--- /dev/null
+class Molby::Molecule
+
+#
+# UFF force field parameters
+# Taken from RDKit source code
+# http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Code/ForceField/UFF/Params.cpp?revision=2044&view=markup
+# Accessed on 2012.5.8.
+#
+# Atom an r1 theta0 x1 D1 zeta Z1 Vi Uj Xi Hard Radius
+UFFParams = [
+["H_", 1, 0.354, 180, 2.886, 0.044, 12, 0.712, 0, 0, 4.528, 6.9452, 0.371],
+["H_b", 1, 0.46, 83.5, 2.886, 0.044, 12, 0.712, 0, 0, 4.528, 6.9452, 0.371],
+["He4+4", 2, 0.849, 90, 2.362, 0.056, 15.24, 0.098, 0, 0, 9.66, 14.92, 1.3],
+["Li", 3, 1.336, 180, 2.451, 0.025, 12, 1.026, 0, 2, 3.006, 2.386, 1.557],
+["Be3+2", 4, 1.074, 109.47, 2.745, 0.085, 12, 1.565, 0, 2, 4.877, 4.443, 1.24],
+["B_3", 5, 0.838, 109.47, 4.083, 0.18, 12.052, 1.755, 0, 2, 5.11, 4.75, 0.822],
+["B_2", 5, 0.828, 120, 4.083, 0.18, 12.052, 1.755, 0, 2, 5.11, 4.75, 0.822],
+["C_3", 6, 0.757, 109.47, 3.851, 0.105, 12.73, 1.912, 2.119, 2, 5.343, 5.063, 0.759],
+["C_R", 6, 0.729, 120, 3.851, 0.105, 12.73, 1.912, 0, 2, 5.343, 5.063, 0.759],
+["C_2", 6, 0.732, 120, 3.851, 0.105, 12.73, 1.912, 0, 2, 5.343, 5.063, 0.759],
+["C_1", 6, 0.706, 180, 3.851, 0.105, 12.73, 1.912, 0, 2, 5.343, 5.063, 0.759],
+["N_3", 7, 0.7, 106.7, 3.66, 0.069, 13.407, 2.544, 0.45, 2, 6.899, 5.88, 0.715],
+["N_R", 7, 0.699, 120, 3.66, 0.069, 13.407, 2.544, 0, 2, 6.899, 5.88, 0.715],
+["N_2", 7, 0.685, 111.2, 3.66, 0.069, 13.407, 2.544, 0, 2, 6.899, 5.88, 0.715],
+["N_1", 7, 0.656, 180, 3.66, 0.069, 13.407, 2.544, 0, 2, 6.899, 5.88, 0.715],
+["O_3", 8, 0.658, 104.51, 3.5, 0.06, 14.085, 2.3, 0.018, 2, 8.741, 6.682, 0.669],
+["O_3_z", 8, 0.528, 146, 3.5, 0.06, 14.085, 2.3, 0.018, 2, 8.741, 6.682, 0.669],
+["O_R", 8, 0.68, 110, 3.5, 0.06, 14.085, 2.3, 0, 2, 8.741, 6.682, 0.669],
+["O_2", 8, 0.634, 120, 3.5, 0.06, 14.085, 2.3, 0, 2, 8.741, 6.682, 0.669],
+["O_1", 8, 0.639, 180, 3.5, 0.06, 14.085, 2.3, 0, 2, 8.741, 6.682, 0.669],
+["F_", 9, 0.668, 180, 3.364, 0.05, 14.762, 1.735, 0, 2, 10.874, 7.474, 0.706],
+["Ne4+4", 10, 0.92, 90, 3.243, 0.042, 15.44, 0.194, 0, 2, 11.04, 10.55, 1.768],
+["Na", 11, 1.539, 180, 2.983, 0.03, 12, 1.081, 0, 1.25, 2.843, 2.296, 2.085],
+["Mg3+2", 12, 1.421, 109.47, 3.021, 0.111, 12, 1.787, 0, 1.25, 3.951, 3.693, 1.5],
+["Al3", 13, 1.244, 109.47, 4.499, 0.505, 11.278, 1.792, 0, 1.25, 4.06, 3.59, 1.201],
+["Si3", 14, 1.117, 109.47, 4.295, 0.402, 12.175, 2.323, 1.225, 1.25, 4.168, 3.487, 1.176],
