From 77737514a3a8fa2526e86720d31d461fb1116d98 Mon Sep 17 00:00:00 2001
From: Merle Stahl <merle.stahl@studium.uni-hamburg.de>
Date: Tue, 7 Dec 2021 15:31:35 +0100
Subject: [PATCH] =?UTF-8?q?git=20aufger=C3=A4umt?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
Output/{cn_26_11_1.js => Graph/cn.js} | 0
Output/{ => Graph}/index.html | 2 +-
Output/{ => Graph}/json_text.json | 0
.../cn_Zeitstrahl.js} | 6 +-
Output/Graph_mit_Zeitstrahl/index.html | 59 ++++++++
Output/Graph_mit_Zeitstrahl/json_text.json | 134 ++++++++++++++++++
Output/ToDo.txt | 26 ++--
7 files changed, 209 insertions(+), 18 deletions(-)
rename Output/{cn_26_11_1.js => Graph/cn.js} (100%)
rename Output/{ => Graph}/index.html (97%)
rename Output/{ => Graph}/json_text.json (100%)
rename Output/{cn.js => Graph_mit_Zeitstrahl/cn_Zeitstrahl.js} (98%)
create mode 100644 Output/Graph_mit_Zeitstrahl/index.html
create mode 100644 Output/Graph_mit_Zeitstrahl/json_text.json
diff --git a/Output/cn_26_11_1.js b/Output/Graph/cn.js
similarity index 100%
rename from Output/cn_26_11_1.js
rename to Output/Graph/cn.js
diff --git a/Output/index.html b/Output/Graph/index.html
similarity index 97%
rename from Output/index.html
rename to Output/Graph/index.html
index 7b1f7ad..dea8b6e 100644
--- a/Output/index.html
+++ b/Output/Graph/index.html
@@ -85,7 +85,7 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/d3-legend/2.13.0/d3-legend.js"></script>
<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>
- <script type="text/javascript" src="cn_26_11_1.js"></script>
+ <script type="text/javascript" src="cn.js"></script>
</body>
</html>
\ No newline at end of file
diff --git a/Output/json_text.json b/Output/Graph/json_text.json
similarity index 100%
rename from Output/json_text.json
rename to Output/Graph/json_text.json
diff --git a/Output/cn.js b/Output/Graph_mit_Zeitstrahl/cn_Zeitstrahl.js
similarity index 98%
rename from Output/cn.js
rename to Output/Graph_mit_Zeitstrahl/cn_Zeitstrahl.js
index b9a5da2..f78f653 100644
--- a/Output/cn.js
+++ b/Output/Graph_mit_Zeitstrahl/cn_Zeitstrahl.js
@@ -51,7 +51,7 @@ var simulation = d3.forceSimulation()
.force("collide", d3.forceCollide(60))
.force("charge", d3.forceManyBody().strength(-50))
.force("center", d3.forceCenter(width/2, height/2+50))
- //.force("xscale", d3.forceX().strength(1).x(function(d) {return xscale(parseFloat(d.year))}))
+ .force("xscale", d3.forceX().strength(1).x(function(d) {return xscale(parseFloat(d.year))}))
.force("yscale", d3.forceY().strength(1).y(function(d) {return yscale(d.group)}));
/**
@@ -61,7 +61,7 @@ var g = svg.append("g")
.attr("class", "everything")
/**
-* creates XAxis element
+* creates xAxis element
*/
var xAxis = d3.axisBottom()
.tickFormat(function(d) {return d;})
@@ -311,7 +311,7 @@ function dragged(node) {
function dragended(node) {
if (!d3.event.active) simulation.alphaTarget(.03);
node.fx = null;
- node.fy = null;
+ //node.fy = null;
}
/**
diff --git a/Output/Graph_mit_Zeitstrahl/index.html b/Output/Graph_mit_Zeitstrahl/index.html
new file mode 100644
index 0000000..9cdd0bd
--- /dev/null
+++ b/Output/Graph_mit_Zeitstrahl/index.html
@@ -0,0 +1,59 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+ <meta charset="utf-8">
+
+ <style type="text/css">
+ /*
+ button {
+ width: 150px;
+ font-size: 15px;
+ padding: 7px;
+ border-radius: 3px;
+ border: 3px solid #999;
+ color: black;
+ cursor: pointer;
+ position : absolute;
+ top: 500px;
+ right: 550px;
+ } */
+
+ /* textbox */
+ div {
+ width:270px;
