From cdab4a56cb35f2bf5bd41942e82edcc3dc9bb744 Mon Sep 17 00:00:00 2001
From: Clemens Barth <barth@root-1.de>
Date: Fri, 9 Nov 2012 21:53:49 +0000
Subject: [PATCH] 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
---
io_mesh_pdb/__init__.py | 35 ++++------
io_mesh_pdb/export_pdb.py | 38 ++++-------
io_mesh_pdb/import_pdb.py | 132 ++++++++++++++++++--------------------
3 files changed, 87 insertions(+), 118 deletions(-)
diff --git a/io_mesh_pdb/__init__.py b/io_mesh_pdb/__init__.py
index 22e4e7104..62c7ca67a 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 : 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__":
diff --git a/io_mesh_pdb/export_pdb.py b/io_mesh_pdb/export_pdb.py
index cdd3e818d..515f9482b 100644
--- a/io_mesh_pdb/export_pdb.py
+++ b/io_mesh_pdb/export_pdb.py
@@ -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" % (
diff --git a/io_mesh_pdb/import_pdb.py b/io_mesh_pdb/import_pdb.py
index eb0e26687..fec026b44 100644
--- a/io_mesh_pdb/import_pdb.py
+++ b/io_mesh_pdb/import_pdb.py
@@ -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]
--
GitLab