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+
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t=0===this.__listening.length;this.__listening.push(e),t&&C(this.__listening)},updateDisplay:function(){S.each(this.__controllers,function(e){e.updateDisplay()}),S.each(this.__folders,function(e){e.updateDisplay()})}});var pe={Color:I,math:N,interpret:R},fe={Controller:z,BooleanController:K,OptionController:Y,StringController:J,NumberController:W,NumberControllerBox:Q,NumberControllerSlider:q,FunctionController:Z,ColorController:$},me={dom:X},ge={GUI:he},be=he,ve={color:pe,controllers:fe,dom:me,gui:ge,GUI:be};e.color=pe,e.controllers=fe,e.dom=me,e.gui=ge,e.GUI=be,e.default=ve,Object.defineProperty(e,"__esModule",{value:!0})}); diff --git a/js/data.js b/js/data.js new file mode 100644 index 0000000..cd71016 --- /dev/null +++ b/js/data.js @@ -0,0 +1,384 @@ +C0 = 0.0478487627793223584957428264710 +C1 = 0.0820874952323578596367661535721 +C2 = 0.0919831947610306166536978645902 +C3 = 0.104185866120626902522184256527 +C4 = 0.159508419728932319992375824582 +C5 = 0.1787372607291718755716205007246 +C6 = 0.180669120116622322543727539983 +C7 = 0.210241281833874424403594384522 +C8 = 0.2707204554902024922253183653148 +C9 = 0.34319353022244057407246218081548 +C10 = 0.347313533259692355979268469051 +C11 = 0.3602517244988994027025508153653 +C12 = 0.393388829036478811293779158091 +C13 = 0.425281025454798433709228334388 +C14 = 0.439296728020722972632966333641 +C15 = 0.457779235446372389179242869890 +C16 = 0.502701949951372894064838005397 +C17 = 0.542220764553627610820757130110 +C18 = 0.5828995347449824144241690772051 +C19 = 0.606611170963521188706220841909 +C20 = 0.635522307288672858112822718909 +C21 = 0.683371070067995216608565545380 +C22 = 0.728499690936574881404561235204 +C23 = 0.735967916735595431954156281793 +C24 = 0.765540078452847533814023126332 +C25 = 0.785348431692693064277841342634 +C26 = 0.832685557057201783926745491732 +C27 = 0.847627573685205393450789279904 +C28 = 0.889534297813319966800025599161 +C29 = 0.8954763364645277519465321063751 +C30 = 0.943151259243881817126719892570 +C31 = 0.9462091985694698563577506663151 + +const NODES = [[ C2, C3, 1.0],[ C2, -C3, -1.0],[ -C2, -C3, 1.0],[ -C2, C3, -1.0],[ 1.0, C2, C3],[ 1.0, -C2, -C3],[-1.0, -C2, C3],[-1.0, C2, -C3],[ C3, 1.0, C2],[ C3, -1.0, -C2],[ -C3, -1.0, C2],[ -C3, 1.0, -C2],[ C9, C0, C31],[ C9, -C0, -C31],[ -C9, -C0, C31],[ -C9, C0, -C31],[ C31, C9, C0],[ C31, -C9, -C0],[-C31, -C9, C0],[-C31, C9, -C0],[ C0, C31, C9],[ C0, -C31, -C9],[ -C0, -C31, C9],[ -C0, C31, -C9],[ 0.0, C11, C30],[ 0.0, C11, -C30],[ 0.0, -C11, C30],[ 0.0, -C11, -C30],[ C30, 0.0, C11],[ C30, 0.0, -C11],[-C30, 0.0, C11],[-C30, 0.0, -C11],[ C11, C30, 0.0],[ C11, -C30, 0.0],[-C11, C30, 0.0],[-C11, -C30, 0.0],[ C13, -C6, C29],[ C13, C6, -C29],[-C13, C6, C29],[-C13, -C6, -C29],[ C29, -C13, C6],[ C29, C13, -C6],[-C29, C13, C6],[-C29, -C13, -C6],[ C6, -C29, C13],[ C6, C29, -C13],[ -C6, C29, C13],[ -C6, -C29, -C13],[ C8, -C12, C28],[ C8, C12, -C28],[ -C8, C12, C28],[ -C8, -C12, -C28],[ C28, -C8, C12],[ C28, C8, -C12],[-C28, C8, C12],[-C28, -C8, -C12],[ C12, -C28, C8],[ C12, C28, -C8],[-C12, C28, C8],[-C12, -C28, -C8],[ C16, C7, C27],[ C16, -C7, -C27],[-C16, -C7, C27],[-C16, C7, -C27],[ C27, C16, C7],[ C27, -C16, -C7],[-C27, -C16, C7],[-C27, C16, -C7],[ C7, C27, C16],[ C7, -C27, -C16],[ -C7, -C27, C16],[ -C7, C27, -C16],[ C5, C17, C26],[ C5, -C17, -C26],[ -C5, -C17, C26],[ -C5, C17, -C26],[ C26, C5, C17],[ C26, -C5, -C17],[-C26, -C5, C17],[-C26, C5, -C17],[ C17, C26, C5],[ C17, -C26, -C5],[-C17, -C26, C5],[-C17, C26, -C5],[ C14, C15, C25],[ C14, -C15, -C25],[-C14, -C15, C25],[-C14, C15, -C25],[ C25, C14, C15],[ C25, -C14, -C15],[-C25, -C14, C15],[-C25, C14, -C15],[ C15, C25, C14],[ C15, -C25, -C14],[-C15, -C25, C14],[-C15, C25, -C14],[ C20, -C4, C24],[ C20, C4, -C24],[-C20, C4, C24],[-C20, -C4, -C24],[ C24, -C20, C4],[ C24, C20, -C4],[-C24, C20, C4],[-C24, -C20, -C4],[ C4, -C24, C20],[ C4, C24, -C20],[ -C4, C24, C20],[ -C4, -C24, -C20],[ C21, C1, C23],[ C21, -C1, -C23],[-C21, -C1, C23],[-C21, C1, -C23],[ C23, C21, C1],[ C23, -C21, -C1],[-C23, -C21, C1],[-C23, C21, -C1],[ C1, C23, C21],[ C1, -C23, -C21],[ -C1, -C23, C21],[ -C1, C23, -C21],[ C10, -C19, C22],[ C10, C19, -C22],[-C10, C19, C22],[-C10, -C19, -C22],[ C22, -C10, C19],[ C22, C10, -C19],[-C22, C10, C19],[-C22, -C10, -C19],[ C19, -C22, C10],[ C19, C22, -C10],[-C19, C22, C10],[-C19, -C22, -C10],[ C18, C18, C18],[ C18, C18, -C18],[ C18, -C18, C18],[ C18, -C18, -C18],[-C18, C18, C18],[-C18, C18, -C18],[-C18, -C18, C18],[-C18, -C18, -C18]] + +const FACES = [ +[ 24, 0, 12, 60, 84, 72 ], +[ 24, 72, 116, 106, 122, 50 ], +[ 24, 50, 38, 14, 2, 0 ], +[ 25, 3, 15, 63, 87, 75 ], +[ 25, 75, 119, 105, 121, 49 ], +[ 25, 49, 37, 13, 1, 3 ], +[ 26, 2, 14, 62, 86, 74 ], +[ 26, 74, 118, 104, 120, 48 ], +[ 26, 48, 36, 12, 0, 2 ], +[ 27, 1, 13, 61, 85, 73 ], +[ 27, 73, 117, 107, 123, 51 ], +[ 27, 51, 39, 15, 3, 1 ], +[ 28, 4, 16, 64, 88, 76 ], +[ 28, 76, 108, 96, 124, 52 ], +[ 28, 52, 40, 17, 5, 4 ], +[ 29, 5, 17, 65, 89, 77 ], +[ 29, 77, 109, 97, 125, 53 ], +[ 29, 53, 41, 16, 4, 5 ], +[ 30, 6, 18, 66, 90, 78 ], +[ 30, 78, 110, 98, 126, 54 ], +[ 30, 54, 42, 19, 7, 6 ], +[ 31, 7, 19, 67, 91, 79 ], +[ 31, 79, 111, 99, 127, 55 ], +[ 31, 55, 43, 18, 6, 7 ], +[ 32, 8, 20, 68, 92, 80 ], +[ 32, 80, 112, 101, 129, 57 ], +[ 32, 57, 45, 23, 11, 8 ], +[ 33, 9, 21, 69, 93, 81 ], +[ 33, 81, 113, 100, 128, 56 ], +[ 33, 56, 44, 22, 10, 9 ], +[ 34, 11, 23, 71, 95, 83 ], +[ 34, 83, 115, 102, 130, 58 ], +[ 34, 58, 46, 20, 8, 11 ], +[ 35, 10, 22, 70, 94, 82 ], +[ 35, 82, 114, 103, 131, 59 ], +[ 35, 59, 47, 21, 9, 10 ], +[ 132, 84, 60, 108, 76, 88 ], +[ 132, 88, 64, 112, 80, 92 ], +[ 132, 92, 68, 116, 72, 84 ], +[ 133, 121, 105, 45, 57, 129 ], +[ 133, 129, 101, 41, 53, 125 ], +[ 133, 125, 97, 37, 49, 121 ], +[ 134, 120, 104, 44, 56, 128 ], +[ 134, 128, 100, 40, 52, 124 ], +[ 134, 124, 96, 36, 48, 120 ], +[ 135, 85, 61, 109, 77, 89 ], +[ 135, 89, 65, 113, 81, 93 ], +[ 135, 93, 69, 117, 73, 85 ], +[ 136, 122, 106, 46, 58, 130 ], +[ 136, 