0), 0.93, 0.93, 0.49 ),
( 3, "Lithium", "Li", ( 0.8, 0.50, 1.0), 1.23, 1.23, 2.05 , 1 , 0.68 ),
......@@ -152,14 +149,14 @@ ATOM_PDB_ELEMENTS_DEFAULT = (
# This list here contains all data of the elements and will be used during
# runtime. It is a list of classes.
# During executing Atomic Blender, the list will be initialized with the fixed
# data from above via the class structure below (CLASS_atom_pdb_Elements). We
# data from above via the class structure below (ElementProp). We
# have then one fixed list (above), which will never be changed, and a list of
# classes with same data. The latter can be modified via loading a separate
# custom data file.
ATOM_PDB_ELEMENTS = []
ELEMENTS = []
# This is the class, which stores the properties for one element.
class CLASS_atom_pdb_Elements(object):
class ElementProp(object):
__slots__ = ('number', 'name', 'short_name', 'color', 'radii', 'radii_ionic')
def __init__(self, number, name, short_name, color, radii, radii_ionic):
self.number = number
......@@ -170,7 +167,7 @@ class CLASS_atom_pdb_Elements(object):
self.radii_ionic = radii_ionic
# This is the class, which stores the properties of one atom.
class CLASS_atom_pdb_atom(object):
class AtomProp(object):
__slots__ = ('element', 'name', 'location', 'radius', 'color', 'material')
def __init__(self, element, name, location, radius, color, material):
self.element = element
......@@ -181,7 +178,7 @@ class CLASS_atom_pdb_atom(object):
self.material = material
# This is the class, which stores the two atoms of one stick.
class CLASS_atom_pdb_stick(object):
class StickProp(object):
__slots__ = ('atom1', 'atom2', 'number', 'dist')
def __init__(self, atom1, atom2, number, dist):
self.atom1 = atom1
......@@ -189,15 +186,14 @@ class CLASS_atom_pdb_stick(object):
self.number = number
self.dist = dist
# -----------------------------------------------------------------------------
# Some basic routines
def DEF_atom_pdb_read_elements():
def read_elements():
ATOM_PDB_ELEMENTS[:] = []
ELEMENTS[:] = []
for item in ATOM_PDB_ELEMENTS_DEFAULT:
for item in ELEMENTS_DEFAULT:
# All three radii into a list
radii = [item[4],item[5],item[6]]
......@@ -205,22 +201,22 @@ def DEF_atom_pdb_read_elements():
# empty list.
radii_ionic = []
li = CLASS_atom_pdb_Elements(item[0],item[1],item[2],item[3],
li = ElementProp(item[0],item[1],item[2],item[3],
radii,radii_ionic)
ATOM_PDB_ELEMENTS.append(li)
ELEMENTS.append(li)
# filepath_pdb: path to pdb file
# radiustype : '0' default
# '1' atomic radii
# '2' van der Waals
def DEF_atom_pdb_read_pdb_file(filepath_pdb,radiustype):
def read_pdb_file(filepath_pdb, radiustype):
# The list of all atoms as read from the PDB file.
all_atoms = []
# Open the pdb file ...
filepath_pdb_p = io.open(filepath_pdb, "r")
filepath_pdb_p = open(filepath_pdb, "r")
#Go to the line, in which "ATOM" or "HETATM" appears.
for line in filepath_pdb_p:
......@@ -249,7 +245,7 @@ def DEF_atom_pdb_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(CLASS_atom_pdb_atom(short_name,
all_atoms.append(AtomProp(short_name,
name,
location,
radius,
......@@ -283,7 +279,7 @@ def DEF_atom_pdb_read_pdb_file(filepath_pdb,radiustype):
if short_name2.isalpha() == True:
FOUND = False
for element in ATOM_PDB_ELEMENTS:
for element in ELEMENTS:
if str.upper(short_name2) == str.upper(element.short_name):
FOUND = True
break
......@@ -291,10 +287,9 @@ def DEF_atom_pdb_read_pdb_file(filepath_pdb,radiustype):
