-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathmolecule.py
1202 lines (964 loc) · 33 KB
/
molecule.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
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
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
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
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
import bpy
from .base import DummyObject, Material, LazyMaterial
from .collections import ObjectCollection, MaterialCollection
from . import meshes, curves
from . import Blender
from .marching_cube import triangulate, triangulate_par
from .materials import getColor, make_lazy_material, make_glas_material
import numpy as np
import sys,os
sys.path.append(os.getcwd())
from lib import AttrDict, Filter, utils as pyutils, VolumeData
import lib.molecule as pymol
from lib.utils import TimerCollection as Timer
from lib.volume import BoundaryVolumeData
atom_radii_period = {1: 0.4, 2: 0.7, 3: 1.0, 4: 1.3, 5: 1.7, 6:1.8}
def make_atom_material(name):#, color=(0., 0., 1., 1), shader="Glossy", roughness=0.0):
mat = bpy.data.materials.new(name) # create new material
mat.use_nodes = True # use nodes
return mat
"""
def make_atom_material(name, **kw):
print("KWWW", kw)
mat = {
'diffuse_color': (.2, .5, .2)
}
for k, v in mat.items():
kw[k] = v if k not in kw else kw[k]
return make_lazy_material(name, **kw)
"""
def make_lobe_material(name, **kw):
mat = bpy.data.materials.new(name) # create new material
mat.use_nodes = True # use nodes
return mat
Materials = {
None: make_atom_material('DefaultMaterial'),
'Atom': make_atom_material('AtomMaterial'),
'Path': make_glas_material('PathMaterial'),
'Lobe': make_lobe_material('Lobe'),
'Bond': make_lazy_material('Bond'),
'Ring': make_lazy_material('Ring', alpha=0.5),
}
Colors = {
None: getColor('grey'),
'Element': {None: getColor('grey'),
1: getColor('lightgrey'),
6: getColor('darkgrey'),
7: getColor('blue'),
8: getColor('red'),
9: getColor('pink'),
13: getColor('tan'),
15: getColor('tan'),
17: getColor('lightgreen'),
47: getColor('silver'),
77: getColor('silver'),
79: getColor('gold'),
},
'Residue': {'ALA': getColor('grey'),
},
'Path': getColor('red'),
'Ring': { 3: getColor('orange'),
4: getColor('red'),
5: getColor('blue'),
6: getColor('lightgreen'),
},
'IsoSign': { +1: getColor('red'), -1: getColor('blue') },
}
default_options = AttrDict({
'colors': Colors,
'materials': Materials,
'carbon_color': getColor('darkgrey'),
'shader': "Diffuse",
'roughness': 0.5,
'atom_scale': 1.,
'stick_size': 0.2,
'line_size': 0.05,
'stick_resolution': 2,
'ball_resolution': 6,
'atom_size': 'period',
'atom_style': 'Nurbs',
'atom_color': 'Element',
'atom_material': 'Atom',
'bond_twocolor': True,
'bond_style': 'Nurbs',
''
'auto_bonds': False,
'bond_tolerance': 1.2,
'align_com': False,
'path_material': 'Path',
'path_color': 'Path',
'path_size': 0.8,
'path_resolution': 16,
'surface_material': 'Lobe',
'surface_color': getColor('red'),
'ring_material': 'Ring',
'ring_color': 'Ring',
'ring_edge_bevel': 0.02,
'triangulation_method': 'cube',
'volume_material': 'Lobe',
'volume_color': 'IsoSign',
'volume_resolution': 4,
})
def make_options(options, **kw):
kw = AttrDict(kw)
options = AttrDict(options.copy())
rest = AttrDict()
for opt, optval in kw.items():
if opt in options:
options[opt] = optval
else:
rest[opt] = optval
return options, rest
def make_default_options(**kw):
return make_options(default_options, **kw)
def get_option(name, **kw):
return kw[name] if name in kw else (default_options[name] if name in default_options else None)
def make_atom_object(radius, style, resolution):
if style == None or style.lower() == 'dummy' or radius == 0 or radius == None:
obj = DummyObject()
elif style.lower() == 'uvsphere':
obj = meshes.UVsphere(size = radius, subdivisions = resolution**3/2)
obj.addAutoKey('location')
elif style.lower() == 'icosphere':
obj = meshes.Icosphere(size = radius, subdivisions = resolution)
elif style.lower() == 'nurbs':
obj = curves.NurbsSurface(type = 'SPHERE', radius = radius)
elif style.lower() == 'metaball':
