api and pep8 edits

2 files changed, 257 insertions, 225 deletions

diff --git a/io_mesh_pdb/__init__.py b/io_mesh_pdb/__init__.py
index b8b4b98c..3a2068f8 100644
--- a/io_mesh_pdb/__init__.py
+++ b/io_mesh_pdb/__init__.py
@@ -16,6 +16,8 @@
 #
 # ##### END GPL LICENSE BLOCK #####
 
+# <pep8-80 compliant>
+
 bl_info = {
     "name": "Import/Export: PDB format",
     "author": "Mariusz Maximus & Jong89",
@@ -48,11 +50,12 @@ from bpy.props import (StringProperty,
 
 from bpy_extras.io_utils import ImportHelper
 
+
 class ImportPDB(bpy.types.Operator, ImportHelper):
     """Import from PDB file format (.pdb)"""
     bl_idname = 'import_scene.pdb'
     bl_label = 'Import PDB'
-    bl_options= {'REGISTER', 'UNDO'}
+    bl_options = {'REGISTER', 'UNDO'}
 
     filename_ext = ".pdb"
     filter_glob = StringProperty(default="*.pdb", options={'HIDDEN'})
@@ -60,7 +63,7 @@ class ImportPDB(bpy.types.Operator, ImportHelper):
     filepath = StringProperty(
             name="File Path",
             description="Filepath used for importing the PDB file",
-            maxlen= 1024,
+            maxlen=1024,
             )
     multi_models = BoolProperty(
             name="Import all models",
@@ -70,14 +73,15 @@ class ImportPDB(bpy.types.Operator, ImportHelper):
     multimers = BoolProperty(
             name="Import Biomolecules",
             description="Import all file-listed biomolecules and multimers, "
-                        "disable to import default biomolecule with all chains",
+                        "disable to import default biomolecule with "
+                        "all chains",
             default=False,
             )
     retain_alts = BoolProperty(
             name="Retain Alternative Atoms",
             description="Select to retain alternative atoms. "
                         "Some PDB files label coordinates of entries "
-                        "in multiple models as alternates" ,
+                        "in multiple models as alternates",
             default=False,
             )
     atom_subdivisions = IntProperty(
@@ -89,25 +93,20 @@ class ImportPDB(bpy.types.Operator, ImportHelper):
     atom_size = FloatProperty(
             name="Atom Size",
             description="Multiplier for the van der Waals radius of the atoms",
-            min=0, max=5,
-            default=1,
+            min=0.0, max=5.0,
+            default=1.0,
             )
     scene_scale = FloatProperty(
             name="Scene Scale Factor",
             description="Number of Blender units equivalent to 1 angstrom",
-            min=0, max=10,
-            default=1,
+            min=0.0, max=10.0,
+            default=1.0,
             )
 
     def execute(self, context):
         from . import import_pdb
-        import_pdb.load_pdb(self.filepath, context,
-                            self.atom_size,
-                            self.scene_scale,
-                            self.atom_subdivisions,
-                            self.retain_alts,
-                            self.multi_models,
-                            self.multimers)
+        keywords = self.as_keywords(ignore=("filter_glob", ))
+        import_pdb.load_pdb(context, **keywords)
         return {'FINISHED'}
 
     def invoke(self, context, event):
@@ -115,13 +114,16 @@ class ImportPDB(bpy.types.Operator, ImportHelper):
         wm.fileselect_add(self)
         return {'RUNNING_MODAL'}
 
+
 def menu_func(self, context):
     self.layout.operator(ImportPDB.bl_idname, text='Protein Databank (.pdb)')
 
+
 def register():
     bpy.utils.register_module(__name__)
     bpy.types.INFO_MT_file_import.append(menu_func)
 
+
 def unregister():
     bpy.utils.unregister_module(__name__)
     bpy.types.INFO_MT_file_import.remove(menu_func)
diff --git a/io_mesh_pdb/import_pdb.py b/io_mesh_pdb/import_pdb.py
index 6f81c847..8c4ab70c 100644
--- a/io_mesh_pdb/import_pdb.py
+++ b/io_mesh_pdb/import_pdb.py
@@ -16,20 +16,27 @@
 #
 # ##### END GPL LICENSE BLOCK #####
 
+# <pep8 compliant>
+
+# TODO, currently imported names are assumed to make valid blender names
+#       this is _not_ assured, so we should use a reliable dict mapping.
+
 import bpy
 
+
 class Element:
-    '''Element class with properties ([R, G, B], cov_radius, vdw_radius, name)'''
+    """Element class with properties ([R, G, B], cov_radius, vdw_radius, name)"""
     def __init__(self, color, cov_radius, vdw_radius, name):
         self.color = color
         self.cov_radius = cov_radius
         self.vdw_radius = vdw_radius
         self.name = name
 
+
 class Atom:
-    '''Atom class with properties (serial, name, altloc, resname,chainid,
-        resseq, icode, x, y, z, occupancy, tempfactor, element, charge)'''
-    
+    """Atom class with properties (serial, name, altloc, resname,chainid,
+        resseq, icode, x, y, z, occupancy, tempfactor, element, charge)"""
+
     def __init__(self, serial, name, altloc, resname, chainid, resseq, icode,
                  x, y, z, occupancy, tempfactor, element, charge):
         self.serial = serial
@@ -47,8 +54,9 @@ class Atom:
         self.element = element
         self.charge = charge
 