+ min-height:200px;
+ max-height:370px;
+ padding: 10px;
+ border: 1px solid #999;
+ position: absolute;
+ top: 20px;
+ left: 980px;
+ display: inline-block;
+ overflow-y: scroll;
+ margin: 0;
+ }
+ </style>
+</head>
+
+<body>
+ <!-- for testing -->
+ <p id="id"></p> <!--for commenting with document.getElementById("id").innerHTML = "text"; -->
+
+ <!-- graph -->
+ <svg width="960" height="600"></svg>
+
+ <!-- textbox -->
+ <div id = "textbox" style="border:1px solid">Click node</div>
+
+ <!-- reset-buttons -->
+ <button onclick="javascript:location.reload();">Reload</button>
+ <button onclick="resetGraph()">Reset graph</button>
+ <button onclick="resetZoom()">Reset zoom</button>
+ <button onclick="center()">Center</button>
+
+ <!-- link D3 (version 5) -->
+ <script src="https://d3js.org/d3.v5.min.js"></script>
+ <script type="text/javascript" src="cn_Zeitstrahl.js"></script>
+
+</body>
+</html>
\ No newline at end of file
diff --git a/Output/Graph_mit_Zeitstrahl/json_text.json b/Output/Graph_mit_Zeitstrahl/json_text.json
new file mode 100644
index 0000000..1a080a0
--- /dev/null
+++ b/Output/Graph_mit_Zeitstrahl/json_text.json
@@ -0,0 +1,134 @@
+{
+ "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":"2001",
+ "doi": "https://doi.org/10.1021/acs.jcim.9b00249",
+ "group": "input",
+ "citations": 0
+ },
+ {
+ "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":"1967",
+ "doi": "https://doi.org/10.1021/acs.chemrev.1c00107",
+ "group": "citing",
+ "citations": 140
+ },
+ {
+ "name": "Disconnected Maximum Common Substructures under Constraints ",
+ "author": "Robert Schmidt, Florian Krull, Anna Lina Heinzke, Matthias Rarey. ",
+ "year":"1991",
+ "doi": "https://doi.org/10.1021/acs.jcim.0c00741",
+ "group": "citing",
+ "citations": 300
+ },
+ {
+ "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":"1990",
+ "doi": "https://doi.org/10.1021/acs.jmedchem.0c01332",
+ "group": "input",
+ "citations": 250
+ },
+ {
+ "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":"2021",
+ "doi": "https://doi.org/10.1021/acs.jcim.9b00250",
+ "group": "cited",
+ "citations": 130
+ },
+ {
+ "name": "Machine learning accelerates quantum mechanics predictions of molecular crystals ",
+ "author": "Yanqiang Han, Imran Ali, Zhilong Wang, Junfei Cai, Sicheng Wu, Jiequn Tang, Lin Zhang, Jiahao Ren, Rui Xiao, Qianqian Lu, Lei Hang, Hongyuan Luo, Jinjin Li. ",
+ "year":"2011",
+ "doi": "https://doi.org/10.1016/j.physrep.2021.08.002",
+ "group": "cited",
+ "citations": 170
+ },
+ {
+ "name": "The Growing Importance of Chirality in 3D Chemical Space Exploration and Modern Drug Discovery Approaches for Hit-ID ",
+ "author": "Ilaria Proietti Silvestri, Paul J. J. Colbon. ",
+ "year":"2001",
+ "doi": "https://doi.org/10.1021/acsmedchemlett.1c00251",
+ "group": "cited",
+ "citations": 210
+ },
+ {
+ "name": "Target-Based Evaluation of \u201cDrug-Like\u201d Properties and Ligand Efficiencies ",
+ "author": "Paul D. Leeson, A. Patricia Bento, Anna Gaulton, Anne Hersey, Emma J. Manners, Chris J. Radoux, Andrew R. Leach. ",
+ "year":"2003",
+ "doi": "https://doi.org/10.1021/acs.jmedchem.1c00416",
+ "group": "cited",
+ "citations": 10
+ },
+ {
+ "name": "BonMOLi\u00e8re: Small-Sized Libraries of Readily Purchasable Compounds, Optimized to Produce Genuine Hits in Biological Screens across the Protein Space ",
+ "author": "Neann Mathai, Conrad Stork, Johannes Kirchmair. ",
+ "year":"2003",
+ "doi": "https://doi.org/10.3390/ijms22157773",
+ "group": "cited",
+ "citations": 80
