forked from willsheffler/pymol
/
symgen_test.py
489 lines (426 loc) · 17.9 KB
/
symgen_test.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
from symgen import SymElem, generate_sym_trie, BuildCGO, ComponentCenterVisitor, CountFrames
from pymol import cmd
def test_D2TET(depth=6,cell=60, **kwargs):
G = [
# SymElem("C2",axis=Vec( 1,0,0),cen=Vec( 0 ,cell/2.0, cell/4.0)),
# SymElem("C3",axis=Vec(-1,1,1),cen=Vec(-cell/6.0,cell/6.0,-cell/3.0)),
# SymElem("C2",axis=Vec(1,1,0),cen=cell*Vec(0,0.0,0.0)),
# SymElem("C3",axis=Vec(-1,1,1),cen=Vec(0,0,0)),
# SymElem("C2",axis=Vec(0,1,0)),
SymElem("C3",axis=Vec(1,1,1)),
# SymElem("C2",axis=Vec(0,1,0),cen=Vec(1,1,1)*cell/2.0), # other T
# SymElem("C3",axis=Vec(1,1,1),cen=Vec(1,1,1)*cell/2.0), # other T
# SymElem("C4",axis=Vec(1,0,0),cen=Vec(1,1,1)*cell/2.0),
SymElem("D2",cen=Vec(0,0,cell/2.0)),
# SymElem("D2",cen=Vec(0,cell/2.0,cell/2.0)), # other D2
]
# for elem in G: print elem
symtrie = generate_sym_trie(G,depth=depth)
buildcgo = BuildCGO( nodes=[ ], origin=Vec(0.5,0.5,0.5)*cell, **kwargs )
# buildcgo = BuildCGO( nodes=[ Vec(6,6,30), ] )
symtrie.visit(buildcgo)
buildcgo.show()
cube( Vec(0,0,0), cell*Vec(1,1,1) )
for g in G:
print "show",g
g.show(radius=2.0,sphereradius=4.0)
def test_D4OCT(depth=4):
CELL = 30
G = [
# SymElem("C2",axis=Vec( 1,0,0),cen=Vec( 0 ,CELL/2.0, CELL/4.0)),
# SymElem("C3",axis=Vec(-1,1,1),cen=Vec(-CELL/6.0,CELL/6.0,-CELL/3.0)),
# SymElem("C2",axis=Vec(1,1,0),cen=CELL*Vec(0,0.0,0.0)),
# SymElem("C3",axis=Vec(-1,1,1),cen=Vec(0,0,0)),
SymElem("C2",axis=Vec(1,1,0),cen=Vec(0,0,CELL)),
SymElem("C3",axis=Vec(1,1,1),cen=Vec(0,0,CELL)),
SymElem("C4",axis=Vec(1,0,0),cen=Vec(0,0,CELL)),
SymElem("C4",axis=Vec(0,0,1)),
SymElem("C2",axis=Vec(1,0,0)),
SymElem("C2",axis=Vec(0,1,0)),
]
# for elem in G: print elem
symtrie = generate_sym_trie(G,depth=depth)
# buildcgo = BuildCGO( nodes=[ Vec(2,4,3), Vec(-6,-2,35), ] )
buildcgo = BuildCGO( nodes=[ Vec(-6,-2,CELL+5), Vec(2,4,3), ] )
# buildcgo = BuildCGO( nodes=[ Vec(-6,-2,35), ] )
# buildcgo = BuildCGO( nodes=[ Vec(2,4,3), ] )
symtrie.visit(buildcgo)
buildcgo.show()
def test_xtal(G,cell,depth=4,mindepth=0,symdef=1,shownodes=1,**kwargs):
v = cmd.get_view()
CEN = [g.cen for g in G]
FN = list()
tag = "test" if not "tag" in kwargs else kwargs['tag']
for d in range(mindepth,depth+1):
symtrie = generate_sym_trie(G,depth=d)
# buildcgo = BuildCGO( nodes=[ CEN1+Vec(2,3,4), CEN2+Vec(2,4,3), ] )
nodes = []
if "component_pos" in kwargs.keys():
raise NotImplementedError("component_pos is no longer used")
# nodes = kwargs["component_pos"][:1]
buildcgo = BuildCGO( nodes=nodes, label=tag+"_DEPTH%i"%d,**kwargs )
symtrie.visit(buildcgo)
buildcgo.show()
if shownodes:
