1 Clazz.declarePackage ("javajs.util");
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2 Clazz.load (["javajs.util.V3"], "javajs.util.Measure", ["java.lang.Float", "javajs.api.Interface", "javajs.util.Lst", "$.P3", "$.P4", "$.Quat"], function () {
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3 c$ = Clazz.declareType (javajs.util, "Measure");
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4 c$.computeAngle = Clazz.defineMethod (c$, "computeAngle",
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5 function (pointA, pointB, pointC, vectorBA, vectorBC, asDegrees) {
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6 vectorBA.sub2 (pointA, pointB);
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7 vectorBC.sub2 (pointC, pointB);
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8 var angle = vectorBA.angle (vectorBC);
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9 return (asDegrees ? angle / 0.017453292 : angle);
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10 }, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3,~B");
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11 c$.computeAngleABC = Clazz.defineMethod (c$, "computeAngleABC",
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12 function (pointA, pointB, pointC, asDegrees) {
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13 var vectorBA = new javajs.util.V3 ();
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14 var vectorBC = new javajs.util.V3 ();
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15 return javajs.util.Measure.computeAngle (pointA, pointB, pointC, vectorBA, vectorBC, asDegrees);
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16 }, "javajs.util.T3,javajs.util.T3,javajs.util.T3,~B");
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17 c$.computeTorsion = Clazz.defineMethod (c$, "computeTorsion",
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18 function (p1, p2, p3, p4, asDegrees) {
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19 var ijx = p1.x - p2.x;
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20 var ijy = p1.y - p2.y;
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21 var ijz = p1.z - p2.z;
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22 var kjx = p3.x - p2.x;
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23 var kjy = p3.y - p2.y;
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24 var kjz = p3.z - p2.z;
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25 var klx = p3.x - p4.x;
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26 var kly = p3.y - p4.y;
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27 var klz = p3.z - p4.z;
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28 var ax = ijy * kjz - ijz * kjy;
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29 var ay = ijz * kjx - ijx * kjz;
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30 var az = ijx * kjy - ijy * kjx;
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31 var cx = kjy * klz - kjz * kly;
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32 var cy = kjz * klx - kjx * klz;
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33 var cz = kjx * kly - kjy * klx;
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34 var ai2 = 1 / (ax * ax + ay * ay + az * az);
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35 var ci2 = 1 / (cx * cx + cy * cy + cz * cz);
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36 var ai = Math.sqrt (ai2);
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37 var ci = Math.sqrt (ci2);
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38 var denom = ai * ci;
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39 var cross = ax * cx + ay * cy + az * cz;
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40 var cosang = cross * denom;
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45 }var torsion = Math.acos (cosang);
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46 var dot = ijx * cx + ijy * cy + ijz * cz;
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47 var absDot = Math.abs (dot);
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48 torsion = (dot / absDot > 0) ? torsion : -torsion;
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49 return (asDegrees ? torsion / 0.017453292 : torsion);
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50 }, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.T3,~B");
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51 c$.computeHelicalAxis = Clazz.defineMethod (c$, "computeHelicalAxis",
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52 function (a, b, dq) {
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53 var vab = new javajs.util.V3 ();
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55 var theta = dq.getTheta ();
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56 var n = dq.getNormal ();
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57 var v_dot_n = vab.dot (n);
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58 if (Math.abs (v_dot_n) < 0.0001) v_dot_n = 0;
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59 var va_prime_d = new javajs.util.V3 ();
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60 va_prime_d.cross (vab, n);
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61 if (va_prime_d.dot (va_prime_d) != 0) va_prime_d.normalize ();
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62 var vda = new javajs.util.V3 ();
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63 var vcb = javajs.util.V3.newV (n);
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64 if (v_dot_n == 0) v_dot_n = 1.4E-45;
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65 vcb.scale (v_dot_n);
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66 vda.sub2 (vcb, vab);
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68 va_prime_d.scale (theta == 0 ? 0 : (vda.length () / Math.tan (theta / 2 / 180 * 3.141592653589793)));
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69 var r = javajs.util.V3.newV (va_prime_d);
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70 if (theta != 0) r.add (vda);
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71 var pt_a_prime = javajs.util.P3.newP (a);
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73 if (v_dot_n != 1.4E-45) n.scale (v_dot_n);
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74 var pt_b_prime = javajs.util.P3.newP (pt_a_prime);
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76 theta = javajs.util.Measure.computeTorsion (a, pt_a_prime, pt_b_prime, b, true);
