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Dynamic Molecules - Cytosine
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| { | |
| "nodes": [ | |
| {"atom": "N", "size": 6, "color": "#0033CC"}, | |
| {"atom": "C", "size": 5, "color": "#272727"}, | |
| {"atom": "N", "size": 6, "color": "#0033CC"}, | |
| {"atom": "C", "size": 5, "color": "#272727"}, | |
| {"atom": "N", "size": 6, "color": "#0033CC"}, | |
| {"atom": "C", "size": 5, "color": "#272727"}, | |
| {"atom": "C", "size": 5, "color": "#272727"}, | |
| {"atom": "H", "size": 3, "color": "#E9E9E9"}, | |
| {"atom": "H", "size": 3, "color": "#E9E9E9"}, | |
| {"atom": "O", "size": 6, "color": "#FF1919"}, | |
| {"atom": "H", "size": 3, "color": "#E9E9E9"}, | |
| {"atom": "H", "size": 3, "color": "#E9E9E9"}, | |
| {"atom": "H", "size": 3, "color": "#E9E9E9"} | |
| ], | |
| "links": [ | |
| {"source": 0, "target": 1, "bond": 1}, | |
| {"source": 1, "target": 2, "bond": 2}, | |
| {"source": 2, "target": 3, "bond": 1}, | |
| {"source": 3, "target": 4, "bond": 1}, | |
| {"source": 4, "target": 5, "bond": 1}, | |
| {"source": 5, "target": 6, "bond": 2}, | |
| {"source": 6, "target": 1, "bond": 1}, | |
| {"source": 7, "target": 0, "bond": 1}, | |
| {"source": 8, "target": 0, "bond": 1}, | |
| {"source": 9, "target": 3, "bond": 2}, | |
| {"source": 10, "target": 4, "bond": 1}, | |
| {"source": 11, "target": 5, "bond": 1}, | |
| {"source": 12, "target": 6, "bond": 1} | |
| ] | |
| } |
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| <!DOCTYPE html> | |
| <meta charset="utf-8"> | |
| <style> | |
| .link line { | |
| stroke: #000000; | |
| stroke-opacity: 0.7; | |
| stroke-width:1.5; | |
| } | |
| .link line.separator { | |
| stroke: #fff; | |
| stroke-width: 2px; | |
| } | |
| .node circle { | |
| stroke: #000; | |
| stroke-width: 3px; | |
| } | |
| .node text { | |
| font: 14px sans-serif; | |
| pointer-events: none; | |
| } | |
| </style> | |
| <script src="http://d3js.org/d3.v3.min.js"></script> | |
| <body> | |
| <div id="chart"></div> | |
| <script> | |
| var margin = {top: -5, right: -5, bottom: -5, left: -5}; | |
| var width = 550 - margin.left - margin.right, | |
| height = 350- margin.top - margin.bottom, | |
| r = 15; | |
| var radius = d3.scale.sqrt() | |
| .range([0, 6]); | |
| var svg = d3.select("body").append("svg") | |
| .attr("width", width) | |
| .attr("height", height); | |
| var vis = d3.select("#chart") | |
| .append("svg:svg") | |
| .attr("width", width) | |
| .attr("height", height) | |
| .append('svg:g'); | |
| vis.append('svg:rect') | |
| .attr('width', width) | |
| .attr('height', height) | |
| .attr('fill', 'white'); | |
| d3.json("cytosine.json", function(graph) { | |
| var force = d3.layout.force() | |
| .nodes(graph.nodes) | |
| .size([width + margin.left + margin.right, height + margin.top + margin.bottom]) | |
| .links(graph.links) | |
| .charge(-350) | |
| .gravity(0.15) | |
| .linkDistance(20) | |
| .on("tick", tick) | |
| .start(); | |
| var link = vis.selectAll(".link") | |
| .data(graph.links) | |
| .enter().append("g") | |
| .attr("class", "link"); | |
| link.append("line") | |
| .style("stroke-width", function(d) { return (d.bond * 3 - 1) * 2 + "px"; }); | |
| link.filter(function(d) { return d.bond > 1; }).append("line") | |
| .attr("class", "separator"); | |
| var node = vis.selectAll(".node") | |
| .data(graph.nodes) | |
| .enter().append("circle") | |
| .attr("class", "node") | |
| .call(force.drag) | |
| .style("fill", function(d) { return d.color; }) | |
| .attr("r", function(d) { return radius(d.size); }) | |
| .style("stroke", "black")//function(d) {return d3.rgb(d.color).darker(); }) | |
| .style("stroke-width", 3) | |
| .style("stroke-opacity", 0.9); | |
| node.append("text") | |
| .attr("dy", ".35em") | |
| .attr("text-anchor", "middle") | |
| .text(function(d) { return d.atom; }) | |
| .style("fill", function(d) { return d.color; }); | |
| function tick() { | |
| link.selectAll("line") | |
| .attr("x1", function(d) { return d.source.x; }) | |
| .attr("y1", function(d) { return d.source.y; }) | |
| .attr("x2", function(d) { return d.target.x; }) | |
| .attr("y2", function(d) { return d.target.y; }) | |
| node.attr("cx", function(d) { return d.x = Math.max(r, Math.min(width - r, d.x)); }) | |
| .attr("cy", function(d) { return d.y = Math.max(r, Math.min(height - r, d.y)); }) | |
| node.each(collide(0.5)) | |
| } | |
| var padding = 1; | |
| function collide(alpha) { | |
| var quadtree = d3.geom.quadtree(graph.nodes); | |
| return function(d) { | |
| var rb = 2*radius + padding, | |
| nx1 = d.x - rb, | |
| nx2 = d.x + rb, | |
| ny1 = d.y - rb, | |
| ny2 = d.y + rb; | |
| quadtree.visit(function(quad, x1, y1, x2, y2) { | |
| if (quad.point && (quad.point !== d)) { | |
| var x = d.x - quad.point.x, | |
| y = d.y - quad.point.y, | |
| l = Math.sqrt(x * x + y * y); | |
| if (l < rb) { | |
| l = (l - rb) / l * alpha; | |
| d.x -= x *= l; | |
| d.y -= y *= l; | |
| quad.point.x += x; | |
| quad.point.y += y; | |
| } | |
| } | |
| return x1 > nx2 || x2 < nx1 || y1 > ny2 || y2 < ny1; | |
| }); | |
| }; | |
| } | |
| }); | |
| </script> |
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