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glshape.js
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glshape.js
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/**
* A GLShape is a collection of user specified shapes.
*
* @constructor $3Dmol.GLShape
* @extends {ShapeSpec}
* @param {number} sid - Unique identifier
* @param {ShapeSpec} stylespec - shape style specification
*/
$3Dmol.GLShape = (function() {
// Marching cube, to match with protein surface generation
var ISDONE = 2;
var finalizeGeo = function(geo) {
//to avoid creating a bunch of geometries, we leave geoGroup untruncated
//until render is called, at which point we truncate;
//successive called up updateGeo will return a new geometry
var geoGroup = geo.updateGeoGroup(0);
if(geoGroup.vertices > 0) {
geoGroup.truncateArrayBuffers(true, true);
}
};
/**
*
* @param {$3Dmol.Geometry}
* geo
* @param {$3Dmol.Color |
* colorlike} color
*/
var updateColor = function(geo, color) {
color = color || $3Dmol.CC.color(color);
geo.colorsNeedUpdate = true;
var r,g,b;
if(color.constructor !== Array) {
r = color.r;
g = color.g;
b = color.b;
}
for ( var gg in geo.geometryGroups) {
var geoGroup = geo.geometryGroups[gg];
var colorArr = geoGroup.colorArray;
for (var i = 0, il = geoGroup.vertices; i < il; ++i) {
if( color.constructor === Array) {
var c = color[i];
r = c.r;
g = c.g;
b = c.b;
}
colorArr[i * 3] = r;
colorArr[i * 3 + 1] = g;
colorArr[i * 3 + 2] = b;
}
}
};
/**
* @param {$3Dmol.GLShape}
* shape
* @param {geometryGroup}
* geoGroup
* @param {ArrowSpec}
* spec
*/
var drawArrow = function(shape, geo, spec) {
var from = spec.start, end = spec.end, radius = spec.radius, radiusRatio = spec.radiusRatio, mid = spec.mid;
if (!(from && end))
return;
var geoGroup = geo.updateGeoGroup(51);
// vertices
var dir = end.clone();
dir.sub(from).multiplyScalar(mid);
var to = from.clone().add(dir);
var negDir = dir.clone().negate();
shape.intersectionShape.cylinder.push(new $3Dmol.Cylinder(from.clone(),
to.clone(), radius));
shape.intersectionShape.sphere.push(new $3Dmol.Sphere(from.clone(),
radius));
// get orthonormal vector
var nvecs = [];
nvecs[0] = dir.clone();
if (Math.abs(nvecs[0].x) > 0.0001)
nvecs[0].y += 1;
else
nvecs[0].x += 1;
nvecs[0].cross(dir);
nvecs[0].normalize();
nvecs[0] = nvecs[0];
// another orth vector
nvecs[4] = nvecs[0].clone();
nvecs[4].crossVectors(nvecs[0], dir);
nvecs[4].normalize();
nvecs[8] = nvecs[0].clone().negate();
nvecs[12] = nvecs[4].clone().negate();
// now quarter positions
nvecs[2] = nvecs[0].clone().add(nvecs[4]).normalize();
nvecs[6] = nvecs[4].clone().add(nvecs[8]).normalize();
nvecs[10] = nvecs[8].clone().add(nvecs[12]).normalize();
nvecs[14] = nvecs[12].clone().add(nvecs[0]).normalize();
// eights
nvecs[1] = nvecs[0].clone().add(nvecs[2]).normalize();
nvecs[3] = nvecs[2].clone().add(nvecs[4]).normalize();
nvecs[5] = nvecs[4].clone().add(nvecs[6]).normalize();
nvecs[7] = nvecs[6].clone().add(nvecs[8]).normalize();
nvecs[9] = nvecs[8].clone().add(nvecs[10]).normalize();
nvecs[11] = nvecs[10].clone().add(nvecs[12]).normalize();
nvecs[13] = nvecs[12].clone().add(nvecs[14]).normalize();
nvecs[15] = nvecs[14].clone().add(nvecs[0]).normalize();
var start = geoGroup.vertices;
var vertexArray = geoGroup.vertexArray;
var faceArray = geoGroup.faceArray;
var normalArray = geoGroup.normalArray;
var lineArray = geoGroup.lineArray;
