Viewing Program

Program Data

Program thumbnail for "{props.program.title}"

Title	3D double stranded DNA
ID	1170514481
Created	13 years ago, 1353847176596
Updated	12 years ago, 1366376274434
Code	/*************************************************** * 3D molecule viewer - Single stranded DNA * Double stranded DNA of sequence ACCGACGTCGGT * In the B-form helix * * Use the mouse or keyboard to rotate the molecule * * Red: Oxygen atoms * Blue: Nitrogen atoms * Dark Grey: Carbon atoms * * Need to add double bonds * * Coordinates from: * http://oca.weizmann.ac.il/oca-bin/send-pdb?id=1bna **************************************************/ var atomSize = 4; var bondThickness = 3; var bondColour = color(64, 61, 64, 160); var backgroundColour = color(250, 250, 255); var Atom = function(element, x, y, z) { this.element = element; this.x = x; this.y = y; this.z = z; if (element === "H") { this.colour = color(180, 180, 180, 220); this.size = atomSize 1.2; } else if (element === "C") { this.colour = color(64, 61, 64, 220); this.size = atomSize * 1.7; } else if (element === "N") { this.colour = color(68, 75, 219, 220); this.size = atomSize * 1.55; } else if (element === "O") { this.colour = color(250, 15, 15, 220); this.size = atomSize * 1.52; } else if (element === "P") { this.colour = color(237, 107, 7, 220); this.size = atomSize * 1.8; } this.draw = function() { var fade = 1 - (this.z + 300) / 600; //fill(lerpColor(this.colour, backgroundColour, fade)); fill(this.colour); ellipse(this.x, this.y, this.size, this.size); }; }; // Coordinates for molecule from http://www.rcsb.org/pdb var atoms = [ new Atom("O", 1.440, 67.674, 10.147), new Atom("C", 0.178, 67.371, 9.545), new Atom("C", 0.390, 67.200, 8.054), new Atom("O", 1.355, 66.152, 7.837), new Atom("C", -0.824, 66.777, 7.247), new Atom("O", -0.814, 67.518, 6.036), new Atom("C", -0.685, 65.302, 7.011), new Atom("C", 0.814, 65.128, 7.001), new Atom("N", 1.340, 63.917, 7.611), new Atom("C", 0.990, 63.338, 8.795), new Atom("N", 1.649, 62.259, 9.061), new Atom("C", 2.508, 62.125, 7.951), new Atom("C", 3.496, 61.159, 7.609), new Atom("N", 3.709, 60.156, 8.444), new Atom("N", 4.141, 61.350, 6.444), new Atom("C", 3.838, 62.403, 5.682), new Atom("N", 2.945, 63.394, 5.855), new Atom("C", 2.332, 63.138, 7.051), new Atom("P", -1.908, 67.112, 4.930), new Atom("O", -2.236, 68.343, 4.176), new Atom("O", -2.953, 66.275, 5.562), new Atom("O", -1.078, 66.144, 3.953), new Atom("C", 0.057, 66.730, 3.314), new Atom("C", 0.530, 65.771, 2.242), new Atom("O", 1.035, 64.575, 2.870), new Atom("C", -0.533, 65.284, 1.264), new Atom("O", 0.051, 65.279, -0.029), new Atom("C", -0.935, 63.924, 1.764), new Atom("C", 0.382, 63.425, 2.331), new Atom("N", 0.344, 62.490, 3.465), new Atom("C", 1.191, 61.402, 3.495), new Atom("O", 2.018, 61.172, 2.568), new Atom("N", 1.143, 60.551, 4.548), new Atom("C", 0.268, 60.782, 5.548), new Atom("N", 0.268, 59.912, 6.553), new Atom("C", -0.612, 61.894, 5.537), new Atom("C", -0.565, 62.741, 4.495), new Atom("P", -0.797, 65.134, -1.372), new Atom("O", -0.056, 65.821, -2.475), new Atom("O", -2.218, 65.453, -1.151), new Atom("O", -0.702, 63.565, -1.718), new