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Commit 71ad41e3 authored by Katja's avatar Katja
Browse files

auto zoom

parent 37d667cb
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2 merge requests!10Output,!9Main
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Output.zip 0 → 100644
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View file @ 71ad41e3
File added
Output/Graph/cn.js
+ 58
− 70
View file @ 71ad41e3
...@@ -13,7 +13,7 @@ width = svg.attr("width"), ...@@ -13,7 +13,7 @@ width = svg.attr("width"),
height = svg.attr("height"); height = svg.attr("height");
var textinfo=''; var textinfo='';
var textabstract=''; var textabstract='';
var perc;
/** /**
* creates node object and associated attributes * creates node object and associated attributes
*/ */
...@@ -54,7 +54,7 @@ var svglegend = d3.select("svg.legendsvg"), ...@@ -54,7 +54,7 @@ var svglegend = d3.select("svg.legendsvg"),
legendposition = [65,95,125], legendposition = [65,95,125],
arrowlegendposition = [0,25], arrowlegendposition = [0,25],
arrowgroupnames = ["citation","self-citation"], arrowgroupnames = ["citation","self-citation"],
groupnames = ["citing","input","cited"]; groupnames = ["cited by","input","reference"];
var legend = svglegend.selectAll(".legend") var legend = svglegend.selectAll(".legend")
.data(legendposition) .data(legendposition)
...@@ -105,13 +105,33 @@ legendarrow.append("text") ...@@ -105,13 +105,33 @@ legendarrow.append("text")
* updates the positions of the links and nodes when the * updates the positions of the links and nodes when the
state of the layout has changed (simulation has advanced by a tick) 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(150).y(function(d) {return yscale(d.group)}))
.force("yscale", d3.forceY().strength(function(d){
if (d.group == "input") {return 1000;}
else {return 50;}
}).y(function(d) {return yscale(d.group)}))
.alpha(0.005)
.on("end", zoomTo);
/*
var simulation = d3.forceSimulation() var simulation = d3.forceSimulation()
.force("link", d3.forceLink().id(function(d) {return d.doi;}).distance(200)) .force("link", d3.forceLink().id(function(d) {return d.doi;}).distance(200))
.force("collide", d3.forceCollide(50).strength(0.5)) .force("collide", d3.forceCollide(50).strength(0.5))
.force("charge", d3.forceManyBody()) .force("charge", d3.forceManyBody())
.force("center", d3.forceCenter(width/2, height/2+20)) .force("center", d3.forceCenter(width/2, height/2+20))
.force("yscale", d3.forceY().strength(1).y(function(d) {return yscale(d.group)})) .force("yscale", d3.forceY().strength(1).y(function(d) {return yscale(d.group)}))
.alpha(0.1); .alpha(0.1)
.on("end", zoomTo,ahaa);*/
/** /**
* creates group element * creates group element
...@@ -122,7 +142,7 @@ var g = svg.append("g") ...@@ -122,7 +142,7 @@ var g = svg.append("g")
/** /**
* loads JSON data and calls the update function * loads JSON data and calls the update function
*/ */
d3.json("json_text.json").then(function(graph) { d3.json("json_with_citations.json").then(function(graph) {
update(graph.links, graph.nodes); update(graph.links, graph.nodes);
}) })
...@@ -145,8 +165,13 @@ function update(links, nodes) { ...@@ -145,8 +165,13 @@ function update(links, nodes) {
link.attr('marker-end', function(d) {return updateMarker("#999", d.target);}) link.attr('marker-end', function(d) {return updateMarker("#999", d.target);})
.style("stroke-dasharray",function(d){return self_cit(d.source,d.target)? ("8,8"): ("1,0")}); .style("stroke-dasharray",function(d){return self_cit(d.source,d.target)? ("8,8"): ("1,0")});
zoomTo();
} }
function ahaa(){
d3.selectAll(".node").attr("initial_x", function(d) {return d.dx;})
.attr("initial_y", function(d) {return d.dy;})
}
function zoomTo() { function zoomTo() {
node_bounds = d3.selectAll("svg.graph").node().getBBox(); node_bounds = d3.selectAll("svg.graph").node().getBBox();
...@@ -162,65 +187,10 @@ function zoomTo() { ...@@ -162,65 +187,10 @@ function zoomTo() {