+["P_3+3", 15, 1.101, 93.8, 4.147, 0.305, 13.072, 2.863, 2.4, 1.25, 5.463, 4, 1.102],
+["P_3+5", 15, 1.056, 109.47, 4.147, 0.305, 13.072, 2.863, 2.4, 1.25, 5.463, 4, 1.102],
+["P_3+q", 15, 1.056, 109.47, 4.147, 0.305, 13.072, 2.863, 2.4, 1.25, 5.463, 4, 1.102],
+["S_3+2", 16, 1.064, 92.1, 4.035, 0.274, 13.969, 2.703, 0.484, 1.25, 6.928, 4.486, 1.047],
+["S_3+4", 16, 1.049, 103.2, 4.035, 0.274, 13.969, 2.703, 0.484, 1.25, 6.928, 4.486, 1.047],
+["S_3+6", 16, 1.027, 109.47, 4.035, 0.274, 13.969, 2.703, 0.484, 1.25, 6.928, 4.486, 1.047],
+["S_R", 16, 1.077, 92.2, 4.035, 0.274, 13.969, 2.703, 0, 1.25, 6.928, 4.486, 1.047],
+["S_2", 16, 0.854, 120, 4.035, 0.274, 13.969, 2.703, 0, 1.25, 6.928, 4.486, 1.047],
+["Cl", 17, 1.044, 180, 3.947, 0.227, 14.866, 2.348, 0, 1.25, 8.564, 4.946, 0.994],
+["Ar4+4", 18, 1.032, 90, 3.868, 0.185, 15.763, 0.3, 0, 1.25, 9.465, 6.355, 2.108],
+["K_", 19, 1.953, 180, 3.812, 0.035, 12, 1.165, 0, 0.7, 2.421, 1.92, 2.586],
+["Ca6+2", 20, 1.761, 90, 3.399, 0.238, 12, 2.141, 0, 0.7, 3.231, 2.88, 2],
+["Sc3+3", 21, 1.513, 109.47, 3.295, 0.019, 12, 2.592, 0, 0.7, 3.395, 3.08, 1.75],
+["Ti3+4", 22, 1.412, 109.47, 3.175, 0.017, 12, 2.659, 0, 0.7, 3.47, 3.38, 1.607],
+["Ti6+4", 22, 1.412, 90, 3.175, 0.017, 12, 2.659, 0, 0.7, 3.47, 3.38, 1.607],
+["V_3+5", 23, 1.402, 109.47, 3.144, 0.016, 12, 2.679, 0, 0.7, 3.65, 3.41, 1.47],
+["Cr6+3", 24, 1.345, 90, 3.023, 0.015, 12, 2.463, 0, 0.7, 3.415, 3.865, 1.402],
+["Mn6+2", 25, 1.382, 90, 2.961, 0.013, 12, 2.43, 0, 0.7, 3.325, 4.105, 1.533],
+["Fe3+2", 26, 1.27, 109.47, 2.912, 0.013, 12, 2.43, 0, 0.7, 3.76, 4.14, 1.393],
+["Fe6+2", 26, 1.335, 90, 2.912, 0.013, 12, 2.43, 0, 0.7, 3.76, 4.14, 1.393],
+["Co6+3", 27, 1.241, 90, 2.872, 0.014, 12, 2.43, 0, 0.7, 4.105, 4.175, 1.406],
+["Ni4+2", 28, 1.164, 90, 2.834, 0.015, 12, 2.43, 0, 0.7, 4.465, 4.205, 1.398],
+["Cu3+1", 29, 1.302, 109.47, 3.495, 0.005, 12, 1.756, 0, 0.7, 4.2, 4.22, 1.434],
+["Zn3+2", 30, 1.193, 109.47, 2.763, 0.124, 12, 1.308, 0, 0.7, 5.106, 4.285, 1.4],
+["Ga3+3", 31, 1.26, 109.47, 4.383, 0.415, 11, 1.821, 0, 0.7, 3.641, 3.16, 1.211],
+["Ge3", 32, 1.197, 109.47, 4.28, 0.379, 12, 2.789, 0.701, 0.7, 4.051, 3.438, 1.189],
+["As3+3", 33, 1.211, 92.1, 4.23, 0.309, 13, 2.864, 1.5, 0.7, 5.188, 3.809, 1.204],
+["Se3+2", 34, 1.19, 90.6, 4.205, 0.291, 14, 2.764, 0.335, 0.7, 6.428, 4.131, 1.224],