130, 102, 42, 54, 126 ], +[ 136, 126, 98, 38, 50, 122 ], +[ 137, 87, 63, 111, 79, 91 ], +[ 137, 91, 67, 115, 83, 95 ], +[ 137, 95, 71, 119, 75, 87 ], +[ 138, 86, 62, 110, 78, 90 ], +[ 138, 90, 66, 114, 82, 94 ], +[ 138, 94, 70, 118, 74, 86 ], +[ 139, 123, 107, 47, 59, 131 ], +[ 139, 131, 103, 43, 55, 127 ], +[ 139, 127, 99, 39, 51, 123 ], +[ 12, 36, 96, 108, 60 ], +[ 13, 37, 97, 109, 61 ], +[ 14, 38, 98, 110, 62 ], +[ 15, 39, 99, 111, 63 ], +[ 16, 41, 101, 112, 64 ], +[ 17, 40, 100, 113, 65 ], +[ 18, 43, 103, 114, 66 ], +[ 19, 42, 102, 115, 67 ], +[ 20, 46, 106, 116, 68 ], +[ 21, 47, 107, 117, 69 ], +[ 22, 44, 104, 118, 70 ], +[ 23, 45, 105, 119, 71 ], +] + +BONDS = [ + [0,1,2], + [0,2,2], + [0,8,1], + [0,60,0], + [0,36,1], + [0,38,2], + + [1,2,2], + [1,38,1], + [1,68,0], + [1,48,1], + [1,50,2], + + [2,50,1], + [2,8,2], + [2,6,1], + [2,62,0], + + [3,4,2], + [3,5,2], + [3,11,1], + [3,63,0], + [3,51,1], + [3,53,2], + + [4,5,2], + [4,53,1], + [4,41,2], + [4,39,1], + [4,71,0], + + [5,11,2], + [5,9,1], + [5,61,0], + [5,41,1], + + [6,56,2], + [6,54,1], + [6,62,0], + [6,8,2], + [6,7,2], + + [7,44,2], + [7,42,1], + [7,70,0], + [7,56,1], + [7,8,2], + + [8,44,1], + [8,60,0], + + [9,10,2], + [9,11,2], + [9,61,0], + [9,45,1], + [9,47,2], + + [10,11,2], + [10,59,2], + [10,57,1], + [10,69,0], + [10,47,1], + + [11,59,1], + [11,63,0], + + [12,36,2], + [12,37,1], + [12,64,0], + [12,17,1], + [12,14,2], + [12,13,2], + + [13,43,2], + [13,44,1], + [13,60,0], + [13,36,1], + [13,14,2], + + [14,17,2], + [14,15,1], + [14,65,0], + [14,43,1], + + [15,45,2], + [15,46,1], + [15,65,0], + [15,17,2], + [15,16,2], + + [16,17,2], + [16,45,1], + [16,61,0], + [16,41,1], + [16,40,2], + + [17,40,1], + [17,64,0], + + [18,19,2], + [18,20,2], + [18,23,1], + [18,66,0], + [18,55,1], + [18,54,2], + + [19,20,2], + [19,54,1], + [19,62,0], + [19,50,1], + [19,49,2], + + [20,49,1], + [20,67,0], + [20,21,1], + [20,23,2], + + [21,22,2], + [21,23,2], + [21,67,0], + [21,52,1], + [21,51,2], + + [22,23,2], + [22,51,1], + [22,63,0], + [22,59,1], + [22,58,2], + + [23,58,1], + [23,66,0], + + [24,25,2], + [24,26,2], + [24,32,1], + [24,68,0], + [24,38,1], + [24,37,2], + + [25,26,2], + [25,37,1], + [25,64,0], + [25,40,1], + [25,39,2], + + [26,39,1], + [26,71,0], + [26,30,1], + [26,32,2], + + [27,28,2], + [27,29,2], + [27,35,1], + [27,69,0], + [27,47,1], + [27,46,2], + + [28,29,2], + [28,46,1], + [28,65,0], + [28,43,1], + [28,42,2], + + [29,42,1], + [29,70,0], + [29,33,1], + [29,35,2], + + [30,31,2], + [30,32,2], + [30,71,0], + [30,53,1], + [30,52,2], + + [31,32,2], + [31,52,1], + [31,67,0], + [31,49,1], + [31,48,2], + + [32,48,1], + [32,68,0], + + [33,34,2], + [33,35,2], + [33,70,0], + [33,56,1], + [33,55,2], + + [34,35,2], + [34,55,1], + [34,66,0], + [34,58,1], + [34,57,2], + + [35,57,1], + [35,69,0], + + [36,37,2], + [36,38,2], + [36,60,0], + + [37,38,2], + [37,64,0], + + [38,68,0], + + [39,40,2], + [39,41,2], + [39,71,0], + + [40,41,2], + [40,64,0], + + [41,61,0], + + [42,43,2], + [42,44,2], + [42,70,0], + + [43,44,2], + [43,65,0], + + [44,60,0], + + [45,46,2], + [45,47,2], + [45,61,0], + + [46,47,2], + [46,65,0], + + [47,69,0], + + [48,49,2], + [48,50,2], + [48,68,0], + + [49,50,2], + [49,67,0], + + [50,62,0], + + [51,52,2], + [51,53,2], + [51,63,0], + + [52,53,2], + [52,67,0], + + [53,71,0], + + [54,55,2], + [54,56,2], + [54,62,0], + + [55,56,2], + [55,66,0], + + [56,70,0], + + [57,58,2], + [57,59,2], + [57,69,0], + + [58,59,2], + [58,66,0], + + [59,63,0], + + + +] diff --git a/js/sketch.js b/js/sketch.js new file mode 100644 index 0000000..aa97574 --- /dev/null +++ b/js/sketch.js @@ -0,0 +1,200 @@ +let camera + +let size = 200 +let offsetFactor = 1.07 + +let removedBondTypes = [] +let displayedFaces = [] +let settings = { + displayPentagons: true, + displayHexagons: true, + displayNetwork: true, + + pentagonColour: "#800080", + hexagonColour: "#FFFFFF", + + edgesWeight: 1, + edgesColour: "#646464", + + networkEdgesWeight: 2, + networkAcolour: "#fA0000", + networkBcolour: "#0064F0", + networkCcolour: "#FAAC10", + networkNodesSize: 15, + networkNodesColour: "#000000", + + backgroundColour: "#FFFFFF", + + displayType: 0, // 0: display all faces, 1: randomly remove some faces, 2: display one pentamer and the surrounding tiles + + removalProbability: 0.5, +} + +//GUI + +let probaController; + +let gui = new dat.GUI({name: 'Polyomavirus interaction network',width: 300}); +let tilesGui = gui.addFolder('Tiles'); +var networkGui = gui.addFolder('Network'); + +gui.addColor(settings,"backgroundColour").name("background") +gui.add(settings,"displayType",0,2,1).name("display").onFinishChange(() => { + updateDisplayedFaces(); + if(settings.displayType == 1) { + probaController = gui.add(settings,"removalProbability",0,1,0.1).name("Fraction removed").onFinishChange(updateDisplayedFaces) + }else { + gui.remove(probaController) + } +}) + +tilesGui.add(settings, 'displayPentagons', 0, 1, 1).name("show pentagons"); +tilesGui.add(settings, 'displayHexagons', 0, 1, 1).name("show hexagons"); +tilesGui.add(settings, 'edgesWeight', 0, 10, 1).name("edges weight"); +tilesGui.addColor(settings, 'pentagonColour').name("pentagons colour"); +tilesGui.addColor(settings, 'hexagonColour').name("hexagons colour"); + +networkGui.add(settings,'displayNetwork',0,1,1).name("show network") +networkGui.add(settings, 'networkNodesSize', 0, 50, 1).name("nodes size"); +networkGui.add(settings,'networkEdgesWeight',0,10,1).name("edges weight") +networkGui.addColor(settings, 'networkBcolour').name("B bonds colour"); +networkGui.addColor(settings, 'networkAcolour').name("A bonds colour"); +networkGui.addColor(settings, 'networkCcolour').name("C bonds colour"); + + +function updateDisplayedFaces() { + displayedFaces = [] + for(let i = 0; i < 72; i++) { + if (settings.displayType == 1 && Math.random() > settings.removalProbability) { + displayedFaces.push(i); + }else if(settings.displayType == 0) { + displayedFaces.push(i); + } + } + if(settings.displayType == 2) { + displayedFaces = [65,14,15,28,43,46]; + } +} + +function