var offset, i, n;
// add vertices, opposing vertices paired together
for (i = 0, n = nvecs.length; i < n; ++i) {
offset = 3 * (start + 3 * i);
var bottom = nvecs[i].clone().multiplyScalar(radius).add(from);
var top = nvecs[i].clone().multiplyScalar(radius).add(to);
var conebase = nvecs[i].clone()
.multiplyScalar(radius * radiusRatio).add(to);
vertexArray[offset] = bottom.x;
vertexArray[offset + 1] = bottom.y;
vertexArray[offset + 2] = bottom.z;
vertexArray[offset + 3] = top.x;
vertexArray[offset + 4] = top.y;
vertexArray[offset + 5] = top.z;
vertexArray[offset + 6] = conebase.x;
vertexArray[offset + 7] = conebase.y;
vertexArray[offset + 8] = conebase.z;
if (i > 0) {
var prev_x = vertexArray[offset - 3];
var prev_y = vertexArray[offset - 2];
var prev_z = vertexArray[offset - 1];
var c = new $3Dmol.Vector3(prev_x, prev_y, prev_z);
var b = end.clone(), b2 = to.clone();
var a = new $3Dmol.Vector3(conebase.x, conebase.y, conebase.z);
shape.intersectionShape.triangle.push(new $3Dmol.Triangle(a, b,
c));
shape.intersectionShape.triangle.push(new $3Dmol.Triangle(c
.clone(), b2, a.clone()));
}
}
geoGroup.vertices += 48;
offset = geoGroup.vertices * 3;
// caps
vertexArray[offset] = from.x;
vertexArray[offset + 1] = from.y;
vertexArray[offset + 2] = from.z;
vertexArray[offset + 3] = to.x;
vertexArray[offset + 4] = to.y;
vertexArray[offset + 5] = to.z;
vertexArray[offset + 6] = end.x;
vertexArray[offset + 7] = end.y;
vertexArray[offset + 8] = end.z;
geoGroup.vertices += 3;
// now faces
var face, norm, faceoffset, lineoffset;
var t1, t2, t2b, t3, t3b, t4, t1offset, t2offset, t2boffset, t3offset, t3boffset, t4offset;
var n1, n2, n3, n4;
var fromi = geoGroup.vertices - 3, toi = geoGroup.vertices - 2, endi = geoGroup.vertices - 1;
var fromoffset = fromi * 3, tooffset = toi * 3, endoffset = endi * 3;
for (i = 0, n = nvecs.length - 1; i < n; ++i) {
var ti = start + 3 * i;
offset = ti * 3;
faceoffset = geoGroup.faceidx;
lineoffset = geoGroup.lineidx;
t1 = ti;
t1offset = t1 * 3;
t2 = ti + 1;
t2offset = t2 * 3;
t2b = ti + 2;
t2boffset = t2b * 3;
t3 = ti + 4;
t3offset = t3 * 3;
t3b = ti + 5;
t3boffset = t3b * 3;
t4 = ti + 3;
t4offset = t4 * 3;
// face = [t1, t2, t4], [t2, t3, t4];
// face = [t1, t2, t3, t4];
norm = [ nvecs[i], nvecs[i], nvecs[i + 1], nvecs[i + 1] ];
n1 = n2 = nvecs[i];
n3 = n4 = nvecs[i + 1];
normalArray[t1offset] = n1.x;
normalArray[t2offset] = n2.x;
normalArray[t4offset] = n4.x;
normalArray[t1offset + 1] = n1.y;
normalArray[t2offset + 1] = n2.y;
normalArray[t4offset + 1] = n4.y;
normalArray[t1offset + 2] = n1.z;
normalArray[t2offset + 2] = n2.z;
normalArray[t4offset + 2] = n4.z;
normalArray[t2offset] = n2.x;
normalArray[t3offset] = n3.x;
normalArray[t4offset] = n4.x;
normalArray[t2offset + 1] = n2.y;
normalArray[t3offset + 1] = n3.y;
normalArray[t4offset + 1] = n4.y;
normalArray[t2offset + 2] = n2.z;
normalArray[t3offset + 2] = n3.z;
normalArray[t4offset + 2] = n4.z;
normalArray[t2boffset] = n2.x;
normalArray[t3boffset] = n3.x;
normalArray[t2boffset + 1] = n2.y;
normalArray[t3boffset + 1] = n3.y;
normalArray[t2boffset + 2] = n2.z;
normalArray[t3boffset + 2] = n3.z;
// sides
faceArray[faceoffset] = t1;
faceArray[faceoffset + 1] = t2;
faceArray[faceoffset + 2] = t4;
faceArray[faceoffset + 3] = t2;
faceArray[faceoffset + 4] = t3;
faceArray[faceoffset + 5] = t4;
// caps
faceArray[faceoffset + 6] = t1;