Atom("C", 0.623, 63.016, -1.773), new Atom("C", 0.526, 61.521, -1.927), new Atom("O", 0.330, 60.907, -0.629), new Atom("C", -0.641, 61.011, -2.767), new Atom("O", -0.091, 60.279, -3.856), new Atom("C", -1.486, 60.167, -1.858), new Atom("C", -0.514, 59.751, -0.793), new Atom("N", -0.959, 59.528, 0.594), new Atom("C", -0.496, 58.429, 1.293), new Atom("O", 0.289, 57.584, 0.836), new Atom("N", -0.909, 58.244, 2.566), new Atom("C", -1.754, 59.128, 3.099), new Atom("N", -2.162, 58.942, 4.354), new Atom("C", -2.251, 60.275, 2.411), new Atom("C", -1.827, 60.442, 1.145), new Atom("P", -1.069, 59.672, -4.979), new Atom("O", -0.303, 59.590, -6.258), new Atom("O", -2.361, 60.413, -4.938), new Atom("O", -1.355, 58.203, -4.466), new Atom("C", -0.268, 57.293, -4.298), new Atom("C", -0.817, 56.036, -3.686), new Atom("O", -1.239, 56.316, -2.323), new Atom("C", -2.039, 55.462, -4.384), new Atom("O", -1.897, 54.069, -4.482), new Atom("C", -3.208, 55.857, -3.508), new Atom("C", -2.527, 55.717, -2.153), new Atom("N", -3.215, 56.395, -1.070), new Atom("C", -3.989, 57.511, -1.116), new Atom("N", -4.490, 57.900, 0.053), new Atom("C", -3.979, 56.936, 0.899), new Atom("C", -4.140, 56.768, 2.333), new Atom("O", -4.803, 57.512, 3.044), new Atom("N", -3.448, 55.666, 2.745), new Atom("C", -2.695, 54.794, 2.025), new Atom("N", -2.087, 53.748, 2.665), new Atom("N", -2.543, 54.941, 0.715), new Atom("C", -3.199, 56.006, 0.252), new Atom("P", -2.491, 53.169, -5.667), new Atom("O", -1.688, 53.368, -6.887), new Atom("O", -3.966, 53.424, -5.721), new Atom("O", -2.260, 51.700, -5.101), new Atom("C", -0.956, 51.404, -4.578), new Atom("C", -1.131, 50.374, -3.484), new Atom("O", -1.753, 51.046, -2.355), new Atom("C", -2.029, 49.179, -3.760), new Atom("O", -1.428, 48.037, -3.146), new Atom("C", -3.368, 49.548, -3.184), new Atom("C", -2.976, 50.393, -1.993), new Atom("N", -3.870, 51.487, -1.621), new Atom("C", -4.395, 52.438, -2.456), new Atom("N", -5.159, 53.310, -1.887), new Atom("C", -5.159, 52.916, -0.528), new Atom("C", -5.815, 53.484, 0.574), new Atom("N", -6.612, 54.571, 0.535), new Atom("N", -5.612, 52.865, 1.781), new Atom("C", -4.831, 51.804, 1.801), new Atom("N", -4.163, 51.187, 0.815), new Atom("C", -4.361, 51.795, -0.374), new Atom("P", -1.999, 46.548, -3.380), new Atom("O", -0.957, 45.565, -2.990), new Atom("O", -2.673, 46.485, -4.686), new Atom("O", -3.144, 46.444, -2.252), new Atom("C", -2.679, 46.518, -0.892), new Atom("C", -3.886, 46.518, 0.017), new Atom("O", -4.582, 47.780, -0.099), new Atom("C", -4.944, 45.467, -0.287), new Atom("O", -4.883, 44.541, 0.789), new Atom("C", -6.258, 46.192, -0.402), new Atom("C", -5.963, 47.525, 0.245), new Atom("N", -6.627, 48.742, -0.216), new Atom("C", -7.320, 49.539, 0.701), new Atom("O", -7.364, 49.192, 1.934), new Atom("N", -7.892, 50.624, 0.223), new Atom("C", -7.865, 51.020, -1.064), new Atom("N", -8.456, 52.106, -1.460), new Atom("C", -7.148, 50.204, -2.026), new Atom("C", -6.567, 49.102, -1.538), new Atom("P", -5.731, 43.195, 0.848), new Atom("O", -5.102, 42.273, 1.836), new Atom("O", -6.026, 42.730, -0.537), new Atom("O", -7.143, 43.636, 1.463), new Atom("C", -7.163, 44.196, 2.782), new