mc-react-structure-visualizer 0.4.0 → 0.4.1

package/README.md

@@ -1,74 +1,74 @@
-# React Materials Cloud Structure Visualizer
-
-A React component to visualize structures on the Materials Cloud platform.
-
-# Getting Started with Create React App
-
-This project was bootstrapped with [Create React App](https://github.com/facebook/create-react-app).
-
-## Available Scripts
-
-In the project directory, you can run:
-
-### `npm start`
-
-Runs the app in the development mode.\
-Open [http://localhost:3000](http://localhost:3000) to view it in your browser.
-
-The page will reload when you make changes.\
-You may also see any lint errors in the console.
-
-### `npm test`
-
-Launches the test runner in the interactive watch mode.\
-See the section about [running tests](https://facebook.github.io/create-react-app/docs/running-tests) for more information.
-
-### `npm run build`
-
-Builds the app for production to the `build` folder.\
-It correctly bundles React in production mode and optimizes the build for the best performance.
-
-The build is minified and the filenames include the hashes.\
-Your app is ready to be deployed!
-
-See the section about [deployment](https://facebook.github.io/create-react-app/docs/deployment) for more information.
-
-### `npm run eject`
-
-**Note: this is a one-way operation. Once you `eject`, you can't go back!**
-
-If you aren't satisfied with the build tool and configuration choices, you can `eject` at any time. This command will remove the single build dependency from your project.
-
-Instead, it will copy all the configuration files and the transitive dependencies (webpack, Babel, ESLint, etc) right into your project so you have full control over them. All of the commands except `eject` will still work, but they will point to the copied scripts so you can tweak them. At this point you're on your own.
-
-You don't have to ever use `eject`. The curated feature set is suitable for small and middle deployments, and you shouldn't feel obligated to use this feature. However we understand that this tool wouldn't be useful if you couldn't customize it when you are ready for it.
-
-## Learn More
-
-You can learn more in the [Create React App documentation](https://facebook.github.io/create-react-app/docs/getting-started).
-
-To learn React, check out the [React documentation](https://reactjs.org/).
-
-### Code Splitting
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/code-splitting](https://facebook.github.io/create-react-app/docs/code-splitting)
-
-### Analyzing the Bundle Size
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size](https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size)
-
-### Making a Progressive Web App
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app](https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app)
-
-### Advanced Configuration
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/advanced-configuration](https://facebook.github.io/create-react-app/docs/advanced-configuration)
-
-### Deployment
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/deployment](https://facebook.github.io/create-react-app/docs/deployment)
-
-### `npm run build` fails to minify
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify](https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify)
+# React Materials Cloud Structure Visualizer
+
+A React component to visualize structures on the Materials Cloud platform.
+
+# Getting Started with Create React App
+
+This project was bootstrapped with [Create React App](https://github.com/facebook/create-react-app).
+
+## Available Scripts
+
+In the project directory, you can run:
+
+### `npm start`
+
+Runs the app in the development mode.\
+Open [http://localhost:3000](http://localhost:3000) to view it in your browser.
+
+The page will reload when you make changes.\
+You may also see any lint errors in the console.
+
+### `npm test`
+
+Launches the test runner in the interactive watch mode.\
+See the section about [running tests](https://facebook.github.io/create-react-app/docs/running-tests) for more information.
+
+### `npm run build`
+
+Builds the app for production to the `build` folder.\
+It correctly bundles React in production mode and optimizes the build for the best performance.
+
+The build is minified and the filenames include the hashes.\
+Your app is ready to be deployed!
+
+See the section about [deployment](https://facebook.github.io/create-react-app/docs/deployment) for more information.
+
+### `npm run eject`
+
+**Note: this is a one-way operation. Once you `eject`, you can't go back!**
+
+If you aren't satisfied with the build tool and configuration choices, you can `eject` at any time. This command will remove the single build dependency from your project.
+
+Instead, it will copy all the configuration files and the transitive dependencies (webpack, Babel, ESLint, etc) right into your project so you have full control over them. All of the commands except `eject` will still work, but they will point to the copied scripts so you can tweak them. At this point you're on your own.
+
+You don't have to ever use `eject`. The curated feature set is suitable for small and middle deployments, and you shouldn't feel obligated to use this feature. However we understand that this tool wouldn't be useful if you couldn't customize it when you are ready for it.
+
+## Learn More
+
+You can learn more in the [Create React App documentation](https://facebook.github.io/create-react-app/docs/getting-started).
+
+To learn React, check out the [React documentation](https://reactjs.org/).
+
+### Code Splitting
+
+This section has moved here: [https://facebook.github.io/create-react-app/docs/code-splitting](https://facebook.github.io/create-react-app/docs/code-splitting)
+
+### Analyzing the Bundle Size
+
+This section has moved here: [https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size](https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size)
+
+### Making a Progressive Web App
+
+This section has moved here: [https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app](https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app)
+
+### Advanced Configuration
+
+This section has moved here: [https://facebook.github.io/create-react-app/docs/advanced-configuration](https://facebook.github.io/create-react-app/docs/advanced-configuration)
+
+### Deployment
+
+This section has moved here: [https://facebook.github.io/create-react-app/docs/deployment](https://facebook.github.io/create-react-app/docs/deployment)
+
+### `npm run build` fails to minify
+
+This section has moved here: [https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify](https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify)