perc = d3.min([perc_x, perc_y]) perc = d3.min([perc_x, perc_y])
//console.log(perc_x, perc) //console.log(perc_x, perc)
d3.select('svg') d3.select('svg')
.transition()
.call(zoom.scaleBy, perc); .call(zoom.scaleBy, perc);
} }
/*
function zoomTo() {
var bounds = root.node().getBBox();
//var bounds = d3.select(".node").node().getBBox();
var parent = root.node().parentElement;
var fullWidth = parent.clientWidth,
fullHeight = parent.clientHeight;
var width = bounds.width,
height = bounds.height;
var midX = bounds.x + width / 2,
midY = bounds.y + height / 2;
if (width == 0 || height == 0) return; // nothing to fit
var scale = (0.75) / Math.max(width / fullWidth, height / fullHeight);
var translate = [fullWidth / 2 - scale * midX, fullHeight / 2 - scale * midY];
console.trace("zoomFit", translate, scale);
root
.transition()
.call(zoom.translate(translate).scale(scale).event);
}
*/
/*function zoomTo() {
x_array = [];
y_array = [];
d3.selectAll(".node").each(function(d) {
//ctm = d[0][0].getCTM();
//xy_trans = d3.translate(d.x, d.y);
//x_array.push(xy_trans[0]);
// x_array.push(ctm.e + d.x*ctm.a + d.y*ctm.c);
x_array.push(d.x);
y_array.push(d.y)
console.log(d.x, d.y)
})
var max_x = d3.max(x_array);
var min_x = d3.min(x_array);
var diff_x = max_x-min_x-50;
perc_y = (diff_x*13)/width;
//if (perc_y < 1) {perc_y = perc_y+1;}
var max_y = d3.max(y_array);
var min_y = d3.min(y_array);
var diff_y = max_y-min_y-50;
perc_x = (diff_y*13)/height;
//if (perc_x < 1) {perc_x = perc_y+1;}
console.log(max_y, min_y)
perc = d3.max([perc_x, perc_y])
console.log(perc_x, perc)
d3.select('svg')
.transition()
.call(zoom.scaleBy, perc);
}*/
/** /**
* initializes and shows links * initializes and shows links
...@@ -249,8 +219,6 @@ function updateNodes(nodes) { ...@@ -249,8 +219,6 @@ function updateNodes(nodes) {
.enter() .enter()
.append("g") .append("g")
.attr("class", "node") .attr("class", "node")
.attr("initial_x", function(d) {return d.dx;})
.attr("initial_y", function(d) {return d.dy;})
//.attr("abs_x", function(d) {return parseInt(d.attr("cx")) + d[0][0].getCTM().e}) //.attr("abs_x", function(d) {return parseInt(d.attr("cx")) + d[0][0].getCTM().e})
//.attr("abs_y", function(d) {return parseInt(d.attr("cy")) + d[0][0].getCTM().f}) //.attr("abs_y", function(d) {return parseInt(d.attr("cy")) + d[0][0].getCTM().f})
.call(d3.drag() .call(d3.drag()
...@@ -301,6 +269,7 @@ function updateMarker(color, target) { ...@@ -301,6 +269,7 @@ function updateMarker(color, target) {
* @param {object} node - node * @param {object} node - node
*/ */
function clickNode(node) { function clickNode(node) {
d3.select(this.parentNode).raise();
fix_nodes(node); fix_nodes(node);
if(toRemove){ if(toRemove){
d3.select(toRemove).selectAll(".circle").style("stroke","none") d3.select(toRemove).selectAll(".circle").style("stroke","none")
...@@ -376,7 +345,7 @@ function textfunc(node){ ...@@ -376,7 +345,7 @@ function textfunc(node){
function highlightbutton(btn){ function highlightbutton(btn){
resetbuttonhighlight(); resetbuttonhighlight();
document.getElementById(btn).style.background="#DCDCDC"; document.getElementById(btn).style.background="#cacaca";
} }
function resetbuttonhighlight(){ function resetbuttonhighlight(){
document.getElementById("overview").style.background=''; document.getElementById("overview").style.background='';
...@@ -413,6 +382,7 @@ function tickHandler() { ...@@ -413,6 +382,7 @@ function tickHandler() {
* @param {object} node - data of current node * @param {object} node - data of current node
*/ */
function dragstarted(node) { function dragstarted(node) {
d3.select(this).raise();
if (!d3.event.active) if (!d3.event.active)
simulation.alphaTarget(0.3).restart() simulation.alphaTarget(0.3).restart()
node.fx = node.x; node.fx = node.x;
...@@ -443,10 +413,16 @@ function fix_nodes(this_node) { ...@@ -443,10 +413,16 @@ function fix_nodes(this_node) {