Atom("C", -8.588, 44.673, 2.999), new Atom("O", -8.796, 45.838, 2.167), new Atom("C", -9.708, 43.730, 2.612), new Atom("O", -10.348, 43.327, 3.824), new Atom("C", -10.626, 44.484, 1.665), new Atom("C", -10.204, 45.909, 1.882), new Atom("N", -10.264, 46.836, 0.754), new Atom("C", -9.735, 46.617, -0.498), new Atom("N", -9.933, 47.609, -1.305), new Atom("C", -10.625, 48.543, -0.570), new Atom("C", -11.101, 49.802, -0.938), new Atom("O", -11.008, 50.389, -2.040), new Atom("N", -11.769, 50.475, 0.089), new Atom("C", -11.919, 49.897, 1.342), new Atom("N", -12.563, 50.591, 2.266), new Atom("N", -11.480, 48.715, 1.707), new Atom("C", -10.833, 48.060, 0.718), new Atom("P", -11.631, 42.383, 3.833), new Atom("O", -11.669, 41.648, 5.133), new Atom("O", -11.688, 41.594, 2.571), new Atom("O", -12.874, 43.378, 3.817), new Atom("C", -12.876, 44.358, 4.878), new Atom("C", -14.071, 45.243, 4.628), new Atom("O", -13.766, 46.086, 3.484), new Atom("C", -15.369, 44.546, 4.278), new Atom("O", -16.292, 44.818, 5.336), new Atom("C", -15.827, 45.101, 2.965), new Atom("C", -14.983, 46.353, 2.810), new Atom("N", -14.583, 46.724, 1.436), new Atom("C", -14.875, 47.994, 0.992), new Atom("O", -15.445, 48.845, 1.664), new Atom("N", -14.463, 48.232, -0.299), new Atom("C", -13.806, 47.373, -1.179), new Atom("O", -13.503, 47.749, -2.318), new Atom("C", -13.546, 46.067, -0.624), new Atom("C", -12.848, 45.032, -1.461), new Atom("C", -13.943, 45.813, 0.634), new Atom("P", -17.803, 44.320, 5.383), new Atom("O", -18.197, 44.219, 6.817), new Atom("O", -17.978, 43.101, 4.525), new Atom("O", -18.668, 45.474, 4.688), new Atom("C", -18.527, 46.798, 5.182), new Atom("C", -19.048, 47.829, 4.223), new Atom("O", -18.187, 47.857, 3.043), new Atom("C", -20.419, 47.615, 3.618), new Atom("O", -21.416, 48.136, 4.486), new Atom("C", -20.417, 48.354, 2.304), new Atom("C", -18.955, 48.516, 2.002), new Atom("N", -18.407, 47.863, 0.809), new Atom("C", -18.223, 48.678, -0.327), new Atom("O", -18.541, 49.852, -0.210), new Atom("N", -17.721, 48.086, -1.408), new Atom("C", -17.401, 46.817, -1.463), new Atom("N", -16.908, 46.356, -2.623), new Atom("C", -17.570, 45.930, -0.320), new Atom("C", -18.080, 46.516, 0.783), new Atom("P", -22.942, 47.712, 4.188), new Atom("O", -23.718, 47.977, 5.442), new Atom("O", -22.986, 46.336, 3.625), new Atom("O", -23.418, 48.731, 3.070), new Atom("C", -23.358, 50.144, 3.273), new Atom("C", -23.818, 50.848, 2.024), new Atom("O", -22.945, 50.489, 0.920), new Atom("C", -25.220, 50.500, 1.532), new Atom("O", -25.805, 51.707, 1.090), new Atom("C", -25.025, 49.481, 0.442), new Atom("C", -23.710, 49.947, -0.156), new Atom("N", -22.860, 48.910, -0.706), new Atom("C", -22.572, 47.682, -0.130), new Atom("N", -21.769, 46.966, -0.875), new Atom("C", -21.524, 47.752, -1.983), new Atom("C", -20.706, 47.442, -3.114), new Atom("O", -20.050, 46.440, -3.360), new Atom("N", -20.755, 48.528, -3.975), new Atom("C", -21.448, 49.680, -3.794), new Atom("N", -21.350, 50.616, -4.777), new Atom("N", -22.217, 49.984, -2.743), new Atom("C", -22.177, 48.949, -1.908), new Atom("P", -27.313, 51.693, 0.526), new Atom("O", -27.904, 53.031, 0.764), new Atom("O", -28.008, 