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77 if (Float.isNaN (theta) || r.length () < 0.0001) theta = dq.getThetaDirectedV (n);
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78 var residuesPerTurn = Math.abs (theta == 0 ? 0 : 360 / theta);
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79 var pitch = Math.abs (v_dot_n == 1.4E-45 ? 0 : n.length () * (theta == 0 ? 1 : 360 / theta));
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80 return Clazz.newArray (-1, [pt_a_prime, n, r, javajs.util.P3.new3 (theta, pitch, residuesPerTurn), pt_b_prime]);
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81 }, "javajs.util.P3,javajs.util.P3,javajs.util.Quat");
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82 c$.getPlaneThroughPoints = Clazz.defineMethod (c$, "getPlaneThroughPoints",
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83 function (pointA, pointB, pointC, vNorm, vAB, plane) {
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84 var w = javajs.util.Measure.getNormalThroughPoints (pointA, pointB, pointC, vNorm, vAB);
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85 plane.set4 (vNorm.x, vNorm.y, vNorm.z, w);
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87 }, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3,javajs.util.P4");
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88 c$.getPlaneThroughPoint = Clazz.defineMethod (c$, "getPlaneThroughPoint",
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89 function (pt, normal, plane) {
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90 plane.set4 (normal.x, normal.y, normal.z, -normal.dot (pt));
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91 }, "javajs.util.T3,javajs.util.V3,javajs.util.P4");
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92 c$.distanceToPlane = Clazz.defineMethod (c$, "distanceToPlane",
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93 function (plane, pt) {
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94 return (plane == null ? NaN : (plane.dot (pt) + plane.w) / Math.sqrt (plane.dot (plane)));
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95 }, "javajs.util.P4,javajs.util.T3");
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96 c$.directedDistanceToPlane = Clazz.defineMethod (c$, "directedDistanceToPlane",
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97 function (pt, plane, ptref) {
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98 var f = plane.dot (pt) + plane.w;
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99 var f1 = plane.dot (ptref) + plane.w;
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100 return Math.signum (f1) * f / Math.sqrt (plane.dot (plane));
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101 }, "javajs.util.P3,javajs.util.P4,javajs.util.P3");
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102 c$.distanceToPlaneD = Clazz.defineMethod (c$, "distanceToPlaneD",
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103 function (plane, d, pt) {
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104 return (plane == null ? NaN : (plane.dot (pt) + plane.w) / d);
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105 }, "javajs.util.P4,~N,javajs.util.P3");
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106 c$.distanceToPlaneV = Clazz.defineMethod (c$, "distanceToPlaneV",
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107 function (norm, w, pt) {
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108 return (norm == null ? NaN : (norm.dot (pt) + w) / Math.sqrt (norm.dot (norm)));
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109 }, "javajs.util.V3,~N,javajs.util.P3");
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110 c$.calcNormalizedNormal = Clazz.defineMethod (c$, "calcNormalizedNormal",
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111 function (pointA, pointB, pointC, vNormNorm, vAB) {
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112 vAB.sub2 (pointB, pointA);
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113 vNormNorm.sub2 (pointC, pointA);
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114 vNormNorm.cross (vAB, vNormNorm);
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115 vNormNorm.normalize ();
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116 }, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3");
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117 c$.getDirectedNormalThroughPoints = Clazz.defineMethod (c$, "getDirectedNormalThroughPoints",
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118 function (pointA, pointB, pointC, ptRef, vNorm, vAB) {
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119 var nd = javajs.util.Measure.getNormalThroughPoints (pointA, pointB, pointC, vNorm, vAB);
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120 if (ptRef != null) {
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121 var pt0 = javajs.util.P3.newP (pointA);
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123 var d = pt0.distance (ptRef);
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124 pt0.sub2 (pointA, vNorm);
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125 if (d > pt0.distance (ptRef)) {
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129 }, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3");
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130 c$.getNormalThroughPoints = Clazz.defineMethod (c$, "getNormalThroughPoints",
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131 function (pointA, pointB, pointC, vNorm, vTemp) {
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132 javajs.util.Measure.calcNormalizedNormal (pointA, pointB, pointC, vNorm, vTemp);
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133 vTemp.setT (pointA);
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134 return -vTemp.dot (vNorm);
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135 }, "javajs.util.T3,javajs.util.T3,javajs.util.T3,javajs.util.V3,javajs.util.V3");
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136 c$.getPlaneProjection = Clazz.defineMethod (c$, "getPlaneProjection",
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137 function (pt, plane, ptProj, vNorm) {
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138 var dist = javajs.util.Measure.distanceToPlane (plane, pt);
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139 vNorm.set (plane.x, plane.y, plane.z);
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140 vNorm.normalize ();
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141 vNorm.scale (-dist);