faceArray[faceoffset + 7] = t4;
faceArray[faceoffset + 8] = fromi;
faceArray[faceoffset + 9] = t2b;
faceArray[faceoffset + 10] = toi;
faceArray[faceoffset + 11] = t3b;
// arrowhead
faceArray[faceoffset + 12] = t2b;
faceArray[faceoffset + 13] = endi;
faceArray[faceoffset + 14] = t3b;
// sides
lineArray[lineoffset] = t1;
lineArray[lineoffset + 1] = t2;
lineArray[lineoffset + 2] = t1;
lineArray[lineoffset + 3] = t4;
// lineArray[lineoffset+4] = t2, lineArray[lineoffset+5] = t3;
lineArray[lineoffset + 4] = t3;
lineArray[lineoffset + 5] = t4;
// caps
lineArray[lineoffset + 6] = t1;
lineArray[lineoffset + 7] = t4;
// lineArray[lineoffset+10] = t1, lineArray[lineoffset+11] = fromi;
// lineArray[lineoffset+12] = t4, lineArray[lineoffset+13] = fromi;
lineArray[lineoffset + 8] = t2b;
lineArray[lineoffset + 9] = t2; // toi
lineArray[lineoffset + 10] = t2b;
lineArray[lineoffset + 11] = t3b;
lineArray[lineoffset + 12] = t3;
lineArray[lineoffset + 13] = t3b; // toi
// arrowhead
lineArray[lineoffset + 14] = t2b;
lineArray[lineoffset + 15] = endi;
lineArray[lineoffset + 16] = t2b;
lineArray[lineoffset + 17] = t3b;
lineArray[lineoffset + 18] = endi;
lineArray[lineoffset + 19] = t3b;
geoGroup.faceidx += 15;
geoGroup.lineidx += 20;
}
// final face
face = [ start + 45, start + 46, start + 1, start, start + 47,
start + 2 ];
norm = [ nvecs[15], nvecs[15], nvecs[0], nvecs[0] ];
faceoffset = geoGroup.faceidx;
lineoffset = geoGroup.lineidx;
t1 = face[0];
t1offset = t1 * 3;
t2 = face[1];
t2offset = t2 * 3;
t2b = face[4];
t2boffset = t2b * 3;
t3 = face[2];
t3offset = t3 * 3;
t3b = face[5];
t3boffset = t3b * 3;
t4 = face[3];
t4offset = t4 * 3;
n1 = n2 = nvecs[15];
n3 = n4 = nvecs[0];
normalArray[t1offset] = n1.x;
normalArray[t2offset] = n2.x;
normalArray[t4offset] = n4.x;
normalArray[t1offset + 1] = n1.y;
normalArray[t2offset + 1] = n2.y;
normalArray[t4offset + 1] = n4.y;
normalArray[t1offset + 2] = n1.z;
normalArray[t2offset + 2] = n2.z;
normalArray[t4offset + 2] = n4.z;
normalArray[t2offset] = n2.x;
normalArray[t3offset] = n3.x;
normalArray[t4offset] = n4.x;
normalArray[t2offset + 1] = n2.y;
normalArray[t3offset + 1] = n3.y;
normalArray[t4offset + 1] = n4.y;
normalArray[t2offset + 2] = n2.z;
normalArray[t3offset + 2] = n3.z;
normalArray[t4offset + 2] = n4.z;
normalArray[t2boffset] = n2.x;
normalArray[t3boffset] = n3.x;
normalArray[t2boffset + 1] = n2.y;
normalArray[t3boffset + 1] = n3.y;
normalArray[t2boffset + 2] = n2.z;
normalArray[t3boffset + 2] = n3.z;
// Cap normals
dir.normalize();
negDir.normalize();
normalArray[fromoffset] = negDir.x;
normalArray[tooffset] = normalArray[endoffset] = dir.x;
normalArray[fromoffset + 1] = negDir.y;
normalArray[tooffset + 1] = normalArray[endoffset + 1] = dir.y;
normalArray[fromoffset + 2] = negDir.z;
normalArray[tooffset + 2] = normalArray[endoffset + 2] = dir.z;
// Final side
faceArray[faceoffset] = t1;
faceArray[faceoffset + 1] = t2;
faceArray[faceoffset + 2] = t4;
faceArray[faceoffset + 3] = t2;
faceArray[faceoffset + 4] = t3;
faceArray[faceoffset + 5] = t4;
// final caps
faceArray[faceoffset + 6] = t1;
faceArray[faceoffset + 7] = t4;
faceArray[faceoffset + 8] = fromi;
faceArray[faceoffset + 9] = t2b;
faceArray[faceoffset + 10] = toi;
faceArray[faceoffset + 11] = t3b;
// final arrowhead
faceArray[faceoffset + 12] = t2b;
faceArray[faceoffset + 13] = endi;
faceArray[faceoffset + 14] = t3b;
// sides