* resets the positions of the nodes * resets the positions of the nodes
*/ */
function resetGraph() { function resetGraph() {
d3.selectAll(".node").each(function(d) {
node.each(function(d) {
d.fx = d.initial_x; d.fx = d.initial_x;
d.fy = d.initial_y; d.fy = d.initial_y;
}) });
simulation.tick();
simulation.tick();
simulation.stop();
} }
/** /**
...@@ -456,12 +432,23 @@ function zoomHandler() { ...@@ -456,12 +432,23 @@ function zoomHandler() {
d3.select('g').attr("transform", d3.event.transform); d3.select('g').attr("transform", d3.event.transform);
} }
d3.selection.prototype.moveToFront = function() {
return this.each(function(){
this.parentNode.appendChild(this);
});
};
/** /**
* transforms svg so that that the zoom is reset * transforms svg so that that the zoom is reset
*/ */
function resetZoom() { function resetView() {
d3.select('svg')
.call(zoom.scaleTo, 1)
d3.select('svg')
.call(zoom.translateTo, 0.5 * width, 0.5 * height);
d3.select('svg') d3.select('svg')
.call(zoom.scaleTo, 1); .call(zoom.scaleBy, perc);
} }
/** /**
...@@ -581,3 +568,4 @@ function svgString2Image( svgString, width, height, format, callback ) { ...@@ -581,3 +568,4 @@ function svgString2Image( svgString, width, height, format, callback ) {
image.src = imgsrc; image.src = imgsrc;
} }
Output/Graph/index.html
+ 38
− 37
View file @ 71ad41e3
...@@ -10,36 +10,27 @@ ...@@ -10,36 +10,27 @@
display: flex; display: flex;
justify-content: center; justify-content: center;
position: absolute; position: absolute;
left: 430px; left: 455px;
top: 575px; top: 575px;
transition-duration: 0.4s;
border-radius:3px;
border:1px solid #909090;
}
.button:hover {
background-color: #cacaca;
} }
button.resetGraph {} button.resetGraph {}
button.resetZoom { button.resetZoom {
margin-left: 110px; margin-left: 110px;
} }
button.center {
margin-left: 220px;
}
button.save{ button.save{
margin-left: 330px; margin-left: 220px;
}
div.legendbox {
width: 270px;
height: 170px;
padding: 10px;
/*border: 1px solid #999;*/
position: absolute;
top: 10px;
left: 968px;
display: inline-block;
margin: 0;
} }
button.abstract{ button.abstract{
width:146px; width:146px;
position:absolute; position:absolute;
...@@ -48,7 +39,6 @@ ...@@ -48,7 +39,6 @@
border-radius:0; border-radius:0;
border:1px solid #909090; border:1px solid #909090;
} }
button.overview{ button.overview{
width:147px; width:147px;
position:absolute; position:absolute;
...@@ -59,6 +49,18 @@ ...@@ -59,6 +49,18 @@
border:1px solid #909090; 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{ div.textbox{
width:270px; width:270px;
min-height:200px; min-height:200px;
...@@ -89,10 +91,9 @@ ...@@ -89,10 +91,9 @@
<div class="textbox" id = "textbox">Click node</div> <div class="textbox" id = "textbox">Click node</div>
<!-- reset buttons --> <!-- reset buttons -->
<!-- <button onclick="javascript:location.reload();">Reload</button>--> <button class="resetGraph" onclick="javascript:location.reload();">Reload Graph</button>
<button class="resetGraph" onclick="resetGraph()">Reset graph</button> <!-- <button class="resetGraph" onclick="resetGraph(),fix_all()">Reset graph</button>-->
<button class="resetZoom" onclick="resetZoom()">Reset zoom</button> <button class="resetZoom" onclick="resetView()">Reset View</button>
<button class="center" onclick="center()">Center</button>
<button class="save" onclick="savesvg()">Save</button> <button class="save" onclick="savesvg()">Save</button>
<button id="overview" class="overview" onclick='displayabstract(false),highlightbutton("overview")'>Overview</button> <button id="overview" class="overview" onclick='displayabstract(false),highlightbutton("overview")'>Overview</button>
<button id="abstract" class="abstract" onclick='displayabstract(true),highlightbutton("abstract")'>Abstract</button> <button id="abstract" class="abstract" onclick='displayabstract(true),highlightbutton("abstract")'>Abstract</button>
... ...
......
