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Merge branch 'main' of https://gitlab.rrz.uni-hamburg.de/bax9187/projekt-cis-biochemie-2021-22 into main
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# Projekt CiS-Projekt 2021/22
Citation Network
## Usage
Input: Json-Datei ***json\_text.json*** in directory
```json
{
"nodes": [
{
"name": <title: string>,
"author": [<author1: string>, <author2: string>, ...],
"year": <date: tring>,
"journal": <journal: string>,
"doi": <doi: string>,
"group": <"input"/"height"/"depth">,
"citations": <citation: int>
}, ...
],
"links": [
{
"source": <doi: string>,
"target": <doi: string>
}, ...
]
}
```
Starting a Python-HTTP Server:
```sh
cd <path to file> &&python3 -m http.server <port>
```
Opening Server:
[http://0.0.0.0/:\<port\>](http://0.0.0.0/:<port>)
## Files in directory
- ***index.html***: webpage
- ***cn.js***: javascript code for force-directed graph, text elements and legend
- ***json_text.json***: example data
## Authors
- Katja Ehlers
- Merle Stahl
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/**
* creates a new zoom behavior
*/
var zoom = d3.zoom().on("zoom", handle_zoom);
/**
* creates svg object and associated attributes
* applies the zoom behavior to svg
*/
var svg = d3.select("svg.graph")
.call(zoom),
width = svg.attr("width"),
height = svg.attr("height");
var text_info='';
var text_abstract='';
var perc;
/**
* creates node object and radius
*/
var node,
r=10,
/**
* scale functions that return y coordinate/color of node depending on group
*/
color = d3.scaleOrdinal()
.domain(["height", "input", "depth"])
.range([' #01d7c0', ' #8b90fe ', ' #a15eb2 ']),
y_scale = d3.scaleOrdinal()
.domain(["height", "input", "depth"])
.range([0, 200, 400]),
to_remove;
/**
* creates link object
*/
var link;
/**
* creates a background
* creates a click functionality of the background
*/
var rect = svg.append("rect")
.attr("x", 0)
.attr("y", 0)
.attr("height", height)
.attr("width", width)
.style("fill", 'white')
.on('click', click_rect);
/**
* creates svg object (legend) and associated attributes
*/
var svg_legend = d3.select("svg.legendsvg"),
legend_position = [65,95,125],
arrow_legend_position = [0,25],
arrow_group_names = ["citation","self-citation"],
group_names = ["cited by","input","reference"],
line_type=d3.scaleOrdinal()
.domain(["line","dotted"])
.range([("8,0"),("8,8")]);
var legend = svg_legend.selectAll(".legend")
.data(legend_position)
.enter()
.append("g")
.attr("class","legend")
.attr("transform", function(d,i) {return "translate(0," + d + ")"; });
legend.append("text")
.attr("x", 80)
.attr("y", 0)
.attr("dy", ".35em")
.style("text-anchor", "start")
.text(function(d,i){return group_names[i]});
legend.append("circle")
.attr("r", r)
.attr("cx",30-r)
.style("fill", color);
var legend_arrow = svg_legend.selectAll(".legendarr")
.data(arrow_legend_position)
.enter()
.append("g")
.attr("class","legendarr")
.attr("transform", function(d) { return "translate(0," + d + ")"; });
legend_arrow.append("line")
.attr("x1", 10)
.attr("x2", 50)
.attr("y1", 10)
.attr("y2", 10)
.style("stroke-dasharray",line_type)
.style("stroke", '#999')
.style("stroke-width", "1px")
.style('pointer-events', 'none')
.attr('marker-end',update_marker('#999',this));
legend_arrow.append("text")
.attr("x", 80)
.attr("y", 10)
.attr("dy", ".35em")
.style("text-anchor", "start")
.text(function(d,i){return arrow_group_names[i]});
/**
* creates a new simulation
* updates the positions of the links and nodes when the
state of the layout has changed (simulation has advanced by a tick)
*/
var simulation = d3.forceSimulation()
.force("link", d3.forceLink().id(function(d) {return d.doi;}).distance(50).strength(function(d) {
if (d.group == "input") {return 0;}
else {return 5;}
}))
.force("collide", d3.forceCollide(function(d) {
if (d.group == "input") {return 100;}
else {return 65;}
}).strength(0.5))
.force("charge", d3.forceManyBody().strength(0.001))
.force("center", d3.forceCenter(width/2, height/2+20))
.force("yscale", d3.forceY().strength(function(d) {
if (d.group == "input") {return 1000;}