+["Br", 35, 1.192, 180, 4.189, 0.251, 15, 2.519, 0, 0.7, 7.79, 4.425, 1.141],
+["Kr4+4", 36, 1.147, 90, 4.141, 0.22, 16, 0.452, 0, 0.7, 8.505, 5.715, 2.27],
+["Rb", 37, 2.26, 180, 4.114, 0.04, 12, 1.592, 0, 0.2, 2.331, 1.846, 2.77],
+["Sr6+2", 38, 2.052, 90, 3.641, 0.235, 12, 2.449, 0, 0.2, 3.024, 2.44, 2.415],
+["Y_3+3", 39, 1.698, 109.47, 3.345, 0.072, 12, 3.257, 0, 0.2, 3.83, 2.81, 1.998],
+["Zr3+4", 40, 1.564, 109.47, 3.124, 0.069, 12, 3.667, 0, 0.2, 3.4, 3.55, 1.758],
+["Nb3+5", 41, 1.473, 109.47, 3.165, 0.059, 12, 3.618, 0, 0.2, 3.55, 3.38, 1.603],
+["Mo6+6", 42, 1.467, 90, 3.052, 0.056, 12, 3.4, 0, 0.2, 3.465, 3.755, 1.53],
+["Mo3+6", 42, 1.484, 109.47, 3.052, 0.056, 12, 3.4, 0, 0.2, 3.465, 3.755, 1.53],
+["Tc6+5", 43, 1.322, 90, 2.998, 0.048, 12, 3.4, 0, 0.2, 3.29, 3.99, 1.5],
+["Ru6+2", 44, 1.478, 90, 2.963, 0.056, 12, 3.4, 0, 0.2, 3.575, 4.015, 1.5],
+["Rh6+3", 45, 1.332, 90, 2.929, 0.053, 12, 3.5, 0, 0.2, 3.975, 4.005, 1.509],
+["Pd4+2", 46, 1.338, 90, 2.899, 0.048, 12, 3.21, 0, 0.2, 4.32, 4, 1.544],
+["Ag1+1", 47, 1.386, 180, 3.148, 0.036, 12, 1.956, 0, 0.2, 4.436, 3.134, 1.622],
+["Cd3+2", 48, 1.403, 109.47, 2.848, 0.228, 12, 1.65, 0, 0.2, 5.034, 3.957, 1.6],
+["In3+3", 49, 1.459, 109.47, 4.463, 0.599, 11, 2.07, 0, 0.2, 3.506, 2.896, 1.404],
+["Sn3", 50, 1.398, 109.47, 4.392, 0.567, 12, 2.961, 0.199, 0.2, 3.987, 3.124, 1.354],
+["Sb3+3", 51, 1.407, 91.6, 4.42, 0.449, 13, 2.704, 1.1, 0.2, 4.899, 3.342, 1.404],
+["Te3+2", 52, 1.386, 90.25, 4.47, 0.398, 14, 2.882, 0.3, 0.2, 5.816, 3.526, 1.38],
+["I_", 53, 1.382, 180, 4.5, 0.339, 15, 2.65, 0, 0.2, 6.822, 3.762, 1.333],
+["Xe4+4", 54, 1.267, 90, 4.404, 0.332, 12, 0.556, 0, 0.2, 7.595, 4.975, 2.459],
+["Cs", 55, 2.57, 180, 4.517, 0.045, 12, 1.573, 0, 0.1, 2.183, 1.711, 2.984],
+["Ba6+2", 56, 2.277, 90, 3.703, 0.364, 12, 2.727, 0, 0.1, 2.814, 2.396, 2.442],
+["La3+3", 57, 1.943, 109.47, 3.522, 0.017, 12, 3.3, 0, 0.1, 2.8355, 2.7415, 2.071],
+["Ce6+3", 58, 1.841, 90, 3.556, 0.013, 12, 3.3, 0, 0.1, 2.774, 2.692, 1.925],
+["Pr6+3", 59, 1.823, 90, 3.606, 0.01, 12, 3.3, 0, 0.1, 2.858, 2.564, 2.007],
+["Nd6+3", 60, 1.816, 90, 3.575, 0.01, 12, 3.3, 0, 0.1, 2.8685, 2.6205, 2.007],
+["Pm6+3", 61, 1.801, 90, 3.547, 0.009, 12, 3.3, 0, 0.1, 2.881, 2.673, 2],
+["Sm6+3", 62, 1.78, 90, 3.52, 0.008, 12, 3.3, 0, 0.1, 2.9115, 2.7195, 1.978],
+["Eu6+3", 63, 1.771, 90, 3.493, 0.008, 12, 3.3, 0, 0.1, 2.8785, 2.7875, 2.227],