lineArray[lineoffset] = t1;
lineArray[lineoffset + 1] = t2;
lineArray[lineoffset + 2] = t1;
lineArray[lineoffset + 3] = t4;
// lineArray[lineoffset+4] = t2, lineArray[lineoffset+5] = t3;
lineArray[lineoffset + 4] = t3;
lineArray[lineoffset + 5] = t4;
// caps
lineArray[lineoffset + 6] = t1;
lineArray[lineoffset + 7] = t4;
// lineArray[lineoffset+10] = t1, lineArray[lineoffset+11] = fromi;
// lineArray[lineoffset+12] = t4, lineArray[lineoffset+13] = fromi;
lineArray[lineoffset + 8] = t2b;
lineArray[lineoffset + 9] = t2; // toi
lineArray[lineoffset + 10] = t2b;
lineArray[lineoffset + 11] = t3b;
lineArray[lineoffset + 12] = t3;
lineArray[lineoffset + 13] = t3b; // toi
// arrowhead
lineArray[lineoffset + 14] = t2b;
lineArray[lineoffset + 15] = endi;
lineArray[lineoffset + 16] = t2b;
lineArray[lineoffset + 17] = t3b;
lineArray[lineoffset + 18] = endi;
lineArray[lineoffset + 19] = t3b;
geoGroup.faceidx += 15;
geoGroup.lineidx += 20;
};
// Update a bounding sphere's position and radius
// from list of centroids and new points
/**
* @param {$3Dmol.Sphere}
* sphere
* @param {Object}
* components, centroid of all objects in shape
* @param {Array}
* points, flat array of all points in shape
* @param {int} numPoints, number of valid poitns in points
*/
var updateBoundingFromPoints = function(sphere, components, points, numPoints) {
sphere.center.set(0, 0, 0);
var i, il;
if (components.length > 0) {
for (i = 0, il = components.length; i < il; ++i) {
var centroid = components[i].centroid;
sphere.center.add(centroid);
}
sphere.center.divideScalar(components.length);
}
var maxRadiusSq = sphere.radius * sphere.radius;
if(points.length/3 < numPoints)
numPoints = points.length/3;
for (i = 0, il = numPoints; i < il; i++) {
var x = points[i * 3], y = points[i * 3 + 1], z = points[i * 3 + 2];
var radiusSq = sphere.center.distanceToSquared({
x : x,
y : y,
z : z
});
maxRadiusSq = Math.max(maxRadiusSq, radiusSq);
}
sphere.radius = Math.sqrt(maxRadiusSq);
};
//helper function for adding an appropriately sized mesh
var addCustomGeo = function(shape, geo, mesh, color, clickable) {
var geoGroup = geo.addGeoGroup();
var vertexArr = mesh.vertexArr, normalArr = mesh.normalArr,
faceArr = mesh.faceArr;
geoGroup.vertices = vertexArr.length;
geoGroup.faceidx = faceArr.length;
var offset, v, a, b, c, i, il, r, g;
var vertexArray = geoGroup.vertexArray;
var colorArray = geoGroup.colorArray;
if(color.constructor !== Array) {
r = color.r;
g = color.g;
b = color.b;
}
for (i = 0, il = geoGroup.vertices; i < il; ++i) {
offset = i * 3;
v = vertexArr[i];
vertexArray[offset] = v.x;
vertexArray[offset + 1] = v.y;
vertexArray[offset + 2] = v.z;
if( color.constructor === Array) {
c = color[i];
r = c.r;
g = c.g;
b = c.b;
}
colorArray[offset] = r;
colorArray[offset + 1] = g;
colorArray[offset + 2] = b;
}
if(clickable) {
for (i = 0, il = geoGroup.faceidx / 3; i < il; ++i) {
offset = i * 3;
a = faceArr[offset];
b = faceArr[offset + 1];
c = faceArr[offset + 2];
var vA = new $3Dmol.Vector3(), vB = new $3Dmol.Vector3(), vC = new $3Dmol.Vector3();
shape.intersectionShape.triangle.push(new $3Dmol.Triangle(vA
.copy(vertexArr[a]), vB.copy(vertexArr[b]), vC
.copy(vertexArr[c])));
}
}
if(clickable) {
var center = new $3Dmol.Vector3(0,0,0);
var cnt = 0;
for(let g = 0; g < geo.geometryGroups.length; g++) {
center.add(geo.geometryGroups[g].getCentroid());
cnt++;
}
