From 71ad41e35aa90ee72d55160e8ba012b31a5d9f12 Mon Sep 17 00:00:00 2001
From: Katja <bax5612@studium.uni-hamburg.de>
Date: Fri, 10 Dec 2021 21:19:19 +0100
Subject: [PATCH] auto zoom
---
Output.zip | Bin 0 -> 18182 bytes
Output/Graph/cn.js | 128 ++--
Output/Graph/index.html | 75 +--
Output/Graph/json_with_citations.json | 819 ++++++++++++++++++++++++++
4 files changed, 915 insertions(+), 107 deletions(-)
create mode 100644 Output.zip
create mode 100644 Output/Graph/json_with_citations.json
diff --git a/Output.zip b/Output.zip
new file mode 100644
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diff --git a/Output/Graph/cn.js b/Output/Graph/cn.js
index 0601cc3..ae6d127 100644
--- a/Output/Graph/cn.js
+++ b/Output/Graph/cn.js
@@ -13,7 +13,7 @@ width = svg.attr("width"),
height = svg.attr("height");
var textinfo='';
var textabstract='';
-
+var perc;
/**
* creates node object and associated attributes
*/
@@ -54,7 +54,7 @@ var svglegend = d3.select("svg.legendsvg"),
legendposition = [65,95,125],
arrowlegendposition = [0,25],
arrowgroupnames = ["citation","self-citation"],
-groupnames = ["citing","input","cited"];
+groupnames = ["cited by","input","reference"];
var legend = svglegend.selectAll(".legend")
.data(legendposition)
@@ -105,13 +105,33 @@ legendarrow.append("text")
* 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(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()
.force("link", d3.forceLink().id(function(d) {return d.doi;}).distance(200))
.force("collide", d3.forceCollide(50).strength(0.5))
.force("charge", d3.forceManyBody())
.force("center", d3.forceCenter(width/2, height/2+20))
.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
@@ -122,7 +142,7 @@ var g = svg.append("g")
/**
* 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);
})
@@ -135,7 +155,7 @@ d3.json("json_text.json").then(function(graph) {
function update(links, nodes) {
updateLinks(links);
updateNodes(nodes);
-
+
simulation
.nodes(nodes)
.on("tick", tickHandler);
@@ -144,10 +164,15 @@ function update(links, nodes) {
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")});
-
- zoomTo();
+
+}
+function ahaa(){
+ d3.selectAll(".node").attr("initial_x", function(d) {return d.dx;})
+ .attr("initial_y", function(d) {return d.dy;})
+
}
+
function zoomTo() {
node_bounds = d3.selectAll("svg.graph").node().getBBox();
svg_bounds = d3.select("rect").node().getBBox();
@@ -162,65 +187,10 @@ function zoomTo() {
perc = d3.min([perc_x, perc_y])
//console.log(perc_x, perc)
d3.select('svg')
- .transition()
.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
@@ -249,8 +219,6 @@ function updateNodes(nodes) {
.enter()
.append("g")
.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_y", function(d) {return parseInt(d.attr("cy")) + d[0][0].getCTM().f})
.call(d3.drag()
@@ -301,6 +269,7 @@ function updateMarker(color, target) {
* @param {object} node - node
*/
function clickNode(node) {
+ d3.select(this.parentNode).raise();
fix_nodes(node);
if(toRemove){
d3.select(toRemove).selectAll(".circle").style("stroke","none")
@@ -376,7 +345,7 @@ function textfunc(node){
function highlightbutton(btn){
resetbuttonhighlight();
- document.getElementById(btn).style.background="#DCDCDC";
+ document.getElementById(btn).style.background="#cacaca";
}
function resetbuttonhighlight(){
document.getElementById("overview").style.background='';
@@ -413,6 +382,7 @@ function tickHandler() {
* @param {object} node - data of current node
*/
function dragstarted(node) {
+ d3.select(this).raise();
if (!d3.event.active)
simulation.alphaTarget(0.3).restart()
node.fx = node.x;
@@ -443,10 +413,16 @@ function fix_nodes(this_node) {
* resets the positions of the nodes
*/
function resetGraph() {
- d3.selectAll(".node").each(function(d) {
+
+ node.each(function(d) {
d.fx = d.initial_x;
d.fy = d.initial_y;
- })
+ });
+ simulation.tick();
+ simulation.tick();
+ simulation.stop();
+
+
}
/**
@@ -456,12 +432,23 @@ function zoomHandler() {
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
*/
-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')
- .call(zoom.scaleTo, 1);
+ .call(zoom.scaleBy, perc);
+
}
/**
@@ -580,4 +567,5 @@ function svgString2Image( svgString, width, height, format, callback ) {
};
image.src = imgsrc;
-}
\ No newline at end of file
+}
+
diff --git a/Output/Graph/index.html b/Output/Graph/index.html
index 9daa68d..8999fad 100644
--- a/Output/Graph/index.html
+++ b/Output/Graph/index.html
@@ -10,27 +10,48 @@
display: flex;
justify-content: center;
position: absolute;
- left: 430px;
+ left: 455px;
top: 575px;
+ transition-duration: 0.4s;
+ border-radius:3px;
+ border:1px solid #909090;
}
+ .button:hover {
+ background-color: #cacaca;
+ }
+
+
button.resetGraph {}
button.resetZoom {
margin-left: 110px;
}
- button.center {
+ button.save{
margin-left: 220px;
}
-
- button.save{
- margin-left: 330px;
+ 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;
+ width:270px;
+ height:170px;
padding: 10px;
/*border: 1px solid #999;*/
position: absolute;
@@ -40,29 +61,10 @@
margin: 0;
}
- 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.textbox {
- width: 270px;
- min-height: 200px;
- max-height: 370px;
+ div.textbox{
+ width:270px;
+ min-height:200px;
+ max-height:370px;
padding: 10px;
border: 1px solid #999;
position: absolute;
@@ -86,16 +88,15 @@
<div class="legendbox"> <svg class="legendsvg"></svg></div>
<!-- textbox -->
- <div class="textbox" id="textbox">Click node</div>
+ <div class="textbox" id = "textbox">Click node</div>
<!-- reset buttons -->
- <!-- <button onclick="javascript:location.reload();">Reload</button>-->
- <button class="resetGraph" onclick="resetGraph()">Reset graph</button>
- <button class="resetZoom" onclick="resetZoom()">Reset zoom</button>
- <button class="center" onclick="center()">Center</button>
+ <button class="resetGraph" onclick="javascript:location.reload();">Reload Graph</button>
+ <!-- <button class="resetGraph" onclick="resetGraph(),fix_all()">Reset graph</button>-->
+ <button class="resetZoom" onclick="resetView()">Reset View</button>
<button class="save" onclick="savesvg()">Save</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="overview" class="overview" onclick='displayabstract(false),highlightbutton("overview")'>Overview</button>
+ <button id="abstract" class="abstract" onclick='displayabstract(true),highlightbutton("abstract")'>Abstract</button>
<!-- link D3 (version 5) -->
diff --git a/Output/Graph/json_with_citations.json b/Output/Graph/json_with_citations.json
new file mode 100644
index 0000000..eb3c1d3
--- /dev/null
+++ b/Output/Graph/json_with_citations.json
@@ -0,0 +1,819 @@
+{
+ "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",
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\ No newline at end of file
--
GitLab