Newer
Older
# ##### 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.
"""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
"""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
# Dictionary of {vertex group: number of group members}
self.vert_group_counts = {}
self.chains = {}
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 = {}
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,
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
"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')
lines = file.readlines()
file.close()
model_list = {}
model_flag = False
biomolecule_flag = False
biomolecule_list = {}
chain_list = []
mat_list = []
# -------------------------------------------------------------------------
# Parse data
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':
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])
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
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(serial)
print('name : ' )
print(name)
print('altloc : ' )
print(altloc)
print('resname : ' )
print(resname)
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_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.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)
# 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:
row1 = transform[0][0:3]
row2 = transform[1][0:3]
row3 = transform[2][0:3]
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
if element not in mat_list:
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
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.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