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142 ptProj.add2 (pt, vNorm);
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143 }, "javajs.util.P3,javajs.util.P4,javajs.util.P3,javajs.util.V3");
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144 c$.getNormalToLine = Clazz.defineMethod (c$, "getNormalToLine",
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145 function (pointA, pointB, vNormNorm) {
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146 vNormNorm.sub2 (pointA, pointB);
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147 vNormNorm.cross (vNormNorm, javajs.util.Measure.axisY);
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148 vNormNorm.normalize ();
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149 if (Float.isNaN (vNormNorm.x)) vNormNorm.set (1, 0, 0);
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150 }, "javajs.util.P3,javajs.util.P3,javajs.util.V3");
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151 c$.getBisectingPlane = Clazz.defineMethod (c$, "getBisectingPlane",
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152 function (pointA, vAB, ptTemp, vTemp, plane) {
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153 ptTemp.scaleAdd2 (0.5, vAB, pointA);
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155 vTemp.normalize ();
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156 javajs.util.Measure.getPlaneThroughPoint (ptTemp, vTemp, plane);
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157 }, "javajs.util.P3,javajs.util.V3,javajs.util.T3,javajs.util.V3,javajs.util.P4");
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158 c$.projectOntoAxis = Clazz.defineMethod (c$, "projectOntoAxis",
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159 function (point, axisA, axisUnitVector, vectorProjection) {
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160 vectorProjection.sub2 (point, axisA);
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161 var projectedLength = vectorProjection.dot (axisUnitVector);
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162 point.scaleAdd2 (projectedLength, axisUnitVector, axisA);
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163 vectorProjection.sub2 (point, axisA);
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164 }, "javajs.util.P3,javajs.util.P3,javajs.util.V3,javajs.util.V3");
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165 c$.calcBestAxisThroughPoints = Clazz.defineMethod (c$, "calcBestAxisThroughPoints",
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166 function (points, axisA, axisUnitVector, vectorProjection, nTriesMax) {
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167 var nPoints = points.length;
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168 axisA.setT (points[0]);
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169 axisUnitVector.sub2 (points[nPoints - 1], axisA);
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170 axisUnitVector.normalize ();
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171 javajs.util.Measure.calcAveragePointN (points, nPoints, axisA);
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173 while (nTries++ < nTriesMax && javajs.util.Measure.findAxis (points, nPoints, axisA, axisUnitVector, vectorProjection) > 0.001) {
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175 var tempA = javajs.util.P3.newP (points[0]);
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176 javajs.util.Measure.projectOntoAxis (tempA, axisA, axisUnitVector, vectorProjection);
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177 axisA.setT (tempA);
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178 }, "~A,javajs.util.P3,javajs.util.V3,javajs.util.V3,~N");
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179 c$.findAxis = Clazz.defineMethod (c$, "findAxis",
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180 function (points, nPoints, axisA, axisUnitVector, vectorProjection) {
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181 var sumXiYi = new javajs.util.V3 ();
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182 var vTemp = new javajs.util.V3 ();
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183 var pt = new javajs.util.P3 ();
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184 var ptProj = new javajs.util.P3 ();
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185 var a = javajs.util.V3.newV (axisUnitVector);
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187 for (var i = nPoints; --i >= 0; ) {
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188 pt.setT (points[i]);
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190 javajs.util.Measure.projectOntoAxis (ptProj, axisA, axisUnitVector, vectorProjection);
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191 vTemp.sub2 (pt, ptProj);
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192 vTemp.cross (vectorProjection, vTemp);
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193 sumXiYi.add (vTemp);
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194 sum_Xi2 += vectorProjection.lengthSquared ();
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196 var m = javajs.util.V3.newV (sumXiYi);
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197 m.scale (1 / sum_Xi2);
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198 vTemp.cross (m, axisUnitVector);
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199 axisUnitVector.add (vTemp);
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200 axisUnitVector.normalize ();
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201 vTemp.sub2 (axisUnitVector, a);
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202 return vTemp.length ();
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203 }, "~A,~N,javajs.util.P3,javajs.util.V3,javajs.util.V3");
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204 c$.calcAveragePoint = Clazz.defineMethod (c$, "calcAveragePoint",
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205 function (pointA, pointB, pointC) {
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206 pointC.set ((pointA.x + pointB.x) / 2, (pointA.y + pointB.y) / 2, (pointA.z + pointB.z) / 2);
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207 }, "javajs.util.P3,javajs.util.P3,javajs.util.P3");
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208 c$.calcAveragePointN = Clazz.defineMethod (c$, "calcAveragePointN",
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209 function (points, nPoints, averagePoint) {