obj = meshes.Metaball(type = 'BALL', size = radius)
else:
raise ValueError(style)
obj.addAutoKey('location')
return obj
def make_bond(iobj, jobj, size, style, twocolor, resolution):
if style == None or size == 0 or size == None or style.lower() == 'dummy':
obj = DummyBond(iobj, jobj)
elif twocolor:
obj = TwoColorBond(style, size, resolution, iobj, jobj)
elif style.lower() == 'nurbs':
obj = NurbsBond(size, resolution, iobj, jobj)
else:
raise ValueError(style)
return obj
class TwoColorBond(ObjectCollection):
__slots__ = ['_atom1', '_atom2', '_style']
__overwrites__ = ['name', 'location','atom1','atom2']
def __init__(self, style, size, resolution, atom1, atom2, material = None):
super().__init__("BOND")
self._atom1 = atom1
self._atom2 = atom2
self._style = style.lower()
if style.lower() == 'nurbs':
c1 = curves.NurbsLine("BOND-1", self.atom1.location, self.location)
c2 = curves.NurbsLine("BOND-2", self.atom2.location, self.location)
c2.data.bevel_depth = c1.data.bevel_depth = size
c2.data.bevel_resolution = c1.data.bevel_resolution = resolution
c2.data.fill_mode = c1.data.fill_mode = 'FULL'
c1.addAutoKey('data.splines.points.co', 'hide_viewport', 'hide_render')
c2.addAutoKey('data.splines.points.co', 'hide_viewport', 'hide_render')
else:
raise ValueError(style)
if not material:
c1.material = self.atom1.material
c2.material = self.atom2.material
else:
c1.material = self._material.copy()
#c2.material.diffuse_color = self.atom1.diffuse_color
c1.material = self._material.copy()
#c2.material.diffuse_color = self.atom2.diffuse_color
self.append(c1)
self.append(c2)
@property
def atom1(self): return self._atom1
@atom1.setter
def atom1(self, value): self._atom1 = value
@property
def atom2(self): return self._atom2
@atom2.setter
def atom2(self, value): self._atom2 = value
@property
def location(self):
return (self.atom1.location + self.atom2.location)/2.
@property
def vector(self):
return (self.atom1.location - self.atom2.location)
@property
def length(self):
return self.vector.length
@location.setter
def location(self, _):
raise RuntimeError("Can not set location of nurbs")
@property
def name(self): return self.getobjattr('name')
@name.setter
def name(self, value):
self.setobjattr('name', value)
for i,o in enumerate(self):
o.setobjattr('name', "%s-%d" % (value, i+1))
o.name = "%s-%d" % (value, i+1)
def update(self):
if self._style == 'nurbs':
self[0].update([self.atom1.location, self.location])
self[1].update([self.atom2.location, self.location])
else:
raise ValueError(self._style)
return self
class NurbsBond(curves.Curve):
__slots__ = ['_atom1', '_atom2', '_style']
__overwrites__ = ['name', 'location','atom1','atom2']
def __init__(self, size, resolution, atom1, atom2, material = None):
super().__init__(curves.NurbsLine("BOND", atom1.location, atom2.location))
self.data.bevel_depth = size
self.data.bevel_resolution = resolution
self.data.fill_mode = 'FULL'
self.addAutoKey('data.splines.points.co', 'hide_viewport', 'hide_render')
if material:
self.material = material
else:
self.material = Materials['Bond']
self._atom1 = atom1
self._atom2 = atom2
@property
def atom1(self): return self._atom1
@atom1.setter
def atom1(self, value): self._atom1 = value
@property
def atom2(self): return self._atom2
@atom2.setter
def atom2(self, value): self._atom2 = value
@property
def location(self):
return (self.atom1.location + self.atom2.location)/2.
@property
def vector(self):
return (self.atom1.location - self.atom2.location)
@property
def length(self):
return self.vector.length
def update(self):
super().update([self.atom1.location, self.atom2.location])
return self
class DummyBond(DummyObject):
__slots__ = ['_atom1', '_atom2']
__overwrites__ = ['atom1','atom2']
def __init__(self, atom1, atom2):
super().__init__()
self._atom1 = atom1
self._atom2 = atom2
@property
def atom1(self): return self._atom1
@atom1.setter
def atom1(self, value): self._atom1 = value
@property
def atom2(self): return self._atom2
@atom2.setter
def atom2(self, value): self._atom2 = value
@property
def location(self):
return (self.atom1.location + self.atom2.location)/2.
