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5 % We define a reference frame attache to each C atom with the
6 % X axis along one of the C-C bonds and with the X-Y plane in
7 % the planed defined by the two bonds coincident in the C.
9 % All distances are in Amstrongs and all angles are in radiants
14 % H-C distance for C the neighbouring C of the C to which H
24 % The firts CC bond is aligned with the X axis and has lenght CCb
25 % The second is in the XY plane at position:
29 % x-y-z position of one of the H w.r.t. a frame attached to the C
30 % The second H is symmetrically placed (w.r.t. the X-Y plane).
31 % This H is at (Hx,Hy,Hz) that is at the intersection of three circunferences
32 % Hx^2+Hy^2+Hz^2=HCb^2
33 % (Hx-CCb)^2+Hy^2+Hz^2=HCb2^2
34 % (Hx-CC2x)^2+(Hy-CC2y)^2+Hz^2=HCb2^2
36 Hx:=(HCb^2-HCb2^2+CCb^2)/(2*CCb)
37 Hy:=((Hx-CC2x)^2-(Hx-CCb)^2+CC2y^2)/(2*CC2y)
40 % Radious of the spheres representing atoms (75% Van der Waals radii)
44 % Radious of the cylinders representing bonds
48 % Colors for the atoms
59 C1 : sphere rC (0,0,0) color (Cr,Cg,Cb)
60 cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
61 cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
62 cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
63 cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
64 sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
65 cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
66 cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
67 sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)
69 C2 : sphere rC (0,0,0) color (Cr,Cg,Cb)
70 cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
71 cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
72 cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
73 cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
74 sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
75 cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
76 cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
77 sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)
79 C3 : sphere rC (0,0,0) color (Cr,Cg,Cb)
80 cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
81 cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
82 cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
83 cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
84 sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
85 cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
86 cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
87 sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)
89 C4 : sphere rC (0,0,0) color (Cr,Cg,Cb)
90 cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
91 cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
92 cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
93 cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
94 sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
95 cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
96 cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
97 sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)
99 C5 : sphere rC (0,0,0) color (Cr,Cg,Cb)
100 cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
101 cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
102 cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
103 cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
104 sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
105 cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
106 cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
107 sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)
109 C6 : sphere rC (0,0,0) color (Cr,Cg,Cb)
110 cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
111 cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
112 cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
113 cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
114 sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
115 cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
116 cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
117 sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)
119 C7 : sphere rC (0,0,0) color (Cr,Cg,Cb)
120 cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
121 cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
122 cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
123 cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
124 sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
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 sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)
131 % We define the revolute joints trying to use as much zeros as possible
132 % in the two first points of the two axes in local coordinates. This produces
133 % simpler equation sets.
134 revolute: C1 (CCb,0,0) (0,0,0)
135 C2 (0,0,0) (CC2x,CC2y,0)
137 revolute: C2 (CCb,0,0) (0,0,0)
138 C3 (0,0,0) (CC2x,CC2y,0)
140 revolute: C3 (CCb,0,0) (0,0,0)
141 C4 (0,0,0) (CC2x,CC2y,0)
143 revolute: C4 (CCb,0,0) (0,0,0)
144 C5 (0,0,0) (CC2x,CC2y,0)
146 revolute: C5 (CCb,0,0) (0,0,0)
147 C6 (0,0,0) (CC2x,CC2y,0)
149 revolute: C6 (CCb,0,0) (0,0,0)
150 C7 (0,0,0) (CC2x,CC2y,0)
152 revolute: C7 (CCb,0,0) (0,0,0)
153 C1 (0,0,0) (CC2x,CC2y,0)
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