Deployed new UI with NGL viewer instead of 3Dmol

3D-e-Chem · Dec 2, 2016 · 0414efd · 0414efd
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,10 @@ The file is formatted as described on http://keepachangelog.com/.
 
 ## [Unreleased]
 
+## Changed
+
+* Switched from 3Dmol to NGL (https://github.com/3D-e-Chem/molviewer-tsx/issues/4)
+
 ## [0.1.4] - 2016-11-25
 
 ### Added

diff --git a/NOTICE b/NOTICE
@@ -1,5 +1,4 @@
-Software uses 3Dmol.js
+Software uses NGL (https://github.com/arose/ngl)
 
-Nicholas Rego and David Koes
-3Dmol.js: molecular visualization with WebGL
-Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829
+- AS Rose, AR Bradley, Y Valasatava, JM Duarte, A Prlić and PW Rose. Web-based molecular graphics for large complexes. ACM Proceedings of the 21st International Conference on Web3D Technology (Web3D '16): 185-186, 2016. doi:10.1145/2945292.2945324
+- AS Rose and PW Hildebrand. NGL Viewer: a web application for molecular visualization. Nucl Acids Res (1 July 2015) 43 (W1): W576-W579 first published online April 29, 2015. doi:10.1093/nar/gkv402
diff --git a/README.md b/README.md
@@ -1,9 +1,9 @@
-KNIME node which launches a web browser with a molecule viewer powered by 3Dmol.js.
+KNIME node which launches a web browser with a molecule viewer powered by [NGL](https://github.com/arose/ngl).
 
 [![Build Status](https://travis-ci.org/3D-e-Chem/knime-molviewer.svg?branch=master)](https://travis-ci.org/3D-e-Chem/knime-molviewer)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.168569.svg)](https://doi.org/10.5281/zenodo.168569)
 
-This project uses [Eclipse Tycho](https://www.eclipse.org/tycho/) to perform build steps.
+This project uses a web user interface based on https://github.com/3D-e-Chem/molviewer-tsx .
 
 # Installation
 
@@ -125,3 +125,5 @@ Server sent events are used to inform the web page that:
 * view closed
 * input changed
 * hilite changed
+
+This project uses [Eclipse Tycho](https://www.eclipse.org/tycho/) to perform build steps.
diff --git a/feature/feature.xml b/feature/feature.xml
@@ -12,10 +12,9 @@
    </description>
 
    <copyright>
-      Software uses 3Dmol.js
-Nicholas Rego and David Koes
-3Dmol.js: molecular visualization with WebGL
-Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829
+      Software uses NGL
+      - AS Rose, AR Bradley, Y Valasatava, JM Duarte, A Prlić and PW Rose. Web-based molecular graphics for large complexes. ACM Proceedings of the 21st International Conference on Web3D Technology (Web3D '16): 185-186, 2016. doi:10.1145/2945292.2945324
+      - AS Rose and PW Hildebrand. NGL Viewer: a web application for molecular visualization. Nucl Acids Res (1 July 2015) 43 (W1): W576-W579 first published online April 29, 2015. doi:10.1093/nar/gkv402
    </copyright>
 
    <license url="https://www.apache.org/licenses/LICENSE-2.0.txt">

diff --git a/server/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/server/SwaggerInfo.java b/server/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/server/SwaggerInfo.java
@@ -4,7 +4,7 @@
 import io.swagger.annotations.License;
 import io.swagger.annotations.SwaggerDefinition;
 