@property
def vector(self):
return (self.atom1.location - self.atom2.location)
@property
def length(self):
return self.vector.length
def update(self):
super().update([self.atom1.location, self.atom2.location])
return self
class ReprBase(ObjectCollection):
__slots__ = ['options', 'filter', '_materials', 'timer','_matoptions']
kind = None
order_id = 0
def __init__(self, name, *args, **kw):
super().__init__(name)
self.options, kw = make_default_options(**kw)
self.filter = None if 'filter' not in kw else kw['filter']
self._materials = {}
self._matoptions = kw['matoptions'] if 'matoptions' in kw else {}
self.timer = Timer()
def __lt__(self, other):
if other == None: return False
else:
return self.order_id < other.order_id
def __gt__(self, other):
if other == None: return False
else:
return self.order_id > other.order_id
def __contains__(self, item):
if self.filter == None: return True
elif isinstance(self.filter, bool): return self.filter
elif callable(self.filter):
return self.filter(*item)
else:
print("Invalid filter", self.filter)
return False
def option(self, name):
return get_option(name, **self.options)
def color(self, col_type, *args):
colors = self.options.colors
if callable(col_type):
col = col_type(*args)
col_id = "-".join(args)
col_id, col
elif isinstance(col_type, str) and col_type in colors:
colors = colors[col_type]
col_id = col_type
for arg in args:
if isinstance(colors, (str,tuple)):
break
if isinstance(colors, dict) and arg in colors:
if arg == 6:
colors = self.options.carbon_color
else:
colors = colors[arg]
col_id += '-'+ str(arg)
elif None in colors:
colors = colors[None]
else:
colors = self.options.colors[None]
break
if isinstance(colors, tuple) or len(colors) == 4:
col = colors
elif isinstance(colors, str):
col = getColor(col_type)
return col_id, col
elif isinstance(col_type, tuple):
col = col_type
else:
col = getColor(col_type)
return col_type, col
def material(self, mat_type, *args):
materials = self.options.materials
print("MATTYPE", mat_type)
print("MATERIALSS", materials)
if callable(mat_type):
mat = mat_type(*args)
elif isinstance(mat_type, str) and mat_type in materials:
materials = materials[mat_type]
for arg in args:
if isinstance(materials, (Material, LazyMaterial)):
break
elif isinstance(materials, (dict, list, tuple)) and arg in materials:
materials = materials[arg]
else:
materials = self.options.materials[None]
break
if isinstance(materials, (Material, LazyMaterial)):
mat = materials
elif isinstance(materials, str) or callable(materials):
mat = bpy.data.materials[name]
else:
return materials
#raise ValueError(mat_type)
elif isinstance(mat_type, (Material, LazyMaterial)):
mat = mat_type
else:
raise ValueError(mat_type)
return mat
def make_material(self, mat, col, *args):
mat = self.material(mat, *args)
col_id, col = self.color(col, *args)
if len(args) == 1 and type(args[0]) == int and type(col) == dict:
iso = args[0]
col = col[iso]
name = mat.name + "-"+ str(col_id)
shader = self.options.shader
roughness = self.options.roughness
if name not in self._materials:
mat = mat.copy()
mat.node_tree.nodes.remove(mat.node_tree.nodes[1])
print("SHADERSHADERSHADER", shader)
if shader == "Fancy":
print("COLCOLCOLCOLID", col_id.split("-")[1])
if col_id.split("-")[1] == "7":
shader = mat.node_tree.nodes.new(type="ShaderNodeBsdfPrincipled") # create new node
shader.inputs['Roughness'].default_value = 0.00
shader.inputs['Metallic'].default_value = 0.748
shader.inputs['Specular'].default_value = 0.302
print("INPUT", mat.node_tree.nodes.get("Material Output").inputs)
mat_input = mat.node_tree.nodes.get("Material Output").inputs[0]
mat.node_tree.links.new(shader.outputs["BSDF"], mat_input)
mat.name = name
col = [0.187, 0.209, 1.000]
mat.diffuse_color = [col[0], col[1], col[2], 1.] #col
mat.node_tree.nodes[1].inputs[0].default_value = [col[0], col[1], col[2], 1.]