short_name = short_name2
# ....................................................... to here.
# Go through all elements and find the element of the current atom.
FLAG_FOUND = False
for element in ATOM_PDB_ELEMENTS:
for element in ELEMENTS:
if str.upper(short_name) == str.upper(element.short_name):
# Give the atom its proper names, color and radius:
short_name = str.upper(element.short_name)
......@@ -313,16 +308,16 @@ def DEF_atom_pdb_read_pdb_file(filepath_pdb,radiustype):
if "X" in short_name:
short_name = "VAC"
name = "Vacancy"
radius = float(ATOM_PDB_ELEMENTS[-3].radii[int(radiustype)])
color = ATOM_PDB_ELEMENTS[-3].color
radius = float(ELEMENTS[-3].radii[int(radiustype)])
color = ELEMENTS[-3].color
# ... take what is written in the PDB file. These are somewhat
# unknown atoms. This should never happen, the element list is
# almost complete. However, we do this due to security reasons.
else:
short_name = str.upper(short_name)
name = str.upper(short_name)
radius = float(ATOM_PDB_ELEMENTS[-2].radii[int(radiustype)])
color = ATOM_PDB_ELEMENTS[-2].color
radius = float(ELEMENTS[-2].radii[int(radiustype)])
color = ELEMENTS[-2].color
# x,y and z are at fixed positions in the PDB file.
x = float(line[30:38].rsplit()[0])
......@@ -334,11 +329,11 @@ def DEF_atom_pdb_read_pdb_file(filepath_pdb,radiustype):
j += 1
# Append the atom to the list. Material remains empty so far.
all_atoms.append(CLASS_atom_pdb_atom(short_name,
name,
location,
radius,
color,[]))
all_atoms.append(AtomProp(short_name,
name,
location,
radius,
color,[]))
line = filepath_pdb_p.readline()
line = line[:-1]
......@@ -350,14 +345,13 @@ def DEF_atom_pdb_read_pdb_file(filepath_pdb,radiustype):
return (Number_of_total_atoms, all_atoms)
def DEF_atom_pdb_read_pdb_file_sticks(filepath_pdb,
use_sticks_bonds):
def read_pdb_file_sticks(filepath_pdb, use_sticks_bonds):
# The list of all sticks.
all_sticks = []
# Open the PDB file again.
filepath_pdb_p = io.open(filepath_pdb, "r")
filepath_pdb_p = open(filepath_pdb, "r")
line = filepath_pdb_p.readline()
split_list = line.split(' ')
......@@ -460,7 +454,7 @@ def DEF_atom_pdb_read_pdb_file_sticks(filepath_pdb,
# 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,number,dist_n))
all_sticks.append(StickProp(atom1,atom2,number,dist_n))
Number_of_sticks += 1
j += 1
......@@ -473,7 +467,7 @@ def DEF_atom_pdb_read_pdb_file_sticks(filepath_pdb,
# Routine which produces a cylinder. All is somewhat easy to undertsand.
def DEF_atom_pdb_build_stick(radius, length, sectors):
def build_stick(radius, length, sectors):
dphi = 2.0 * pi/(float(sectors)-1)
......@@ -535,23 +529,23 @@ def DEF_atom_pdb_build_stick(radius, length, sectors):
# -----------------------------------------------------------------------------
# The main routine
def DEF_atom_pdb_main(use_mesh,
Ball_azimuth,
Ball_zenith,
Ball_radius_factor,
radiustype,
Ball_distance_factor,
use_sticks,
use_sticks_color,
use_sticks_smooth,
use_sticks_bonds,
Stick_unit, Stick_dist,
Stick_sectors,
Stick_diameter,
put_to_center,
use_camera,
use_lamp,
filepath_pdb):
def import_pdb(use_mesh,
Ball_azimuth,
Ball_zenith,
Ball_radius_factor,
radiustype,
Ball_distance_factor,
use_sticks,
use_sticks_color,
use_sticks_smooth,
use_sticks_bonds,
Stick_unit, Stick_dist,
Stick_sectors,
Stick_diameter,
put_to_center,
use_camera,
use_lamp,
filepath_pdb):