find_nodes = ComponentCenterVisitor(symelems=G,label=tag+"_NODES%i"%d,**kwargs)
symtrie.visit(find_nodes)
FN.append(find_nodes)
if symdef:
sdef_string = FN[-1].make_symdef(**kwargs)
print "==================== SYMDEF (dump to "+tag+"_"+str(d)+".sym) ===================="
print sdef_string
print "====================================================================="
with open(tag+"_"+str(d)+".sym","w") as out:
out.write(sdef_string)
if 'symdef_check' in kwargs and kwargs['symdef_check']:
sdef = RosettaSymDef()
sdef.parse(sdef_string)
sdef.show("SYMDEF_"+tag)
for fn in FN:
fn.show(**kwargs) # dumb order hack for pymol up/dn
cmd.disable("all")
cmd.enable(tag+"_DEPTH%i"%(depth))
cmd.enable(tag+"_NODES%i"%(depth))
count = CountFrames()
symtrie.visit(count)
print "N Frames:",count.count
cmd.set_view(v)
def test_I432_OD3(cell=120,**kwargs):
X = alignvectors(Vec(1,1,1),Vec(1,0,-1),Vec(0,0,1),Vec(1,0,0))
# G = [ SymElem( "O" , cen=cell*Vec(0.0,0.0,0.0) ),
# SymElem( "D3", cen=cell*Vec(0.25,0.25,0.25), axis=Vec(1,1,1), axis2=Vec(1,-1,0) ), ]
# cube( cell*Vec(-0.5,-0.5,-0.5), cell*Vec(0.5,0.5,0.5) )
G = [ SymElem( "D3", cen=cell*Vec(0.0,0.0,0.0) ),
SymElem( "O" , cen=cell*Vec(0.0,0.0,sqrt(3.0)/4.0), input_xform=X ), ]
cube( cell*Vec(-0.25,-0.25,-0.25), cell*Vec(0.75,0.75,0.75), xform=X )
test_xtal(G,cell,tag="I432_OD3",**kwargs)
def test_P23_TT(cell=100,**kwargs):
# delete all; run ~/pymol/symgen.py; test_P23_TD2B( depth=2, cell=200, symdef_scale=0.000001, generic_names=1 )
G = [ SymElem( "C3" , axis=Vec( 1,-1,-1), cen=cell*Vec(0.0 , 0.0 ,0.0 ) ),
SymElem( "C3" , axis=Vec( 1,-1, 1), cen=cell*Vec(0.25, 0.25,0.0 ) ),
# SymElem( "T" , cen=cell*Vec(0.25,0.25,0.0) ),
]
test_xtal(G,cell,tag="P23_TT",**kwargs)
cube( cell*Vec(1,1,1)*-0.5, cell*Vec(1,1,1)*0.5 )
def test_P432_OD4(cell=80,**kwargs):
G = [ SymElem( "D4", cen=cell*Vec(0.0,0.0,0.0) ),
SymElem( "O" , cen=cell*Vec(0.0,0.0,0.5) ), ]
test_xtal(G,cell,tag="P432_OD4",**kwargs)
def test_P4m_44(cell=80,**kwargs):
G = [ SymElem( "D4", cen=cell*Vec(0.0,0.0,0.0) ),
SymElem( "D4", cen=cell*Vec(0.5,0.0,0.0) ), ]
test_xtal(G,cell,tag="P432_OD4",**kwargs)
def test_P23_TD2A(cell=200,**kwargs):
# delete all; run ~/pymol/symgen.py; test_P23_TD2B( depth=2, cell=200, symdef_scale=0.000001, generic_names=1 )
G = [ SymElem( "D2", cen=cell*Vec(0.0,0.0,0.0) ),
SymElem( "T" , cen=cell*Vec(0.0,0.0,0.5) ), ]
component_pos=[ Vec(-8,-7,6), Vec(-7,0,-11), ]
test_xtal(G,cell,component_pos=component_pos,tag="P23_TD2A",**kwargs)
cube( cell*Vec(0,0,-0.5), cell*Vec(1,1,0.5) )
def test_P23_TC3(cell=200,**kwargs):
# delete all; run ~/pymol/symgen.py; test_P23_TD2B( depth=2, cell=200, symdef_scale=0.000001, generic_names=1 )
G = [ SymElem( "C3" , cen=cell*Vec(0.0,0.0,0.0) ),