50.480, 1.013), new Atom("O", -27.063, 51.511, -1.046), new Atom("C", -26.451, 52.629, -1.747), new Atom("C", -26.455, 52.215, -3.207), new Atom("O", -25.501, 51.142, -3.369), new Atom("C", -27.770, 51.684, -3.744), new Atom("O", -28.188, 52.544, -4.800), new Atom("C", -27.503, 50.278, -4.207), new Atom("C", -25.995, 50.216, -4.329), new Atom("N", -25.389, 48.933, -3.996), new Atom("C", -25.546, 48.180, -2.875), new Atom("N", -24.865, 47.079, -2.881), new Atom("C", -24.186, 47.077, -4.104), new Atom("C", -23.281, 46.155, -4.713), new Atom("O", -22.854, 45.083, -4.293), new Atom("N", -22.865, 46.606, -5.963), new Atom("C", -23.253, 47.759, -6.543), new Atom("N", -22.769, 48.071, -7.763), new Atom("N", -24.096, 48.637, -5.999), new Atom("C", -24.503, 48.214, -4.795), new Atom("P", -29.519, 52.311, -5.654), new Atom("O", -29.964, 53.578, -6.284), new Atom("O", -30.477, 51.509, -4.843), new Atom("O", -29.033, 51.337, -6.848), new Atom("C", -28.214, 51.776, -7.921), new Atom("C", -27.793, 50.631, -8.800), new Atom("O", -27.090, 49.623, -8.013), new Atom("C", -28.884, 49.795, -9.459), new Atom("O", -29.276, 50.436, -10.662), new Atom("C", -28.272, 48.442, -9.686), new Atom("C", -27.025, 48.444, -8.837), new Atom("N", -26.842, 47.373, -7.848), new Atom("C", -25.937, 46.369, -8.106), new Atom("O", -25.300, 46.363, -9.134), new Atom("N", -25.836, 45.426, -7.130), new Atom("C", -26.535, 45.377, -5.942), new Atom("O", -26.323, 44.456, -5.174), new Atom("C", -27.472, 46.456, -5.717), new Atom("C", -28.276, 46.480, -4.438), new Atom("C", -27.579, 47.390, -6.667), new Atom("O", -21.455, 36.281, -10.094), new Atom("C", -20.269, 37.067, -9.948), new Atom("C", -20.261, 38.152, -10.998), new Atom("O", -21.319, 39.106, -10.749), new Atom("C", -19.001, 39.009, -11.049), new Atom("O", -18.802, 39.403, -12.390), new Atom("C", -19.280, 40.158, -10.125), new Atom("C", -20.786, 40.328, -10.244), new Atom("N", -21.453, 40.586, -8.971), new Atom("C", -21.327, 39.943, -7.770), new Atom("N", -22.087, 40.439, -6.806), new Atom("C", -22.770, 41.491, -7.413), new Atom("C", -23.723, 42.409, -6.929), new Atom("N", -24.190, 42.445, -5.685), new Atom("N", -24.199, 43.327, -7.806), new Atom("C", -23.728, 43.285, -9.043), new Atom("N", -22.844, 42.492, -9.638), new Atom("C", -22.390, 41.593, -8.745), new Atom("P", -17.502, 40.265, -12.750), new Atom("O", -17.278, 40.201, -14.217), new Atom("O", -16.411, 39.910, -11.810), new Atom("O", -17.963, 41.770, -12.399), new Atom("C", -18.962, 42.340, -13.249), new Atom("C", -19.312, 43.727, -12.764), new Atom("O", -19.902, 43.654, -11.439), new Atom("C", -18.134, 44.675, -12.631), new Atom("O", -18.446, 45.817, -13.422), new Atom("C", -17.997, 44.964, -11.162), new Atom("C", -19.429, 44.792, -10.695), new Atom("N", -19.710, 44.426, -9.307), new Atom("C", -20.707, 45.141, -8.624), new Atom("O", -21.308, 46.046, -9.199), new Atom("N", -20.938, 44.782, -7.361), new Atom("C", -20.328, 43.814, -6.680), new Atom("N", -20.708, 43.612, -5.422), new Atom("C", -19.306, 43.065, -7.346), new Atom("C", -19.105, 43.456, -8.613), new Atom("P", -17.277, 46.807, -13.906), new Atom("O", -17.440, 47.087, -15.347), new