center.divideScalar(cnt);
updateBoundingFromPoints(shape.boundingSphere, {centroid: center}, vertexArray, geoGroup.vertices);
}
geoGroup.faceArray = new Uint16Array(faceArr);
geoGroup.truncateArrayBuffers(true, true);
if (normalArr.length < geoGroup.vertices)
geoGroup.setNormals();
else {
var normalArray = geoGroup.normalArray = new Float32Array(geoGroup.vertices * 3);
var n;
for (i = 0, il = geoGroup.vertices; i < il; ++i) {
offset = i * 3;
n = normalArr[i];
normalArray[offset] = n.x;
normalArray[offset + 1] = n.y;
normalArray[offset + 2] = n.z;
}
}
geoGroup.setLineIndices();
geoGroup.lineidx = geoGroup.lineArray.length;
};
// handles custom shape generation from user supplied arrays
// May need to generate normal and/or line indices
/**
* @param {$3Dmol.GLShape}
* shape
* @param {geometry}
* geo
* @param {CustomSpec}
* customSpec
*/
var drawCustom = function(shape, geo, customSpec) {
var mesh = customSpec;
var vertexArr = mesh.vertexArr;
var faceArr = mesh.faceArr;
if (vertexArr.length === 0 || faceArr.length === 0) {
console
.warn("Error adding custom shape component: No vertices and/or face indices supplied!");
}
var color = customSpec.color;
if(typeof(color) == 'undefined') {
color = shape.color;
}
color = $3Dmol.CC.color(color);
//var firstgeo = geo.geometryGroups.length;
var splits = $3Dmol.splitMesh(mesh);
for(var i = 0, n = splits.length; i < n; i++) {
addCustomGeo(shape, geo, splits[i], splits[i].colorArr ? splits[i].colorArr : color, customSpec.clickable);
}
};
/**
*
* @param {$3Dmol.GLShape}
* shape
* @param {ShapeSpec}
* stylespec
* @returns {undefined}
*/
var updateFromStyle = function(shape, stylespec) {
if(typeof(stylespec.color) != 'undefined') {
shape.color = stylespec.color || new $3Dmol.Color();
if(! (stylespec.color instanceof $3Dmol.Color))
shape.color = $3Dmol.CC.color(stylespec.color);
} else {
shape.color = $3Dmol.CC.color(0);
}
shape.wireframe = stylespec.wireframe ? true : false;
//opacity is the preferred nomenclature, support alpha for backwards compat
shape.opacity = stylespec.alpha ? $3Dmol.Math.clamp(stylespec.alpha, 0.0,
1.0) : 1.0;
if(typeof(stylespec.opacity) != 'undefined') {
shape.opacity = $3Dmol.Math.clamp(stylespec.opacity, 0.0, 1.0);
}
shape.side = (stylespec.side !== undefined) ? stylespec.side
: $3Dmol.DoubleSide;
shape.linewidth = typeof(stylespec.linewidth) == 'undefined' ? 1 : stylespec.linewidth;
// Click handling
shape.clickable = stylespec.clickable ? true : false;
shape.callback = typeof (stylespec.callback) === "function" ? stylespec.callback
: null;
shape.hoverable = stylespec.hoverable ? true : false;
shape.hover_callback = typeof (stylespec.hover_callback) === "function" ? stylespec.hover_callback
: null;
shape.unhover_callback = typeof (stylespec.unhover_callback) === "function" ? stylespec.unhover_callback
: null;
shape.hidden = stylespec.hidden;
shape.frame = stylespec.frame;
};
/**
* Custom renderable shape
*
* @constructor $3Dmol.GLShape
*
* @param {Object}
* stylespec
* @returns {$3Dmol.GLShape}
*/
function GLShape(stylespec) {
stylespec = stylespec || {};
$3Dmol.ShapeIDCount++;
this.boundingSphere = new $3Dmol.Sphere();
/** @type {IntersectionShapes} */
this.intersectionShape = {
sphere : [],
cylinder : [],
line : [],
triangle : []
};
updateFromStyle(this, stylespec);
// Keep track of shape components and their centroids
var components = [];