else {return 50;}
}).y(function(d) {return y_scale(d.group)}))
.alpha(0.005)
.on("end", zoom_to);
/**
* creates group element
*/
var g = svg.append("g")
.attr("class", "everything")
/**
* loads JSON data and calls the update function
*/
d3.json("json_text.json").then(function(graph) {
update(graph.links, graph.nodes);
})
/**
* calls update functions for links and nodes
* adds the nodes, links and tick functionailty to the simulation
* @param {object} nodes - nodes
* @param {object} links - links
*/
function update(links, nodes) {
update_links(links);
update_nodes(nodes);
simulation
.nodes(nodes)
.on("tick", handle_tick);
simulation.force("link")
.links(links);
link.attr('marker-end', function(d) {return update_marker("#999", d.target);})
.style("stroke-dasharray",function(d){return self_citation(d.source,d.target)? ("8,8"): ("1,0")});
}
/**
* initializes and shows links
* @param {object} links - links
*/
function update_links(links) {
link = g.append("g")
.selectAll(".link")
.data(links)
.enter()
.append("line")
.style("stroke-width", "1px")
.style("stroke", "#999")
.attr("class", "link");
}
/**
* initializes and shows nodes with circles and texts
* creates a new drag behavior and applies it to the circles
* creates a click functionality of the circles and texts
* @param {object} nodes - nodes
*/
function update_nodes(nodes) {
node = g.selectAll(".node")
.data(nodes)
.enter()
.append("g")
.attr("class", "node")
.call(d3.drag()
.on("start", start_drag)
.on("drag", dragged)
);
node.append("circle")
.attr("class", "circle")
.attr("r", function(d) {return 1.5*r+d.citations*0.05})
.style("fill", function(d){ return color(d.group)})
.on('click', click_node);
node.append("text")
.attr("class", "text")
.style("font-size", "15px")
.style('pointer-events', 'auto')
.text(function (d) {const first_author=d.author[0].split(" ")
return first_author[first_author.length-1];})
.on('click', click_node);
}
/**
* creates arrowhead and returns its url
* @param {string} color - color of arrowhead
* @param {string} target - target node
*/
function update_marker(color, target) {
var radius=1.5*r+target.citations*0.05
svg.append('defs').append('marker')
.attr('id',color.replace("#", "")+radius)
.attr('viewBox','-0 -5 10 10')
.attr('refX',radius+9.5)
.attr('refY',0)
.attr('orient','auto')
.attr('markerWidth',10)
.attr('markerHeight',15)
.attr('xoverflow','visible')
.append('svg:path')
.attr('d', 'M 0,-5 L 10 ,0 L 0,5')
.attr('fill', color)
.style('stroke','none');
return "url(" + color + radius + ")";
};
/**
* sets color of circle and its links to black and removes the previous highlights
* displays overview info of node in textbox
* @param {object} node - node
*/
function click_node(node) {
d3.select(this.parentNode).raise();
fix_nodes(node);
if(to_remove){
d3.select(to_remove).selectAll(".circle").style("stroke","none")
}
to_remove = this.parentNode;
d3.select(this.parentNode).selectAll(".circle").style("stroke","black")
mark_link(node)
textbox_content(node)
reset_button_highlight()
highlight_button("overview")
}
/**
* removes the highlights of the circles and their links
*/
function click_rect() {
fix_nodes(node);
d3.selectAll(".circle").style("stroke", "none")
d3.selectAll(".link")
.style("stroke", "#999")
.attr('marker-end', function(d) {return update_marker('#999', d.target);})
text_abstract='';
text_info='';
reset_button_highlight()
document.getElementById('textbox').innerHTML = "Click node";
}
/**
* returns true if journals have a common author (self-citation)
* @param {object} source - node
* @param {object} target - node
*/
function self_citation(source,target){
return source.author.some(item=>target.author.includes(item))
}
/**
* sets color of link (line and arrowhead) to black if it is directly connected to node
* and to grey otherwise
* @param {object} node - node
*/
function mark_link(node){
d3.selectAll(".link")
.style("stroke", function(o) {
return is_link_for_node(node, o) ? "black" : "#999";})
.attr('marker-end', function(o) {
return is_link_for_node(node, o) ? update_marker('#000000', o.target) : update_marker('#999', o.target);})