elif col_id.split("-")[1] == "77":
shader = mat.node_tree.nodes.new(type="ShaderNodeBsdfPrincipled") # create new node
shader.inputs['Roughness'].default_value = 0.245
shader.inputs['Metallic'].default_value = 1.000
shader.inputs['Specular'].default_value = 0.5000
print("INPUT", mat.node_tree.nodes.get("Material Output").inputs)
mat_input = mat.node_tree.nodes.get("Material Output").inputs[0]
mat.node_tree.links.new(shader.outputs["BSDF"], mat_input)
mat.name = name
col = [0.800, 0.047, 0.159]
mat.diffuse_color = [col[0], col[1], col[2], 1.] #col
mat.node_tree.nodes[1].inputs[0].default_value = [col[0], col[1], col[2], 1.]
elif col_id.split("-")[1] == "9":
shader = mat.node_tree.nodes.new(type="ShaderNodeBsdfPrincipled") # create new node
shader.inputs['Roughness'].default_value = 0.00
shader.inputs['Metallic'].default_value = 0.748
shader.inputs['Specular'].default_value = 0.302
print("INPUT", mat.node_tree.nodes.get("Material Output").inputs)
mat_input = mat.node_tree.nodes.get("Material Output").inputs[0]
mat.node_tree.links.new(shader.outputs["BSDF"], mat_input)
mat.name = name
col = [0.637, 0.890, 0.000]
mat.diffuse_color = [col[0], col[1], col[2], 1.] #col
mat.node_tree.nodes[1].inputs[0].default_value = [col[0], col[1], col[2], 1.]
else:
shader = mat.node_tree.nodes.new(type="ShaderNodeBsdfGlossy") # create new node
shader.inputs['Roughness'].default_value = 0.00
print("INPUT", mat.node_tree.nodes.get("Material Output").inputs)
mat_input = mat.node_tree.nodes.get("Material Output").inputs[0]
mat.node_tree.links.new(shader.outputs["BSDF"], mat_input)
mat.name = name
if col != None:
if col_id.split("-")[1] == "6":
col = [0.377, 0.377, 0.377]
if col_id.split("-")[1] == "1":
col = [0.8, 0.8, 0.8]
mat.diffuse_color = [col[0], col[1], col[2], 1.] #col
mat.node_tree.nodes[1].inputs[0].default_value = [col[0], col[1], col[2], 1.]
else:
shader = mat.node_tree.nodes.new(type="ShaderNodeBsdf"+shader) # create new node
shader.inputs['Roughness'].default_value = roughness
print("INPUT", mat.node_tree.nodes.get("Material Output").inputs)
mat_input = mat.node_tree.nodes.get("Material Output").inputs[0]
mat.node_tree.links.new(shader.outputs["BSDF"], mat_input)
mat.name = name
if col != None:
print("COLOR", mat)#, mat.diffuse_color)
mat.diffuse_color = [col[0], col[1], col[2], 1.] #col
mat.node_tree.nodes[1].inputs[0].default_value = [col[0], col[1], col[2], 1.]
for k, w in self._matoptions:
mat['k'] = w
self._materials[name] = mat
else:
mat = self._materials[name]
return mat
def create(self, *args, **kw):
return self
def update(self, *args, **kw):
return self
class MoleculeRepr(ReprBase):
__slots__ = ['atom_objects', 'bond_objects', 'ref_atom']
kind = 'MOL'
def __init__(self, name, *args, **kw):
super().__init__(name, *args, **kw)
self.ref_atom = {}
self.atom_objects = {}
self.bond_objects = {}
def key(self, molecule, atom):
key = self.options.atom_color.lower()
if key == 'element':
return atom.number
if key == 'symbol':
return atom.symbol
elif key == 'name':
return atom.name
elif key == 'resnm':
return atom.residue.resnm if atom.residue != None else 'UNK'
else:
return atom.index
def atom_size(self, molecule, atom):
if isinstance(self, StickRepr):
return self.options.stick_size
else:
type = self.options.atom_size
if isinstance(type, (float, int)):
res = float(type)
elif isinstance(type, str):
type = type.lower()
if type == 'period':
res = atom_radii_period[atom.period]
elif type == 'atomic_radius':
res = atom.atomic_radius
elif type == 'vdw_radius':
res = atom.vdw_radius
else:
res = 1.
