csh2_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 % local coordinates of the H and C atoms from the Carbon corners
47 Hx:=0
48 Hy:=0
49 Hz:=CHb
50 
51 d:= CSb*sqrt(2-2*cos(SCSa))
52 x:= d/sqrt(3)
53 y:= d/2
54 z:=-sqrt(CSb^2-x^2)
55 
56 S1x:= x
57 S1y:= 0
58 S1z:= z
59 
60 S2x:=-x/2
61 S2y:= y
62 S2z:= z
63 
64 S3x:=-x/2
65 S3y:=-y
66 S3z:= z
67 
68 % angle of the C-S bond
69 CSbx:=CSb*cos(CSSa)
70 CSby:=CSb*sin(CSSa)
71 
72 % angle of the S-S bond
73 SSbx:=SSb*cos(SSSa)
74 SSby:=SSb*sin(SSSa)
75 
76 % Reduction over the Van der Waals radious
77 VdWRatio:=0.25 % 0.7
78 
79 % Radious of the spheres representing atoms
80 rC:=1.7*VdWRatio
81 rH:=1.1*VdWRatio
82 rS:=1.8*VdWRatio
83 
84 % Radious of the cylinders representing bonds
85 rCS:=0.15
86 rCH:=0.15
87 rSS:=0.15
88 
89 % Colors for the atoms
90 Cr:=0.2
91 Cg:=0.6
92 Cb:=0.6
93 
94 Hr:=1
95 Hg:=1
96 Hb:=1
97 
98 Sr:=1
99 Sg:=1
100 Sb:=0
101 
102 
103 [LINKS]
104 
105 % Atoms in the main ring
106 
107 C1: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
108  sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
109  cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
110  cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
111  cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
112  cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
113  cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
114 
115 S1: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
116  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
117  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
118 
119 S2: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
120  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
121  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
122 
123 C2: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
124  sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
125  cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
126  cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
127  cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
128  cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
129  cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
130 
131 S3: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
132  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
133  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
134 
135 S4: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
136  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
137  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
138 
139 S5: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
140  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
141  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
142 
143 C3: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
144  sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
145  cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
146  cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
147  cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
148  cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
149  cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
150 
151 S6: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
152  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
153  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
154 
155 S7: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
156  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
157  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
158 
159 S8: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
160  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
161  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
162 
163 C4: sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
164  sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
165  cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
166  cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
167  cylinder rCS (0,0,0) (S1x/2,S1y/2,S1z/2) color (Cr,Cg,Cb) decoration
168  cylinder rCS (0,0,0) (S2x/2,S2y/2,S2z/2) color (Cr,Cg,Cb) decoration
169  cylinder rCS (0,0,0) (S3x/2,S3y/2,S3z/2) color (Cr,Cg,Cb) decoration
170 
171 S9: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
172  cylinder rCS (0,0,0) (CSb/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 S10: 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 % Atoms defining the two other rings (2 S per connection)
180 
181 
182 S11: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
183  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
184  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
185 
186 S12: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
187  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
188  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
189 
190 
191 S13: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
192  cylinder rCS (0,0,0) (CSb/2,0,0) color (Sr,Sg,Sb) decoration
193  cylinder rSS (0,0,0) (SSbx/2,SSby/2,0) color (Sr,Sg,Sb) decoration
194 
195 S14: sphere rS (0,0,0) color (Sr,Sg,Sb) decoration
196  cylinder rCS (0,0,0) (SSb/2,0,0) color (Sr,Sg,Sb) decoration
197  cylinder rSS (0,0,0) (CSbx/2,CSby/2,0) color (Sr,Sg,Sb) decoration
198 
199 
200 [JOINTS]
201 
202 % main ring C-S-S-C-S-S-S-C-S-S-S-C-S-S
203 revolute: C1 (0,0,0) (S1x,S1y,S1z)
204  S1 (CSb,0,0) (0,0,0)
205 
206 revolute: S1 (0,0,0) (SSbx,SSby,0)
207  S2 (SSb,0,0) (0,0,0)
208 
209 revolute: S2 (CSbx,CSby,0) (0,0,0)
210  C2 (0,0,0) (S3x,S3y,S3z)
211 
212 revolute: C2 (0,0,0) (S1x,S1y,S1z)
213  S3 (CSb,0,0) (0,0,0)
214 
215 revolute: S3 (0,0,0) (SSbx,SSby,0)
216  S4 (SSb,0,0) (0,0,0)
217 
218 revolute: S4 (0,0,0) (SSbx,SSby,0)
219  S5 (SSb,0,0) (0,0,0)
220 
221 revolute: S5 (CSbx,CSby,0) (0,0,0)
222  C3 (0,0,0) (S2x,S2y,S2z)
223 
224 revolute: C3 (0,0,0) (S1x,S1y,S1z)
225  S6 (CSb,0,0) (0,0,0)
226 
227 revolute: S6 (0,0,0) (SSbx,SSby,0)
228  S7 (SSb,0,0) (0,0,0)
229 
230 revolute: S7 (0,0,0) (SSbx,SSby,0)
231  S8 (SSb,0,0) (0,0,0)
232 
233 revolute: S8 (CSbx,CSby,0) (0,0,0)
234  C4 (0,0,0) (S3x,S3y,S3z)
235 
236 revolute: C4 (0,0,0) (S1x,S1y,S1z)
237  S9 (CSb,0,0) (0,0,0)
238 
239 revolute: S9 (0,0,0) (SSbx,SSby,0)
240  S10 (SSb,0,0) (0,0,0)
241 
242 revolute: S10 (CSbx,CSby,0) (0,0,0)
243  C1 (0,0,0) (S2x,S2y,S2z)
244 
245 
246 % Connections defining the two other rings
247 
248 revolute: C1 (0,0,0) (S3x,S3y,S3z)
249  S11 (CSb,0,0) (0,0,0)
250 
251 revolute: S11 (0,0,0) (SSbx,SSby,0)
252  S12 (SSb,0,0) (0,0,0)
253 
254 revolute: S12 (CSbx,CSby,0) (0,0,0)
255  C3 (0,0,0) (S3x,S3y,S3z)
256 
257 revolute: C4 (0,0,0) (S2x,S2y,S2z)
258  S13 (CSb,0,0) (0,0,0)
259 
260 revolute: S13 (0,0,0) (SSbx,SSby,0)
261  S14 (SSb,0,0) (0,0,0)
262 
263 revolute: S14 (CSbx,CSby,0) (0,0,0)
264  C2 (0,0,0) (S2x,S2y,S2z)
265 
266 
267 
main
int main(int argc, char **arg)
Main body of the cuik application.
Definition: cuik.c:172