Atom("O", -15.980, 46.302, -13.371), new Atom("O", -17.625, 48.150, -13.080), new Atom("C", -18.934, 48.688, -13.216), new Atom("C", -19.232, 49.669, -12.105), new Atom("O", -19.365, 48.954, -10.851), new Atom("C", -18.180, 50.730, -11.807), new Atom("O", -18.828, 51.957, -12.072), new Atom("C", -17.758, 50.587, -10.370), new Atom("C", -18.912, 49.835, -9.786), new Atom("N", -18.706, 48.868, -8.693), new Atom("C", -19.436, 49.044, -7.513), new Atom("O", -20.210, 50.002, -7.453), new Atom("N", -19.244, 48.149, -6.520), new Atom("C", -18.395, 47.150, -6.654), new Atom("N", -18.238, 46.290, -5.634), new Atom("C", -17.635, 46.954, -7.858), new Atom("C", -17.835, 47.841, -8.833), new Atom("P", -18.089, 53.357, -12.252), new Atom("O", -19.072, 54.296, -12.884), new Atom("O", -16.752, 53.179, -12.848), new Atom("O", -17.908, 53.858, -10.742), new Atom("C", -19.045, 54.366, -10.049), new Atom("C", -18.676, 54.616, -8.606), new Atom("O", -18.474, 53.301, -7.993), new Atom("C", -17.404, 55.373, -8.289), new Atom("O", -17.755, 56.295, -7.276), new Atom("C", -16.398, 54.359, -7.823), new Atom("C", -17.373, 53.434, -7.093), new Atom("N", -16.842, 52.122, -6.794), new Atom("C", -15.977, 51.362, -7.516), new Atom("N", -15.702, 50.233, -6.963), new Atom("C", -16.423, 50.204, -5.780), new Atom("C", -16.524, 49.229, -4.755), new Atom("O", -15.990, 48.130, -4.649), new Atom("N", -17.394, 49.689, -3.762), new Atom("C", -18.055, 50.861, -3.729), new Atom("N", -18.853, 51.103, -2.658), new Atom("N", -17.965, 51.797, -4.699), new Atom("C", -17.140, 51.382, -5.661), new Atom("P", -16.872, 57.480, -6.693), new Atom("O", -17.564, 58.750, -7.082), new Atom("O", -15.443, 57.227, -6.949), new Atom("O", -17.109, 57.288, -5.099), new Atom("C", -18.454, 57.289, -4.622), new Atom("C", -18.532, 56.999, -3.138), new Atom("O", -18.244, 55.594, -2.891), new Atom("C", -17.551, 57.760, -2.257), new Atom("O", -18.243, 58.125, -1.070), new Atom("C", -16.424, 56.816, -2.005), new Atom("C", -17.097, 55.472, -2.049), new Atom("N", -16.270, 54.429, -2.645), new Atom("C", -15.660, 54.488, -3.905), new Atom("N", -14.997, 53.408, -4.140), new Atom("C", -15.150, 52.572, -3.003), new Atom("C", -14.701, 51.314, -2.648), new Atom("N", -13.926, 50.553, -3.418), new Atom("N", -15.030, 50.754, -1.441), new Atom("C", -15.817, 51.581, -0.708), new Atom("N", -16.326, 52.771, -0.885), new Atom("C", -15.946, 53.234, -2.096), new Atom("P", -17.678, 59.268, -0.098), new Atom("O", -18.846, 59.712, 0.727), new Atom("O", -16.851, 60.235, -0.842), new Atom("O", -16.697, 58.480, 0.892), new Atom("C", -17.234, 57.523, 1.818), new Atom("C", -16.068, 56.817, 2.480), new Atom("O", -15.550, 55.782, 1.571), new Atom("C", -14.866, 57.658, 2.819), new Atom("O", -14.351, 57.320, 4.105), new Atom("C", -13.829, 57.336, 1.778), new Atom("C", -14.134, 55.834, 1.667), new Atom("N", -13.540, 55.155, 0.515), new Atom("C", -13.307, 53.776, 0.623), new Atom("O", -13.624, 53.195, 1.706), new Atom("N", -12.759, 53.141, -0.415), new Atom("C", -12.442, 53.813, -1.558), new Atom("N", -11.890, 53.135, -2.600), new Atom("C", -12.669, 55.195, -1.686), new Atom("C", -13.221, 