diff --git a/io_mesh_pdb/__init__.py b/io_mesh_pdb/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..b8b4b98ca121d7ad910a72e4a371a52be9d2dcd7
--- /dev/null
+++ b/io_mesh_pdb/__init__.py
@@ -0,0 +1,130 @@
+# ##### 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 #####
+
+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, max=5,
+ default=1,
+ )
+ scene_scale = FloatProperty(
+ name="Scene Scale Factor",
+ description="Number of Blender units equivalent to 1 angstrom",
+ min=0, max=10,
+ default=1,
+ )
+
+ 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)
+ 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
new file mode 100644
index 0000000000000000000000000000000000000000..6f81c8475b231e2c29a07d20a2807884dd633ca4
--- /dev/null
+++ b/io_mesh_pdb/import_pdb.py
@@ -0,0 +1,465 @@
+# ##### 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 #####
+
+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(filepath, context, atom_size, scene_scale, atom_subdivisions,
+ retain_alts, multi_models, multimers):
+
+ file = open(filepath, 'r')
+ lines = file.readlines()
+ file.close()
+
+ model_list = {}
+ model_flag = False
+ biomolecule_flag = False
+ biomolecule_list = {}
+ chain_list = []
+ mat_list = []
+
+#Parse data
+
+ for line in lines:
+# 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)
+
+
+ if (not multimers) or (not biomolecule_flag):
+ #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].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
+ 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_mesh.name = 'Atom_Template'
+ bpy.ops.object.delete()
+
+ layers = bpy.context.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 = 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)
+
+ 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
+ bpy.context.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:
+ bpy.context.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
+
+ 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[vert_group.name + '.' + str(bm_serial) + '.' + str(model_id)].count = count
+