var shapeObj = null;
var renderedShapeObj = null;
var geo = new $3Dmol.Geometry(true);
var linegeo = new $3Dmol.Geometry(true);
/** Update shape with new style specification
* @function $3Dmol.GLShape#updateStyle
* @param {ShapeSpec} newspec
* @return {$3Dmol.GLShape}
*/
this.updateStyle = function(newspec) {
for ( var prop in newspec) {
stylespec[prop] = newspec[prop];
}
updateFromStyle(this, stylespec);
};
/**
* Creates a custom shape from supplied vertex and face arrays
* @function $3Dmol.GLShape#addCustom
* @param {CustomShapeSpec} customSpec
* @return {$3Dmol.GLShape}
*/
this.addCustom = function(customSpec) {
customSpec.vertexArr = customSpec.vertexArr || [];
customSpec.faceArr = customSpec.faceArr || [];
customSpec.normalArr = customSpec.normalArr || [];
// will split mesh as needed
drawCustom(this, geo, customSpec);
};
/**
* Creates a sphere shape
* @function $3Dmol.GLShape#addSphere
* @param {SphereSpec} sphereSpec
* @return {$3Dmol.GLShape}
@example
viewer.addSphere({center:{x:0,y:0,z:0},radius:10.0,color:'red'});
viewer.render();
*/
this.addSphere = function(sphereSpec) {
sphereSpec.center = sphereSpec.center || {
x : 0,
y : 0,
z : 0
};
sphereSpec.radius = sphereSpec.radius ? $3Dmol.Math.clamp(
sphereSpec.radius, 0, Infinity) : 1.5;
sphereSpec.color = $3Dmol.CC.color(sphereSpec.color);
this.intersectionShape.sphere.push(new $3Dmol.Sphere(
sphereSpec.center, sphereSpec.radius));
$3Dmol.GLDraw.drawSphere(geo, sphereSpec.center,
sphereSpec.radius, sphereSpec.color);
components.push({
centroid : new $3Dmol.Vector3(sphereSpec.center.x,
sphereSpec.center.y, sphereSpec.center.z)
});
var geoGroup = geo.updateGeoGroup(0);
updateBoundingFromPoints(this.boundingSphere, components,
geoGroup.vertexArray, geoGroup.vertices);
};
/**
* Creates a box
* @function $3Dmol.GLShape#addBox
* @param {BoxSpec} boxSpec
* @return {$3Dmol.GLShape}
@example
var shape = viewer.addShape({color:'red'});
shape.addBox({corner: {x:1,y:2,z:0}, dimensions: {w: 4, h: 2, d: 6}});
shape.addBox({corner: {x:-5,y:-3,z:0},
dimensions: { w: {x:1,y:1,z:0},
h: {x:-1,y:1,z:0},
d: {x:0,y:0,z:1} }});
viewer.zoomTo();
viewer.rotate(30);
viewer.render();
*/
this.addBox = function(boxSpec) {
var dim = boxSpec.dimensions || { w: 1, h:1, d: 1};
//dimensions may be scalar or vector quantities
var w = dim.w;
if(typeof(dim.w) == "number") {
w = {x:dim.w,y:0,z:0};
}
var h = dim.h;
if(typeof(dim.h) == "number") {
h = {x:0,y:dim.h,z:0};
}
var d = dim.d;
if(typeof(dim.d) == "number") {
d = {x:0,y:0,z:dim.d};
}
//can position using corner OR center
var c = boxSpec.corner;
if(c == undefined) {
if(boxSpec.center !== undefined) {
c = {x: boxSpec.center.x - 0.5*(w.x+h.x+d.x),
y: boxSpec.center.y - 0.5*(w.y+h.y+d.y),
z: boxSpec.center.z - 0.5*(w.z+h.z+d.z)};
} else { // default to origin
c = {x:0,y:0,z:0};
}
}
//8 vertices
var uv =
[{x: c.x, y: c.y, z:c.z},
{x: c.x+w.x, y: c.y+w.y, z:c.z+w.z},
{x: c.x+h.x, y: c.y+h.y, z:c.z+h.z},
{x: c.x+w.x+h.x, y: c.y+w.y+h.y, z:c.z+w.z+h.z},
{x: c.x+d.x, y: c.y+d.y, z:c.z+d.z},
{x: c.x+w.x+d.x, y: c.y+w.y+d.y, z:c.z+w.z+d.z},
{x: c.x+h.x+d.x, y: c.y+h.y+d.y, z:c.z+h.z+d.z},
{x: c.x+w.x+h.x+d.x, y: c.y+w.y+h.y+d.y, z:c.z+w.z+h.z+d.z}];
//but.. so that we can have sharp issues, we want a unique normal
//for each face - since normals are associated with vertices, need to duplicate
//bottom
// 0 1
// 2 3
//top
// 4 5
// 6 7
