npm - mc-react-structure-visualizer - Versions diffs - 0.3.0 → 0.4.1 - Mend

mc-react-structure-visualizer 0.3.0 → 0.4.1

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Files changed (26) hide show

package/README.md +74 -74
package/dist/ControlBox/index.css +16 -3
package/dist/ControlBox/index.js +21 -19
package/dist/{3dmol → StructureWindow/3dmol}/Visualizer3dmol.js +35 -14
package/dist/StructureWindow/index.css +43 -0
package/dist/StructureWindow/index.js +65 -0
package/dist/index.css +1 -11
package/dist/index.js +47 -16
package/package.json +5 -3
package/public/index.html +43 -43
package/public/manifest.json +25 -25
package/public/robots.txt +3 -3
package/src/App.css +38 -38
package/src/App.js +0 -2
package/src/StructureVisualizer/ControlBox/index.css +16 -3
package/src/StructureVisualizer/ControlBox/index.js +17 -15
package/src/StructureVisualizer/{3dmol → StructureWindow/3dmol}/Visualizer3dmol.js +32 -6
package/src/StructureVisualizer/StructureWindow/index.css +43 -0
package/src/StructureVisualizer/StructureWindow/index.js +49 -0
package/src/StructureVisualizer/index.css +1 -11
package/src/StructureVisualizer/index.js +33 -11
package/src/index.css +13 -13
package/src/index.js +17 -17
package/src/reportWebVitals.js +13 -13
/package/dist/{3dmol → StructureWindow/3dmol}/Visualizer3dmol.css +0 -0
/package/src/StructureVisualizer/{3dmol → StructureWindow/3dmol}/Visualizer3dmol.css +0 -0

package/public/index.html CHANGED Viewed

@@ -1,43 +1,43 @@
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-    <meta charset="utf-8" />
-    <link rel="icon" href="%PUBLIC_URL%/favicon.ico" />
-    <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <meta name="theme-color" content="#000000" />
-    <meta
-      name="description"
-      content="Web site created using create-react-app"
-    />
-    <link rel="apple-touch-icon" href="%PUBLIC_URL%/logo192.png" />
-    <!--
-      manifest.json provides metadata used when your web app is installed on a
-      user's mobile device or desktop. See https://developers.google.com/web/fundamentals/web-app-manifest/
-    -->
-    <link rel="manifest" href="%PUBLIC_URL%/manifest.json" />
-    <!--
-      Notice the use of %PUBLIC_URL% in the tags above.
-      It will be replaced with the URL of the `public` folder during the build.
-      Only files inside the `public` folder can be referenced from the HTML.
-      Unlike "/favicon.ico" or "favicon.ico", "%PUBLIC_URL%/favicon.ico" will
-      work correctly both with client-side routing and a non-root public URL.
-      Learn how to configure a non-root public URL by running `npm run build`.
-    -->
-    <title>React App</title>
-  </head>
-  <body>
-    <noscript>You need to enable JavaScript to run this app.</noscript>
-    <div id="root"></div>
-    <!--
-      This HTML file is a template.
-      If you open it directly in the browser, you will see an empty page.
-      You can add webfonts, meta tags, or analytics to this file.
-      The build step will place the bundled scripts into the <body> tag.
-      To begin the development, run `npm start` or `yarn start`.
-      To create a production bundle, use `npm run build` or `yarn build`.
-    -->
-  </body>
-</html>
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <link rel="icon" href="%PUBLIC_URL%/favicon.ico" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <meta name="theme-color" content="#000000" />
+    <meta
+      name="description"
+      content="Web site created using create-react-app"
+    />
+    <link rel="apple-touch-icon" href="%PUBLIC_URL%/logo192.png" />
+    <!--
+      manifest.json provides metadata used when your web app is installed on a
+      user's mobile device or desktop. See https://developers.google.com/web/fundamentals/web-app-manifest/
+    -->
+    <link rel="manifest" href="%PUBLIC_URL%/manifest.json" />
+    <!--
+      Notice the use of %PUBLIC_URL% in the tags above.
+      It will be replaced with the URL of the `public` folder during the build.
+      Only files inside the `public` folder can be referenced from the HTML.
+      Unlike "/favicon.ico" or "favicon.ico", "%PUBLIC_URL%/favicon.ico" will
+      work correctly both with client-side routing and a non-root public URL.
+      Learn how to configure a non-root public URL by running `npm run build`.
+    -->
+    <title>React App</title>
+  </head>
+  <body>
+    <noscript>You need to enable JavaScript to run this app.</noscript>
+    <div id="root"></div>
+    <!--
+      This HTML file is a template.
+      If you open it directly in the browser, you will see an empty page.
+      You can add webfonts, meta tags, or analytics to this file.
+      The build step will place the bundled scripts into the <body> tag.
+      To begin the development, run `npm start` or `yarn start`.
+      To create a production bundle, use `npm run build` or `yarn build`.
+    -->
+  </body>
+</html>