setup() { + updateDisplayedFaces() + createCanvas(windowWidth, windowHeight, WEBGL); + camera = createCamera(); + camera.setPosition(328.0194072520545,-282.51371090543233,9.448365808553215) + camera.lookAt(0,0,0) +} + +function midPoint(face) { + let x = 0; + let y = 0; + let z = 0; + for(let pid of face) { + let [fx,fy,fz] = NODES[pid] + x += fx; + y += fy; + z += fz; + } + x /= face.length + y /= face.length + z /= face.length + return [x,y,z] +} + +function draw() { + smooth(); + orbitControl(3,3) + background(settings.backgroundColour); + + //Set lighting + ambientLight(20,20,20); + ambientMaterial(255); + strokeWeight(3); + pointLight(255, 255, 255, 220, -220, 220); + directionalLight(255, 255, 255, -1, 1, -1); + + + //Draw the hexamers and pentamers + for(let points of FACES) { + if(displayedFaces.indexOf(FACES.indexOf(points)) != -1 && ((points.length == 5 && settings.displayPentagons) || (points.length == 6 && settings.displayHexagons) )){ + noFill(); + strokeWeight(settings.edgesWeight); + stroke(settings.edgesColour) + beginShape(); + if(points.length == 5) { + fill(settings.pentagonColour) + }else { + fill(settings.hexagonColour) + } + for(id of points) { + let [x,y,z] = NODES[id] + vertex(x*size,y*size,z*size) + } + endShape(CLOSE) + } + } + + + //Draw the interaction network + for(let [id1,id2,type] of BONDS) { + if(removedBondTypes.indexOf(type) == -1 && displayedFaces.indexOf(id1) != -1 && displayedFaces.indexOf(id2) != -1 && settings.displayNetwork){ + strokeWeight(settings.networkEdgesWeight); + if(type==0) { + stroke(settings.networkAcolour) + }else if (type == 1) { + stroke(settings.networkBcolour) + }else { + stroke(settings.networkCcolour) + } + beginShape(); + [x1,y1,z1] = midPoint(FACES[id1]); + [x2,y2,z2] = midPoint(FACES[id2]); + + vertex(size*x1 * offsetFactor,size*y1 * offsetFactor,size*z1 * offsetFactor); + vertex(size*x2 * offsetFactor,size*y2 * offsetFactor,size*z2 * offsetFactor); + endShape() + stroke(settings.networkNodesColour) + strokeWeight(settings.networkNodesSize) + point(size*x1 * offsetFactor,size*y1 * offsetFactor,size*z1 * offsetFactor); + point(size*x2 * offsetFactor,size*y2 * offsetFactor,size*z2 * offsetFactor); + } + } +} + +function mouseDragged(){ + orbitControl(); +} + +// function getAdj(id) { +// let res = [] +// let S = "" +// for(let n of FACES[id]) { +// for(fid in FACES) { +// if(FACES[fid].indexOf(n) != -1 && res.indexOf(fid) == -1) { +// res.push(fid) +// if(fid > id) { +// S += "// [" + id + "," + fid + ",2],\n" +// } +// } +// } +// } +// console.log(S) +// return S +// } + +// function nodeIndex(x,y,z) { +// P = {x,y,z} +// return NODES.findIndex(({x,y,z}) => { +// let D = (x - P.x) * (x - P.x) + (y - P.y) * (y - P.y) + (z - P.z) * (z - P.z) +// return D < 1e-3 +// }) +// } +// EDGES_ = [] +// for(let {x1,y1,z1,x2,y2,z2} of EDGES) { +// let i1 = nodeIndex(x1,y1,z1) +// let i2 = nodeIndex(x2,y2,z2) +// if(i1 == -1) { +// console.log({x1,y1,z1,x2,y2,z2}) +// } +// EDGES_.push([i1,i2]) +// // console.log("[",[nodeIndex(x1,y1,z1),nodeIndex(x2,y2,z2)].toString(),"],") +// }