var verts = [];
var faces = [];
//bottom
verts.splice(verts.length, 0, uv[0],uv[1],uv[2],uv[3]);
faces.splice(faces.length,0, 0,2,1, 1,2,3);
var foff = 4;
//front
verts.splice(verts.length, 0, uv[2],uv[3],uv[6],uv[7]);
faces.splice(faces.length,0, foff+0,foff+2,foff+1, foff+1,foff+2,foff+3);
foff += 4;
//back
verts.splice(verts.length, 0, uv[4],uv[5],uv[0],uv[1]);
faces.splice(faces.length,0, foff+0,foff+2,foff+1, foff+1,foff+2,foff+3);
foff += 4;
//top
verts.splice(verts.length, 0, uv[6],uv[7],uv[4],uv[5]);
faces.splice(faces.length,0, foff+0,foff+2,foff+1, foff+1,foff+2,foff+3);
foff += 4;
//right
verts.splice(verts.length, 0, uv[3],uv[1],uv[7],uv[5]);
faces.splice(faces.length,0, foff+0,foff+2,foff+1, foff+1,foff+2,foff+3);
foff += 4;
//left
verts.splice(verts.length, 0, uv[2],uv[6],uv[0],uv[4]); // fix: was 2 0 6 4 , was flipped! will this ruin anything?
// and is this the reason for having double sided lambert shading? the box had a flipped face
faces.splice(faces.length,0, foff+0,foff+2,foff+1, foff+1,foff+2,foff+3);
foff += 4;
var spec = $.extend({},boxSpec);
spec.vertexArr = verts;
spec.faceArr = faces;
spec.normalArr = [];
drawCustom(this, geo, spec);
var centroid = new $3Dmol.Vector3();
components.push({
centroid : centroid.addVectors(uv[0],uv[7]).multiplyScalar(0.5)
});
var geoGroup = geo.updateGeoGroup(0);
updateBoundingFromPoints(this.boundingSphere, components, geoGroup.vertexArray, geoGroup.vertices);
};
/**
* Creates a cylinder shape
* @function $3Dmol.GLShape#addCylinder
* @param {CylinderSpec} cylinderSpec
* @return {$3Dmol.GLShape}
@example
viewer.addCylinder({start:{x:0.0,y:0.0,z:0.0},
end:{x:10.0,y:0.0,z:0.0},
radius:1.0,
fromCap:1,
toCap:2,
color:'red',
hoverable:true,
clickable:true,
callback:function(){ this.color.setHex(0x00FFFF00);viewer.render( );},
hover_callback: function(){ viewer.render( );},
unhover_callback: function(){ this.color.setHex(0xFF000000);viewer.render( );}
});
viewer.addCylinder({start:{x:0.0,y:2.0,z:0.0},
end:{x:0.0,y:10.0,z:0.0},
radius:0.5,
fromCap:false,
toCap:true,
color:'teal'});
viewer.addCylinder({start:{x:15.0,y:0.0,z:0.0},
end:{x:20.0,y:0.0,z:0.0},
radius:1.0,
color:'black',
fromCap:false,
toCap:false});
viewer.render();
*/
this.addCylinder = function(cylinderSpec) {
cylinderSpec.start = cylinderSpec.start || {};
cylinderSpec.end = cylinderSpec.end || {};
var start = new $3Dmol.Vector3(cylinderSpec.start.x || 0,
cylinderSpec.start.y || 0, cylinderSpec.start.z || 0);
var end = new $3Dmol.Vector3(cylinderSpec.end.x,
cylinderSpec.end.y || 0, cylinderSpec.end.z || 0);
if(typeof(end.x) == 'undefined') end.x = 3; //show something even if undefined
var radius = cylinderSpec.radius || 0.1;
var color = $3Dmol.CC.color(cylinderSpec.color);
this.intersectionShape.cylinder.push(new $3Dmol.Cylinder(start, end, radius));
$3Dmol.GLDraw.drawCylinder(geo, start, end, radius, color, cylinderSpec.fromCap, cylinderSpec.toCap);
var centroid = new $3Dmol.Vector3();
components.push({
centroid : centroid.addVectors(start,end).multiplyScalar(0.5)
});
var geoGroup = geo.updateGeoGroup(0);
updateBoundingFromPoints(this.boundingSphere, components,
geoGroup.vertexArray, geoGroup.vertices);
};
/**
* Creates a dashed cylinder shape
* @function $3Dmol.GLShape#addDashedCylinder
* @param {CylinderSpec} cylinderSpec
* @return {$3Dmol.GLShape}
*/
this.addDashedCylinder = function(cylinderSpec){