package/public/manifest.json CHANGED Viewed

@@ -1,25 +1,25 @@
-{
-  "short_name": "React App",
-  "name": "Create React App Sample",
-  "icons": [
-    {
-      "src": "favicon.ico",
-      "sizes": "64x64 32x32 24x24 16x16",
-      "type": "image/x-icon"
-    },
-    {
-      "src": "logo192.png",
-      "type": "image/png",
-      "sizes": "192x192"
-    },
-    {
-      "src": "logo512.png",
-      "type": "image/png",
-      "sizes": "512x512"
-    }
-  ],
-  "start_url": ".",
-  "display": "standalone",
-  "theme_color": "#000000",
-  "background_color": "#ffffff"
-}
+{
+  "short_name": "React App",
+  "name": "Create React App Sample",
+  "icons": [
+    {
+      "src": "favicon.ico",
+      "sizes": "64x64 32x32 24x24 16x16",
+      "type": "image/x-icon"
+    },
+    {
+      "src": "logo192.png",
+      "type": "image/png",
+      "sizes": "192x192"
+    },
+    {
+      "src": "logo512.png",
+      "type": "image/png",
+      "sizes": "512x512"
+    }
+  ],
+  "start_url": ".",
+  "display": "standalone",
+  "theme_color": "#000000",
+  "background_color": "#ffffff"
+}

package/public/robots.txt CHANGED Viewed

@@ -1,3 +1,3 @@
-# https://www.robotstxt.org/robotstxt.html
-User-agent: *
-Disallow:
+# https://www.robotstxt.org/robotstxt.html
+User-agent: *
+Disallow:

package/src/App.css CHANGED Viewed

@@ -1,38 +1,38 @@
-/* .App {
-  text-align: center;
-}
-.App-logo {
-  height: 40vmin;
-  pointer-events: none;
-}
-@media (prefers-reduced-motion: no-preference) {
-  .App-logo {
-    animation: App-logo-spin infinite 20s linear;
-  }
-}
-.App-header {
-  background-color: #282c34;
-  min-height: 100vh;
-  display: flex;
-  flex-direction: column;
-  align-items: center;
-  justify-content: center;
-  font-size: calc(10px + 2vmin);
-  color: white;
-}
-.App-link {
-  color: #61dafb;
-}
-@keyframes App-logo-spin {
-  from {
-    transform: rotate(0deg);
-  }
-  to {
-    transform: rotate(360deg);
-  }
-} */
+/* .App {
+  text-align: center;
+}
+.App-logo {
+  height: 40vmin;
+  pointer-events: none;
+}
+@media (prefers-reduced-motion: no-preference) {
+  .App-logo {
+    animation: App-logo-spin infinite 20s linear;
+  }
+}
+.App-header {
+  background-color: #282c34;
+  min-height: 100vh;
+  display: flex;
+  flex-direction: column;
+  align-items: center;
+  justify-content: center;
+  font-size: calc(10px + 2vmin);
+  color: white;
+}
+.App-link {
+  color: #61dafb;
+}
+@keyframes App-logo-spin {
+  from {
+    transform: rotate(0deg);
+  }
+  to {
+    transform: rotate(360deg);
+  }
+} */

package/src/App.js CHANGED Viewed

@@ -17,8 +17,6 @@ async function fetchCif() {
   );
   const jsonAiiDACif = await responseAiiDACif.json();
-  console.log(jsonAiiDACif);
   return jsonAiiDACif.data.download.data;
 }