-#collection of biomolecules based on model
-#all chains in model stored here
+
+# collection of biomolecules based on model
+# all chains in model stored here
 class Model:
     '''Model class'''
     def __init__(self, model_id):
@@ -56,14 +64,15 @@ class Model:
         self.atoms = {}
         self.atom_count = 0
         self.vert_list = []
-        #Dictionary of {vert index: [list of vertex groups it belongs to]}
-        #Now element only
+        # Dictionary of {vert index: [list of vertex groups it belongs to]}
+        # Now element only
         self.vert_group_index = {}
-        #Dictionary of {vertex group: number of group members}
+        # Dictionary of {vertex group: number of group members}
         self.vert_group_counts = {}
         self.chains = {}
 
-#new object level class
+
+# new object level class
 class Biomolecule:
     '''Biomolecule'''
     def __init__(self, serial):
@@ -74,136 +83,147 @@ class Biomolecule:
         self.vert_group_counts = {}
         self.chain_transforms = {}
 
-#Atom collection
+
+# Atom collection
 class Chain:
     '''Chain'''
     def __init__(self, chain_id):
         self.chain_id = chain_id
         self.atoms = {}
 
-#Atomic data from http://www.ccdc.cam.ac.uk/products/csd/radii/
-#Color palatte adapted from Jmol
-#"Element symbol":[[Red, Green, Blue], Covalent radius, van der Waals radius,
-#                  Element name]
-#Atomic radii are in angstroms (100 pm)
-#Unknown covalent radii are assigned 1.5 A, unknown van der Waals radiii are
-#assigned 2 A,
+# Atomic data from http://www.ccdc.cam.ac.uk/products/csd/radii/
+# Color palatte adapted from Jmol
+# "Element symbol":[[Red, Green, Blue], Covalent radius, van der Waals radius,
+#                   Element name]
+# Atomic radii are in angstroms (100 pm)
+# Unknown covalent radii are assigned 1.5 A, unknown van der Waals radiii are
+# assigned 2 A,
 