SymElem( "T" , cen=cell*Vec(0.5,0.5,0.5) ), ]
test_xtal(G,cell,tag="P23_TC3",**kwargs)
cube( cell*Vec(0,0,0), cell*Vec(1,1,1) )
# run /Users/sheffler/pymol/symgen.py; delete all; test_P23_TD2B( depth=4 )
def test_P23_TD2B(depth=3,cell=150,**kwargs):
# delete all; run ~/pymol/symgen.py; test_P23_TD2B( depth=2, cell=200, symdef_scale=0.000001, generic_names=1 )
G = [
SymElem( "D2", cen=cell*Vec(0.0,0.0,0.0) ),
SymElem( "T" , cen=cell*Vec(0.0,0.5,0.5) ),
]
test_xtal(G,cell,tag="P23_TD2B",**kwargs)
cube( cell*Vec(0,-0.5,-0.5), cell*Vec(1,0.5,0.5) )
def test_F432_TD2(cell=150,**kwargs):
# delete all; run ~/pymol/symgen.py; test_F432_TD2( depth=2, cell=200, symdef_scale=0.000001, generic_names=1 )
G = [ SymElem( "D2", cen=cell*Vec(0.0,0.0,0.0) ), # , axis2=Vec(1,1,0) ),
SymElem( "T" , cen=cell*Vec(0.0,0.0,0.25), input_xform=RAD(Uz,45) ),
# SymElem( "O" , cen=cell*Vec(0.5,0.5,0.0) ),
]
component_pos=[ Vec(2,4,8), Vec(2,5,-12), Vec(4,6,8) ]
test_xtal(G,cell,component_pos=component_pos,tag="F432_TD2",**kwargs)
cube( cell*Vec(-0.5,-0.5,-0.25), cell*Vec(0.5,0.5,0.75), xform=RAD(Uz,45) )
def test_F432_OTD2(depth=3,cell=80,**kwargs):
# delete all; run /Users/sheffler/pymol/symgen.py; test_P23(depth=1,mindepth=1)
# ODT 96
# TDO 96
G = [
SymElem( "O" , cen=cell*Vec(0.5,0.5,0.0) ),
SymElem( "D2", cen=cell*Vec(0.0,0.0,0.0), axis2=Vec(1,1,0) ),
SymElem( "T" , cen=cell*Vec(0.0,0.0,-0.5) ),
]
component_pos=[ Vec(2,4,8), Vec(2,5,-12), Vec(4,6,8) ]
extranodes = [ cell*Vec(0.0,0.5,0.0)]
test_xtal(G,cell,component_pos=component_pos,tag="F432_TD2",extranodes=extranodes,**kwargs)
cube( cell*Vec(-1,-1,-0.5), cell*Vec(1,1,1.5) )
def test_I432_OD4(cell=80,**kwargs):
# delete all; run /Users/sheffler/pymol/symgen.py; test_F432_OD4( depth=3, cell=200, symdef_scale=0.000001, generic_names=1 )
# G = [ SymElem( "D2", cen=cell*Vec(0.0,0.0,0.0), axis2=Vec(1,1,0) ),
# # SymElem( "T" , cen=cell*Vec(0.0,0.0,-0.5) ),
# SymElem( "O" , cen=cell*Vec(0.5,0.5,0.0) ),
# ]
G = [ SymElem( "D4", cen=cell*Vec(0.0,0.0,0.0)) ,
# SymElem( "T" , cen=cell*Vec(0.0,0.0,-0.5) ),
SymElem( "O" , cen=cell*Vec(0.0,0.0,0.5), input_xform=RAD(Uz,45) ),
]
component_pos=[ Vec(2,4,8), Vec(2,5,-12), Vec(4,6,8) ]
test_xtal(G,cell,component_pos=component_pos,tag="I432_OD4",**kwargs)
cube( cell*Vec(-1,-1,-0.5), cell*Vec(1,1,1.5) )
def test_P442(cell=80,**kwargs):
# delete all; run ~/pymol/symgen.py; test_P4( depth=4, cell=100, symdef_scale=0.000001, generic_names=1 )
G = [ SymElem( "C4", cen=cell*Vec(0.0,0.0,0.0) ),
SymElem( "C2", cen=cell*Vec(0.5,0.0,0.0) ),
]
test_xtal(G,cell,tag='test_P4_42',**kwargs)
def test_P444(cell=100,**kwargs):
G = [ SymElem( "C4", cen=cell*Vec(0.0,0.0,0.0) ),
SymElem( "C4", cen=cell*Vec(0.5,0.0,0.0) ), # moved lattice WRP C2!!!!!
