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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)
14 % in MMFF94 C is 20 and H is 5 ( for this case)
16 % reference bond lenghts
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
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
36 HCHa:=109.107*pi/180.0
41 % distance of non-bonded C-H (with a C in between them)
43 CHb2:=sqrt(CCb^2+CHb^2-2*CCb*CHb*cos(HCCa))
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)
52 % Reduction over the Van der Waals radious
55 % Radious of the spheres representing atoms
59 % Radious of the cylinders representing bonds
63 % Colors for the atoms
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)
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)
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)
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)
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)
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)
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)
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)
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)
162 revolute: C2 (CCb,0,0) (0,0,0)
163 C3 (0,0,0) (CC2x,CC2y,0)
165 revolute: C3 (CCb,0,0) (0,0,0)
166 C4 (0,0,0) (CC2x,CC2y,0)
168 revolute: C4 (CCb,0,0) (0,0,0)
169 C5 (0,0,0) (CC2x,CC2y,0)
171 revolute: C5 (CCb,0,0) (0,0,0)
172 C6 (0,0,0) (CC2x,CC2y,0)
174 revolute: C6 (CCb,0,0) (0,0,0)
175 C7 (0,0,0) (CC2x,CC2y,0)
177 revolute: C7 (CCb,0,0) (0,0,0)
178 C8 (0,0,0) (CC2x,CC2y,0)
180 revolute: C8 (CCb,0,0) (0,0,0)
181 C1 (0,0,0) (CC2x,CC2y,0)
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