+ },
+ {
+ "name": "Accelerating high-throughput virtual screening through molecular pool-based active learning ",
+ "author": "David E. Graff, Eugene I. Shakhnovich, Connor W. Coley. ",
+ "year":"2013",
+ "doi": "https://doi.org/10.1039/D0SC06805E",
+ "group": "cited",
+ "citations": 60
+ },
+ {
+ "name": "Compound Screening ",
+ "author": "Shin Numao.",
+ "year":"2009",
+ "doi": "https://doi.org/10.1016/B978-0-12-820472-6.00078-5",
+ "group": "citing",
+ "citations": 280
+ }
+ ],
+ "links": [
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.9b00249",
+ "target": "https://doi.org/10.1021/acs.chemrev.1c00107"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.9b00249",
+ "target": "https://doi.org/10.1021/acs.jcim.0c00741"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.9b00249",
+ "target": "https://doi.org/10.1021/acs.jmedchem.0c01332"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.9b00249",
+ "target": "https://doi.org/10.1021/acs.jcim.9b00250"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jcim.9b00249",
+ "target": "https://doi.org/10.1016/j.physrep.2021.08.002"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jmedchem.0c01332",
+ "target": "https://doi.org/10.1021/acsmedchemlett.1c00251"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jmedchem.0c01332",
+ "target": "https://doi.org/10.1021/acs.jmedchem.1c00416"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jmedchem.0c01332",
+ "target": "https://doi.org/10.3390/ijms22157773"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jmedchem.0c01332",
+ "target": "https://doi.org/10.1039/D0SC06805E"
+ },
+ {
+ "source": "https://doi.org/10.1021/acs.jmedchem.0c01332",
+ "target": "https://doi.org/10.1016/B978-0-12-820472-6.00078-5"
+ }
+ ]
+}
\ No newline at end of file
diff --git a/Output/ToDo.txt b/Output/ToDo.txt
index 414a1e1..e4905e4 100644
--- a/Output/ToDo.txt
+++ b/Output/ToDo.txt
@@ -1,25 +1,23 @@
Erledigt:
- Graphstruktur mit Knoten und Kanten (+ Schnittstelle mit Verarbeitung (Json))
- 3 senkrechte Schichten für Input, Citing und Cited (+ Farben)
-- Scroll- und Schiebefunktionen des gesamten Graphen
+- Legende
+- Knotengröße nach Zitierungsanzahl
+- Markierung der Selbstzitierung
- Zoom- und Schiebefunktionen des gesamten Graphen
- Schiebefunktionen der einzelnen Knoten
-- Hover-Text mit den zugehörigen Informationen von den Knoten
-- Informationsfenster auf Klick geöffnet
-- Hervorhebung von Knoten und deren verbundenen Kanten auf Klick
-- Knopf zum Neuladen des Programms
+- Hervorhebung von Knoten und deren verbundenen Kanten auf Klick (Knoten oder Beschriftung)
+- Informationsfenster für Knoten auf Klick (Knoten oder Beschriftung)
+-> Zurücksetzen auf Klick (Hintergrund)
- Knopf zum Zurücksetzen der verschobenen Knoten
-- Knopf zum Zurücksetzen des verschobenen Graphen
+- Knopf zum Zurücksetzen des verschobenen Graphen (Zentrieren)
- Knopf zum Zurücksetzen der Zoom-Funktion
+- Zeitstrahl auf x-Achse
Noch offen:
-- Strukturierung und Kommentierung des Codes verbessern
-- Informationsfenster an sehr lange Titel anpassen
-- Ãœberlagerung von Graph und Informationsfenster verhindern
-- Zurücksetzen der Markierungsfunktion
- Skalierung an unterschiedliche Geräte anpassen
- Schnittstelle zu Benutzeroberfläche (!)
-- Informationen zu Funktionen anzeigen (?)
-- Speicherfunktion (?)
-- Suchfunktion
-- X-Achse mit Jahreszahlen
+ - Suchfunktion
+ - Informationen zu Funktionen anzeigen
+ - Zeitstrahl auf x-Achse (optional)
+- Speicherfunktion
--
GitLab