}
/**
* returns true if link is directly connected to node and false if it is not
* @param {object} node - node
* @param {object} link - link
*/
function is_link_for_node(node, link){
return link.source.index == node.index || link.target.index == node.index;
}
/**
* saves text for overview and abstract of node
* outputs node info to textbox
* @param {object} node - node
*/
function textbox_content(node) {
text_info="Title:" + '</br>' + node.name +
'</br>' +'</br>'+"Author:"+ '</br>' +node.author+'</br>'+'</br>'+"Date:"+'</br>'
+node.year+'</br>'+'</br>'+"Journal:"+'</br>'+node.journal+'</br>'+'</br>'+"doi:"+'</br>'+'<a href="'+node.doi+ '">'+node.doi
+'</a>'+'</br>'+'</br>'+"Citations:"+'</br>'+node.citations;
text_abstract=node.abstract;
document.getElementById('textbox').innerHTML = text_info;
}
/**
* sets color of btn to dark gray
* @param {object} btn - button
*/
function highlight_button(btn) {
reset_button_highlight();
document.getElementById(btn).style.background="#CACACA";
}
/**
* sets color of all buttons to default light gray
*/
function reset_button_highlight() {
document.getElementById("overview").style.background='';
document.getElementById("abstract").style.background='';
}
/**
* displays abstract in textbox if a is true, overview text otherwise
* @param {bool} a- bool
*/
function display_abstract(a){
if (text_abstract=='' && text_info=='') {
document.getElementById('textbox').innerHTML="Click node";
}
else {
if (a==true) {
document.getElementById('textbox').innerHTML =text_abstract;
}
else {
document.getElementById('textbox').innerHTML =text_info;
}
}
}
/**
* updates the positions of the links and nodes
*/
function handle_tick() {
link.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 + ")";});
}
/**
* initializes the dragging of the node
* @param {object} node - node
*/
function start_drag(node) {
d3.select(this).raise();
if (!d3.event.active)
simulation.alphaTarget(0.3).restart()
node.fx = node.x;
node.fy = node.y;
fix_nodes(node);
}
/**
* applies the dragging to the node
* @param {object} node - node
*/
function dragged(node) {
node.fx = d3.event.x;
node.fy = d3.event.y;
fix_nodes(node);
}
/**
* fix positions of all nodes except for the current node
* @param {object} this_node - node
*/
function fix_nodes(this_node) {
node.each(function(d) {
if (this_node != d) {
d.fx = d.x;
d.fy = d.y;
}
});
}
/**
* applies the transformation (zooming or dragging) to the g element
*/
function handle_zoom() {
d3.select('g').attr("transform", d3.event.transform);
}
/**
* transforms svg so that the zoom is adapted to the size of the graph
*/
function zoom_to() {
node_bounds = d3.selectAll("svg.graph").node().getBBox();
svg_bounds = d3.select("rect").node().getBBox();
perc_x = width/(node_bounds.width+100);
perc_y = height/(node_bounds.height+100);
perc = d3.min([perc_x, perc_y])
d3.select('svg')
.call(zoom.scaleBy, perc);
}
/**
* transforms svg so that the zoom and drag is reset
*/
function reset_view() {
d3.select('svg')
.call(zoom.scaleTo, 1)
d3.select('svg')
.call(zoom.translateTo, 0.5 * width, 0.5 * height);
d3.select('svg')
.call(zoom.scaleBy, perc);
}
/**
* save svg as png
*/
function save_svg(){
var svgString = get_svg_string(svg.node());
svg_string_to_image( svgString, 2*width, 2*height, 'png', save ); // passes Blob and filesize String to the callback
function save( dataBlob, filesize ){
saveAs( dataBlob, 'D3 vis exported to PNG.png' ); // FileSaver.js function
}
};
/**
* generate svgString
* @param {object} svgNode - node
*/
function get_svg_string( svgNode ) {
svgNode.setAttribute('xlink', 'http://www.w3.org/1999/xlink');
var cssStyleText = get_css_styles( svgNode );
append_css( cssStyleText, svgNode );
var serializer = new XMLSerializer();
var svgString = serializer.serializeToString(svgNode);
svgString = svgString.replace(/(\w+)?:?xlink=/g, 'xmlns:xlink='); // Fix root xlink without namespace
svgString = svgString.replace(/NS\d+:href/g, 'xlink:href'); // Safari NS namespace fix
return svgString;
function get_css_styles( parentElement ) {