]
test_xtal(G,cell,tag='test_P4_44',**kwargs)
def test_P4m44(cell=100,**kwargs):
G = [ SymElem( "D4", cen=cell*Vec(0.0,0.0,0.0) ),
SymElem( "D4", cen=cell*Vec(0.5,0.0,0.0) ), # moved lattice WRP C2!!!!!
]
test_xtal(G,cell,tag='test_P4_44',**kwargs)
def test_I4132(cell=100,**kwargs):
# delete all; test_I4132(depth=7,shownodes=0,cell=200,maxrad=180); run /Users/sheffler/pymol/misc/G222.py; gyroid(200,r=180)
# delete all; run /Users/sheffler/pymol/symgen.py; test_I4132( cell=150, depth=7, shownodes=0, maxrad=150 ); gyroid(150,r=150,c=Vec(75,75,75))
r = random.random
G = [
SymElem( "D3", cen=cell*Vec(0.625,0.625,0.625), axis=Vec(1,1,1), axis2=Vec(1,-1,0), col=(0,1,0) ),
SymElem( "D2", cen=cell*Vec(0.625,0.500,0.750), axis=Vec(1,0,0), axis2=Vec(0,-1,1), col=(0,1,1) ),
SymElem( "D3", cen=cell*Vec(0.375,0.375,0.375), axis=Vec(1,1,1), axis2=Vec(1,-1,0), col=(1,0,0) ),
SymElem( "D2", cen=cell*Vec(0.375,0.500,0.250), axis=Vec(1,0,0), axis2=Vec(0,-1,1), col=(1,1,0) ),
# SymElem( "C3", axis=Vec(1,1,1) ),
# SymElem( "C2", axis=Vec(1,1,0), cen=cell*Vec(-1, 1, 1)/8.0 ),
# SymElem( "C2", axis=Vec(1,1,0), cen=cell*Vec( 1,-1,-1)/8.0 ),
# SymElem( "C2", axis=Vec(1,1,0), cen=cell*Vec( 1,-1,-1)/8.0, col=(1,1,0) ),
# SymElem( "D3", cen=cell*Vec(0.125,0.125,0.125), axis=Vec(1,1,1), axis2=Vec(1,-1,0), col=(0,1,0) ),
# SymElem( "D2", cen=cell*Vec(0.125,0.000,0.250), axis=Vec(1,0,0), axis2=Vec(0,-1,1), col=(0,1,1) ),
# SymElem( "D3", cen=cell*Vec(-0.125,-0.125,-0.125), axis=Vec(1,1,1), axis2=Vec(1,-1,0), col=(1,0,0) ),
# SymElem( "D2", cen=cell*Vec(-0.125,0.000,-0.250), axis=Vec(1,0,0), axis2=Vec(0,-1,1), col=(1,1,0) ),
]
component_pos=[ Vec(-8,-7,6), Vec(-7,0,-11), ]
test_xtal(G,cell,component_pos=component_pos,tag="I4132",origin=cell*Vec(0.5,0.5,0.5),showshape=0,**kwargs)
# cube( cell*Vec(-0.5,-0.5,-0.5), cell*Vec(0.5,0.5,0.5) )
cube( cell*Vec(-0,-0,-0), cell*Vec(1,1,1) )
def test_P213(cell=100,**kwargs):
AXS = [ Vec( 1, 1, 1),
Vec( 1, 1,-1) ]
CEN = [ cell * Vec(0,0,0),
cell * Vec(0.5,0,0.0) ]
G = [
SymElem( "C3", axis=AXS[0], cen=CEN[0] ),
SymElem( "C3", axis=AXS[1], cen=CEN[1] ),
]
component_pos=[ Vec(-18,-17,-16), Vec(7,0,11), ]
test_xtal(G,cell,tag="P213",origin=cell*Vec(0.0,0.0,0.0),showshape=0,**kwargs)
cube( Vec(0,0,0), cell*Vec(1,1,1) )
def test_T32(cell=100,**kwargs):
print "========================================== T32 =========================================="