55.861, -0.635), new Atom("P", -14.764, 58.173, 5.395), new Atom("O", -16.251, 58.176, 5.490), new Atom("O", -14.030, 59.466, 5.406), new Atom("O", -14.176, 57.262, 6.569), new Atom("C", -14.821, 56.036, 6.919), new Atom("C", -13.747, 55.025, 7.232), new Atom("O", -13.199, 54.500, 5.998), new Atom("C", -12.538, 55.551, 8.008), new Atom("O", -12.281, 54.641, 9.083), new Atom("C", -11.418, 55.660, 7.007), new Atom("C", -11.758, 54.518, 6.075), new Atom("N", -11.316, 54.623, 4.690), new Atom("C", -11.533, 55.746, 3.880), new Atom("N", -11.025, 55.535, 2.704), new Atom("C", -10.467, 54.284, 2.719), new Atom("C", -9.786, 53.504, 1.773), new Atom("O", -9.517, 53.828, 0.600), new Atom("N", -9.362, 52.238, 2.181), new Atom("C", -9.588, 51.735, 3.458), new Atom("N", -9.128, 50.513, 3.711), new Atom("N", -10.232, 52.456, 4.368), new Atom("C", -10.641, 53.676, 3.979), new Atom("P", -11.117, 54.973, 10.136), new Atom("O", -11.550, 54.476, 11.478), new Atom("O", -10.673, 56.385, 10.058), new Atom("O", -9.932, 54.036, 9.605), new Atom("C", -10.172, 52.636, 9.518), new Atom("C", -8.907, 51.915, 9.099), new Atom("O", -8.596, 52.236, 7.738), new Atom("C", -7.651, 52.280, 9.892), new Atom("O", -7.040, 51.049, 10.246), new Atom("C", -6.842, 53.157, 8.975), new Atom("C", -7.204, 52.589, 7.619), new Atom("N", -7.232, 53.439, 6.425), new Atom("C", -6.676, 52.925, 5.241), new Atom("O", -6.170, 51.822, 5.146), new Atom("N", -6.760, 53.806, 4.181), new Atom("C", -7.304, 55.059, 4.181), new Atom("O", -7.326, 55.765, 3.176), new Atom("C", -7.852, 55.528, 5.399), new Atom("C", -8.468, 56.882, 5.505), new Atom("C", -7.782, 54.684, 6.458), new Atom("P", -5.847, 50.937, 11.301), new Atom("O", -5.912, 49.536, 11.852), new Atom("O", -5.894, 52.037, 12.285), new Atom("O", -4.513, 51.068, 10.456), new Atom("C", -4.282, 50.075, 9.430), new Atom("C", -3.071, 50.561, 8.674), new Atom("O", -3.471, 51.622, 7.753), new Atom("C", -1.966, 51.158, 9.525), new Atom("O", -0.711, 50.761, 9.013), new Atom("C", -2.193, 52.651, 9.419), new Atom("C", -2.546, 52.692, 7.922), new Atom("N", -3.197, 53.898, 7.419), new Atom("C", -3.192, 54.156, 6.053), new Atom("O", -2.637, 53.375, 5.251), new Atom("N", -3.784, 55.256, 5.574), new Atom("C", -4.387, 56.120, 6.416), new Atom("N", -4.954, 57.188, 5.853), new Atom("C", -4.406, 55.871, 7.808), new Atom("C", -3.808, 54.764, 8.260), new Atom("P", 0.501, 50.108, 9.842), new Atom("O", 0.079, 48.762, 10.270), new Atom("O", 1.030, 51.104, 10.803), new Atom("O", 1.611, 49.947, 8.694), new Atom("C", 1.414, 49.083, 7.585), new Atom("C", 2.225, 49.545, 6.405), new Atom("O", 1.602, 50.718, 5.831), new Atom("C", 3.659, 49.986, 6.694), new Atom("O", 4.440, 49.627, 5.564), new Atom("C", 3.552, 51.462, 6.944), new Atom("C", 2.492, 51.839, 5.920), new Atom("N", 1.651, 52.970, 6.259), new Atom("C", 1.159, 53.316, 7.497), new Atom("N", 0.429, 54.391, 7.485), new Atom("C", 0.421, 54.808, 6.159), new Atom("C", -0.219, 55.929, 5.566), new Atom("O", -0.920, 56.815, 6.035), new Atom("N", 0.051, 55.952, 4.190), new Atom("C", 0.806, 55.045, 3.529), new Atom("N", 0.950, 55.235, 2.215), new Atom("N", 1.402, 54.003, 4.074), new Atom("C", 1.173, 