package/src/StructureVisualizer/ControlBox/index.css CHANGED Viewed

@@ -16,13 +16,25 @@
 }
 .supercell-input {
-  width: 40px;
+  width: 45px;
   height: 25px;
 }
+/* Always show the small arrows (needed for Chrome) */
+.supercell-input::-webkit-inner-spin-button,
+.supercell-input::-webkit-outer-spin-button {
+  opacity: 1;
+}
 .control-box-row {
-  margin: 5px 5px;
+  margin: 5px 0px;
+  padding: 0px 10px;
+  width: 100%;
   line-height: inherit;
+  /* background-color: pink; */
+  display: flex;
+  justify-content: space-between;
+  align-items: stretch;
 }
 .control-box-row label {
@@ -49,6 +61,7 @@
 }
 .control-box-row .camera-controls {
-  margin: 0px 30px;
+  margin-left: auto;
+  margin-right: auto;
   display: inline;
 }

package/src/StructureVisualizer/ControlBox/index.js CHANGED Viewed

@@ -25,18 +25,21 @@ class ControlBox extends React.Component {
     return (
       <div className="control-box">
         <div className="control-box-row">
-          <label>Supercell: </label>
-          {[0, 1, 2].map((index) => (
-            <input
-              key={index}
-              className="supercell-input"
-              type="number"
-              value={this.props.viewerParams.supercell[index]}
-              onChange={(e) =>
-                this.handleSupercellChange(index, e.target.value)
-              }
-            />
-          ))}
+          <div className="supercell-container">
+            <label>Supercell: </label>
+            {[0, 1, 2].map((index) => (
+              <input
+                key={index}
+                className="supercell-input"
+                type="number"
+                min="1"
+                value={this.props.viewerParams.supercell[index]}
+                onChange={(e) =>
+                  this.handleSupercellChange(index, e.target.value)
+                }
+              />
+            ))}
+          </div>
           <div className="camera-controls">
             <label>Camera: </label>
             <button onClick={() => this.handleCameraEvent("x")}>x</button>
@@ -60,9 +63,8 @@ class ControlBox extends React.Component {
               type="checkbox"
               checked={this.props.viewerParams.atomLabels}
               onChange={() => this.handleOptionChange("atomLabels")}
-              disabled={true}
             />
-            Atom Labels
+            Atom labels
           </label>
           <label>
             <input
@@ -72,7 +74,7 @@ class ControlBox extends React.Component {
               onChange={() => this.handleOptionChange("packedCell")}
               disabled={true}
             />
-            Packed Cell
+            Packed cell
           </label>
           <label>
             <input

package/src/StructureVisualizer/{3dmol → StructureWindow/3dmol}/Visualizer3dmol.js RENAMED Viewed

@@ -3,6 +3,7 @@ import React from "react";
 import * as $3Dmol from "3dmol";
 import "./Visualizer3dmol.css";
+import { isLabelWithInternallyDisabledControl } from "@testing-library/user-event/dist/utils";
 class Visualizer3dmol extends React.Component {
   constructor(props) {
@@ -17,12 +18,21 @@ class Visualizer3dmol extends React.Component {
   componentDidMount() {
     // set up the viewer instance
-    let config = { backgroundColor: "mintcream", orthographic: true };
+    let config = { backgroundColor: "white", orthographic: true };
     this.viewer = $3Dmol.createViewer(this.divId, config);
     this.updateView();
   }
+  componentDidUpdate(prevProps) {
+    if (
+      prevProps.viewerParams != this.props.viewerParams ||
+      prevProps.cifText != this.props.cifText
+    ) {
+      this.updateView();
+    }
+  }
   updateView() {
     this.viewer.removeAllModels();
     this.model = this.viewer.addModel(this.props.cifText, "cif");
@@ -42,12 +52,30 @@ class Visualizer3dmol extends React.Component {
     this.viewer.addUnitCell(this.model);
     let sc = this.props.viewerParams.supercell;
     this.viewer.replicateUnitCell(sc[0], sc[1], sc[2], this.model);
     this.model.assignBonds();
-    // console.log(this.viewer.getView());
-    // this.viewer.setView([0.0, 0.0, 0.0, 0.0, 0.5, 0.5, 0.5, 0.5]);
+    this.viewer.removeAllLabels();
+    if (this.props.viewerParams.atomLabels) {
+      this.model.atoms.forEach((atom) => {
+        this.viewer.addLabel(
+          atom.elem,
+          {
+            position: { x: atom.x, y: atom.y, z: atom.z },
+            fontColor: atom.color,
+            fontSize: 18,
+            showBackground: false,
+            backgroundOpacity: 0.5,
+            inFront: false,
+          },
+          null,
+          true
+        );
+      });
+    }
     this.viewer.zoomTo();
+    this.viewer.zoom(1.4);
     this.viewer.render();
   }
@@ -64,13 +92,11 @@ class Visualizer3dmol extends React.Component {
         this.viewer.setView([0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0]);
       }
       this.viewer.zoomTo();
+      this.viewer.zoom(1.4);
     }
   }
   render() {
-    if (this.viewer && this.model) {
-      this.updateView();
-    }
     return (
       <div id={this.divId} className="gldiv">
         No data!