G = [
SymElem( "C3", axis=Vec(1,1,1) ),
SymElem( "C2", axis=Vec(1,0,0), cen=Vec(0.00001,0,0) ),
]
component_pos=[ Vec(8,6,5), Vec(7,2,1), ]
test_xtal(G,cell,component_pos=component_pos,tag="T32",origin=cell*Vec(0.0,0.0,0.0),showshape=0,**kwargs)
def test_I213(depth=16,cell=100,maxrad=9e9):
#C3 and C2 at angle = 54.7356 offset = 0.176777
# C3 axis=[-0.57735,0.57735,0.57735] origin=[-0.166667,0.166667,-0.333333]
# C2 axis=[1,0,0] origin=[0,0.5,0.25]
# AXS = [ Vec(-1,1,1),
# Vec( 1,0,0) ]
# CEN = [ cell * Vec(-1,1,-2)/6.0 ,
# cell * Vec(0,0.5,0.25) ]
AXS = [ Vec(1,1,1),
Vec(1,0,0) ]
CEN = [ cell * Vec(0,0,0) ,
cell * Vec(0,0,0.25) ]
G = [
SymElem( "C3", axis=AXS[0], cen=CEN[0] ),
SymElem( "C2", axis=AXS[1], cen=CEN[1] )
]
symtrie = generate_sym_trie(G,depth=depth)
# buildcgo = BuildCGO( nodes=[ CEN1+Vec(2,3,4), CEN2+Vec(2,4,3), ] )
nodes = [
CEN[0]+projperp(AXS[0],randnorm())*8.0,
CEN[1]+projperp(AXS[1],randnorm())*8.0
]
buildcgo = BuildCGO( nodes=nodes, maxrad=maxrad, origin=cell*Vec(0.5,0.5,0.5), showlinks=True )
symtrie.visit(buildcgo)
buildcgo.show()
cube( Vec(0,0,0), cell*Vec(1,1,1) )
for g in G:
print "show",g
g.show(radius=2.0,sphereradius=4.0)
return AXS,CEN
def test_P4132(depth=8,cell=50,maxrad=80):
#**** P4132 ****
#C2 and C3 at angle = 35.2644 offset = 0.176777
# C2 axis=[-0.707107,0.707107,0] origin=[-0.125,-0.125,-0.125]
# C3 axis=[0.57735,-0.57735,0.57735] origin=[0,-0.5,-0.5]
AXS = [ Vec(-1, 1, 0) ,
Vec( 1,-1, 1) ]
CEN = [ cell * Vec(1,1,1)/-8.0,
cell * Vec(0,1,1)/-2.0 ]
# AXS = [ Vec(-1, 1, 0) ,
# Vec( 1, 1, 1) ]
# CEN = [ cell * Vec(1,1,1)/-8.0,
# cell * Vec(0,0,0) ]
G = [
SymElem( "C2", axis=AXS[0], cen=CEN[0] ),
SymElem( "C3", axis=AXS[1], cen=CEN[1] ),
]
symtrie = generate_sym_trie(G,depth=depth)
# buildcgo = BuildCGO( nodes=[ CEN1+Vec(2,3,4), CEN2+Vec(2,4,3), ] )
cencell = cell/2.0 * Vec(1,1,1)
buildcgo = BuildCGO( nodes=[ CEN[1]+randnorm()*5.0, CEN[0]+randnorm()*8.0 ], origin=cencell, maxrad=maxrad, showlinks=False, showelems=True )
symtrie.visit(buildcgo)
buildcgo.show()
cube( Vec(0,0,0), cell*Vec(1,1,1) )
for g in G:
print "show",g
g.show(radius=2.0,sphereradius=4.0)
return AXS,CEN
def test_F432(depth=6,cell=100,maxrad=90):
#C3 and D2 at angle = 35.2644 offset = 0
# C3 axis=[0.57735,0.57735,0.57735] origin=[0,0,0]
# D2 axis=[1,0,0] axis2=[0,-0.707107,0.707107] origin=[0,0.25,0.25]
AXS = [ Vec(1,1,1),
