removing this PDB importer in preparation to replace with a re-written one which supports more file types

2 files changed, 0 insertions, 628 deletions

diff --git a/io_mesh_pdb/__init__.py b/io_mesh_pdb/__init__.py
deleted file mode 100644
index 3a2068f8..00000000
--- a/io_mesh_pdb/__init__.py
+++ /dev/null
@@ -1,132 +0,0 @@
-# ##### BEGIN GPL LICENSE BLOCK #####
-#
-#  This program is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU General Public License
-#  as published by the Free Software Foundation; either version 2
-#  of the License, or (at your option) any later version.
-#
-#  This program is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#  GNU General Public License for more details.
-#
-#  You should have received a copy of the GNU General Public License
-#  along with this program; if not, write to the Free Software Foundation,
-#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-#
-# ##### END GPL LICENSE BLOCK #####
-
-# <pep8-80 compliant>
-
-bl_info = {
-    "name": "Import/Export: PDB format",
-    "author": "Mariusz Maximus & Jong89",
-    "version": (0, 9, 0),
-    "blender": (2, 6, 0),
-    "api": 35616,
-    "location": "File > Import/Export > PDB",
-    "description": "Import PDB files",
-    "warning": "",
-    "wiki_url": "http://blenderartists.org/forum/showthread.php?t=194336",
-    "tracker_url": "http://blenderartists.org/forum/showthread.php?t=194336",
-    "category": "Import-Export"}
-
-# @todo write the wiki page
-
-# To support reload properly, try to access a package var,
-# if it's there, reload everything
-if "bpy" in locals():
-    import imp
-    if "import_pdb" in locals():
-        imp.reload(import_pdb)
-
-
-import bpy
-from bpy.props import (StringProperty,
-                       BoolProperty,
-                       IntProperty,
-                       FloatProperty,
-                       )
-
-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'}
-
-    filename_ext = ".pdb"
-    filter_glob = StringProperty(default="*.pdb", options={'HIDDEN'})
-
-    filepath = StringProperty(
-            name="File Path",
-            description="Filepath used for importing the PDB file",
-            maxlen=1024,
-            )
-    multi_models = BoolProperty(
-            name="Import all models",
-            description="Import all alternative structures listed in file",
-            default=False,
-            )
-    multimers = BoolProperty(
-            name="Import Biomolecules",
-            description="Import all file-listed biomolecules and multimers, "
-                        "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",
-            default=False,
-            )
-    atom_subdivisions = IntProperty(
-            name="Atom Subdivisions",
-            description="Number of icosphere subdivisions for the atoms",
-            min=1, max=6,
-            default=3,
-            )
-    atom_size = FloatProperty(
-            name="Atom Size",
-            description="Multiplier for the van der Waals radius of the atoms",
-            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=0.0, max=10.0,
-            default=1.0,
-            )
-
-    def execute(self, context):
-        from . import import_pdb
-        keywords = self.as_keywords(ignore=("filter_glob", ))
-        import_pdb.load_pdb(context, **keywords)
-        return {'FINISHED'}
-
-    def invoke(self, context, event):
-        wm = context.window_manager
-        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)
-
-if __name__ == '__main__':
-    register()
diff --git a/io_mesh_pdb/import_pdb.py b/io_mesh_pdb/import_pdb.py
deleted file mode 100644
index 6b39a78c..00000000
--- a/io_mesh_pdb/import_pdb.py
+++ /dev/null
@@ -1,496 +0,0 @@
-# ##### BEGIN GPL LICENSE BLOCK #####
-#
-#  This program is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU General Public License
-#  as published by the Free Software Foundation; either version 2
-#  of the License, or (at your option) any later version.
-#
-#  This program is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#  GNU General Public License for more details.
