Dynamic Molecules - Alanine

<!DOCTYPE html>
<meta charset="utf-8">
<style>

.link line {
    stroke: #000000;
    stroke-opacity: 0.75;
    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>
<body>
    <script src="https://d3js.org/d3.v3.min.js"></script>
<script>

var width = 500,
    height = 350;

var color = d3.scale.category20();

var radius = d3.scale.sqrt()
    .range([0, 6]);

var svg = d3.select("body").append("svg")
    .attr("width", width)
    .attr("height", height);

var force = d3.layout.force()
    .size([width, height])
    .charge(-400)
    .linkDistance(function(d) { return radius(d.source.size) + radius(d.target.size) + 8; });

d3.json("alanine.json", function(graph) {
    force.nodes(graph.nodes)
        .links(graph.links)
        .charge(-450)
        .gravity(0.25)
        .distance(20)
        .on("tick", tick)
        .start();

var link = svg.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 = svg.selectAll(".node")
        .data(graph.nodes)
        .enter().append("g")
        .attr("class", "node")
        .call(force.drag);

node.append("circle")
        .attr("r", function(d) { return radius(d.size); })
        .style("fill", function(d) { return d.color; });

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("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
    }
});

</script>

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

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