cylinderSpec.start = cylinderSpec.start || {};
cylinderSpec.end = cylinderSpec.end || {};
cylinderSpec.dashLength=cylinderSpec.dashLength || 0.25;
cylinderSpec.gapLength=cylinderSpec.gapLength || 0.25;
var start = new $3Dmol.Vector3(cylinderSpec.start.x || 0,
cylinderSpec.start.y || 0, cylinderSpec.start.z || 0);
var end = new $3Dmol.Vector3(cylinderSpec.end.x,
cylinderSpec.end.y || 0, cylinderSpec.end.z || 0);
if(typeof(end.x) == 'undefined') end.x = 3; //show something even if undefined
var radius = cylinderSpec.radius || 0.1;
var color = $3Dmol.CC.color(cylinderSpec.color);
var cylinderLength = Math.sqrt(Math.pow((start.x-end.x),2)+Math.pow((start.y-end.y),2)+Math.pow((start.z-end.z),2));
var count = cylinderLength/(cylinderSpec.gapLength+cylinderSpec.dashLength);
var new_start = new $3Dmol.Vector3(cylinderSpec.start.x || 0,
cylinderSpec.start.y || 0, cylinderSpec.start.z || 0);
var new_end = new $3Dmol.Vector3(cylinderSpec.end.x,
cylinderSpec.end.y || 0, cylinderSpec.end.z || 0);
var gapVector = new $3Dmol.Vector3((end.x-start.x)/(cylinderLength/cylinderSpec.gapLength),(end.y-start.y)/(cylinderLength/cylinderSpec.gapLength),(end.z-start.z)/(cylinderLength/cylinderSpec.gapLength));
var dashVector = new $3Dmol.Vector3((end.x-start.x)/(cylinderLength/cylinderSpec.dashLength),(end.y-start.y)/(cylinderLength/cylinderSpec.dashLength),(end.z-start.z)/(cylinderLength/cylinderSpec.dashLength));
for(var place=0; place < count;place++){
new_end = new $3Dmol.Vector3(new_start.x+dashVector.x,new_start.y+dashVector.y,new_start.z+dashVector.z);
this.intersectionShape.cylinder.push(new $3Dmol.Cylinder(new_start, new_end, radius));
$3Dmol.GLDraw.drawCylinder(geo, new_start, new_end, radius, color, cylinderSpec.fromCap, cylinderSpec.toCap);
new_start = new $3Dmol.Vector3(new_end.x+gapVector.x,new_end.y+gapVector.y,new_end.z+gapVector.z);
}
var centroid = new $3Dmol.Vector3();
components.push({
centroid : centroid.addVectors(start,end).multiplyScalar(0.5)
});
var geoGroup = geo.updateGeoGroup(0);
updateBoundingFromPoints(this.boundingSphere, components,
geoGroup.vertexArray, geoGroup.vertices);
};
/**
* Creates a curved shape
* @function $3Dmol.GLShape#addCurve
* @param {CurveSpec} curveSpec
* @return {$3Dmol.GLShape}
*/
this.addCurve = function(curveSpec) {
curveSpec.points = curveSpec.points || [];
curveSpec.smooth = curveSpec.smooth || 10;
if(typeof(curveSpec.fromCap) == "undefined") curveSpec.fromCap = 2;
if(typeof(curveSpec.toCap) == "undefined") curveSpec.toCap = 2;
//subdivide into smoothed spline points
var points = $3Dmol.subdivide_spline(curveSpec.points, curveSpec.smooth);
if(points.length < 3) {
console.log("Too few points in addCurve");
return;
}
var radius = curveSpec.radius || 0.1;
var color = $3Dmol.CC.color(curveSpec.color);
//TODO TODO - this is very inefficient, should create our
//own water tight model with proper normals...
//if arrows are requested, peel off enough points to fit
//at least 2*r of arrowness
var start = 0;
var end = points.length-1;
var segmentlen = points[0].distanceTo(points[1]);
var npts = Math.ceil(2*radius/segmentlen);
if(curveSpec.toArrow) {
end -= npts;
let arrowspec = { start: points[end],
end: points[points.length-1],
radius: radius,
color: color,
mid: 0.0001
};
this.addArrow(arrowspec);
}
if(curveSpec.fromArrow) {
start += npts;
let arrowspec = { start: points[start],