Go to the documentation of this file.
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 % local coordinates of the H and C atoms from the Carbon corners
51 d:= CSb*sqrt(2-2*cos(SCSa))
68 % angle of the C-S bond
72 % angle of the S-S bond
76 % Reduction over the Van der Waals radious
79 % Radious of the spheres representing atoms
84 % Radious of the cylinders representing bonds
89 % Colors for the atoms
105 % Atoms in the main ring
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
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
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
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
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
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
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
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
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
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
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
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
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
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
179 % Atoms defining the two other rings (2 S per connection)
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
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
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
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
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)
206 revolute: S1 (0,0,0) (SSbx,SSby,0)
209 revolute: S2 (CSbx,CSby,0) (0,0,0)
210 C2 (0,0,0) (S3x,S3y,S3z)
212 revolute: C2 (0,0,0) (S1x,S1y,S1z)
215 revolute: S3 (0,0,0) (SSbx,SSby,0)
218 revolute: S4 (0,0,0) (SSbx,SSby,0)
221 revolute: S5 (CSbx,CSby,0) (0,0,0)
222 C3 (0,0,0) (S2x,S2y,S2z)
224 revolute: C3 (0,0,0) (S1x,S1y,S1z)
227 revolute: S6 (0,0,0) (SSbx,SSby,0)
230 revolute: S7 (0,0,0) (SSbx,SSby,0)
233 revolute: S8 (CSbx,CSby,0) (0,0,0)
234 C4 (0,0,0) (S3x,S3y,S3z)
236 revolute: C4 (0,0,0) (S1x,S1y,S1z)
239 revolute: S9 (0,0,0) (SSbx,SSby,0)
240 S10 (SSb,0,0) (0,0,0)
242 revolute: S10 (CSbx,CSby,0) (0,0,0)
243 C1 (0,0,0) (S2x,S2y,S2z)
246 % Connections defining the two other rings
248 revolute: C1 (0,0,0) (S3x,S3y,S3z)
249 S11 (CSb,0,0) (0,0,0)
251 revolute: S11 (0,0,0) (SSbx,SSby,0)
252 S12 (SSb,0,0) (0,0,0)
254 revolute: S12 (CSbx,CSby,0) (0,0,0)
255 C3 (0,0,0) (S3x,S3y,S3z)
257 revolute: C4 (0,0,0) (S2x,S2y,S2z)
258 S13 (CSb,0,0) (0,0,0)
260 revolute: S13 (0,0,0) (SSbx,SSby,0)
261 S14 (SSb,0,0) (0,0,0)
263 revolute: S14 (CSbx,CSby,0) (0,0,0)
264 C2 (0,0,0) (S2x,S2y,S2z)
int main(int argc, char **arg) Main body of the cuik application.
|
Follow us!