var selectorTextArr = [];
// Add Parent element Id and Classes to the list
selectorTextArr.push( '#'+parentElement.id );
for (var c = 0; c < parentElement.classList.length; c++)
if ( !contains('.'+parentElement.classList[c], selectorTextArr) )
selectorTextArr.push( '.'+parentElement.classList[c] );
// Add Children element Ids and Classes to the list
var nodes = parentElement.getElementsByTagName("*");
for (var i = 0; i < nodes.length; i++) {
var id = nodes[i].id;
if ( !contains('#'+id, selectorTextArr) )
selectorTextArr.push( '#'+id );
var classes = nodes[i].classList;
for (var c = 0; c < classes.length; c++)
if ( !contains('.'+classes[c], selectorTextArr) )
selectorTextArr.push( '.'+classes[c] );
}
// Extract CSS Rules
var extractedCSSText = "";
for (var i = 0; i < document.styleSheets.length; i++) {
var s = document.styleSheets[i];
try {
if(!s.cssRules) continue;
} catch( e ) {
if(e.name !== 'SecurityError') throw e; // for Firefox
continue;
}
var cssRules = s.cssRules;
for (var r = 0; r < cssRules.length; r++) {
if ( contains( cssRules[r].selectorText, selectorTextArr ) )
extractedCSSText += cssRules[r].cssText;
}
}
return extractedCSSText;
function contains(str,arr) {
return arr.indexOf( str ) === -1 ? false : true;
}
}
function append_css( cssText, element ) {
var styleElement = document.createElement("style");
styleElement.setAttribute("type","text/css");
styleElement.innerHTML = cssText;
var refNode = element.hasChildNodes() ? element.children[0] : null;
element.insertBefore( styleElement, refNode );
}
}
/**
* convert svgString to image and export it
* @param {object} svgString - svgString
* @param {object} width - width of image
* @param {object} height - height of image
* @param {object} format - format to save image in
* @param {object} callback - callback function
*/
function svg_string_to_image( svgString, width, height, format, callback ) {
var format = format ? format : 'png';
var imgsrc = 'data:image/svg+xml;base64,'+ btoa( unescape( encodeURIComponent( svgString ) ) ); // Convert SVG string to data URL
var canvas = document.createElement("canvas");
var context = canvas.getContext("2d");
canvas.width = width;
canvas.height = height;
var image = new Image();
image.onload = function() {
context.clearRect ( 0, 0, width, height );
context.drawImage(image, 0, 0, width, height);
canvas.toBlob( function(blob) {
var filesize = Math.round( blob.length/1024 ) + ' KB';
if ( callback ) callback( blob, filesize );
});
};
image.src = imgsrc;
}
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<!-- style specifications for button and div elements -->
<style type="text/css">
button {
width: 100px;
height:20px;
display: flex;
justify-content: center;
position: absolute;
left: 455px;
top: 575px;
transition-duration: 0.4s;
border-radius:3px;
border:1px solid #909090;
}
.button:hover {
background-color: #CACACA;
}
button.resetZoom {
margin-left: 110px;
}
button.save {
margin-left: 220px;
}
button.abstract {
width:146px;
position:absolute;
top: 181px;
left: 1114px;
border-radius:0;
border:1px solid #909090;
}
button.overview {
width:147px;
position:absolute;
display:inline-block;
top: 181px;
left: 968px;
border-radius:0;
border:1px solid #909090;
}
div.legendbox {
width:270px;
height:170px;
padding: 10px;
/*border: 1px solid #999;*/
position: absolute;
top: 10px;
left: 968px;
display: inline-block;
margin: 0;
}
div.textbox {
width:270px;
min-height:200px;
max-height:370px;
padding: 10px;
border: 1px solid #999;
position: absolute;
top: 200px;
left: 968px;
display: inline-block;
overflow-y: scroll;
margin: 0;
}
</style>
</head>
<body>
<!-- graph -->
<svg class="graph" width="960" height="560"></svg>
<!-- legend -->
<div class="legendbox"> <svg class="legendsvg"></svg></div>
<!-- textbox -->
<div class="textbox" id = "textbox">Click node</div>
<button id="overview" class="overview" onclick='display_abstract(false), highlight_button("overview")'>Overview</button>
<button id="abstract" class="abstract" onclick='display_abstract(true), highlight_button("abstract")'>Abstract</button>