+["Gd6+3", 64, 1.735, 90, 3.368, 0.009, 12, 3.3, 0, 0.1, 3.1665, 2.9745, 1.968],
+["Tb6+3", 65, 1.732, 90, 3.451, 0.007, 12, 3.3, 0, 0.1, 3.018, 2.834, 1.954],
+["Dy6+3", 66, 1.71, 90, 3.428, 0.007, 12, 3.3, 0, 0.1, 3.0555, 2.8715, 1.934],
+["Ho6+3", 67, 1.696, 90, 3.409, 0.007, 12, 3.416, 0, 0.1, 3.127, 2.891, 1.925],
+["Er6+3", 68, 1.673, 90, 3.391, 0.007, 12, 3.3, 0, 0.1, 3.1865, 2.9145, 1.915],
+["Tm6+3", 69, 1.66, 90, 3.374, 0.006, 12, 3.3, 0, 0.1, 3.2514, 2.9329, 2],
+["Yb6+3", 70, 1.637, 90, 3.355, 0.228, 12, 2.618, 0, 0.1, 3.2889, 2.965, 2.158],
+["Lu6+3", 71, 1.671, 90, 3.64, 0.041, 12, 3.271, 0, 0.1, 2.9629, 2.4629, 1.896],
+["Hf3+4", 72, 1.611, 109.47, 3.141, 0.072, 12, 3.921, 0, 0.1, 3.7, 3.4, 1.759],
+["Ta3+5", 73, 1.511, 109.47, 3.17, 0.081, 12, 4.075, 0, 0.1, 5.1, 2.85, 1.605],
+["W_6+6", 74, 1.392, 90, 3.069, 0.067, 12, 3.7, 0, 0.1, 4.63, 3.31, 1.538],
+["W_3+4", 74, 1.526, 109.47, 3.069, 0.067, 12, 3.7, 0, 0.1, 4.63, 3.31, 1.538],
+["W_3+6", 74, 1.38, 109.47, 3.069, 0.067, 12, 3.7, 0, 0.1, 4.63, 3.31, 1.538],
+["Re6+5", 75, 1.372, 90, 2.954, 0.066, 12, 3.7, 0, 0.1, 3.96, 3.92, 1.6],
+["Re3+7", 75, 1.314, 109.47, 2.954, 0.066, 12, 3.7, 0, 0.1, 3.96, 3.92, 1.6],
+["Os6+6", 76, 1.372, 90, 3.12, 0.037, 12, 3.7, 0, 0.1, 5.14, 3.63, 1.7],
+["Ir6+3", 77, 1.371, 90, 2.84, 0.073, 12, 3.731, 0, 0.1, 5, 4, 1.866],
+["Pt4+2", 78, 1.364, 90, 2.754, 0.08, 12, 3.382, 0, 0.1, 4.79, 4.43, 1.557],
+["Au4+3", 79, 1.262, 90, 3.293, 0.039, 12, 2.625, 0, 0.1, 4.894, 2.586, 1.618],
+["Hg1+2", 80, 1.34, 180, 2.705, 0.385, 12, 1.75, 0, 0.1, 6.27, 4.16, 1.6],
+["Tl3+3", 81, 1.518, 120, 4.347, 0.68, 11, 2.068, 0, 0.1, 3.2, 2.9, 1.53],
+["Pb3", 82, 1.459, 109.47, 4.297, 0.663, 12, 2.846, 0.1, 0.1, 3.9, 3.53, 1.444],
+["Bi3+3", 83, 1.512, 90, 4.37, 0.518, 13, 2.47, 1, 0.1, 4.69, 3.74, 1.514],
+["Po3+2", 84, 1.5, 90, 4.709, 0.325, 14, 2.33, 0.3, 0.1, 4.21, 4.21, 1.48],
+["At", 85, 1.545, 180, 4.75, 0.284, 15, 2.24, 0, 0.1, 4.75, 4.75, 1.47],
+["Rn4+4", 86, 1.42, 90, 4.765, 0.248, 16, 0.583, 0, 0.1, 5.37, 5.37, 2.2],
+["Fr", 87, 2.88, 180, 4.9, 0.05, 12, 1.847, 0, 0, 2, 2, 2.3],
+["Ra6+2", 88, 2.512, 90, 3.677, 0.404, 12, 2.92, 0, 0, 2.843, 2.434, 2.2],
+["Ac6+3", 89, 1.983, 90, 3.478, 0.033, 12, 3.9, 0, 0, 2.835, 2.835, 2.108],
+["Th6+4", 90, 1.721, 90, 3.396, 0.026, 12, 4.202, 0, 0, 3.175, 2.905, 2.018],
+["Pa6+4", 91, 1.711, 90, 3.424, 0.022, 12, 3.9, 0, 0, 2.985, 2.905, 1.8],
