cs_orig.world
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1 
3 % Note that this world is not the one generated from a pdb and, thus
4 % it is not valid to be used with the cuikbio tools.
5 % This file is used to generate samples strictly fulfill the rigid
6 % geometry assumption (atom coordiantes in the pdb typically do
7 % not fullfil this assumption). This sample is latter used
8 % to generate atom coordiantes (with cuikatoms) to replace
9 % those in the pdb during the process to generate a world
10 % "syncronized" with the pdb (using cuikbio)
11 
12 [CONSTANTS]
13 
14 % in MMFF94 C is 1, S is 15, and H is 5 (for this case)
15 
16 % ---------------------------------------------------------
17 % Parameters taken from the force field definition
18 % reference bond lenghts
19 % CHb:=1.093
20 % CSb:=1.805
21 % SSb:=2.050
22 
23 % reference angles
24 % SCSa:=111.896*pi/180 % 15 1 15
25 % HCSa:=109.609*pi/180 % 5 1 15
26 % CSSa:=100.316*pi/180 % 1 15 15
27 % SSSa:=104.893*pi/180 % 15 15 15
28 
29 % ---------------------------------------------------------
30 
31 % ---------------------------------------------------------
32 % Artificial parameters used in previous papers
33 % reference bond lenghts
34 CHb:=1.120
35 CSb:=1.805
36 SSb:=2.019
37 
38 % reference angles
39 SCSa:=109.5*pi/180 % 15 1 15
40 HCSa:=109.5*pi/180 % 5 1 15
41 CSSa:=135.0*pi/180 % 1 15 15
42 SSSa:=135.0*pi/180 % 15 15 15
43 
44 % ---------------------------------------------------------
45 
46 d:= CSb*sqrt(2-2*cos(SCSa))
47 x:= d/sqrt(3)
48 y:= d/2
49 z:=-sqrt(CSb^2-x^2)
50 
51 S0x:= 0
52 S0y:= 0
53 S0z:= CSb
54 
55 S1x:= x
56 S1y:= 0
57 S1z:= z
58 
59 S2x:=-x/2
60 S2y:= y
61 S2z:= z
62 
63 S3x:=-x/2
64 S3y:=-y
65 S3z:= z
66 
67 % angle of the C-S bond
68 CSbx:=CSb*cos(CSSa)
69 CSby:=CSb*sin(CSSa)
70 
71 % angle of the S-S bond
72 SSbx:=SSb*cos(SSSa)
73 SSby:=SSb*sin(SSSa)
74 
75 % Reduction over the Van der Waals radious
76 VdWRatio:=0.25 % 0.7
77 
78 % Radious of the spheres representing atoms
79 rC:=1.7*VdWRatio
80 rH:=1.1*VdWRatio
81 rS:=1.8*VdWRatio
82 
83 % Radious of the cylinders representing bonds
84 rCS:=0.15
85 rCH:=0.15
86 rSS:=0.15
87 
88 % Colors for the atoms
89 Cr:=0.2
90 Cg:=0.6
91 Cb:=0.6
92 
93 Hr:=1
94 Hg:=1
95 Hb:=1
96 
97 Sr:=1
98 Sg:=1
99 Sb:=0
100 
101 
102 [LINKS]
103 
104 % Atoms in the main ring
105 
106 C1: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
107  cylinder rCS (0,0,0) (S0x/2,S0y/2,S0z/2) color (Cr,Cg,Cb) decoration
108  cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
109  cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
110  cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
111 
112 S1: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
113  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
114  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
115 
116 S2: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
117  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
118  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
119 
120 S3: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
121  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
122  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
123 
124 C2: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
125  cylinder rCS (0,0,0) (S0x/2,S0y/2,S0z/2) color (Cr,Cg,Cb) decoration
126  cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
127  cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
128  cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
129 
130 S4: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
131  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
132  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
133 
134 S5: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
135  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
136  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
137 
138 S6: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
139  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
140  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
141 
142 C3: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
143  cylinder rCS (0,0,0) (S0x/2,S0y/2,S0z/2) red % color (Cr,Cg,Cb) decoration
144  cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) green % color (Cr,Cg,Cb) decoration
145  cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) blue % color (Cr,Cg,Cb) decoration
146  cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
147 
148 
149 S7: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
150  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