<!-- buttons -->
<button onclick="location.reload()">Reload Graph</button>
<button class="resetZoom" onclick="reset_view()">Reset View</button>
<button class="save" onclick="save_svg()">Save</button>
<!-- D3 (version 5) -->
<script src="https://d3js.org/d3.v5.min.js"></script>
<!-- scripts to save svg element as png -->
<script src="https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js"></script>
<script src="https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js"></script>
<!-- javascript for force-directed graph -->
<script type="text/javascript" id="cn" src="cn.js"></script>
</body>
</html>
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{
"nodes": [
{
"name": "Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis",
"author": [
"Emanuel S. R. Ehmki",
"Robert Schmidt",
"Farina Ohm",
"Matthias Rarey"
],
"year": "May 24, 2019",
"journal": "Journal of Chemical Information and Modeling",
"doi": "https://doi.org/10.1021/acs.jcim.9b00249",
"group": "input",
"citations": 5
},
{
"name": "Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems",
"author": [
"John A. Keith",
"Valentin Vassilev-Galindo",
"Bingqing Cheng",
"Stefan Chmiela",
"Michael Gastegger",
"Klaus-Robert M\u00fcller",
"Alexandre Tkatchenko"
],
"year": "July 7, 2021",
"journal": "Chem. Rev.",
"doi": "https://doi.org/10.1021/acs.chemrev.1c00107",
"group": "height",
"citations": 1
},
{
"name": "Disconnected Maximum Common Substructures under Constraints",
"author": [
"Robert Schmidt",
"Florian Krull",
"Anna Lina Heinzke",
"Matthias Rarey"
],
"year": "December 16, 2020",
"journal": "Journal of Chemical Information and Modeling",
"doi": "https://doi.org/10.1021/acs.jcim.0c00741",
"group": "height",
"citations": 0
},
{
"name": "Evolution of Novartis\u2019 Small Molecule Screening Deck Design",
"author": [
"Ansgar Schuffenhauer",
"Nadine Schneider",
"Samuel Hintermann",
"Douglas Auld",
"Jutta Blank",
"Simona Cotesta",
"Caroline Engeloch",
"Nikolas Fechner",
"Christoph Gaul",
"Jerome Giovannoni",
"Johanna Jansen",
"John Joslin",
"Philipp Krastel",
"Eugen Lounkine",
"John Manchester",
"Lauren G. Monovich",
"Anna Paola Pelliccioli",
"Manuel Schwarze",
"Michael D. Shultz",
"Nikolaus Stiefl",
"Daniel K. Baeschlin"
],
"year": "November 3, 2020",
"journal": "Journal of Medicinal Chemistry",
"doi": "https://doi.org/10.1021/acs.jmedchem.0c01332",
"group": "height",
"citations": 8
},
{
"name": "Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms",
"author": [
"Robert Schmidt",
"Emanuel S. R. Ehmki",
"Farina Ohm",
"Hans-Christian Ehrlich",
"Andriy Mashychev",
"Matthias Rarey"
],
"year": "May 23, 2019",
"journal": "Journal of Chemical Information and Modeling",
"doi": "https://doi.org/10.1021/acs.jcim.9b00250",
"group": "height",
"citations": 12
},
{
"name": "AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings",
"author": [
"Jerome Eberhardt",
"Diogo Santos-Martins",
"Andreas F. Tillack",
"Stefano Forli"
],
"year": "July 19, 2021",
"journal": "Journal of Chemical Information and Modeling",
"doi": "https://doi.org/10.1021/acs.jcim.1c00203",
"group": "input",
"citations": 1
},
{
"name": "Accelerating AutoDock4 with GPUs and Gradient-Based Local Search",
"author": [
"Diogo Santos-Martins",
"Leonardo Solis-Vasquez",
"Andreas F Tillack",
"Michel F Sanner",
"Andreas Koch",
"Stefano Forli"
],
"year": "January 6, 2021",
"journal": "Journal of Chemical Theory and Computation",
"doi": "https://doi.org/10.1021/acs.jctc.0c01006",
"group": "depth",
"citations": 14
},
{
"name": "Docking Flexible Cyclic Peptides with AutoDock CrankPep",
"author": [
"Yuqi Zhang",
"Michel F. Sanner"
],
"year": "September 11, 2019",
"journal": "Journal of Chemical Theory and Computation",
"doi": "https://doi.org/10.1021/acs.jctc.9b00557",
"group": "depth",
"citations": 9
},
{
"name": "Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise",
"author": [
"David Ryan Koes",
"Matthew P. Baumgartner",
"Carlos J. Camacho"
],
"year": "February 4, 2013",
"journal": "Journal of Chemical Information and Modeling",
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