return max(res * self.options.atom_scale, self.options.stick_size)
def bond_size(self, molecule, iatom, jatom):
if isinstance(self, LineRepr):
return self.options.line_size
else:
return self.options.stick_size
def create(self, molecule, *args, **kw):
print(" Generate Atoms")
atom_mat = self.options.atom_material
atom_col = self.options.atom_color
self.timer.reset('atoms')
wm = Blender.window_manager
wm.progress_begin(0, len(molecule))
for i, (atom, coords) in enumerate(molecule):
if (molecule, atom) in self:
self.timer.tick('atoms')
key = self.key(molecule, atom)
atom_size = self.atom_size(molecule, atom)
name = 'Atom-%04d' % i
if key not in self.ref_atom:
obj = make_atom_object(1, self.options.atom_style, self.options.ball_resolution)
obj.name = name
obj.scale = atom_size
obj.material = self.make_material(atom_mat, atom_col, key)
print(obj.name)
self.ref_atom[key] = obj
else:
obj = self.ref_atom[key].copy()
obj.name = name
obj.scale = atom_size
obj.location = coords
self.append(obj)
self.atom_objects[i] = obj
self.timer.tock('atoms')
wm.progress_update(i)
wm.progress_end()
print(" Generate Bonds")
self.timer.reset('bonds')
nbonds = len(molecule.bonds)
wm.progress_begin(0, nbonds)
bonds = [b for b in molecule.bonds \
if (molecule, molecule.atoms[b[0]]) in self \
or (molecule, molecule.atoms[b[1]]) in self]
nbonds = len(bonds)
for n, (i,j) in enumerate(bonds):
iatom, jatom = molecule.atoms[i], molecule.atoms[j]
irep = (molecule, iatom) in self
jrep = (molecule, jatom) in self
if irep or jrep:
self.timer.tick('bonds')
self.create_bond(molecule, i,j, irep, jrep)
self.timer.tock('bonds')
if nbonds > 100:
if (n % int(0.1*nbonds)) == 0:
print(" %3.0f%% %4d/%d bonds processed (t = %.3f)" \
% (n/float(nbonds)*100, n, nbonds, self.timer['bonds'].total))
wm.progress_update(n)
wm.progress_end()
print(" Added %d atoms and %d bonds" \
% (len(self.atom_objects), len(self.bond_objects)))
print(self.timer)
return super().create(molecule, *args, **kw)
def create_bond(self, molecule, i, j, irep, jrep):
if not irep and not jrep: return None
elif irep and jrep:
ir = jr = self
else:
ir = jr = self
if not irep:
ir = molecule.find_atom_repr(molecule.atoms[i])
if not ir or ir > self: return None
elif not jrep:
jr = molecule.find_atom_repr(molecule.atoms[j])
if not jr or jr > self: return None
print("BONDINDICES", i, j, ir.atom_objects, molecule.atoms, ir)
iobj = ir.atom_objects[i]
jobj = jr.atom_objects[j]
bond_style = self.options.bond_style
bond_reso = 0 if isinstance(self, LineRepr) else self.options.stick_resolution
twocolor = self.options.bond_twocolor
size = self.bond_size(molecule, i, j)
name = 'Bond-%04d-%04d' % (i,j)
print(i,j,bond_style, twocolor, bond_reso)
obj = make_bond(iobj, jobj, size, bond_style, twocolor, bond_reso)
obj.name = name
obj.hide = True
#obj.notify('hide_viewport', 'hide_render', frame=0)
obj.hide = False
self.bond_objects[(i,j)] = obj
self.append(obj)
return obj
def update(self, molecule, *args, **kw):
print(" Update positions of %d atoms and %d bonds" \
% (len(self.atom_objects), len(self.bond_objects)))
for i, obj in self.atom_objects.items():
obj.location = molecule.coords[i]
if molecule.options.auto_bonds:
bonds = list(molecule.bonds)
hidebonds, unhidebonds,addbonds = 0, 0, 0
for i,j in bonds:
if (i,j) not in self.bond_objects:
iatom, jatom = molecule.atoms[i], molecule.atoms[j]
irep = (molecule, iatom) in self
jrep = (molecule, jatom) in self
obj = self.create_bond(molecule, i, j, irep, jrep)
addbonds += 1
for (i,j), obj in self.bond_objects.items():