151  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
152 
153 S8: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
154  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
155  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
156 
157 S9: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
158  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
159  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
160 
161 C4: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
162  cylinder rCS (0,0,0) (S0x/2,S0y/2,S0z/2) color (Cr,Cg,Cb) decoration
163  cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
164  cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
165  cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
166 
167 S10: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
168  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
169  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
170 
171 S11: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
172  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
173  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
174 
175 S12: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
176  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
177  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
178 
179 % C1
180 
181 % other loops
182 
183 % C1
184 S13: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
185  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
186  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
187 
188 S14: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
189  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
190  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
191 
192 C5: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
193  cylinder rCS (0,0,0) (S0x/2,S0y/2,S0z/2) color (Cr,Cg,Cb) decoration
194  cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
195  cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
196  cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
197 
198 S15: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
199  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
200  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
201 
202 S16: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
203  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
204  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
205 % C3
206 
207 % C3
208 S17: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
209  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
210  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
211 
212 S18: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
213  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
214  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
215 
216 C6: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
217  cylinder rCS (0,0,0) (S0x/2,S0y/2,S0z/2) color (Cr,Cg,Cb) decoration
218  cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
219  cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
220  cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
221 
222 S19: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
223  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
224  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
225 
226 S20: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
227  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
228  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
229 % C1
230 
231 % C2
232 S21: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
233  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
234  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
235 
236 S22: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
237  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
238  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
239 
240 S23: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
241  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
242  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
243 
244 % C5
245 S24: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
246  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
247  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
248 
249 S25: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
250  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
251  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
252 
253 S26: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
254  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
