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Dynamic Molecules - Alanine
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{ | |
"nodes": [ | |
{"atom": "C", "size": 5, "color": "#272727"}, | |
{"atom": "C", "size": 5, "color": "#272727"}, | |
{"atom": "C", "size": 5, "color": "#272727"}, | |
{"atom": "N", "size": 6, "color": "#0033CC"}, | |
{"atom": "H", "size": 3, "color": "#E9E9E9"}, | |
{"atom": "O", "size": 6, "color": "#FF1919"}, | |
{"atom": "O", "size": 6, "color": "#FF1919"}, | |
{"atom": "H", "size": 3, "color": "#E9E9E9"}, | |
{"atom": "H", "size": 3, "color": "#E9E9E9"}, | |
{"atom": "H", "size": 3, "color": "#E9E9E9"}, | |
{"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": 1}, | |
{"source": 1, "target": 3, "bond": 1}, | |
{"source": 2, "target": 5, "bond": 1}, | |
{"source": 2, "target": 6, "bond": 2}, | |
{"source": 1, "target": 4, "bond": 1}, | |
{"source": 3, "target": 10, "bond": 1}, | |
{"source": 3, "target": 11, "bond": 1}, | |
{"source": 0, "target": 7, "bond": 1}, | |
{"source": 0, "target": 8, "bond": 1}, | |
{"source": 0, "target": 9, "bond": 1}, | |
{"source": 5, "target": 12, "bond": 1} | |
] | |
} |
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<!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="http://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; }); | |
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("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; }); | |
} | |
}); | |
</script> |
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