Vec(1,0,0) ]
CEN = [ cell * Vec(0,0,0) ,
cell * Vec(0,0.25,0.25) ]
G = [
SymElem( "C2", axis=Vec(1,1,0), cen=Vec(0,0,0) ),
SymElem( "C3", axis=AXS[0], cen=CEN[0] ),
SymElem( "C4", axis=Vec(1,0,0), cen=Vec(0,0,0) ),
SymElem( "D2", axis=AXS[1], axis2=Vec(0,-1,1), cen=CEN[1] )
]
symtrie = generate_sym_trie(G,depth=depth)
# buildcgo = BuildCGO( nodes=[ CEN1+Vec(2,3,4), CEN2+Vec(2,4,3), ] )
nodes = [
CEN[0]+projperp(AXS[0],randnorm())*8.0,
CEN[1]+projperp(AXS[1],randnorm())*8.0
]
buildcgo = BuildCGO( nodes=nodes, maxrad=maxrad, origin=cell*Vec(0.5,0.5,0.5), showlinks=False )
symtrie.visit(buildcgo)
buildcgo.show()
cube( Vec(0,0,0), cell*Vec(1,1,1) )
for g in G:
print "show",g
g.show(radius=2.0,sphereradius=4.0)
return AXS,CEN
def test_quasi( depth=8, cell=20.0, maxrad=9e9 ):
G = [
SymElem( "C2", axis=Vec(1,0,0) ),
SymElem( "C2", axis=Vec(0,1,0) ),
SymElem( "C2", axis=Vec(0,0,1) ),
SymElem( "C3", axis=Vec(+1,+1,+1) ),
SymElem( "C3", axis=Vec(+1,-1,-1) ),
SymElem( "C3", axis=Vec(-1,+1,-1) ),
SymElem( "C3", axis=Vec(-1,-1,+1) ),
SymElem( "C2", axis=Vec(2,-1,-1), cen=cell*Vec(1,1,1) ),
]
nodes = [ ]
symtrie = generate_sym_trie(G,depth=depth)
symtrie.visit(print_node)
print symtrie
buildcgo = BuildCGO( nodes=nodes, maxrad=maxrad, origin=cell*Vec(0.5,0.5,0.5), showlinks=False, showelems=True )
symtrie.visit(buildcgo)
buildcgo.show()
def test_I432( depth=6, cell=50, **kwargs ):
#**** I432 ****
#C2 and D3 at angle = 35.2644 offset = 0.353553
# C2 axis=[-0.707107,0.707107,0] origin=[0.25,0.25,0.25]
# D3 axis=[-0.57735,0.57735,0.57735] axis2=[0.707107,0.707107,0] origin=[0,0,0]
G = [
SymElem( "C2", axis=Vec(-1,1,0), cen=Vec(1,1,1)/4.0*cell ),
SymElem( "D3", axis=Vec(-1,1,1), axis2=Vec(1,1,0) )
]
symtrie = generate_sym_trie(G,depth=depth)
# buildcgo = BuildCGO( nodes=[ CEN1+Vec(2,3,4), CEN2+Vec(2,4,3), ] )
nodes = []
buildcgo = BuildCGO( nodes=nodes, origin=cell*Vec(0.5,0.5,0.5), showlinks=False, **kwargs )
symtrie.visit(buildcgo)
buildcgo.show()
cube( Vec(0,0,0), cell*Vec(1,1,1) )
for g in G:
print "show",g
g.show(radius=2.0,sphereradius=4.0)
def test_icos( depth=3, cell=30, **kwargs ):
# dodec
# (+-1, +-1, +-1)
# (0, +-1/p, +-p)
# (+-1/p, +-p, 0)
# (+-p, 0, +-1/p)
# icos
# (0, +-1, +-p)
# (+-1, +-p, 0)
# (+-p, 0, +-1)
p = (1.0+sqrt(5.0))/2.0
q = 1.0/p