 atom_data = {
-'H' :	Element([1.00000, 1.00000, 1.00000],	0.23,	1.09,	'Hydrogen'  ),
-'HE':	Element([0.85098, 1.00000, 1.00000],	1.5 ,	1.4 ,	'Helium'    ),
-'LI':	Element([0.80000, 0.50196, 1.00000],	1.28,	1.82,	'Lithium'   ),
-'BE':	Element([0.76078, 1.00000, 0.00000],	0.96,	2   ,	'Beryllium' ),
-'B' :	Element([1.00000, 0.70980, 0.70980],	0.83,	2   ,	'Boron'     ),
-'C' :	Element([0.56471, 0.56471, 0.56471],	0.68,	1.7 ,	'Carbon'    ),
-'N' :	Element([0.18824, 0.31373, 0.97255],	0.68,	1.55,	'Nitrogen'  ),
-'O' :   Element([1.00000, 0.05098, 0.05098],	0.68,	1.52,	'Oxygen'    ),
-'F' :	Element([0.56471, 0.87843, 0.31373],	0.64,	1.47,	'Fluorine'  ),
-'NE':	Element([0.70196, 0.89020, 0.96078],	1.5 ,	1.54,	'Neon'      ),
-'NA':	Element([0.67059, 0.36078, 0.94902],	1.66,	2.27,	'Sodium'    ),
-'MG':	Element([0.54118, 1.00000, 0.00000],	1.41,	1.73,	'Magnesium' ),
-'AL':	Element([0.74902, 0.65098, 0.65098],	1.21,	2   ,	'Aluminum'  ),
-'SI':	Element([0.94118, 0.78431, 0.62745],	1.2 ,	2.1 ,	'Silicon'   ),
-'P' :	Element([1.00000, 0.50196, 0.00000],	1.05,	1.8 ,	'Phosphorus'),
-'S' :	Element([1.00000, 1.00000, 0.18824],	1.02,	1.8 ,	'Sulfur'    ),
-'CL':	Element([0.12157, 0.94118, 0.12157],	0.99,	1.75,	'Chlorine'  ),
-'AR':	Element([0.50196, 0.81961, 0.89020],	1.51,	1.88,	'Argon'     ),
-'K' :	Element([0.56078, 0.25098, 0.83137],	2.03,	2.75,	'Potassium' ),
-'CA':	Element([0.23922, 1.00000, 0.00000],	1.76,	2   ,	'Calcium'   ),
-'SC':	Element([0.90196, 0.90196, 0.90196],	1.7 ,	2   ,	'Scandium'  ),
-'TI':	Element([0.74902, 0.76078, 0.78039],	1.6 ,	2   ,	'Titanium'  ),
-'V' :	Element([0.65098, 0.65098, 0.67059],	1.53,	2   ,	'Vanadium'  ),
-'CR':	Element([0.54118, 0.60000, 0.78039],	1.39,	2   ,	'Chromium'  ),
-'MN':	Element([0.61176, 0.47843, 0.78039],	1.61,	2   ,	'Manganese' ),
-'FE':	Element([0.87843, 0.40000, 0.20000],	1.52,	2   ,	'Iron'      ),
-'CO':	Element([0.94118, 0.56471, 0.62745],	1.26,	2   ,	'Cobalt'    ),
-'NI':	Element([0.31373, 0.81569, 0.31373],	1.24,	1.63,	'Nickel'    ),
-'CU':	Element([0.78431, 0.50196, 0.20000],	1.32,	1.4 ,	'Copper'    ),
-'ZN':	Element([0.49020, 0.50196, 0.69020],	1.22,	1.39,	'Zinc'      ),
-'GA':	Element([0.76078, 0.56078, 0.56078],	1.22,	1.87,	'Gallium'   ),
-'GE':	Element([0.40000, 0.56078, 0.56078],	1.17,	2   ,	'Germanium' ),
-'AS':	Element([0.74118, 0.50196, 0.89020],	1.21,	1.85,	'Arsenic'   ),
-'SE':	Element([1.00000, 0.63137, 0.00000],	1.22,	1.9 ,	'Selenium'  ),
-'BR':	Element([0.65098, 0.16078, 0.16078],	1.21,	1.85,	'Bromine'   ),
-'KR':	Element([0.36078, 0.72157, 0.81961],	1.5 ,	2.02,	'Krypton'   ),
-'RB':	Element([0.43922, 0.18039, 0.69020],	2.2 ,	2   ,	'Rubidium'  ),
-'SR':	Element([0.00000, 1.00000, 0.00000],	1.95,	2   ,	'Strontium' ),
-'Y' :	Element([0.58039, 1.00000, 1.00000],	1.9 ,	2   ,	'Yttrium'   ),
-'ZR':	Element([0.58039, 0.87843, 0.87843],	1.75,	2   ,	'Zirconium' ),
-'NB':	Element([0.45098, 0.76078, 0.78824],	1.64,	2   ,	'Niobium'   ),
-'MO':	Element([0.32941, 0.70980, 0.70980],	1.54,	2   ,	'Molybdenum'),
-'TC':	Element([0.23137, 0.61961, 0.61961],	1.47,	2   ,	'Technetium'),
-'RU':	Element([0.14118, 0.56078, 0.56078],	1.46,	2   ,	'Ruthenium' ),
-'RH':	Element([0.03922, 0.49020, 0.54902],	1.45,	2   ,	'Rhodium'   ),
-'PD':	Element([0.00000, 0.41176, 0.52157],	1.39,	1.63,	'Palladium' ),
-'AG':	Element([0.75294, 0.75294, 0.75294],	1.45,	1.72,	'Silver'    ),
-'CD':	Element([1.00000, 0.85098, 0.56078],	1.44,	1.58,	'Cadmium'   ),
-'IN':	Element([0.65098, 0.45882, 0.45098],	1.42,	1.93,	'Indium'    ),
-'SN':	Element([0.40000, 0.50196, 0.50196],	1.39,	2.17,	'Tin'       ),
-'SB':	Element([0.61961, 0.38824, 0.70980],	1.39,	2   ,	'Antimony'  ),
-'TE':	Element([0.83137, 0.47843, 0.00000],	1.47,	2.06,	'Tellurium' ),
-'I' :	Element([0.58039, 0.00000, 0.58039],	1.4 ,	1.98,	'Iodine'    ),
-'XE':	Element([0.25882, 0.61961, 0.69020],	1.5 ,	2.16,	'Xenon'     ),
-'CS':	Element([0.34118, 0.09020, 0.56078],	2.44,	2   ,	'Cesium'    ),
-'BA':	Element([0.00000, 0.78824, 0.00000],	2.15,	2   ,	'Barium'    ),
-'LA':	Element([0.43922, 0.83137, 1.00000],	2.07,	2   ,	'Lanthanum' ),
-'CE':	Element([1.00000, 1.00000, 0.78039],	2.04,	2   ,	'Cerium'    ),
-'PR':	Element([0.85098, 1.00000, 0.78039],	2.03,	2   ,	'Praseodymium'),
-'ND':	Element([0.78039, 1.00000, 0.78039],	2.01,	2   ,	'Neodymium' ),
-'PM':	Element([0.63922, 1.00000, 0.78039],	1.99,	2   ,	'Promethium'),
-'SM':	Element([0.56078, 1.00000, 0.78039],	1.98,	2   ,	'Samarium'  ),
-'EE':	Element([0.38039, 1.00000, 0.78039],	1.98,	2   ,	'Europium'  ),
-'GD':	Element([0.27059, 1.00000, 0.78039],	1.96,	2   ,	'Gadolinium'),
-'TB':	Element([0.18824, 1.00000, 0.78039],	1.94,	2   ,	'Terbium'   ),
-'DY':	Element([0.12157, 1.00000, 0.78039],	1.92,	2   ,	'Dysprosium'),
-'HO':	Element([0.00000, 1.00000, 0.61176],	1.92,	2   ,	'Holmium'   ),
-'ER':	Element([0.00000, 0.90196, 0.45882],	1.89,	2   ,	'Erbium'    ),
-'TM':	Element([0.00000, 0.83137, 0.32157],	1.9 ,	2   ,	'Thulium'   ),
-'YB':	Element([0.00000, 0.74902, 0.21961],	1.87,	2   ,	'Ytterbium' ),
-'LU':	Element([0.00000, 0.67059, 0.14118],	1.87,	2   ,	'Lutetium'  ),
-'HF':	Element([0.30196, 0.76078, 1.00000],	1.75,	2   ,	'Hafnium'   ),
-'TA':	Element([0.30196, 0.65098, 1.00000],	1.7 ,	2   ,	'Tantalum'  ),
-'W' :	Element([0.12941, 0.58039, 0.83922],	1.62,	2   ,	'Tungsten'  ),
-'RE':	Element([0.14902, 0.49020, 0.67059],	1.51,	2   ,	'Rhenium'   ),
-'OS':	Element([0.14902, 0.40000, 0.58824],	1.44,	2   ,	'Osmium'    ),
-'IR':	Element([0.09020, 0.32941, 0.52941],	1.41,	2   ,	'Iridium'   ),