package/src/StructureVisualizer/StructureWindow/index.css ADDED Viewed

@@ -0,0 +1,43 @@
+.structure-window-outer {
+  position: relative;
+}
+.structure-window {
+  position: relative;
+  z-index: 2;
+  height: 370px;
+  width: 450px;
+  background: white;
+  text-align: center;
+  border: 1px solid #999;
+  display: flex;
+  justify-content: center;
+  align-items: center;
+  border-radius: 5px;
+}
+.disable-mouse {
+  pointer-events: none;
+}
+.mouse-disabled-note {
+  background-color: #fff1f1;
+  border: 1px solid black;
+  color: #353434;
+  padding: 2px 6px;
+  border-radius: 5px;
+  position: absolute;
+  top: 10px;
+  left: 10px;
+  z-index: 3;
+  cursor: pointer;
+  user-select: none;
+}
+.on {
+  background-color: #e9ffe7;
+}
+.mouse-disabled-note:hover {
+  filter: brightness(90%);
+}

package/src/StructureVisualizer/StructureWindow/index.js ADDED Viewed

@@ -0,0 +1,49 @@
+import React from "react";
+import Visualizer3dmol from "./3dmol/Visualizer3dmol";
+import "./index.css";
+class StructureWindow extends React.Component {
+  constructor(props) {
+    super(props);
+  }
+  render() {
+    let swClassName = "structure-window";
+    if (!this.props.mouseEnabled) swClassName += " disable-mouse";
+    let mouseNoteText = "Interaction off";
+    let mouseNoteClass = "mouse-disabled-note";
+    if (this.props.mouseEnabled) {
+      mouseNoteText = "Interaction on";
+      mouseNoteClass = "mouse-disabled-note on";
+    }
+    return (
+      <div>
+        <div
+          className="structure-window-outer"
+          onClick={() => this.props.setMouseEnabledState(true)}
+        >
+          <div className={swClassName}>
+            <Visualizer3dmol
+              ref={this.props.visualizerRef}
+              viewerParams={this.props.viewerParams}
+              cifText={this.props.cifText}
+            />
+          </div>
+        </div>
+        <div
+          className={mouseNoteClass}
+          onClick={() =>
+            this.props.setMouseEnabledState(!this.props.mouseEnabled)
+          }
+        >
+          {mouseNoteText}
+        </div>
+      </div>
+    );
+  }
+}
+export default StructureWindow;

package/src/StructureVisualizer/index.css CHANGED Viewed

@@ -1,13 +1,3 @@
-.structure-window {
-  position: relative;
-  z-index: 2;
-  height: 370px;
+.structure-visualizer {
   width: 450px;
-  background: #f5fffa;
-  text-align: center;
-  border: 1px solid #999;
-  display: flex;
-  justify-content: center;
-  align-items: center;
-  border-radius: 5px;
 }

