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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 % ---------------------------------------------------------
29 % ---------------------------------------------------------
30 % Artificial parameters used in previous papers
31 % reference bond lenghts
37 SCSa:=109.5*pi/180 % 15 1 15
38 HCSa:=109.5*pi/180 % 5 1 15
39 CSSa:=135.0*pi/180 % 1 15 15
40 % ---------------------------------------------------------
42 % local coordinates of the H and C atoms from the Carbon corners
47 d:= CSb*sqrt(2-2*cos(SCSa))
64 % Rotation of the C-S bond
68 % Reduction over the Van der Waals radious
71 % Radious of the spheres representing atoms
76 % Radious of the cylinders representing bonds
81 % Colors for the atoms
97 % Atoms in the first ring
99 C1: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
100 sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
101 cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
102 cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
103 cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
104 cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
105 cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
107 S1: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
108 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
109 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
111 S2: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
112 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
113 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
115 C2: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
116 sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
117 cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
118 cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
119 cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
120 cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
121 cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
123 S3: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
124 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
125 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
127 S4: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
128 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
129 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
131 C3: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
132 sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
133 cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
134 cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
135 cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
136 cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
137 cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
139 S5: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
140 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
141 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
143 S6: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
144 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
145 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
147 C4: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
148 sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
149 cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
150 cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
151 cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
152 cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
153 cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
155 S7: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
156 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
157 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
159 S8: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
160 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
161 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
163 % Atoms in the second ring
165 C5: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
166 sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
167 cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
168 cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
169 cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
170 cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
171 cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
173 S9: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
174 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
175 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
177 S10: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
178 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
179 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
181 C6: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
182 sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
183 cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
184 cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
185 cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
186 cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
187 cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
189 S11: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
190 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
191 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
193 S12: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
194 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
195 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
197 C7: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
198 sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
199 cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
200 cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
201 cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
202 cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
203 cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
205 S13: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
206 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
207 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
209 S14: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
210 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
211 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
213 C8: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
214 sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
215 cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
216 cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
217 cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
218 cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
219 cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
221 S15: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
222 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
223 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
225 S16: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
226 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
227 cylinder rSS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
229 % Sulfulre atoms joining the two rings
231 S17: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
232 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
233 cylinder rSS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
235 S18: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
236 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
237 cylinder rSS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
239 S19: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
240 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
241 cylinder rSS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
243 S20: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
244 cylinder rCS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
245 cylinder rSS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
249 % first ring C-S-S-C-S-S-C-S-S-C-S-S
250 revolute: C1 (0,0,0) (S1x,S1y,S1z)
251 S1 (CSbx,CSby,0) (0,0,0)
253 revolute: S1 (0,0,0) (SSb,0,0)
256 revolute: C2 (0,0,0) (S2x,S2y,S2z)
257 S2 (CSbx,CSby,0) (0,0,0)
259 revolute: C2 (0,0,0) (S1x,S1y,S1z)
260 S3 (CSbx,CSby,0) (0,0,0)
262 revolute: S3 (0,0,0) (SSb,0,0)
265 revolute: C3 (0,0,0) (S2x,S2y,S2z)
266 S4 (CSbx,CSby,0) (0,0,0)
268 revolute: C3 (0,0,0) (S1x,S1y,S1z)
269 S5 (CSbx,CSby,0) (0,0,0)
271 revolute: S5 (0,0,0) (SSb,0,0)
274 revolute: C4 (0,0,0) (S2x,S2y,S2z)
275 S6 (CSbx,CSby,0) (0,0,0)
277 revolute: C4 (0,0,0) (S1x,S1y,S1z)
278 S7 (CSbx,CSby,0) (0,0,0)
280 revolute: S7 (0,0,0) (SSb,0,0)
283 revolute: C1 (0,0,0) (S2x,S2y,S2z)
284 S8 (CSbx,CSby,0) (0,0,0)
287 % second ring C-S-S-C-S-S-C-S-S-C-S-S
288 revolute: C5 (0,0,0) (S3x,S3y,S3z)
289 S9 (CSbx,CSby,0) (0,0,0)
291 revolute: S9 (0,0,0) (SSb,0,0)
292 S10 (SSb,0,0) (0,0,0)
294 revolute: C6 (0,0,0) (S2x,S2y,S2z)
295 S10 (CSbx,CSby,0) (0,0,0)
297 revolute: C6 (0,0,0) (S3x,S3y,S3z)
298 S11 (CSbx,CSby,0) (0,0,0)
300 revolute: S11 (0,0,0) (SSb,0,0)
301 S12 (SSb,0,0) (0,0,0)
303 revolute: C7 (0,0,0) (S2x,S2y,S2z)
304 S12 (CSbx,CSby,0) (0,0,0)
306 revolute: C7 (0,0,0) (S3x,S3y,S3z)
307 S13 (CSbx,CSby,0) (0,0,0)
309 revolute: S13 (0,0,0) (SSb,0,0)
310 S14 (SSb,0,0) (0,0,0)
312 revolute: C8 (0,0,0) (S2x,S2y,S2z)
313 S14 (CSbx,CSby,0) (0,0,0)
315 revolute: C8 (0,0,0) (S3x,S3y,S3z)
316 S15 (CSbx,CSby,0) (0,0,0)
318 revolute: S15 (0,0,0) (SSb,0,0)
319 S16 (SSb,0,0) (0,0,0)
321 revolute: C5 (0,0,0) (S2x,S2y,S2z)
322 S16 (CSbx,CSby,0) (0,0,0)
325 % joining the two rings
327 revolute: C1 (0,0,0) (S3x,S3y,S3z)
328 S17 (CSbx,CSby,0) (0,0,0)
330 revolute: C5 (0,0,0) (S1x,S1y,S1z)
331 S17 (CSb,0,0) (0,0,0)
333 revolute: C2 (0,0,0) (S3x,S3y,S3z)
334 S18 (CSbx,CSby,0) (0,0,0)
336 revolute: C6 (0,0,0) (S1x,S1y,S1z)
337 S18 (CSb,0,0) (0,0,0)
339 revolute: C3 (0,0,0) (S3x,S3y,S3z)
340 S19 (CSbx,CSby,0) (0,0,0)
342 revolute: C7 (0,0,0) (S1x,S1y,S1z)
343 S19 (CSb,0,0) (0,0,0)
345 revolute: C4 (0,0,0) (S3x,S3y,S3z)
346 S20 (CSbx,CSby,0) (0,0,0)
348 revolute: C8 (0,0,0) (S1x,S1y,S1z)
349 S20 (CSb,0,0) (0,0,0)
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