-'PT':	Element([0.81569, 0.81569, 0.87843],	1.36,	1.72,	'Platinum'  ),
-'AU':	Element([1.00000, 0.81961, 0.13725],	1.5 ,	1.66,	'Gold'      ),
-'HG':	Element([0.72157, 0.72157, 0.81569],	1.32,	1.55,	'Mercury'   ),
-'TL':	Element([0.65098, 0.32941, 0.30196],	1.45,	1.96,	'Thallium'  ),
-'PB':	Element([0.34118, 0.34902, 0.38039],	1.46,	2.02,	'Lead'      ),
-'BI':	Element([0.61961, 0.30980, 0.70980],	1.48,	2   ,	'Bismuth'   ),
-'PO':	Element([0.67059, 0.36078, 0.00000],	1.4 ,	2   ,	'Polonium'  ),
-'AT':	Element([0.45882, 0.30980, 0.27059],	1.21,	2   ,	'Astatine'  ),
-'RN':	Element([0.25882, 0.50980, 0.58824],	1.5 ,	2   ,	'Radon'     ),
-'FR':	Element([0.25882, 0.00000, 0.40000],	2.6 ,	2   ,	'Francium'  ),
-'RA':	Element([0.00000, 0.49020, 0.00000],	2.21,	2   ,	'Radium'    ),
-'AC':	Element([0.43922, 0.67059, 0.98039],	2.15,	2   ,	'Actinium'  ),
-'TH':	Element([0.00000, 0.72941, 1.00000],	2.06,	2   ,	'Thorium'   ),
-'PA':	Element([0.00000, 0.63137, 1.00000],	2   ,	2   ,	'Protactinium'),
-'U' :	Element([0.00000, 0.56078, 1.00000],	1.96,	1.86,	'Uranium'   ),
-'NP':	Element([0.00000, 0.50196, 1.00000],	1.9 ,	2   ,	'Neptunium' ),
-'PU':	Element([0.00000, 0.41961, 1.00000],	1.87,	2   ,	'Plutonium' ),
-'AM':	Element([0.32941, 0.36078, 0.94902],	1.8 ,	2   ,	'Americium' ),
-'CM':	Element([0.47059, 0.36078, 0.89020],	1.69,	2   ,	'Curium'    ),
-'BK':	Element([0.54118, 0.30980, 0.89020],	1.54,	2   ,	'Berkelium' ),
-'CF':	Element([0.63137, 0.21176, 0.83137],	1.83,	2   ,	'Californium'),
-'ES':	Element([0.70196, 0.12157, 0.83137],	1.5 ,	2   ,	'Einsteinium'),
-'FM':	Element([0.70196, 0.12157, 0.72941],	1.5 ,	2   ,	'Fermium'   ),
-'MD':	Element([0.70196, 0.05098, 0.65098],	1.5 ,	2   ,	'Mendelevium'),
-'NO':	Element([0.74118, 0.05098, 0.52941],	1.5 ,	2   ,	'Nobelium'  ),
-'LR':	Element([0.78039, 0.00000, 0.40000],	1.5 ,	2   ,	'Lawrencium'),
-'RF':	Element([0.80000, 0.00000, 0.34902],	1.5 ,	2   ,	'Rutherfordium'),
-'DB':	Element([0.81961, 0.00000, 0.30980],	1.5 ,	2   ,	'Dubnium'   ),
-'SG':	Element([0.85098, 0.00000, 0.27059],	1.5 ,	2   ,	'Seaborgium'),
-'BH':	Element([0.87843, 0.00000, 0.21961],	1.5 ,	2   ,	'Bohrium'   ),
-'HS':	Element([0.90196, 0.00000, 0.18039],	1.5 ,	2   ,	'Hassium'   ),
-'MT':	Element([0.92157, 0.00000, 0.14902],	1.5 ,	2   ,	'Meitnerium'),
-'DS':	Element([0.93725, 0.00000, 0.12157],	1.5 ,	2   ,	'Darmstadtium')
+    "H" : Element((1.00000, 1.00000, 1.00000), 0.23, 1.09, "Hydrogen"     ),
+    "HE": Element((0.85098, 1.00000, 1.00000), 1.5 , 1.4 , "Helium"       ),
+    "LI": Element((0.80000, 0.50196, 1.00000), 1.28, 1.82, "Lithium"      ),
+    "BE": Element((0.76078, 1.00000, 0.00000), 0.96, 2   , "Beryllium"    ),
+    "B" : Element((1.00000, 0.70980, 0.70980), 0.83, 2   , "Boron"        ),
+    "C" : Element((0.56471, 0.56471, 0.56471), 0.68, 1.7 , "Carbon"       ),
+    "N" : Element((0.18824, 0.31373, 0.97255), 0.68, 1.55, "Nitrogen"     ),
+    "O" : Element((1.00000, 0.05098, 0.05098), 0.68, 1.52, "Oxygen"       ),
+    "F" : Element((0.56471, 0.87843, 0.31373), 0.64, 1.47, "Fluorine"     ),
+    "NE": Element((0.70196, 0.89020, 0.96078), 1.5 , 1.54, "Neon"         ),
+    "NA": Element((0.67059, 0.36078, 0.94902), 1.66, 2.27, "Sodium"       ),
+    "MG": Element((0.54118, 1.00000, 0.00000), 1.41, 1.73, "Magnesium"    ),
+    "AL": Element((0.74902, 0.65098, 0.65098), 1.21, 2   , "Aluminum"     ),
+    "SI": Element((0.94118, 0.78431, 0.62745), 1.2 , 2.1 , "Silicon"      ),
+    "P" : Element((1.00000, 0.50196, 0.00000), 1.05, 1.8 , "Phosphorus"   ),
+    "S" : Element((1.00000, 1.00000, 0.18824), 1.02, 1.8 , "Sulfur"       ),
+    "CL": Element((0.12157, 0.94118, 0.12157), 0.99, 1.75, "Chlorine"     ),
+    "AR": Element((0.50196, 0.81961, 0.89020), 1.51, 1.88, "Argon"        ),
+    "K" : Element((0.56078, 0.25098, 0.83137), 2.03, 2.75, "Potassium"    ),
+    "CA": Element((0.23922, 1.00000, 0.00000), 1.76, 2   , "Calcium"      ),
+    "SC": Element((0.90196, 0.90196, 0.90196), 1.7 , 2   , "Scandium"     ),
+    "TI": Element((0.74902, 0.76078, 0.78039), 1.6 , 2   , "Titanium"     ),
+    "V" : Element((0.65098, 0.65098, 0.67059), 1.53, 2   , "Vanadium"     ),
+    "CR": Element((0.54118, 0.60000, 0.78039), 1.39, 2   , "Chromium"     ),
+    "MN": Element((0.61176, 0.47843, 0.78039), 1.61, 2   , "Manganese"    ),
+    "FE": Element((0.87843, 0.40000, 0.20000), 1.52, 2   , "Iron"         ),
+    "CO": Element((0.94118, 0.56471, 0.62745), 1.26, 2   , "Cobalt"       ),
+    "NI": Element((0.31373, 0.81569, 0.31373), 1.24, 1.63, "Nickel"       ),
+    "CU": Element((0.78431, 0.50196, 0.20000), 1.32, 1.4 , "Copper"       ),
+    "ZN": Element((0.49020, 0.50196, 0.69020), 1.22, 1.39, "Zinc"         ),
+    "GA": Element((0.76078, 0.56078, 0.56078), 1.22, 1.87, "Gallium"      ),
+    "GE": Element((0.40000, 0.56078, 0.56078), 1.17, 2   , "Germanium"    ),
+    "AS": Element((0.74118, 0.50196, 0.89020), 1.21, 1.85, "Arsenic"      ),
+    "SE": Element((1.00000, 0.63137, 0.00000), 1.22, 1.9 , "Selenium"     ),
+    "BR": Element((0.65098, 0.16078, 0.16078), 1.21, 1.85, "Bromine"      ),
+    "KR": Element((0.36078, 0.72157, 0.81961), 1.5 , 2.02, "Krypton"      ),
+    "RB": Element((0.43922, 0.18039, 0.69020), 2.2 , 2   , "Rubidium"     ),
+    "SR": Element((0.00000, 1.00000, 0.00000), 1.95, 2   , "Strontium"    ),
+    "Y" : Element((0.58039, 1.00000, 1.00000), 1.9 , 2   , "Yttrium"      ),
+    "ZR": Element((0.58039, 0.87843, 0.87843), 1.75, 2   , "Zirconium"    ),