package/src/StructureVisualizer/index.js CHANGED Viewed

@@ -2,7 +2,7 @@ import React from "react";
 import ControlBox from "./ControlBox";
-import Visualizer3dmol from "./3dmol/Visualizer3dmol";
+import StructureWindow from "./StructureWindow";
 import "./index.css";
@@ -13,19 +13,42 @@ class StructureVisualizer extends React.Component {
     this.state = {
       viewerParams: {
         supercell: [2, 2, 2],
-        orientation: "x",
         bonds: true,
         atomLabels: false,
         packedCell: false,
         vdwRadius: false,
       },
+      mouseEnabled: false,
     };
     // use Ref to send events to the visualizer backend
     this.visualizerRef = React.createRef();
+    // Ref to detect click outside
+    this.wrapperRef = React.createRef();
+    this.handleClickOutside = this.handleClickOutside.bind(this);
     this.handleViewerParamChange = this.handleViewerParamChange.bind(this);
     this.handleViewerEvent = this.handleViewerEvent.bind(this);
+    this.setMouseEnabledState = this.setMouseEnabledState.bind(this);
+  }
+  componentDidMount() {
+    document.addEventListener("mousedown", this.handleClickOutside);
+  }
+  componentWillUnmount() {
+    document.removeEventListener("mousedown", this.handleClickOutside);
+  }
+  handleClickOutside(event) {
+    if (this.wrapperRef && !this.wrapperRef.current.contains(event.target)) {
+      this.setState({ mouseEnabled: false });
+    }
+  }
+  setMouseEnabledState(state) {
+    this.setState({ mouseEnabled: state });
   }
   handleViewerParamChange(param, value) {
@@ -42,16 +65,15 @@ class StructureVisualizer extends React.Component {
   }
   render() {
-    // console.log("CIF", this.props.cifText);
     return (
-      <div className="structure-visualizer">
-        <div className="structure-window">
-          <Visualizer3dmol
-            ref={this.visualizerRef}
-            viewerParams={this.state.viewerParams}
-            cifText={this.props.cifText}
-          />
-        </div>
+      <div ref={this.wrapperRef} className="structure-visualizer">
+        <StructureWindow
+          visualizerRef={this.visualizerRef}
+          viewerParams={this.state.viewerParams}
+          cifText={this.props.cifText}
+          mouseEnabled={this.state.mouseEnabled}
+          setMouseEnabledState={this.setMouseEnabledState}
+        />
         <ControlBox
           viewerParams={this.state.viewerParams}
           onViewerParamChange={this.handleViewerParamChange}

package/src/index.css CHANGED Viewed

@@ -1,13 +1,13 @@
-body {
-  margin: 0;
-  font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', 'Roboto', 'Oxygen',
-    'Ubuntu', 'Cantarell', 'Fira Sans', 'Droid Sans', 'Helvetica Neue',
-    sans-serif;
-  -webkit-font-smoothing: antialiased;
-  -moz-osx-font-smoothing: grayscale;
-}
-code {
-  font-family: source-code-pro, Menlo, Monaco, Consolas, 'Courier New',
-    monospace;
-}
+body {
+  margin: 0;
+  font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', 'Roboto', 'Oxygen',
+    'Ubuntu', 'Cantarell', 'Fira Sans', 'Droid Sans', 'Helvetica Neue',
+    sans-serif;
+  -webkit-font-smoothing: antialiased;
+  -moz-osx-font-smoothing: grayscale;
+}
+code {
+  font-family: source-code-pro, Menlo, Monaco, Consolas, 'Courier New',
+    monospace;
+}

package/src/index.js CHANGED Viewed

@@ -1,17 +1,17 @@
-import React from 'react';
-import ReactDOM from 'react-dom/client';
-import './index.css';
-import App from './App';
-import reportWebVitals from './reportWebVitals';
-const root = ReactDOM.createRoot(document.getElementById('root'));
-root.render(
-  <React.StrictMode>
-    <App />
-  </React.StrictMode>
-);
-// If you want to start measuring performance in your app, pass a function
-// to log results (for example: reportWebVitals(console.log))
-// or send to an analytics endpoint. Learn more: https://bit.ly/CRA-vitals
-reportWebVitals();
+import React from 'react';
+import ReactDOM from 'react-dom/client';
+import './index.css';
+import App from './App';
+import reportWebVitals from './reportWebVitals';
+const root = ReactDOM.createRoot(document.getElementById('root'));
+root.render(
+  <React.StrictMode>
+    <App />
+  </React.StrictMode>
+);
+// If you want to start measuring performance in your app, pass a function
+// to log results (for example: reportWebVitals(console.log))
+// or send to an analytics endpoint. Learn more: https://bit.ly/CRA-vitals
+reportWebVitals();