if (i,j) not in bonds and not obj.hide:
obj.hide = True
hidebonds += 1
elif (i,j) in bonds and obj.hide:
obj.hide = False
unhidebonds += 1
if not obj.hide:
obj.update()
print(" Created %d bonds, %d bonds hidden and %d bonds unhidden" \
% (addbonds, hidebonds, unhidebonds))
else:
for (i,j), obj in self.bond_objects.items():
obj.update()
return super().update(molecule, *args, **kw)
class StickAndBallRepr(MoleculeRepr):
order_id = 0
def __init__(self, name = 'StickAndBall', *args, **kw):
super().__init__(name, *args, **kw)
class StickRepr(MoleculeRepr):
order_id = 1
def __init__(self, name = 'Stick', *args, **kw):
super().__init__(name, *args, **kw)
class LineRepr(MoleculeRepr):
order_id = 2
def __init__(self, name = 'Line', *args, **kw):
super().__init__(name, *args, **kw)
self.options.atom_style = None
class VdwRepr(MoleculeRepr):
order_id = 2
def __init__(self, name = 'Vdw', *args, **kw):
super().__init__(name, *args, **kw)
if 'atom_size' not in kw:
self.options.atom_size = 'vdw_radius'
if 'atom_scale' not in kw:
self.options.atom_scale = self.options.atom_scale * 0.6
if 'atom_style' not in kw:
self.options.atom_style = 'metaball'
self.options.bond_style = None
class WireframeRepr(MoleculeRepr):
order_id = 2
def __init__(self, name = 'Wireframe', *args, **kw):
super().__init__(name, *args, **kw)
self.options.bond_style = None
self.options.atom_style = None
def create(self, molecule, *args, **kw):
if len(molecule.bonds) == 0:
print("No bonds available for wireframe representation")
return self
context = bpy.context
verts = [x for i, x in enumerate(molecule.coords) if (molecule, i) in self]
edges = [(i,j) for i,j in molecule.bonds if (molecule, i) in self and (molecule, j) in self]
mesh = bpy.data.meshes.new(self.name)
mesh.from_pydata(verts, edges, [])
mesh.update()
obj = bpy.data.objects.new(self.name, mesh)
bpy.context.scene.objects.link(obj)
Blender.select_all(False)
obj.select = True
bpy.context.scene.objects.active = obj
bpy.ops.object.convert(target='CURVE')
obj = context.object
obj.data.fill_mode = 'FULL'
obj.data.render_resolution_u = self.options.stick_size
obj.data.bevel_depth = self.options.line_size
obj.data.bevel_resolution = self.options.stick_size
bpy.ops.object.shade_smooth()
self.append(obj)
return super().update(molecule, *args, **kw)
def update(self, *args, **kw):
return super().update(*args, **kw)
class RingsRepr(ReprBase):
order_id = 2
def __init__(self, name = 'Rings', *args, **kw):
super().__init__(name, *args, **kw)
self._rings = {}
def key(self, molecule, ring):
key = self.options.ring_color
if key == 'Ring':
return len(ring)
def create_ring(self, molecule, ring):
ring_mat = self.options.ring_material
ring_col = self.options.ring_color
edge_bevel = self.options.ring_edge_bevel
ring = tuple(ring)
key = self.key(molecule, ring)
verts = [molecule.coords[i] for i in ring]
edges = [[i, (i + 1) % len(ring)] for i,_ in enumerate(ring)]
mat = self.make_material(ring_mat, ring_col, key)
obj = meshes.Mesh("Ring")
obj.create(verts, edges, [range(len(ring))])
obj.material = mat
obj.addAutoKey('data.vertices.co')#, 'hide_viewport', 'hide_render')
self.append(obj)
self._rings[tuple(ring)] = obj
return obj
def create(self, molecule, *args, **kw):
rings = molecule.rings()
for i,ring in enumerate(rings):
if ring in self:
name = "%s%d-%02d" % (self.name, len(ring), i)
obj = self.create_ring(molecule, ring)
obj.name = name
return super().create(molecule, *args, **kw)
def update(self, molecule, **kw):
newrings = molecule.rings()