Output/Graph/json_with_citations.json 0 → 100644
+ 819
− 0
View file @ 71ad41e3
{
"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",
"doi": "https://doi.org/10.1021/ci300604z",
"group": "depth",
"citations": 100
},
{
"name": "Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking",
"author": [
"Anita K. Nivedha",
"David F. Thieker",
"Spandana Makeneni",
"Huimin Hu",
"Robert J. Woods"
],
"year": "January 8, 2016",
"journal": "Journal of Chemical Theory and Computation",
"doi": "https://doi.org/10.1021/acs.jctc.5b00834",
"group": "depth",
"citations": 48
},
{
"name": "Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems",
"author": [
"Stefano Forli",
"Maurizio Botta"
],
"year": "June 22, 2007",
"journal": "Journal of Chemical Information and Modeling",
"doi": "https://doi.org/10.1021/ci700036j",
"group": "depth",
"citations": 32
},
{
"name": "AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins",
"author": [
"Diogo Santos-Martins",
"Stefano Forli",
"Maria Jo\u00e3o Ramos",
"Arthur J. Olson"
],
"year": "June 15, 2014",
"journal": "Journal of Chemical Information and Modeling",
"doi": "https://doi.org/10.1021/ci500209e",
"group": "depth",
"citations": 100
},
{
"name": "A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking",
"author": [
"Stefano Forli",
"Arthur J. Olson"
],
"year": "December 9, 2011",
"journal": "Journal of Medicinal Chemistry",
"doi": "https://doi.org/10.1021/jm2005145",
"group": "depth",
"citations": 100
},
{
"name": "Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context",
"author": [
"Douglas R. Houston",
"Malcolm D. Walkinshaw"
],
"year": "January 27, 2013",
"journal": "Journal of Chemical Information and Modeling",
"doi": "https://doi.org/10.1021/ci300399w",
"group": "depth",
"citations": 100
},
{
"name": "Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. Theory",
"author": [
"Themis Lazaridis"
],
"year": "April 14, 1998",
"journal": "Journal of Physical Chemistry B",
"doi": "https://doi.org/10.1021/jp9723574",
"group": "depth",
"citations": 100
},
{
"name": "Inhomogeneous Fluid Approach to Solvation Thermodynamics. 2. Applications to Simple Fluids",
"author": [
"Themis Lazaridis"
],
"year": "April 14, 1998",
"journal": "Journal of Physical Chemistry B",
"doi": "https://doi.org/10.1021/jp972358w",
"group": "depth",
"citations": 100
},
{
"name": "ZINC20\u2014A Free Ultralarge-Scale Chemical Database for Ligand Discovery",
"author": [
"John J. Irwin",
"Khanh G. Tang",
"Jennifer Young",
"Chinzorig Dandarchuluun",
"Benjamin R. Wong",
"Munkhzul Khurelbaatar",
"Yurii S. Moroz",
"John Mayfield",
"Roger A. Sayle"
],
"year": "October 29, 2020",
"journal": "Journal of Chemical Information and Modeling",
"doi": "https://doi.org/10.1021/acs.jcim.0c00675",
"group": "depth",
"citations": 25
},
{
"name": "Structural Biology-Inspired Discovery of Novel KRAS\u2013PDE\u03b4 Inhibitors",
"author": [
"Yan Jiang",
"Chunlin Zhuang",
"Long Chen",
"Junjie Lu",
"Guoqiang Dong",
"Zhenyuan Miao",
"Wannian Zhang",
"Jian Li",
"Chunquan Sheng"
],
"year": "September 20, 2017",
"journal": "Journal of Medicinal Chemistry",
"doi": "https://doi.org/10.1021/acs.jmedchem.7b01243",
"group": "depth",
"citations": 12
},
{
"name": "Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking",
"author": [
"Michael M. Mysinger",
"Michael Carchia",
"John. J. Irwin",
"Brian K. Shoichet"
],
"year": "June 20, 2012",
"journal": "Journal of Medicinal Chemistry",
"doi": "https://doi.org/10.1021/jm300687e",
"group": "depth",
"citations": 100
},
{
"name": "Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark",
"author": [
"Thomas Gaillard"
],
"year": "July 10, 2018",
"journal": "Journal of Chemical Information and Modeling",
"doi": "https://doi.org/10.1021/acs.jcim.8b00312",
"group": "depth",
"citations": 74
},
{
"name": "Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity",
"author": [
"Nguyen Thanh Nguyen",
"Trung Hai Nguyen",
"T. Ngoc Han Pham",
"Nguyen Truong Huy",
"Mai Van Bay",
"Minh Quan Pham",
"Pham Cam Nam",
"Van V. Vu",
"Son Tung Ngo"
],
"year": "December 30, 2019",
"journal": "Journal of Chemical Information and Modeling",
"doi": "https://doi.org/10.1021/acs.jcim.9b00778",
"group": "depth",
"citations": 65
},
{
"name": "Glide:\u2009 A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy",
"author": [
"Richard A. Friesner",
"Jay L. Banks",
"Robert B. Murphy",
"Thomas A. Halgren",
"Jasna J. Klicic",
"Daniel T. Mainz",
"Matthew P. Repasky",
"Eric H. Knoll",
"Mee Shelley",
"Jason K. Perry",
"David E. Shaw",
"Perry Francis",
"Peter S. Shenkin"
],
"year": "February 27, 2004",
"journal": "Journal of Medicinal Chemistry",
"doi": "https://doi.org/10.1021/jm0306430",
"group": "depth",
"citations": 97
},
{
"name": "Surflex:\u2009 Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine",
"author": [
"Ajay N. Jain"
],
"year": "January 21, 2003",
"journal": "Journal of Medicinal Chemistry",
"doi": "https://doi.org/10.1021/jm020406h",
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