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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)
14 % in MMFF94 C is 1, S is 15, and H is 5 ( for this case)
16 % ---------------------------------------------------------
17 % Parameters taken from the force field definition
18 % reference bond lenghts
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
29 % ---------------------------------------------------------
31 % ---------------------------------------------------------
32 % Artificial parameters used in previous papers
33 % reference bond lenghts
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
44 % ---------------------------------------------------------
46 d:= CSb*sqrt(2-2*cos(SCSa))
67 % angle of the C-S bond
71 % angle of the S-S bond
75 % Reduction over the Van der Waals radious
78 % Radious of the spheres representing atoms
83 % Radious of the cylinders representing bonds
88 % Colors for the atoms
104 % Atoms in the main ring
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
288 revolute: C1 (0,0,0) (S1x,S1y,S1z)
291 revolute: S1 (0,0,0) (SSbx,SSby,0)
294 revolute: S2 (0,0,0) (SSbx,SSby,0)
297 revolute: S3 (CSbx,CSby,0) (0,0,0)
298 C2 (0,0,0) (S0x,S0y,S0z)
300 revolute: C2 (0,0,0) (S1x,S1y,S1z)
303 revolute: S4 (0,0,0) (SSbx,SSby,0)
306 revolute: S5 (0,0,0) (SSbx,SSby,0)
309 revolute: S6 (CSbx,CSby,0) (0,0,0)
310 C3 (0,0,0) (S1x,S1y,S1z)
312 revolute: C3 (0,0,0) (S2x,S2y,S2z)
315 revolute: S7 (0,0,0) (SSbx,SSby,0)
318 revolute: S8 (0,0,0) (SSbx,SSby,0)
321 revolute: S9 (CSbx,CSby,0) (0,0,0)
322 C4 (0,0,0) (S1x,S1y,S1z)
324 revolute: C4 (0,0,0) (S0x,S0y,S0z)
325 S10 (CSb,0,0) (0,0,0)
327 revolute: S10 (0,0,0) (SSbx,SSby,0)
328 S11 (SSb,0,0) (0,0,0)
330 revolute: S11 (0,0,0) (SSbx,SSby,0)
331 S12 (SSb,0,0) (0,0,0)
333 revolute: S12 (CSbx,CSby,0) (0,0,0)
334 C1 (0,0,0) (S3x,S3y,S3z)
336 % Connections defining the two other rings
338 revolute: C1 (0,0,0) (S0x,S0y,S0z)
339 S13 (CSb,0,0) (0,0,0)
341 revolute: S13 (0,0,0) (SSbx,SSby,0)
342 S14 (SSb,0,0) (0,0,0)
344 revolute: S14 (CSbx,CSby,0) (0,0,0)
345 C5 (0,0,0) (S0x,S0y,S0z)
348 revolute: C5 (0,0,0) (S2x,S2y,S2z)
349 S15 (CSb,0,0) (0,0,0)
351 revolute: S15 (0,0,0) (SSbx,SSby,0)
352 S16 (SSb,0,0) (0,0,0)
354 revolute: S16 (CSbx,CSby,0) (0,0,0)
355 C3 (0,0,0) (S0x,S0y,S0z)
358 revolute: C3 (0,0,0) (S3x,S3y,S3z)
359 S17 (CSb,0,0) (0,0,0)
361 revolute: S17 (0,0,0) (SSbx,SSby,0)
362 S18 (SSb,0,0) (0,0,0)
364 revolute: S18 (CSbx,CSby,0) (0,0,0)
365 C6 (0,0,0) (S3x,S3y,S3z)
368 revolute: C6 (0,0,0) (S0x,S0y,S0z)
369 S19 (CSb,0,0) (0,0,0)
371 revolute: S19 (0,0,0) (SSbx,SSby,0)
372 S20 (SSb,0,0) (0,0,0)
374 revolute: S20 (CSbx,CSby,0) (0,0,0)
375 C1 (0,0,0) (S2x,S2y,S2z)
378 revolute: C2 (0,0,0) (S3x,S3y,S3z)
379 S21 (CSb,0,0) (0,0,0)
381 revolute: S21 (0,0,0) (SSbx,SSby,0)
382 S22 (SSb,0,0) (0,0,0)
384 revolute: S22 (0,0,0) (SSbx,SSby,0)
385 S23 (SSb,0,0) (0,0,0)
387 revolute: S23 (CSbx,CSby,0) (0,0,0)
388 C5 (0,0,0) (S3x,S3y,S3z)
390 revolute: C5 (0,0,0) (S1x,S1y,S1z)
391 S24 (CSb,0,0) (0,0,0)
393 revolute: S24 (0,0,0) (SSbx,SSby,0)
394 S25 (SSb,0,0) (0,0,0)
396 revolute: S25 (0,0,0) (SSbx,SSby,0)
397 S26 (SSb,0,0) (0,0,0)
399 revolute: S26 (CSbx,CSby,0) (0,0,0)
400 C4 (0,0,0) (S2x,S2y,S2z)
403 revolute: C4 (0,0,0) (S3x,S3y,S3z)
404 S27 (CSb,0,0) (0,0,0)
406 revolute: S27 (0,0,0) (SSbx,SSby,0)
407 S28 (SSb,0,0) (0,0,0)
409 revolute: S28 (0,0,0) (SSbx,SSby,0)
410 S29 (SSb,0,0) (0,0,0)
412 revolute: S29 (CSbx,CSby,0) (0,0,0)
413 C6 (0,0,0) (S1x,S1y,S1z)
416 revolute: C6 (0,0,0) (S2x,S2y,S2z)
417 S30 (CSb,0,0) (0,0,0)
419 revolute: S30 (0,0,0) (SSbx,SSby,0)
420 S31 (SSb,0,0) (0,0,0)
422 revolute: S31 (0,0,0) (SSbx,SSby,0)
423 S32 (SSb,0,0) (0,0,0)
425 revolute: S32 (CSbx,CSby,0) (0,0,0)
426 C2 (0,0,0) (S2x,S2y,S2z)
int main(int argc, char **arg) Main body of the cuik application.
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