+["U_6+4", 92, 1.684, 90, 3.395, 0.022, 12, 3.9, 0, 0, 3.341, 2.853, 1.713],
+["Np6+4", 93, 1.666, 90, 3.424, 0.019, 12, 3.9, 0, 0, 3.549, 2.717, 1.8],
+["Pu6+4", 94, 1.657, 90, 3.424, 0.016, 12, 3.9, 0, 0, 3.243, 2.819, 1.84],
+["Am6+4", 95, 1.66, 90, 3.381, 0.014, 12, 3.9, 0, 0, 2.9895, 3.0035, 1.942],
+["Cm6+3", 96, 1.801, 90, 3.326, 0.013, 12, 3.9, 0, 0, 2.8315, 3.1895, 1.9],
+["Bk6+3", 97, 1.761, 90, 3.339, 0.013, 12, 3.9, 0, 0, 3.1935, 3.0355, 1.9],
+["Cf6+3", 98, 1.75, 90, 3.313, 0.013, 12, 3.9, 0, 0, 3.197, 3.101, 1.9],
+["Es6+3", 99, 1.724, 90, 3.299, 0.012, 12, 3.9, 0, 0, 3.333, 3.089, 1.9],
+["Fm6+3", 100, 1.712, 90, 3.286, 0.012, 12, 3.9, 0, 0, 3.4, 3.1, 1.9],
+["Md6+3", 101, 1.689, 90, 3.274, 0.011, 12, 3.9, 0, 0, 3.47, 3.11, 1.9],
+["No6+3", 102, 1.679, 90, 3.248, 0.011, 12, 3.9, 0, 0, 3.475, 3.175, 1.9],
+["Lw6+3", 103, 1.698, 90, 3.236, 0.011, 12, 3.9, 0, 0, 3.5, 3.2, 1.9]
+]
+
+# Calculate UFF bond length
+def uff_bond_length(r1, r2, x1, x2, bond_order)
+ bond_order_correction = -0.1332 * (r1 + r2) * log(bond_order)
+ sq = sqrt(x1) - sqrt(x2)
+ electronegativity_correction = r1 * r2 * (sqrt(x1) - sqrt(x2)) ** 2 / (x1 * r1 + x2 * r2)
+ return r1 + r2 + bond_order_correction + electronegativity_correction
+end
+
+# UFF bond force constant
+def uff_bond_force(idx1, idx2, bond_order)
+ r1 = UFFParams[idx1][2]
+ r2 = UFFParams[idx2][2]
+ r12 = uff_bond_length(r1, r2, UFFParams[idx1][10], UFFParams[idx2][10], bond_order)
+ return 332.06 * UFFParams[idx1][7] * UFFParams[idx2][7] / (r12 ** 3)
+end
+
+# UFF angle force constant (equilibrium angle should be given in degree)
+def uff_angle_force(idx1, idx2, idx3, bond_order_12, bond_order_23, angle)
+ r1 = UFFParams[idx1][2]
+ r2 = UFFParams[idx2][2]
+ r3 = UFFParams[idx3][2]
+ cost = cos(angle * 3.1415927 / 180.0)
+ r12 = uff_bond_length(r1, r2, UFFParams[idx1][10], UFFParams[idx2][10], bond_order_12)
+ r23 = uff_bond_length(r2, r3, UFFParams[idx2][10], UFFParams[idx3][10], bond_order_23)
+ r13 = sqrt(r12 * r12 + r23 * r23 - 2 * r12 * r23 * cost)
+ return 332.06 * UFFParams[idx1][7] * UFFParams[idx3][7] / (r13 ** 5) * (r12 * r23 * (1.0 - cost * cost) - r13 * r13 * cost)
+end
+
+def guess_uff_parameter_dialog(current_value, indices)
+
+ indices = indices.split(/-/)
+
+ if indices.length == 2
+ par_type = "bond"
+ elsif indices.length == 3
+ par_type = "angle"
+ else