v33a = ( Vec(1,1,1).normalized() - Vec(q,p,0).normalized() ).normalized()
v33b = ( Vec(1,1,1).normalized() - Vec(p,0,q).normalized() ).normalized()
v33c = ( Vec(1,1,1).normalized() - Vec(0,q,p).normalized() ).normalized()
icsang = angle_degrees( Vec(1,1,1),V0, v33a )
tetang = 180.0-math.acos(-1.0/3.0)*180.0/math.pi
print icsang, tetang
delta_deg = icsang-tetang
v33a = RAD(v33a.cross(Vec(1,1,1)),delta_deg) * v33a
v33b = RAD(v33b.cross(Vec(1,1,1)),delta_deg) * v33b
v33c = RAD(v33c.cross(Vec(1,1,1)),delta_deg) * v33c
print angle_degrees(Vec(1,1,1),V0,v33a)
print angle_degrees(Vec(1,1,1),V0,v33b)
print angle_degrees(Vec(1,1,1),V0,v33c)
G = [
# icos 3folds
SymElem("C3",Vec(+1,+1,+1)),
SymElem("C3",Vec(+1,+1,-1)),
SymElem("C3",Vec(+1,-1,+1)),
SymElem("C3",Vec(-1,+1,+1)),
SymElem("C3",Vec( 0,+q,+p)),
SymElem("C3",Vec( 0,+q,-p)),
SymElem("C3",Vec(+q,+p, 0)),
SymElem("C3",Vec(+q,-p, 0)),
SymElem("C3",Vec(+p, 0,+q)),
SymElem("C3",Vec(-p, 0,+q)),
SymElem("C5",Vec( 0,+p, 1)),
SymElem("C5",Vec( 0,-p, 1)),
SymElem("C5",Vec(+p, 1, 0)),
SymElem("C5",Vec(-p, 1, 0)),
SymElem("C5",Vec( 1, 0, +p)),
SymElem("C5",Vec( 1, 0, -p)),
# tet
SymElem("C3",Vec(1,1,1),cen=cell*Vec(1,1,1)),
SymElem("C3",v33a,cen=cell*Vec(1,1,1)),
SymElem("C3",v33b,cen=cell*Vec(1,1,1)),
SymElem("C3",v33c,cen=cell*Vec(1,1,1)),
SymElem("C2",v33a+v33b,cen=cell*Vec(1,1,1)),
SymElem("C2",v33b+v33c,cen=cell*Vec(1,1,1)),
SymElem("C2",v33c+v33a,cen=cell*Vec(1,1,1)),
]
symtrie = generate_sym_trie(G,depth=depth)
# symtrie.visit(print_node)
nodes = [ ]
buildcgo = BuildCGO( nodes=nodes, origin=cell*Vec(0.5,0.5,0.5), showelems=True, **kwargs )
symtrie.visit(buildcgo)
buildcgo.show()
#def test_F23_C2_T(cell=100,**kwargs):
# #delete all ; run ~/pymolscripts/symgen.py; test_F23_C2_T(cell=100, depth=2)
# G = [ SymElem( 'C2', cen=cell* Vec ( 0.0,0.0,0.0 ) , axis=Vec(0,0,1), #axis2=Vec(-,-,-)
# ),
# SymElem( 'T', cen=cell*Vec(0.25,0.25,0.0), axis=Vec(0.57735,-0.57735,0.57735), #axis2=Vec(,,)
# ),
#
# ]
# test_xtal(G,cell,tag='test_F23_C2_T',**kwargs)
#
#
# from una
def test_F23_C2_T(cell=100,**kwargs):
# delete all; run ~/pymol/symgen.py; test_P4( depth=4, cell=100, symdef_scale=0.000001, generic_names=1 )
G = [ SymElem( 'T' , cen=cell*Vec( 0.0 , 0.0 , 0.0 ), axis=Vec(-1,1,1) ),
SymElem( 'C2', cen=cell*Vec( 0.25, 0.25, 0.0 ), axis=Vec(0,0,1) )
]
test_xtal(G,cell,tag='test_F23_C2_T',**kwargs)