-#
-#  You should have received a copy of the GNU General Public License
-#  along with this program; if not, write to the Free Software Foundation,
-#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-#
-# ##### 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)"""
-    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)"""
-
-    def __init__(self, serial, name, altloc, resname, chainid, resseq, icode,
-                 x, y, z, occupancy, tempfactor, element, charge):
-        self.serial = serial
-        self.name = name
-        self.altloc = altloc
-        self.resname = resname
-        self.chainid = chainid
-        self.resseq = resseq
-        self.icode = icode
-        self.x = x
-        self.y = y
-        self.z = z
-        self.occupancy = occupancy
-        self.tempfactor = tempfactor
-        self.element = element
-        self.charge = charge
-
-
-# collection of biomolecules based on model
-# all chains in model stored here
-class Model:
-    '''Model class'''
-    def __init__(self, model_id):
-        self.model_id = model_id
-        self.atoms = {}
-        self.atom_count = 0
-        self.vert_list = []
-        # 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}
-        self.vert_group_counts = {}
-        self.chains = {}
-
-
-# new object level class
-class Biomolecule:
-    '''Biomolecule'''
-    def __init__(self, serial):
-        self.serial = serial
-        self.atom_count = 0
-        self.vert_list = []
-        self.vert_group_index = {}
-        self.vert_group_counts = {}
-        self.chain_transforms = {}
-
-
-# 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,
-
-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" )
-}
-
-
-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')
-
-    model_list = {}
-    model_flag = False
-    biomolecule_flag = False
-    biomolecule_list = {}
-    chain_list = []
-    mat_list = []
-
-    # -------------------------------------------------------------------------
-    # Parse data
-
-    for line in file:
-        # 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()
-                        chain_list.append(chain_id)
-                        s = 17 + i
-                    elif line[16 + i:17 + i] == ';':
-                        chain_id = line[s:16 + i].strip()
-                        chain_list.append(chain_id)
-                        break
-                    elif i == len(line[17:]):
-                        chain_id = line[s:].strip()
-                        chain_list.append(chain_id)
-        elif line[:10] == 'REMARK 300':
-            if line[11:23] == 'BIOMOLECULE:':
-                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])
-                        biomolecule_list[bm_serial] = Biomolecule(bm_serial)
-                        s = 23 + i
-                    elif i == len(line[23:]):
-                        bm_serial = int(line[s:])
-                        biomolecule_list[bm_serial] = Biomolecule(bm_serial)
-
-        elif line[:10] == 'REMARK 350':
-            if line[11:23] == 'BIOMOLECULE:':
-                cur_biomolecule = biomolecule_list[int(line[23:].strip())]
-            elif line[11:41] == 'APPLY THE FOLLOWING TO CHAINS:':
-                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
-                    elif i == len(line[41:]):
-                        cur_chain_list.append(line[s:].strip())
-                cur_biomolecule.chain_transforms[tuple(cur_chain_list)] = []
-            elif line[13:18] == 'BIOMT':
-                if line[18:19] == '1':
-                    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]),
-                            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)
-            cur_model = model_list[model_id]
-            model_flag = True
-            for chain in chain_list:
-                cur_model.chains[chain] = Chain(chain)
-        elif line[:6] == 'ENDMDL':
-            cur_model = None
-        elif line[:4] == 'ATOM':
-            if not model_flag:
-                model_list[1] = Model(1)
-                cur_model = model_list[1]
-                model_flag = True
-                for chain in chain_list:
-                    cur_model.chains[chain] = Chain(chain)
-
-            serial = int(line[6:11])
-            name = line[12:16].strip()
-            altloc = line[16:17]
-            resname = line[17:20]
-            chainid = line[21:22]
-            resseq = int(line[22:26])
-            icode = line[26:28].strip()
-            x = float(line[30:38]) * scene_scale
-            y = float(line[38:46]) * scene_scale
-            z = float(line[46:54]) * scene_scale
-            occupancy = float(line[54:60])
-            tempfactor = float(line[60:66])
-            element = line[76:78].strip()
-            charge = line[78:80].strip()
-
-            '''
-            print('******')
-            print('serial       : ' )
-            print(serial)