+    "NB": Element((0.45098, 0.76078, 0.78824), 1.64, 2   , "Niobium"      ),
+    "MO": Element((0.32941, 0.70980, 0.70980), 1.54, 2   , "Molybdenum"   ),
+    "TC": Element((0.23137, 0.61961, 0.61961), 1.47, 2   , "Technetium"   ),
+    "RU": Element((0.14118, 0.56078, 0.56078), 1.46, 2   , "Ruthenium"    ),
+    "RH": Element((0.03922, 0.49020, 0.54902), 1.45, 2   , "Rhodium"      ),
+    "PD": Element((0.00000, 0.41176, 0.52157), 1.39, 1.63, "Palladium"    ),
+    "AG": Element((0.75294, 0.75294, 0.75294), 1.45, 1.72, "Silver"       ),
+    "CD": Element((1.00000, 0.85098, 0.56078), 1.44, 1.58, "Cadmium"      ),
+    "IN": Element((0.65098, 0.45882, 0.45098), 1.42, 1.93, "Indium"       ),
+    "SN": Element((0.40000, 0.50196, 0.50196), 1.39, 2.17, "Tin"          ),
+    "SB": Element((0.61961, 0.38824, 0.70980), 1.39, 2   , "Antimony"     ),
+    "TE": Element((0.83137, 0.47843, 0.00000), 1.47, 2.06, "Tellurium"    ),
+    "I" : Element((0.58039, 0.00000, 0.58039), 1.4 , 1.98, "Iodine"       ),
+    "XE": Element((0.25882, 0.61961, 0.69020), 1.5 , 2.16, "Xenon"        ),
+    "CS": Element((0.34118, 0.09020, 0.56078), 2.44, 2   , "Cesium"       ),
+    "BA": Element((0.00000, 0.78824, 0.00000), 2.15, 2   , "Barium"       ),
+    "LA": Element((0.43922, 0.83137, 1.00000), 2.07, 2   , "Lanthanum"    ),
+    "CE": Element((1.00000, 1.00000, 0.78039), 2.04, 2   , "Cerium"       ),
+    "PR": Element((0.85098, 1.00000, 0.78039), 2.03, 2   , "Praseodymium" ),
+    "ND": Element((0.78039, 1.00000, 0.78039), 2.01, 2   , "Neodymium"    ),
+    "PM": Element((0.63922, 1.00000, 0.78039), 1.99, 2   , "Promethium"   ),
+    "SM": Element((0.56078, 1.00000, 0.78039), 1.98, 2   , "Samarium"     ),
+    "EE": Element((0.38039, 1.00000, 0.78039), 1.98, 2   , "Europium"     ),
+    "GD": Element((0.27059, 1.00000, 0.78039), 1.96, 2   , "Gadolinium"   ),
+    "TB": Element((0.18824, 1.00000, 0.78039), 1.94, 2   , "Terbium"      ),
+    "DY": Element((0.12157, 1.00000, 0.78039), 1.92, 2   , "Dysprosium"   ),
+    "HO": Element((0.00000, 1.00000, 0.61176), 1.92, 2   , "Holmium"      ),
+    "ER": Element((0.00000, 0.90196, 0.45882), 1.89, 2   , "Erbium"       ),
+    "TM": Element((0.00000, 0.83137, 0.32157), 1.9 , 2   , "Thulium"      ),
+    "YB": Element((0.00000, 0.74902, 0.21961), 1.87, 2   , "Ytterbium"    ),
+    "LU": Element((0.00000, 0.67059, 0.14118), 1.87, 2   , "Lutetium"     ),
+    "HF": Element((0.30196, 0.76078, 1.00000), 1.75, 2   , "Hafnium"      ),
+    "TA": Element((0.30196, 0.65098, 1.00000), 1.7 , 2   , "Tantalum"     ),
+    "W" : Element((0.12941, 0.58039, 0.83922), 1.62, 2   , "Tungsten"     ),
+    "RE": Element((0.14902, 0.49020, 0.67059), 1.51, 2   , "Rhenium"      ),
+    "OS": Element((0.14902, 0.40000, 0.58824), 1.44, 2   , "Osmium"       ),
+    "IR": Element((0.09020, 0.32941, 0.52941), 1.41, 2   , "Iridium"      ),
+    "PT": Element((0.81569, 0.81569, 0.87843), 1.36, 1.72, "Platinum"     ),
+    "AU": Element((1.00000, 0.81961, 0.13725), 1.5 , 1.66, "Gold"         ),
+    "HG": Element((0.72157, 0.72157, 0.81569), 1.32, 1.55, "Mercury"      ),
+    "TL": Element((0.65098, 0.32941, 0.30196), 1.45, 1.96, "Thallium"     ),
+    "PB": Element((0.34118, 0.34902, 0.38039), 1.46, 2.02, "Lead"         ),
+    "BI": Element((0.61961, 0.30980, 0.70980), 1.48, 2   , "Bismuth"      ),
+    "PO": Element((0.67059, 0.36078, 0.00000), 1.4 , 2   , "Polonium"     ),
+    "AT": Element((0.45882, 0.30980, 0.27059), 1.21, 2   , "Astatine"     ),
+    "RN": Element((0.25882, 0.50980, 0.58824), 1.5 , 2   , "Radon"        ),
+    "FR": Element((0.25882, 0.00000, 0.40000), 2.6 , 2   , "Francium"     ),
+    "RA": Element((0.00000, 0.49020, 0.00000), 2.21, 2   , "Radium"       ),
+    "AC": Element((0.43922, 0.67059, 0.98039), 2.15, 2   , "Actinium"     ),
+    "TH": Element((0.00000, 0.72941, 1.00000), 2.06, 2   , "Thorium"      ),
+    "PA": Element((0.00000, 0.63137, 1.00000), 2   , 2   , "Protactinium" ),
+    "U" : Element((0.00000, 0.56078, 1.00000), 1.96, 1.86, "Uranium"      ),
+    "NP": Element((0.00000, 0.50196, 1.00000), 1.9 , 2   , "Neptunium"    ),
+    "PU": Element((0.00000, 0.41961, 1.00000), 1.87, 2   , "Plutonium"    ),
+    "AM": Element((0.32941, 0.36078, 0.94902), 1.8 , 2   , "Americium"    ),
+    "CM": Element((0.47059, 0.36078, 0.89020), 1.69, 2   , "Curium"       ),
+    "BK": Element((0.54118, 0.30980, 0.89020), 1.54, 2   , "Berkelium"    ),
+    "CF": Element((0.63137, 0.21176, 0.83137), 1.83, 2   , "Californium"  ),
+    "ES": Element((0.70196, 0.12157, 0.83137), 1.5 , 2   , "Einsteinium"  ),
+    "FM": Element((0.70196, 0.12157, 0.72941), 1.5 , 2   , "Fermium"      ),
+    "MD": Element((0.70196, 0.05098, 0.65098), 1.5 , 2   , "Mendelevium"  ),
+    "NO": Element((0.74118, 0.05098, 0.52941), 1.5 , 2   , "Nobelium"     ),
+    "LR": Element((0.78039, 0.00000, 0.40000), 1.5 , 2   , "Lawrencium"   ),
+    "RF": Element((0.80000, 0.00000, 0.34902), 1.5 , 2   , "Rutherfordium"),
+    "DB": Element((0.81961, 0.00000, 0.30980), 1.5 , 2   , "Dubnium"      ),
+    "SG": Element((0.85098, 0.00000, 0.27059), 1.5 , 2   , "Seaborgium"   ),
+    "BH": Element((0.87843, 0.00000, 0.21961), 1.5 , 2   , "Bohrium"      ),
+    "HS": Element((0.90196, 0.00000, 0.18039), 1.5 , 2   , "Hassium"      ),
+    "MT": Element((0.92157, 0.00000, 0.14902), 1.5 , 2   , "Meitnerium"   ),
+    "DS": Element((0.93725, 0.00000, 0.12157), 1.5 , 2   , "Darmstadtium" )
 }
 
