Dynamic Molecules - Cytosine

<!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>

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");

node.append("text")
        .attr("dy", ".35em")
        .attr("text-anchor", "middle")
        .text(function(d) { return d.atom; })
        .style("fill", function(d) { return d.color; });

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>

Modified http://d3js.org/d3.v3.min.js to a secure url

https://d3js.org/d3.v3.min.js