diff --git a/io_mesh_pdb/__init__.py b/io_mesh_pdb/__init__.py
deleted file mode 100644
index 3a2068f8152e9f9b092ac01912f3afc3f8e86ac1..0000000000000000000000000000000000000000
--- 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 6b39a78cdd08cfae080c565cc527f9520cee8bbb..0000000000000000000000000000000000000000
--- 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