255  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
256 % C4
257 
258 % C4
259 S27: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
260  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
261  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
262 
263 S28: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
264  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
265  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
266 
267 S29: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
268  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
269  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
270 
271 % C6
272 S30: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
273  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
274  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
275 
276 S31: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
277  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
278  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
279 
280 S32: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
281  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
282  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
283 % C2
284 
285 [JOINTS]
286 
287 % main ring
288 revolute: C1 (0,0,0) (S1x,S1y,S1z)
289  S1 (CSb,0,0) (0,0,0)
290 
291 revolute: S1 (0,0,0) (SSbx,SSby,0)
292  S2 (SSb,0,0) (0,0,0)
293 
294 revolute: S2 (0,0,0) (SSbx,SSby,0)
295  S3 (SSb,0,0) (0,0,0)
296 
297 revolute: S3 (CSbx,CSby,0) (0,0,0)
298  C2 (0,0,0) (S0x,S0y,S0z)
299 
300 revolute: C2 (0,0,0) (S1x,S1y,S1z)
301  S4 (CSb,0,0) (0,0,0)
302 
303 revolute: S4 (0,0,0) (SSbx,SSby,0)
304  S5 (SSb,0,0) (0,0,0)
305 
306 revolute: S5 (0,0,0) (SSbx,SSby,0)
307  S6 (SSb,0,0) (0,0,0)
308 
309 revolute: S6 (CSbx,CSby,0) (0,0,0)
310  C3 (0,0,0) (S1x,S1y,S1z)
311 
312 revolute: C3 (0,0,0) (S2x,S2y,S2z)
313  S7 (CSb,0,0) (0,0,0)
314 
315 revolute: S7 (0,0,0) (SSbx,SSby,0)
316  S8 (SSb,0,0) (0,0,0)
317 
318 revolute: S8 (0,0,0) (SSbx,SSby,0)
319  S9 (SSb,0,0) (0,0,0)
320 
321 revolute: S9 (CSbx,CSby,0) (0,0,0)
322  C4 (0,0,0) (S1x,S1y,S1z)
323 
324 revolute: C4 (0,0,0) (S0x,S0y,S0z)
325  S10 (CSb,0,0) (0,0,0)
326 
327 revolute: S10 (0,0,0) (SSbx,SSby,0)
328  S11 (SSb,0,0) (0,0,0)
329 
330 revolute: S11 (0,0,0) (SSbx,SSby,0)
331  S12 (SSb,0,0) (0,0,0)
332 
333 revolute: S12 (CSbx,CSby,0) (0,0,0)
334  C1 (0,0,0) (S3x,S3y,S3z)
335 
336 % Connections defining the two other rings
337 
338 revolute: C1 (0,0,0) (S0x,S0y,S0z)
339  S13 (CSb,0,0) (0,0,0)
340 
341 revolute: S13 (0,0,0) (SSbx,SSby,0)
342  S14 (SSb,0,0) (0,0,0)
343 
344 revolute: S14 (CSbx,CSby,0) (0,0,0)
345  C5 (0,0,0) (S0x,S0y,S0z)
346 
347 
348 revolute: C5 (0,0,0) (S2x,S2y,S2z)
349  S15 (CSb,0,0) (0,0,0)
350 
351 revolute: S15 (0,0,0) (SSbx,SSby,0)
352  S16 (SSb,0,0) (0,0,0)
353 
354 revolute: S16 (CSbx,CSby,0) (0,0,0)
355  C3 (0,0,0) (S0x,S0y,S0z)
356 
357 
358 revolute: C3 (0,0,0) (S3x,S3y,S3z)
359  S17 (CSb,0,0) (0,0,0)
360 
361 revolute: S17 (0,0,0) (SSbx,SSby,0)
362  S18 (SSb,0,0) (0,0,0)
363 
364 revolute: S18 (CSbx,CSby,0) (0,0,0)
365  C6 (0,0,0) (S3x,S3y,S3z)
366 
367 
368 revolute: C6 (0,0,0) (S0x,S0y,S0z)
369  S19 (CSb,0,0) (0,0,0)
370 
371 revolute: S19 (0,0,0) (SSbx,SSby,0)
372  S20 (SSb,0,0) (0,0,0)
373 
374 revolute: S20 (CSbx,CSby,0) (0,0,0)
375  C1 (0,0,0) (S2x,S2y,S2z)
376 
377 
378 revolute: C2 (0,0,0) (S3x,S3y,S3z)
379  S21 (CSb,0,0) (0,0,0)
380 
381 revolute: S21 (0,0,0) (SSbx,SSby,0)
382  S22 (SSb,0,0) (0,0,0)
383 
384 revolute: S22 (0,0,0) (SSbx,SSby,0)
385  S23 (SSb,0,0) (0,0,0)
386 
387 revolute: S23 (CSbx,CSby,0) (0,0,0)
388  C5 (0,0,0) (S3x,S3y,S3z)
389 
390 revolute: C5 (0,0,0) (S1x,S1y,S1z)
391  S24 (CSb,0,0) (0,0,0)
392 
393 revolute: S24 (0,0,0) (SSbx,SSby,0)
394  S25 (SSb,0,0) (0,0,0)
395 
396 revolute: S25 (0,0,0) (SSbx,SSby,0)
397  S26 (SSb,0,0) (0,0,0)
398 
399 revolute: S26 (CSbx,CSby,0) (0,0,0)
400  C4 (0,0,0) (S2x,S2y,S2z)
401 
402 
403 revolute: C4 (0,0,0) (S3x,S3y,S3z)
404  S27 (CSb,0,0) (0,0,0)
405 
406 revolute: S27 (0,0,0) (SSbx,SSby,0)
407  S28 (SSb,0,0) (0,0,0)
408 
409 revolute: S28 (0,0,0) (SSbx,SSby,0)
410  S29 (SSb,0,0) (0,0,0)
411 
412 revolute: S29 (CSbx,CSby,0) (0,0,0)
413  C6 (0,0,0) (S1x,S1y,S1z)
414 
415 
416 revolute: C6 (0,0,0) (S2x,S2y,S2z)
417  S30 (CSb,0,0) (0,0,0)
418 
419 revolute: S30 (0,0,0) (SSbx,SSby,0)
420  S31 (SSb,0,0) (0,0,0)
421 
422 revolute: S31 (0,0,0) (SSbx,SSby,0)
423  S32 (SSb,0,0) (0,0,0)
424 
425 revolute: S32 (CSbx,CSby,0) (0,0,0)
426  C2 (0,0,0) (S2x,S2y,S2z)
427 
428 
int main(int argc, char **arg)
Main body of the cuik application.
Definition: cuik.c:172