-            print('name         : ' )
-            print(name)
-            print('altloc       : ' )
-            print(altloc)
-            print('resname      : ' )
-            print(resname)
-            print('chainid      : ' )
-            print(chainid)
-            print('resseq       : ' )
-            print(resseq)
-            print('icode        : ' )
-            print(icode)
-            print('x            : ' )
-            print(x)
-            print('y            : ' )
-            print(y)
-            print('z            : ' )
-            print(z)
-            print('occupancy    : ' )
-            print(occupancy)
-            print('tempfactor   : ' )
-            print(tempfactor)
-            print('element      : ' )
-            print(element)
-            print('charge       : ' )
-            print(charge)
-            print('******')
-            '''
-
-            cur_model.chains[chainid].atoms[serial] = Atom(serial, name, altloc,
-                                                           resname, chainid,
-                                                           resseq, icode,
-                                                           x, y, z, occupancy,
-                                                           tempfactor, element,
-                                                           charge)
-
-    file.close()
-
-    if (not multimers) or (not biomolecule_flag):
-        # Create a default biomolecule w/ all chains and identity transform
-        # Overwrites original biomolecule_list
-        biomolecule_flag = True
-        bm_serial = 1
-        biomolecule = Biomolecule(bm_serial)
-        biomolecule.chain_transforms[tuple(chain_list)] = [(((1.0, 0.0, 0.0, 0.0),
-                                                             (0.0, 1.0, 0.0, 0.0),
-                                                             (0.0, 0.0, 1.0, 0.0)))]
-        biomolecule_list = {bm_serial: biomolecule}
-
-    # -------------------------------------------------------------------------
-    # 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_obj = scene.objects.active
-    atom_mesh = atom_obj.data
-    atom_mesh.name = 'Atom_Template'
-    scene.objects.unlink(atom_obj)
-    bpy.data.objects.remove(atom_obj)
-
-    layers = scene.layers
-
-    # 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_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
-                        row1 = transform[0][0:3]
-                        row2 = transform[1][0:3]
-                        row3 = transform[2][0:3]
-                        # 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)
-                            if (atom.altloc == ' ' or atom.altloc == 'A') or retain_alts:
-
-                                element = atom_data[atom.element].name
-
-                                # Generate master element models
-                                if element not in mat_list:
-
-                                    # 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.layers = layers
-                                    master_atom.name = element  # why set again?
-                                    scene.objects.link(master_atom)
-
-                                    mat_list.append(element)
-                                else:
-                                    pass
-
-                                # Generate element vertex groups
-                                if element not in cur_biom.vertex_groups:
-                                    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)
-                                if element not in cur_biom.particle_systems:
-                                    scene.objects.active = cur_biom
-                                    bpy.ops.object.particle_system_add()
-
-                                    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
-                                biomolecule.atom_count += 1
-                                tx = atom.x * row1[0] + atom.y * row1[1] + atom.z * row1[2] + (dx * scene_scale)
-                                ty = atom.x * row2[0] + atom.y * row2[1] + atom.z * row2[2] + (dy * scene_scale)
-                                tz = atom.x * row3[0] + atom.y * row3[1] + atom.z * row3[2] + (dz * scene_scale)
-                                biomolecule.vert_list.extend([tx, ty, tz])
-                            else:
-                                pass
-
-            biom_mesh.vertices.add(biomolecule.atom_count)
-            biom_mesh.vertices.foreach_set('co', biomolecule.vert_list)
-
-            for vert_index, vert_group in biomolecule.vert_group_index.items():
-                aa = []  # neeed array to vertex_groups.assign
-                aa.append(vert_index)
-                vert_group.add(aa, 1, "ADD")
-
-            for vert_group, count in biomolecule.vert_group_counts.items():
-                bpy.data.particles["%s.%d.%d" % (vert_group.name, bm_serial, model_id)].count = count