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210 averagePoint.setT (points[0]);
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211 for (var i = 1; i < nPoints; i++) averagePoint.add (points[i]);
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213 averagePoint.scale (1 / nPoints);
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214 }, "~A,~N,javajs.util.P3");
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215 c$.transformPoints = Clazz.defineMethod (c$, "transformPoints",
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216 function (vPts, m4, center) {
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217 var v = new javajs.util.Lst ();
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218 for (var i = 0; i < vPts.size (); i++) {
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219 var pt = javajs.util.P3.newP (vPts.get (i));
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226 }, "javajs.util.Lst,javajs.util.M4,javajs.util.P3");
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227 c$.isInTetrahedron = Clazz.defineMethod (c$, "isInTetrahedron",
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228 function (pt, ptA, ptB, ptC, ptD, plane, vTemp, vTemp2, fullyEnclosed) {
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229 var b = (javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptC, ptD, ptA, vTemp, vTemp2, plane), pt) >= 0);
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230 if (b != (javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptA, ptD, ptB, vTemp, vTemp2, plane), pt) >= 0)) return false;
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231 if (b != (javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptB, ptD, ptC, vTemp, vTemp2, plane), pt) >= 0)) return false;
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232 var d = javajs.util.Measure.distanceToPlane (javajs.util.Measure.getPlaneThroughPoints (ptA, ptB, ptC, vTemp, vTemp2, plane), pt);
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233 if (fullyEnclosed) return (b == (d >= 0));
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234 var d1 = javajs.util.Measure.distanceToPlane (plane, ptD);
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235 return d1 * d <= 0 || Math.abs (d1) > Math.abs (d);
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236 }, "javajs.util.P3,javajs.util.P3,javajs.util.P3,javajs.util.P3,javajs.util.P3,javajs.util.P4,javajs.util.V3,javajs.util.V3,~B");
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237 c$.getIntersectionPP = Clazz.defineMethod (c$, "getIntersectionPP",
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238 function (plane1, plane2) {
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247 var norm1 = javajs.util.V3.new3 (a1, b1, c1);
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248 var norm2 = javajs.util.V3.new3 (a2, b2, c2);
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249 var nxn = new javajs.util.V3 ();
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250 nxn.cross (norm1, norm2);
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251 var ax = Math.abs (nxn.x);
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252 var ay = Math.abs (nxn.y);
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253 var az = Math.abs (nxn.z);
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258 var type = (ax > ay ? (ax > az ? 1 : 3) : ay > az ? 2 : 3);
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262 diff = (b1 * c2 - b2 * c1);
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263 if (Math.abs (diff) < 0.01) return null;
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264 y = (c1 * d2 - c2 * d1) / diff;
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265 z = (b2 * d1 - d2 * b1) / diff;
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268 diff = (a1 * c2 - a2 * c1);
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269 if (Math.abs (diff) < 0.01) return null;
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270 x = (c1 * d2 - c2 * d1) / diff;
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272 z = (a2 * d1 - d2 * a1) / diff;
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276 diff = (a1 * b2 - a2 * b1);
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277 if (Math.abs (diff) < 0.01) return null;
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278 x = (b1 * d2 - b2 * d1) / diff;
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279 y = (a2 * d1 - d2 * a1) / diff;
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282 var list = new javajs.util.Lst ();
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283 list.addLast (javajs.util.P3.new3 (x, y, z));
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285 list.addLast (nxn);
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287 }, "javajs.util.P4,javajs.util.P4");
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288 c$.getIntersection = Clazz.defineMethod (c$, "getIntersection",
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289 function (pt1, v, plane, ptRet, tempNorm, vTemp) {
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290 javajs.util.Measure.getPlaneProjection (pt1, plane, ptRet, tempNorm);
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291 tempNorm.set (plane.x, plane.y, plane.z);
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292 tempNorm.normalize ();
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293 if (v == null) v = javajs.util.V3.newV (tempNorm);
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294 var l_dot_n = v.dot (tempNorm);
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295 if (Math.abs (l_dot_n) < 0.01) return null;
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296 vTemp.sub2 (ptRet, pt1);
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297 ptRet.scaleAdd2 (vTemp.dot (tempNorm) / l_dot_n, v, pt1);
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299 }, "javajs.util.P3,javajs.util.V3,javajs.util.P4,javajs.util.P3,javajs.util.V3,javajs.util.V3");
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300 c$.calculateQuaternionRotation = Clazz.defineMethod (c$, "calculateQuaternionRotation",
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301 function (centerAndPoints, retStddev) {
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302 retStddev[1] = NaN;
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303 var q = new javajs.util.Quat ();
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304 if (centerAndPoints[0].length == 1 || centerAndPoints[0].length != centerAndPoints[1].length) return q;