+ message_box("UFF parameter guess of this type is not implemented.", "Guess UFF Force", "OK")
+ end
+
+ # Look up the UFFParams entry
+ uff_types = indices.map { |i|
+ ap = atoms[i]
+ sel = []
+ UFFParams.each_with_index { |p, j|
+ if p[1] == ap.atomic_number
+ sel.push(j)
+ end
+ }
+ if sel.length == 0
+ message_box("No UFF parameter is available for atom #{ap.name}", "Guess UFF Force", "OK")
+ return nil
+ end
+ sel
+ }
+ names = indices.map { |i| sprintf("%d:%s", atoms[i].res_seq, atoms[i].name) }
+ types = indices.map { |i| atoms[i].atom_type }
+ names_str = names.join("-")
+ types_str = types.join("-")
+ recalc = proc { |i1, i2, i3, b1, b2|
+ i1 = uff_types[0][i1] rescue 0
+ i2 = uff_types[1][i2] rescue 0
+ i3 = uff_types[2][i3] rescue 0
+ if par_type == "bond"
+ k = uff_bond_force(i1, i2, b1)
+ else
+ k = uff_angle_force(i1, i2, i3, b1, b2, current_value.to_f)
+ end
+ sprintf("%.5f", k)
+ }
+ hash = Dialog.run("Guess UFF Force", "Accept", "Cancel") {
+ action_proc = proc { |it|
+ t1 = value("uff_type_0").to_i rescue 0
+ t2 = value("uff_type_1").to_i rescue 0
+ t3 = value("uff_type_2").to_i rescue 0
+ b1 = value("bond_order_0").to_f rescue 1.0
+ b2 = value("bond_order_1").to_f rescue 1.0
+ set_value("guessed", recalc.call(t1, t2, t3, b1, b2))
+ }
+ type_selects = []
+ uff_types.each_with_index { |p, i|
+ type_selects.push(item(:text, :title=>names[i] + "->"))
+ if p.length == 1
+ type_selects.push(item(:text, :title=>UFFParams[p[0]][0]))
+ else
+ type_selects.push(item(:popup, :subitems=>p.map { |pp| UFFParams[pp][0] }, :tag=>"uff_type_#{i}", :action=>action_proc))
+ end
+ }
+ bond_orders = []
+ (0..indices.length - 2).each { |i|
+ bond_orders.push(item(:text, :title=>names[i] + "-" + names[i + 1]))
+ bond_orders.push(item(:textfield, :width=>60, :value=>"1.0", :tag=>"bond_order_#{i}", :action=>action_proc))
+ }
+ layout(1,
+ item(:text, :title=>"Guess UFF force parameter from atom types and bond order"),
+ layout(2,
+ item(:text, :title=>"UFF Atom Types:"),
+ item(:text, :title=>"Bond order:"),
+ layout(2, *type_selects),
+ layout(2, *bond_orders)
+ ),
+ layout(2,
+ item(:text, :title=>"Guessed value = "),
+ item(:textfield, :editable=>false, :width=>100, :value=>recalc.call(0, 0, 0, 1.0, 1.0), :tag=>"guessed")
+ )
+ )
+ }
+ if hash[:status] == 0
+ return hash["guessed"]
+ else
+ return nil
+ end
+end
+
+end
+
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