53.934, 5.399), new Atom("P", 6.036, 49.700, 5.535), new Atom("O", 6.540, 48.503, 4.800), new Atom("O", 6.547, 50.011, 6.893), new Atom("O", 6.341, 50.973, 4.607), new Atom("C", 5.790, 50.913, 3.291), new Atom("C", 6.191, 52.129, 2.499), new Atom("O", 5.262, 53.209, 2.768), new Atom("C", 7.560, 52.732, 2.807), new Atom("O", 8.123, 53.063, 1.560), new Atom("C", 7.314, 53.928, 3.676), new Atom("C", 5.963, 54.378, 3.142), new Atom("N", 5.145, 55.054, 4.137), new Atom("C", 5.048, 54.604, 5.459), new Atom("N", 4.253, 55.385, 6.150), new Atom("C", 3.837, 56.359, 5.230), new Atom("C", 2.984, 57.453, 5.392), new Atom("O", 2.410, 57.778, 6.427), new Atom("N", 2.795, 58.215, 4.242), new Atom("C", 3.405, 57.908, 3.055), new Atom("N", 3.107, 58.751, 2.065), new Atom("N", 4.202, 56.896, 2.879), new Atom("C", 4.391, 56.154, 3.977), new Atom("P", 9.564, 53.711, 1.352), new Atom("O", 9.983, 53.353, -0.038), new Atom("O", 10.441, 53.419, 2.503), new Atom("O", 9.263, 55.281, 1.362), new Atom("C", 8.598, 55.903, 0.257), new Atom("C", 8.329, 57.333, 0.629), new Atom("O", 7.406, 57.383, 1.751), new Atom("C", 9.501, 58.158, 1.143), new Atom("O", 10.226, 58.659, 0.034), new Atom("C", 8.873, 59.241, 1.976), new Atom("C", 7.482, 58.712, 2.274), new Atom("N", 7.124, 58.580, 3.698), new Atom("C", 6.259, 59.542, 4.216), new Atom("O", 5.870, 60.404, 3.465), new Atom("N", 5.963, 59.365, 5.546), new Atom("C", 6.395, 58.401, 6.398), new Atom("O", 6.065, 58.339, 7.578), new Atom("C", 7.304, 57.418, 5.794), new Atom("C", 7.802, 56.345, 6.685), new Atom("C", 7.590, 57.592, 4.496) ]; var Bond = function(a, b) { this.atom1 = atoms[a]; this.atom2 = atoms[b]; this.draw = function() { var atom1 = this.atom1; var atom2 = this.atom2; var dx = atom1.x - atom2.x; var dy = atom1.y - atom2.y; var theta = atan2(dx, dy); var x1 = atom1.x - 0.5 * atom1.size * sin(theta); var y1 = atom1.y - 0.5 * atom1.size * cos(theta); var x2 = atom2.x + 0.5 * atom2.size * sin(theta); var y2 = atom2.y + 0.5 * atom2.size * cos(theta); line(x1, y1, x2, y2); }; }; var addGroup = function(bonds, group, n) { for (var i=0; i<group.length; i++){ bonds.push(new Bond (n + group[i][0], n + group[i][1])); } return bonds; }; // Nucleoside bonds var phosphate = [[0,1], [0,2], [0,3]]; var ribose = [[0, 1], [1, 2], [2, 3], [2, 4], [4, 5], [4, 6], [6, 7], [7, 3]]; var adenine = [[0, 1], [1, 2], [2, 3], [3, 4], [4, 5], [5, 6], [5, 7], [7, 8], [8, 9], [9, 10], [10, 1], [10, 4]]; var guanine = [[0, 1], [1, 2], [2, 3], [3, 4], [4, 5], [5, 6], [5, 7], [7, 8], [8, 9], [8, 10], [11, 4], [10, 11], [11,1]]; var cytosine = [[0, 1], [1, 2], [2, 3], [2, 4], [4, 5], [5, 6], [5, 7], [7, 8], [8, 1]]; var thymine = [[0, 1], [1, 2], [2, 3], [2, 4], [4, 5], [5, 6], [5, 7], [7, 8], [7, 9], [9, 1]]; var createSequence =function(seq) { var bonds = []; var baseBonds; var n = 0; for (var s=1; s<=2; s++) { for (var i=0; i<seq.length; i++) { bonds = addGroup(bonds, ribose, n); n += 7; if (seq.charAt(i) === "A") { bonds = addGroup(bonds, adenine, n); baseBonds = 11; } else if (seq.charAt(i) === "C") { bonds = addGroup(bonds, cytosine, n); baseBonds = 9; } else if (seq.charAt(i) === "G") { bonds = addGroup(bonds, guanine, n); baseBonds = 12; } else if (seq.charAt(i) === "T") { bonds = addGroup(bonds, thymine, n); baseBonds = 10; } // Add phosphate backbone if (i !