-def load_pdb(filepath, context, atom_size, scene_scale, atom_subdivisions,
-             retain_alts, multi_models, multimers):
+
+def load_pdb(context,
+             filepath="",
+             atom_size=1.0,
+             scene_scale=1.0,
+             atom_subdivisions=3,
+             retain_alts=False,
+             multi_models=False,
+             multimers=False,
+             ):
+
+    scene = context.scene
 
     file = open(filepath, 'r')
     lines = file.readlines()
@@ -216,20 +236,21 @@ def load_pdb(filepath, context, atom_size, scene_scale, atom_subdivisions,
     chain_list = []
     mat_list = []
 
-#Parse data
-    
+    # -------------------------------------------------------------------------
+    # Parse data
+
     for line in lines:
-#        print(line)
+        # print(line)
         if line[:6] == 'COMPND':
             if line[11:17] == 'CHAIN:':
                 s = 17
                 for i in range(1, (len(line[17:]) + 1)):
-                    if line[16+i:17+i] == ',':
-                        chain_id = line[s:16+i].strip()
+                    if line[16 + i:17 + i] == ',':
+                        chain_id = line[s:16 + i].strip()
                         chain_list.append(chain_id)
                         s = 17 + i
-                    elif line[16+i:17+i] == ';':
-                        chain_id = line[s:16+i].strip()
+                    elif line[16 + i:17 + i] == ';':
+                        chain_id = line[s:16 + i].strip()
                         chain_list.append(chain_id)
                         break
                     elif i == len(line[17:]):
@@ -240,8 +261,8 @@ def load_pdb(filepath, context, atom_size, scene_scale, atom_subdivisions,
                 biomolecule_flag = True
                 s = 23
                 for i in range(1, (len(line[23:]) + 1)):
-                    if line[22+i:23+i] == ',':
-                        bm_serial = int(line[s:22+i])
+                    if line[22 + i:23 + i] == ',':
+                        bm_serial = int(line[s:22 + i])
                         biomolecule_list[bm_serial] = Biomolecule(bm_serial)
                         s = 23 + i
                     elif i == len(line[23:]):
@@ -255,9 +276,9 @@ def load_pdb(filepath, context, atom_size, scene_scale, atom_subdivisions,
                 s = 41
                 cur_chain_list = []
                 for i in range(1, (len(line[41:]) + 1)):
-                    if line[40+i:41+i] == ',':
-                        cur_chain_list.append(line[s:40+i].strip())
-                        s = 41+i
+                    if line[40 + i:41 + i] == ',':
+                        cur_chain_list.append(line[s:40 + i].strip())
+                        s = 41 + i
                     elif i == len(line[41:]):
                         cur_chain_list.append(line[s:].strip())
                 cur_biomolecule.chain_transforms[tuple(cur_chain_list)] = []
@@ -266,14 +287,13 @@ def load_pdb(filepath, context, atom_size, scene_scale, atom_subdivisions,
                     row1 = [float(line[24:33]), float(line[34:43]),
                             float(line[44:53]), float(line[60:68])]
                 elif line[18:19] == '2':
-                    row2 =[float(line[24:33]), float(line[34:43]),
+                    row2 = [float(line[24:33]), float(line[34:43]),
                             float(line[44:53]), float(line[60:68])]
                 elif line[18:19] == '3':
                     row3 = [float(line[24:33]), float(line[34:43]),
                             float(line[44:53]), float(line[60:68])]
                     cur_biomolecule.chain_transforms[tuple(cur_chain_list)].append([row1, row2, row3])
-                    
-                        
+
         elif line[:5] == 'MODEL':
             model_id = int(line[10:14])
             model_list[model_id] = Model(model_id)
@@ -305,142 +325,153 @@ def load_pdb(filepath, context, atom_size, scene_scale, atom_subdivisions,
             tempfactor = float(line[60:66])
             element = line[76:78].strip()
             charge = line[78:80].strip()
-            '''print('******************************************************************')
+
+            '''
+            print('******')
             print('serial       : ' )
-            print(serial) 
-            print('name         : ' ) 
-            print(name) 
-            print('altloc       : ' ) 
-            print(altloc) 
-            print('resname      : ' ) 
-            print(resname) 
+            print(serial)
+            print('name         : ' )
+            print(name)
+            print('altloc       : ' )
+            print(altloc)
+            print('resname      : ' )
+            print(resname)
             print('chainid      : ' )
-            print(chainid) 
+            print(chainid)
             print('resseq       : ' )
-            print(resseq) 
+            print(resseq)
             print('icode        : ' )
-            print(icode) 
+            print(icode)
             print('x            : ' )
-            print(x) 
+            print(x)
             print('y            : ' )
-            print(y) 
+            print(y)
             print('z            : ' )
-            print(z) 
+            print(z)
             print('occupancy    : ' )
-            print(occupancy) 
+            print(occupancy)
             print('tempfactor   : ' )
-            print(tempfactor) 
+            print(tempfactor)
             print('element      : ' )
-            print(element) 
+            print(element)
             print('charge       : ' )
-            print(charge) 
-            print('******************************************************************')'''
+            print(charge)
+            print('******')
+            '''
+
             cur_model.chains[chainid].atoms[serial] = Atom(serial, name, altloc,
                                                            resname, chainid,
                                                            resseq, icode,
                                                            x, y, z, occupancy,
                                                            tempfactor, element,
                                                            charge)
-    
 