# List of materials
......@@ -561,17 +555,15 @@ def DEF_atom_pdb_main(use_mesh,
# structure.
atom_object_list = []
# ------------------------------------------------------------------------
# INITIALIZE THE ELEMENT LIST
DEF_atom_pdb_read_elements()
read_elements()
# ------------------------------------------------------------------------
# READING DATA OF ATOMS
(Number_of_total_atoms, all_atoms) = DEF_atom_pdb_read_pdb_file(filepath_pdb,
radiustype)
(Number_of_total_atoms, all_atoms) = read_pdb_file(filepath_pdb, radiustype)
# ------------------------------------------------------------------------
# MATERIAL PROPERTIES FOR ATOMS
......@@ -631,9 +623,7 @@ def DEF_atom_pdb_main(use_mesh,
# ------------------------------------------------------------------------
# READING DATA OF STICKS
all_sticks = DEF_atom_pdb_read_pdb_file_sticks(filepath_pdb,
use_sticks_bonds)
all_sticks = read_pdb_file_sticks(filepath_pdb, use_sticks_bonds)
# So far, all atoms, sticks and materials have been registered.
......@@ -695,12 +685,12 @@ def DEF_atom_pdb_main(use_mesh,
# Assume that the object is put into the global origin. Then, the
# camera is moved in x and z direction, not in y. The object has its
# size at distance math.sqrt(object_size) from the origin. So, move the
# size at distance sqrt(object_size) from the origin. So, move the
# camera by this distance times a factor of camera_factor in x and z.
# Then add x, y and z of the origin of the object.
object_camera_vec = Vector((math.sqrt(object_size) * camera_factor,
object_camera_vec = Vector((sqrt(object_size) * camera_factor,
0.0,
math.sqrt(object_size) * camera_factor))
sqrt(object_size) * camera_factor))
camera_xyz_vec = object_center_vec + object_camera_vec
# Create the camera
......@@ -728,7 +718,7 @@ def DEF_atom_pdb_main(use_mesh,
# camera position and view onto the object.
bpy.ops.object.select_all(action='DESELECT')
camera.select = True
bpy.ops.transform.rotate(value=(90.0*2*math.pi/360.0),
bpy.ops.transform.rotate(value=(90.0*2*pi/360.0),
axis=object_camera_vec,
constraint_axis=(False, False, False),
constraint_orientation='GLOBAL',
......@@ -744,7 +734,7 @@ def DEF_atom_pdb_main(use_mesh,
# This is the distance from the object measured in terms of %
# of the camera distance. It is set onto 50% (1/2) distance.
lamp_dl = math.sqrt(object_size) * 15 * 0.5
lamp_dl = sqrt(object_size) * 15 * 0.5
# This is a factor to which extend the lamp shall go to the right
# (from the camera point of view).
lamp_dy_right = lamp_dl * (3.0/4.0)
......@@ -874,8 +864,8 @@ def DEF_atom_pdb_main(use_mesh,
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
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 = []
......@@ -917,7 +907,7 @@ def DEF_atom_pdb_main(use_mesh,
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)))
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])
......@@ -978,9 +968,9 @@ def DEF_atom_pdb_main(use_mesh,
n_b = b / b.length
if use_sticks_color == True:
loops = int(math.ceil(dv.length / (2.0 * dl)))
loops = int(ceil(dv.length / (2.0 * dl)))
else:
loops = int(math.ceil(dv.length / dl))
loops = int(ceil(dv.length / dl))
for j in range(loops):
......@@ -1004,7 +994,7 @@ def DEF_atom_pdb_main(use_mesh,
bpy.context.scene.objects.link(new_mesh)
current_layers = bpy.context.scene.layers
object_stick = DEF_atom_pdb_build_stick(Stick_diameter, dl, Stick_sectors)
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]
......
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