-@SwaggerDefinition(info = @Info(description = "Datastore for 3DMol.js based molecule viewer",
+@SwaggerDefinition(info = @Info(description = "Datastore for WebGL based molecule viewer",
 		// TODO read version from pom.xml or MANIFEST.MF
 		version = "1.0.0", title = "The Molviewer API", license = @License(name = "Apache 2.0", url = "http://www.apache.org/licenses/LICENSE-2.0")), consumes = {
 				"application/json" }, produces = { "application/json", "text/event-stream" }, schemes = {

diff --git a/server/src/main/resources/index.html b/server/src/main/resources/index.html
@@ -1 +1 @@
-<!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width,initial-scale=1"><link rel="shortcut icon" href="/favicon.ico"><title>Molviewer</title><link href="/static/css/main.534a40ae.css" rel="stylesheet"></head><body><div id="root"></div><script type="text/javascript" src="/static/js/3Dmol-min.js"></script><script type="text/javascript" src="/static/js/main.c71886df.js"></script></body></html>
+<!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width,initial-scale=1"><link rel="shortcut icon" href="/favicon.ico"><title>Molviewer</title><link href="/static/css/main.3e482447.css" rel="stylesheet"></head><body><div id="root" style="height:100%"></div><script type="text/javascript" src="/static/js/ngl.js"></script><script type="text/javascript" src="/static/js/main.f5700504.js"></script></body></html>
diff --git a/...in/resources/static/css/main.534a40ae.css → ...in/resources/static/css/main.3e482447.css b/...in/resources/static/css/main.534a40ae.css → ...in/resources/static/css/main.3e482447.css
diff --git a/server/src/main/resources/static/js/3Dmol-min.js b/server/src/main/resources/static/js/3Dmol-min.js
diff --git a/server/src/main/resources/static/js/main.c71886df.js b/server/src/main/resources/static/js/main.c71886df.js
diff --git a/server/src/main/resources/static/js/main.f5700504.js b/server/src/main/resources/static/js/main.f5700504.js
diff --git a/server/src/main/resources/static/js/ngl.js b/server/src/main/resources/static/js/ngl.js
diff --git a/...center/e3dchem/knime/molviewer/ligandsandproteins/LigandsAndProteinsViewerServerTest.java b/...center/e3dchem/knime/molviewer/ligandsandproteins/LigandsAndProteinsViewerServerTest.java
@@ -74,7 +74,7 @@ public void testRest() throws ClientProtocolException, IOException, URISyntaxExc
 	public void testSwaggerYaml() throws URISyntaxException, ClientProtocolException, IOException {
 		URI uri = server.getBaseUri().resolve("/api/swagger.yaml");
 		String response = Request.Get(uri).execute().returnContent().asString();
-		assertTrue(response.contains("3DMol.js"));
+		assertTrue(response.contains("WebGL"));
 		assertTrue(response.contains("ligands"));
 		assertTrue(response.contains("hilite"));
 		assertTrue(response.contains("event-stream"));
@@ -84,7 +84,7 @@ public void testSwaggerYaml() throws URISyntaxException, ClientProtocolException
 	public void testSwaggerJson() throws URISyntaxException, ClientProtocolException, IOException {
 		URI uri = server.getBaseUri().resolve("/api/swagger.json");
 		String response = Request.Get(uri).execute().returnContent().asString();
-		assertTrue(response.contains("3DMol.js"));
+		assertTrue(response.contains("WebGL"));
 		assertTrue(response.contains("ligands"));
 		assertTrue(response.contains("hilite"));
 		assertTrue(response.contains("event-stream"));
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		<!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width,initial-scale=1"><link rel="shortcut icon" href="/favicon.ico"><title>Molviewer</title><link href="/static/css/main.534a40ae.css" rel="stylesheet"></head><body><div id="root"></div><script type="text/javascript" src="/static/js/3Dmol-min.js"></script><script type="text/javascript" src="/static/js/main.c71886df.js"></script></body></html>
		<!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width,initial-scale=1"><link rel="shortcut icon" href="/favicon.ico"><title>Molviewer</title><link href="/static/css/main.3e482447.css" rel="stylesheet"></head><body><div id="root" style="height:100%"></div><script type="text/javascript" src="/static/js/ngl.js"></script><script type="text/javascript" src="/static/js/main.f5700504.js"></script></body></html>