     if (not multimers) or (not biomolecule_flag):
-        #Create a default biomolecule w/ all chains and identity transform
-        #Overwrites original biomolecule_list
+        # Create a default biomolecule w/ all chains and identity transform
+        # Overwrites original biomolecule_list
         biomolecule_flag = True
-        biomolecule_list = {1:Biomolecule(1)}
+        biomolecule_list = {1: Biomolecule(1)}
         biomolecule_list[1].chain_transforms[tuple(chain_list)] = []
         biomolecule_list[1].chain_transforms[tuple(chain_list)].append([[1, 0, 0, 0],
                                                                         [0, 1, 0, 0],
                                                                         [0, 0, 1, 0]])
-        
-#Create atom mesh template
+
+    # -------------------------------------------------------------------------
+    # Create atom mesh template
+    bpy.ops.object.select_all(action='DESELECT')
+
     bpy.ops.mesh.primitive_ico_sphere_add(subdivisions=atom_subdivisions,
                                           size=(atom_size * scene_scale))
     bpy.ops.object.shade_smooth()
-    atom_mesh = bpy.context.active_object.data
+    atom_obj = scene.objects.active
+    atom_mesh = atom_obj.data
     atom_mesh.name = 'Atom_Template'
-    bpy.ops.object.delete()
+    scene.objects.unlink(atom_obj)
+    bpy.data.objects.remove(atom_obj)
 