== seq.length - 1) { bonds.push(new Bond (n - 2, n + baseBonds)); n += baseBonds; bonds = addGroup(bonds, phosphate, n); n += 3; } } n += 10; } return bonds; }; // List of bond joining atoms by index. var bonds = createSequence("ACCGACGTCGGT"); var currentX = false; var currentY = false; var moveObjectToCentre = function(atoms) { // Find range of x values and scale to fill screen var minValue = atoms[0].y; var maxValue = atoms[0].y; for (var i=0; i<atoms.length; i++){ if (atoms[i].y > maxValue) { maxValue = atoms[i].y; } else if (atoms[i].y < minValue) { minValue = atoms[i].y; } } var scaleValue = 300 / (maxValue - minValue); scaleValue = 8; // Scale and shift everything var dims = ['x', 'y', 'z']; for (var d = 0; d<3; d++) { // Find mean values for each dimension var meanValue = 0; var dimension = dims[d]; for (i=0; i<atoms.length; i++) { meanValue += atoms[i][dimension]; } meanValue /= atoms.length; for (i=0; i<atoms.length; i++) { atoms[i][dimension] = scaleValue * (atoms[i][dimension] - meanValue); } } }; moveObjectToCentre(atoms); var rotateY3D = function(theta) { var ct = cos(theta); var st = sin(theta); var x, z; for (var i = 0; i < atoms.length; i+=1) { x = atoms[i].x; z = atoms[i].z; atoms[i].x = ctx + stz; atoms[i].z = -stx + ctz; } }; var rotateX3D = function(theta){ var ct = cos(theta); var st = sin(theta); var y, z; for (var i = 0; i < atoms.length; i+=1) { y = atoms[i].y; z = atoms[i].z; atoms[i].y = cty - stz; atoms[i].z = sty + ctz; } }; // Return the difference of the z-coordinate var sortByZ = function(a, b) { return a.z - b.z; }; // Move to centre of screen translate(200, 200); var draw = function() { var i; atoms.sort(sortByZ); background(backgroundColour); // Draw bonds stroke(bondColour); strokeWeight(bondThickness); for (i = 0; i < bonds.length; i+=1) { bonds[i].draw(); } // Draw atoms noStroke(); for (i = 0; i < atoms.length; i+=1) { atoms[i].draw(); } if (mouseIsPressed) { if (currentX !== false) { rotateY3D(-(currentX - mouseX)PI/10); rotateX3D((currentY - mouseY)PI/10); } currentX = mouseX; currentY = mouseY; } else { currentX = false; } }; var keyPressed = function() { if (keyCode === LEFT) { rotateY3D(-3); } else if (keyCode === RIGHT) { rotateY3D(3); } else if (keyCode === UP) { rotateX3D(-3); } else if (keyCode === DOWN) { rotateX3D(3); } }; // Let go when mouse leaves canvas var mouseOut = function(){ mouseIsPressed = false; }; // Initial rotations rotateY3D(20);
Folds
Fork	false
Key	ag5zfmtoYW4tYWNhZGVteXIUCxIKU2NyYXRjaHBhZBixxJKuBAw
Votes	173
Spin-Offs	10
Type	PJS
Width	400
Height	400
User Flagged	false
Origin Scratchpad	{"id":"1169364753","title":"Single stranded DNA","deleted":"false","official":"false"}
Hidden From Hotlist	false
Restricted Posting	false
By Child	false
Author Nick	Peter Collingridge
Author Name	peterwcollingridge
Author ID	kaid_1128810778687926889052316
Author Profile Access	COACH

Archive Data

Added	10 months ago, 1739280048938
Updated	10 months ago, 1739280048938
Source Deleted	unknown