csh_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 % ---------------------------------------------------------
28 
29 % ---------------------------------------------------------
30 % Artificial parameters used in previous papers
31 % reference bond lenghts
32 CHb:=1.120
33 CSb:=1.805
34 SSb:=2.019
35 
36 % reference angles
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 % ---------------------------------------------------------
41 
42 % local coordinates of the H and C atoms from the Carbon corners
43 Hx:=0
44 Hy:=0
45 Hz:=CHb
46 
47 d:= CSb*sqrt(2-2*cos(SCSa))
48 x:= d/sqrt(3)
49 y:= d/2
50 z:=-sqrt(CSb^2-x^2)
51 
52 S1x:= x
53 S1y:= 0
54 S1z:= z
55 
56 S2x:=-x/2
57 S2y:= y
58 S2z:= z
59 
60 S3x:=-x/2
61 S3y:=-y
62 S3z:= z
63 
64 % Rotation of the C-S bond
65 CSbx:=CSb*cos(CSSa)
66 CSby:=CSb*sin(CSSa)
67 
68 % Reduction over the Van der Waals radious
69 VdWRatio:=0.25 % 0.7
70 
71 % Radious of the spheres representing atoms
72 rC:=1.7*VdWRatio
73 rH:=1.1*VdWRatio
74 rS:=1.8*VdWRatio
75 
76 % Radious of the cylinders representing bonds
77 rCS:=0.15
78 rCH:=0.15
79 rSS:=0.15
80 
81 % Colors for the atoms
82 Cr:=0.2
83 Cg:=0.6
84 Cb:=0.6
85 
86 Hr:=1
87 Hg:=1
88 Hb:=1
89 
90 Sr:=1
91 Sg:=1
92 Sb:=0
93 
94 
95 [LINKS]
96 
97 % Atoms in the first ring
98 
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
106 
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
110 
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
114 
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
122 
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
126 
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
130 
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
138 
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
142 
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
146 
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
154 
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
158 
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
162 
163 % Atoms in the second ring
164 
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
172 
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
176 
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
180 
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
188 
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
192 
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
196 
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
204 
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
208 
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
212 
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
220 
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
224 
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
228 
229 % Sulfulre atoms joining the two rings
230 
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
234 
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
238 
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
242 
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
246 
247 [JOINTS]
248 
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)
252 
253 revolute: S1 (0,0,0) (SSb,0,0)
254  S2 (SSb,0,0) (0,0,0)
255 
256 revolute: C2 (0,0,0) (S2x,S2y,S2z)
257  S2 (CSbx,CSby,0) (0,0,0)
258 
259 revolute: C2 (0,0,0) (S1x,S1y,S1z)
260  S3 (CSbx,CSby,0) (0,0,0)
261 
262 revolute: S3 (0,0,0) (SSb,0,0)
263  S4 (SSb,0,0) (0,0,0)
264 
265 revolute: C3 (0,0,0) (S2x,S2y,S2z)
266  S4 (CSbx,CSby,0) (0,0,0)
267 
268 revolute: C3 (0,0,0) (S1x,S1y,S1z)
269  S5 (CSbx,CSby,0) (0,0,0)
270 
271 revolute: S5 (0,0,0) (SSb,0,0)
272  S6 (SSb,0,0) (0,0,0)
273 
274 revolute: C4 (0,0,0) (S2x,S2y,S2z)
275  S6 (CSbx,CSby,0) (0,0,0)
276 
277 revolute: C4 (0,0,0) (S1x,S1y,S1z)
278  S7 (CSbx,CSby,0) (0,0,0)
279 
280 revolute: S7 (0,0,0) (SSb,0,0)
281  S8 (SSb,0,0) (0,0,0)
282 
283 revolute: C1 (0,0,0) (S2x,S2y,S2z)
284  S8 (CSbx,CSby,0) (0,0,0)
285 
286 
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)
290 
291 revolute: S9 (0,0,0) (SSb,0,0)
292  S10 (SSb,0,0) (0,0,0)
293 
294 revolute: C6 (0,0,0) (S2x,S2y,S2z)
295  S10 (CSbx,CSby,0) (0,0,0)
296 
297 revolute: C6 (0,0,0) (S3x,S3y,S3z)
298  S11 (CSbx,CSby,0) (0,0,0)
299 
300 revolute: S11 (0,0,0) (SSb,0,0)
301  S12 (SSb,0,0) (0,0,0)
302 
303 revolute: C7 (0,0,0) (S2x,S2y,S2z)
304  S12 (CSbx,CSby,0) (0,0,0)
305 
306 revolute: C7 (0,0,0) (S3x,S3y,S3z)
307  S13 (CSbx,CSby,0) (0,0,0)
308 
309 revolute: S13 (0,0,0) (SSb,0,0)
310  S14 (SSb,0,0) (0,0,0)
311 
312 revolute: C8 (0,0,0) (S2x,S2y,S2z)
313  S14 (CSbx,CSby,0) (0,0,0)
314 
315 revolute: C8 (0,0,0) (S3x,S3y,S3z)
316  S15 (CSbx,CSby,0) (0,0,0)
317 
318 revolute: S15 (0,0,0) (SSb,0,0)
319  S16 (SSb,0,0) (0,0,0)
320 
321 revolute: C5 (0,0,0) (S2x,S2y,S2z)
322  S16 (CSbx,CSby,0) (0,0,0)
323 
324 
325 % joining the two rings
326 
327 revolute: C1 (0,0,0) (S3x,S3y,S3z)
328  S17 (CSbx,CSby,0) (0,0,0)
329 
330 revolute: C5 (0,0,0) (S1x,S1y,S1z)
331  S17 (CSb,0,0) (0,0,0)
332 
333 revolute: C2 (0,0,0) (S3x,S3y,S3z)
334  S18 (CSbx,CSby,0) (0,0,0)
335 
336 revolute: C6 (0,0,0) (S1x,S1y,S1z)
337  S18 (CSb,0,0) (0,0,0)
338 
339 revolute: C3 (0,0,0) (S3x,S3y,S3z)
340  S19 (CSbx,CSby,0) (0,0,0)
341 
342 revolute: C7 (0,0,0) (S1x,S1y,S1z)
343  S19 (CSb,0,0) (0,0,0)
344 
345 revolute: C4 (0,0,0) (S3x,S3y,S3z)
346  S20 (CSbx,CSby,0) (0,0,0)
347 
348 revolute: C8 (0,0,0) (S1x,S1y,S1z)
349  S20 (CSb,0,0) (0,0,0)
350 
351