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305 var n = centerAndPoints[0].length - 1;
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306 if (n < 2) return q;
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316 var ptA = new javajs.util.P3 ();
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317 var ptB = new javajs.util.P3 ();
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318 for (var i = n + 1; --i >= 1; ) {
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319 var aij = centerAndPoints[0][i];
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320 var bij = centerAndPoints[1][i];
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321 ptA.sub2 (aij, centerAndPoints[0][0]);
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322 ptB.sub2 (bij, centerAndPoints[0][1]);
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323 Sxx += ptA.x * ptB.x;
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324 Sxy += ptA.x * ptB.y;
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325 Sxz += ptA.x * ptB.z;
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326 Syx += ptA.y * ptB.x;
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327 Syy += ptA.y * ptB.y;
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328 Syz += ptA.y * ptB.z;
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329 Szx += ptA.z * ptB.x;
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330 Szy += ptA.z * ptB.y;
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331 Szz += ptA.z * ptB.z;
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333 retStddev[0] = javajs.util.Measure.getRmsd (centerAndPoints, q);
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334 var N = Clazz.newDoubleArray (4, 4, 0);
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335 N[0][0] = Sxx + Syy + Szz;
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336 N[0][1] = N[1][0] = Syz - Szy;
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337 N[0][2] = N[2][0] = Szx - Sxz;
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338 N[0][3] = N[3][0] = Sxy - Syx;
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339 N[1][1] = Sxx - Syy - Szz;
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340 N[1][2] = N[2][1] = Sxy + Syx;
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341 N[1][3] = N[3][1] = Szx + Sxz;
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342 N[2][2] = -Sxx + Syy - Szz;
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343 N[2][3] = N[3][2] = Syz + Szy;
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344 N[3][3] = -Sxx - Syy + Szz;
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345 var v = (javajs.api.Interface.getInterface ("javajs.util.Eigen")).setM (N).getEigenvectorsFloatTransposed ()[3];
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346 q = javajs.util.Quat.newP4 (javajs.util.P4.new4 (v[1], v[2], v[3], v[0]));
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347 retStddev[1] = javajs.util.Measure.getRmsd (centerAndPoints, q);
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350 c$.getTransformMatrix4 = Clazz.defineMethod (c$, "getTransformMatrix4",
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351 function (ptsA, ptsB, m, centerA) {
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352 var cptsA = javajs.util.Measure.getCenterAndPoints (ptsA);
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353 var cptsB = javajs.util.Measure.getCenterAndPoints (ptsB);
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354 var retStddev = Clazz.newFloatArray (2, 0);
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355 var q = javajs.util.Measure.calculateQuaternionRotation ( Clazz.newArray (-1, [cptsA, cptsB]), retStddev);
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356 var r = q.getMatrix ();
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357 if (centerA == null) r.rotate (cptsA[0]);
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358 else centerA.setT (cptsA[0]);
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359 var t = javajs.util.V3.newVsub (cptsB[0], cptsA[0]);
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361 return retStddev[1];
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362 }, "javajs.util.Lst,javajs.util.Lst,javajs.util.M4,javajs.util.P3");
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363 c$.getCenterAndPoints = Clazz.defineMethod (c$, "getCenterAndPoints",
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365 var n = vPts.size ();
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366 var pts = new Array (n + 1);
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367 pts[0] = new javajs.util.P3 ();
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369 for (var i = 0; i < n; i++) {
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370 pts[0].add (pts[i + 1] = vPts.get (i));
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372 pts[0].scale (1 / n);
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374 }, "javajs.util.Lst");
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375 c$.getRmsd = Clazz.defineMethod (c$, "getRmsd",
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376 function (centerAndPoints, q) {
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378 var ptsA = centerAndPoints[0];
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379 var ptsB = centerAndPoints[1];
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382 var n = ptsA.length - 1;
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383 var ptAnew = new javajs.util.P3 ();
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384 for (var i = n + 1; --i >= 1; ) {
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385 ptAnew.sub2 (ptsA[i], cA);
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386 q.transform2 (ptAnew, ptAnew).add (cB);
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387 sum2 += ptAnew.distanceSquared (ptsB[i]);
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389 return Math.sqrt (sum2 / n);
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390 }, "~A,javajs.util.Quat");
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391 Clazz.defineStatics (c$,
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392 "radiansPerDegree", (0.017453292519943295));
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393 c$.axisY = c$.prototype.axisY = javajs.util.V3.new3 (0, 1, 0);
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git://source.jalview.org / jalviewjs.git / blob