oldrings = self._rings.keys()
for i,ring in enumerate(newrings):
ring = tuple(ring)
if ring not in oldrings and ring in self:
name = "%s%d-%02d" % (self.name, len(ring), i)
obj = self.create_ring(molecule, ring)
obj.name = name
obj.hide = True
obj.notify(frame = 0)
obj.hide = False
obj.notify()
for i,ring in enumerate(oldrings):
obj = self._rings[ring]
if ring not in newrings and not obj.hide:
obj.hide = True
elif ring in newrings and obj.hide:
obj.hide = False
verts = [molecule.coords[i] for i in ring]
for x,v in zip(verts, obj.data.vertices):
v.co = x
obj.notify('data.vertices.co')
return super().create(molecule, *args, **kw)
class PathRepr(ReprBase):
__slots__ = ['_paths']
kind = 'PATH'
def __init__(self, name = 'Path', *args, **kw):
super().__init__(name, *args, **kw)
self._paths = []
def vertices(self, molecule, path):
if callable(path):
return path(molecule)
elif hasattr(path, "__iter__"):
return path
else:
return None
def append(self, path):
self._paths.append(path)
return self
def create(self, molecule, *args, **kw):
size = self.options.path_size
reso = self.options.path_resolution
mat = self.make_material(self.options.path_material, self.options.path_color)
for p in self._paths:
verts = self.vertices(molecule, p)
if verts != None and hasattr(verts, "__iter__"):
obj = curves.NurbsPath(self.name, verts)
obj.data.bevel_depth = size
obj.data.bevel_resolution = reso
obj.data.fill_mode = 'FULL'
obj.material = mat
super().append(obj)
return super().create(molecule, *args, **kw)
def update(self, molecule, *args, **kw):
off = 0
for i, p in enumerate(self._paths):
verts = self.vertices(molecule, p)
if verts and hasattr(verts, "__iter__"):
self[i-off].update(verts)
else:
off += 1
return super().update(molecule, *args, **kw)
class Isosurface(ReprBase):
__slots__ = ['_isovals', 'on_update','draw_box', '_lastvol']
kind = 'VOLUME'
def __init__(self, name, isovals, *args, **kw):
super().__init__(name, *args, **kw)
self.on_update = kw['on_update'] if 'on_update' in kw else 'hide'
self.draw_box = 'draw_box' in kw and bool(kw['draw_box'])
if isinstance(isovals, float):
isovals = [isovals]
self._isovals = isovals
self._lastvol = None
def set_iso(self,isovals):
if isinstance(isovals, float):
isovals = [isovals]
self._isovals = isovals
def key(self, molecule, iso):
if self.options.volume_color == 'IsoSign':
return int(iso/abs(iso))
else:
return None
def create_box(self, mol, V):
context = bpy.context
ox, oy, oz = V.origin
mx, my, mz = V.max
verts = [[ ox, oy, oz ], # 0 0
[ mx, oy, oz ], # 1 x
[ ox, my, oz ], # 2 y
[ ox, oy, mz ], # 3 z
[ mx, my, oz ], # 4 xy
[ ox, my, mz ], # 5 yz
[ mx, oy, mz ], # 6 xz
[ mx, my, mz ]] # 7 xyz
edges = [[0,1], [0,2], [0,3],
[1,4], [1,6],
[2,4], [2,5],
[3,5], [3,6],
[4,7], [5,7],[6,7]
]
mesh = bpy.data.meshes.new(self.name +"-Box")
mesh.from_pydata(verts, edges, [])
mesh.update()
obj = bpy.data.objects.new(self.name, mesh)
bpy.context.scene.objects.link(obj)
bpy.ops.object.shade_smooth()
self.append(obj)
def create_volume(self, mol, V):
import time
nthreads = Blender.get_nthreads()
print(" Triangulate surface of %d points using %d threads" % (len(V), nthreads))
#t = time.time()
#triList = triangulate(V, self._isovals, Blender.window_manager)
#print("Serial = %lf, %d" % (time.time()-t, len(triList[0])))
#t = time.time()
#triList = triangulate_par(nthreads, V, self._isovals, Blender.window_manager)
#print("Parallel = %lf, %d" % (time.time()-t, len(triList[0])))
if nthreads == 1:
triList = triangulate(V, self._isovals, Blender.window_manager)