-    layers = bpy.context.scene.layers
+    layers = scene.layers
 
-#After parsing and preparing the templates, generate the output
+    # After parsing and preparing the templates, generate the output
     for model_id, model in model_list.items():
         if (not multi_models) and model_id != 1:
             break
 
         for bm_serial, biomolecule in biomolecule_list.items():
-            biom_mesh = bpy.data.meshes.new('Biomolecule' + str(bm_serial) + '.' + 
-                                        str(model_id))
-            cur_biom = bpy.data.objects.new('Biomolecule' + str(bm_serial) +
-                                               '.' + str(model_id), biom_mesh)
-            bpy.context.scene.objects.link(cur_biom)
-        
+            biom_mesh_name = "Biomolecule%d.%d" % (bm_serial, model_id)
+            biom_mesh = bpy.data.meshes.new(biom_mesh_name)
+            cur_biom = bpy.data.objects.new(biom_mesh_name, biom_mesh)
+            scene.objects.link(cur_biom)
+
             for chain_clones, transforms in biomolecule.chain_transforms.items():
                 for chain in chain_clones:
 
                     for transform in transforms:
-                        #rotations
+                        # rotations
                         row1 = transform[0][0:3]
                         row2 = transform[1][0:3]
                         row3 = transform[2][0:3]
-                        #translations
+                        # translations
                         dx = transform[0][3]
                         dy = transform[1][3]
                         dz = transform[2][3]
 
                         for serial, atom in model.chains[chain].atoms.items():
-                            #Prunes alternative locations for the atoms
-                            #(should pick the one with highest occupancy but doesn't)
+                            # Prunes alternative locations for the atoms
+                            # (should pick the one with highest occupancy but doesn't)
                             if (atom.altloc == ' ' or atom.altloc == 'A') or retain_alts:
 
                                 element = atom_data[atom.element].name
 
-                                #Generate master element models
+                                # Generate master element models
                                 if element not in mat_list:
 
-                                    #Create a master atom
+                                    # Create a master atom
                                     mesh = atom_mesh.copy()
                                     mesh.name = element
                                     mat = bpy.data.materials.new(element)
                                     mat.diffuse_color = atom_data[atom.element].color
                                     mesh.materials.append(mat)
                                     master_atom = bpy.data.objects.new(element, mesh)
-                                    master_atom.scale = [atom_data[atom.element].vdw_radius]*3
+                                    master_atom.scale = [atom_data[atom.element].vdw_radius] * 3
                                     master_atom.layers = layers
-                                    master_atom.name = element
-                                    bpy.context.scene.objects.link(master_atom)
+                                    master_atom.name = element  # why set again?
+                                    scene.objects.link(master_atom)
 
                                     mat_list.append(element)
                                 else:
                                     pass
 
-                                #Generate element vertex groups
+                                # Generate element vertex groups
                                 if element not in cur_biom.vertex_groups:
-                                    cur_vert_group = cur_biom.vertex_groups.new(element) 
+                                    cur_vert_group = cur_biom.vertex_groups.new(element)
                                     #Adds a key in the vert_group_count
                                     biomolecule.vert_group_counts[cur_vert_group] = 0
-                    
+
                                 else:
                                     cur_vert_group = cur_biom.vertex_groups[element]
 
-                #Generate particle systems (can be merged with vertex group generator)
+                                # Generate particle systems
+                                # (can be merged with vertex group generator)
                                 if element not in cur_biom.particle_systems:
-                                    bpy.context.scene.objects.active = cur_biom
+                                    scene.objects.active = cur_biom
                                     bpy.ops.object.particle_system_add()
-                                    cur_particle = cur_biom.particle_systems.active
-                                    cur_particle.name = element
-                                    cur_particle.settings.name = (element + '.' + str(bm_serial) + '.' + str(model_id))
-                                    cur_particle.settings.frame_start = 0
-                                    cur_particle.settings.frame_end = 0
-                                    cur_particle.settings.lifetime = 10000
-                                    cur_particle.settings.emit_from = 'VERT'
-                                    cur_particle.settings.use_emit_random = False
-                                    cur_particle.settings.normal_factor = 0
-                                    cur_particle.settings.particle_size = 1
-                                    cur_particle.settings.render_type = 'OBJECT' 
-                                    cur_particle.settings.dupli_object = bpy.data.objects[element]
-                                    cur_particle.settings.effector_weights.gravity = 0
-                                    cur_particle.vertex_group_density = element
+
+                                    psys = cur_biom.particle_systems.active
+                                    part = psys.settings
+
+                                    psys.name = element
+                                    part.name = "%s.%d.%d" % (element, bm_serial, model_id)
+                                    part.frame_start = 0
+                                    part.frame_end = 0
+                                    part.lifetime = 10000
+                                    part.emit_from = 'VERT'
+                                    part.use_emit_random = False
+                                    part.normal_factor = 0
+                                    part.particle_size = 1
+                                    part.render_type = 'OBJECT'
+                                    part.dupli_object = bpy.data.objects[element]
+                                    part.effector_weights.gravity = 0
+                                    psys.vertex_group_density = element
 
                                 biomolecule.vert_group_index[biomolecule.atom_count] = cur_vert_group
                                 biomolecule.vert_group_counts[cur_vert_group] += 1
@@ -461,5 +492,4 @@ def load_pdb(filepath, context, atom_size, scene_scale, atom_subdivisions,
                 vert_group.add(aa, 1, "ADD")
 
             for vert_group, count in biomolecule.vert_group_counts.items():
-                bpy.data.particles[vert_group.name + '.' + str(bm_serial) + '.' + str(model_id)].count = count
-
+                bpy.data.particles["%s.%d.%d" % (vert_group.name, bm_serial, model_id)].count = count