c8_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 liable to be used with the cuikbio tools.
5 % This pdb 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 20 and H is 5 (for this case)
15 
16 % reference bond lenghts
17 CHb:=1.093
18 CCb:=1.526
19 
20 % reference angles
21 % MMFF94 defines two references values for CCC angle
22 % the first one seems better (using 90 deg for the CCC
23 % angle produces extrange cyclooctane configurations
24 CCCa:=108.644*pi/180.0
25 % CCCa:=90.294*pi/180.0
26 
27 % MMFF94 uses 113.94 as a reference for HCC angle
28 % but 109.77 adjusts better the HCH angle (otherwise
29 % the HCH angle is about 91 which is quite different
30 % from the reference (109.107). Something in
31 % betwen 109 and 113 (110.02) produces less combined error.
32 % HCCa:=113.94*pi/180.0
33 HCCa:=110.02*pi/180.0
34 % HCCa:=109.77*pi/180
35 
36 HCHa:=109.107*pi/180.0
37 
38 CC2x:=CCb*cos(CCCa)
39 CC2y:=CCb*sin(CCCa)
40 
41 % distance of non-bonded C-H (with a C in between them)
42 % cosine rule
43 CHb2:=sqrt(CCb^2+CHb^2-2*CCb*CHb*cos(HCCa))
44 
45 % The positions of H are determined intersecting 3 spheres
46 % One with radius CHb at (0,0,0)
47 % Two with radious CHb2 at (CCb,0,0) and (CC2x,CC2y,0)
48 Hx:=(CHb^2-CHb2^2+CCb^2)/(2*CCb)
49 Hy:=((Hx-CC2x)^2-(Hx-CCb)^2+CC2y^2)/(2*CC2y)
50 Hz:=sqrt(CHb^2-Hx^2-Hy^2)
51 
52 % Reduction over the Van der Waals radious
53 VdWRatio:=0.7
54 
55 % Radious of the spheres representing atoms
56 rC:=1.7*VdWRatio
57 rH:=1.1*VdWRatio
58 
59 % Radious of the cylinders representing bonds
60 rCC:=0.15
61 rCH:=0.15
62 
63 % Colors for the atoms
64 Cr:=0.2
65 Cg:=0.6
66 Cb:=0.6
67 
68 Hr:=1
69 Hg:=1
70 Hb:=1
71 
72 [LINKS]
73 
74 C1 : sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
75  cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
76  cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
77  cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
78  cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
79  sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
80  cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
81  cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
82  sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)
83 
84 C2 : sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
85  cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
86  cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
87  cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
88  cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
89  sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
90  cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
91  cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
92  sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)
93 
94 C3 : sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
95  cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
96  cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
97  cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
98  cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
99  sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
100  cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
101  cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
102  sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)
103 
104 C4 : sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
105  cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
106  cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
107  cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
108  cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
109  sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
110  cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
111  cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
112  sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)
113 
114 C5 : sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
115  cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
116  cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) 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  sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
120  cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
121  cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
122  sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)
123 
124 C6 : sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
125  cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
126  cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
127  cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
128  cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
129  sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
130  cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
131  cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
132  sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)
133 
134 C7 : sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
135  cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
136  cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
137  cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
138  cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
139  sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
140  cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
141  cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
142  sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)
143 
144 C8 : sphere rC (0,0,0) color (Cr,Cg,Cb) decoration
145  cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
146  cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
147  cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
148  cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
149  sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
150  cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
151  cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
152  sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)
153 
154 [JOINTS]
155 
156 % We define the revolute joints trying to use as much zeros as possible
157 % in the two first points of the two axes in local coordinates. This produces
158 % simpler equation sets.
159 revolute: C1 (CCb,0,0) (0,0,0)
160  C2 (0,0,0) (CC2x,CC2y,0)
161 
162 revolute: C2 (CCb,0,0) (0,0,0)
163  C3 (0,0,0) (CC2x,CC2y,0)
164 
165 revolute: C3 (CCb,0,0) (0,0,0)
166  C4 (0,0,0) (CC2x,CC2y,0)
167 
168 revolute: C4 (CCb,0,0) (0,0,0)
169  C5 (0,0,0) (CC2x,CC2y,0)
170 
171 revolute: C5 (CCb,0,0) (0,0,0)
172  C6 (0,0,0) (CC2x,CC2y,0)
173 
174 revolute: C6 (CCb,0,0) (0,0,0)
175  C7 (0,0,0) (CC2x,CC2y,0)
176 
177 revolute: C7 (CCb,0,0) (0,0,0)
178  C8 (0,0,0) (CC2x,CC2y,0)
179 
180 revolute: C8 (CCb,0,0) (0,0,0)
181  C1 (0,0,0) (CC2x,CC2y,0)
182 
183 
184 [COLLISIONS]
185 
186 check:all
187 
188 /*
189 do not check: all
190 
191 check : C1,C4
192 check : C1,C5
193 check : C1,C6
194 
195 check : C2,C5
196 check : C2,C6
197 check : C2,C7
198 
199 check : C3,C6
200 check : C3,C7
201 check : C3,C8
202 
203 check : C4,C7
204 check : C4,C8
205 
206 check : C5,C8
207 */
208