package/dist/ControlBox/index.css

@@ -27,8 +27,14 @@
 }
 
 .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 {
@@ -55,6 +61,7 @@
 }
 
 .control-box-row .camera-controls {
-  margin: 0px 30px;
+  margin-left: auto;
+  margin-right: auto;
   display: inline;
 }

package/dist/ControlBox/index.js

@@ -3,10 +3,10 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.default = void 0;
+exports["default"] = void 0;
 var _react = _interopRequireDefault(require("react"));
 require("./index.css");
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
+function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { "default": obj }; }
 function _typeof(obj) { "@babel/helpers - typeof"; return _typeof = "function" == typeof Symbol && "symbol" == typeof Symbol.iterator ? function (obj) { return typeof obj; } : function (obj) { return obj && "function" == typeof Symbol && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }, _typeof(obj); }
 function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
 function _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, _toPropertyKey(descriptor.key), descriptor); } }
@@ -45,12 +45,14 @@ var ControlBox = /*#__PURE__*/function (_React$Component) {
     key: "render",
     value: function render() {
       var _this2 = this;
-      return /*#__PURE__*/_react.default.createElement("div", {
+      return /*#__PURE__*/_react["default"].createElement("div", {
         className: "control-box"
-      }, /*#__PURE__*/_react.default.createElement("div", {
+      }, /*#__PURE__*/_react["default"].createElement("div", {
         className: "control-box-row"
-      }, /*#__PURE__*/_react.default.createElement("label", null, "Supercell: "), [0, 1, 2].map(function (index) {
-        return /*#__PURE__*/_react.default.createElement("input", {
+      }, /*#__PURE__*/_react["default"].createElement("div", {
+        className: "supercell-container"
+      }, /*#__PURE__*/_react["default"].createElement("label", null, "Supercell: "), [0, 1, 2].map(function (index) {
+        return /*#__PURE__*/_react["default"].createElement("input", {
           key: index,
           className: "supercell-input",
           type: "number",
@@ -60,38 +62,37 @@ var ControlBox = /*#__PURE__*/function (_React$Component) {
             return _this2.handleSupercellChange(index, e.target.value);
           }
         });
-      }), /*#__PURE__*/_react.default.createElement("div", {
+      })), /*#__PURE__*/_react["default"].createElement("div", {
         className: "camera-controls"
-      }, /*#__PURE__*/_react.default.createElement("label", null, "Camera: "), /*#__PURE__*/_react.default.createElement("button", {
+      }, /*#__PURE__*/_react["default"].createElement("label", null, "Camera: "), /*#__PURE__*/_react["default"].createElement("button", {
         onClick: function onClick() {
           return _this2.handleCameraEvent("x");
         }
-      }, "x"), /*#__PURE__*/_react.default.createElement("button", {
+      }, "x"), /*#__PURE__*/_react["default"].createElement("button", {
         onClick: function onClick() {
           return _this2.handleCameraEvent("y");
         }
-      }, "y"), /*#__PURE__*/_react.default.createElement("button", {
+      }, "y"), /*#__PURE__*/_react["default"].createElement("button", {
         onClick: function onClick() {
           return _this2.handleCameraEvent("z");
         }
-      }, "z"))), /*#__PURE__*/_react.default.createElement("div", {
+      }, "z"))), /*#__PURE__*/_react["default"].createElement("div", {
         className: "control-box-row"
-      }, /*#__PURE__*/_react.default.createElement("label", null, /*#__PURE__*/_react.default.createElement("input", {
+      }, /*#__PURE__*/_react["default"].createElement("label", null, /*#__PURE__*/_react["default"].createElement("input", {
         className: "option-checkbox",
         type: "checkbox",
         checked: this.props.viewerParams.bonds,
         onChange: function onChange() {
           return _this2.handleOptionChange("bonds");
         }
-      }), "Bonds"), /*#__PURE__*/_react.default.createElement("label", null, /*#__PURE__*/_react.default.createElement("input", {
+      }), "Bonds"), /*#__PURE__*/_react["default"].createElement("label", null, /*#__PURE__*/_react["default"].createElement("input", {
         className: "option-checkbox",
         type: "checkbox",
         checked: this.props.viewerParams.atomLabels,
         onChange: function onChange() {
           return _this2.handleOptionChange("atomLabels");
-        },
-        disabled: true
-      }), "Atom Labels"), /*#__PURE__*/_react.default.createElement("label", null, /*#__PURE__*/_react.default.createElement("input", {
+        }
+      }), "Atom labels"), /*#__PURE__*/_react["default"].createElement("label", null, /*#__PURE__*/_react["default"].createElement("input", {
         className: "option-checkbox",
         type: "checkbox",
         checked: this.props.viewerParams.packedCell,
@@ -99,7 +100,7 @@ var ControlBox = /*#__PURE__*/function (_React$Component) {
           return _this2.handleOptionChange("packedCell");
         },
         disabled: true
-      }), "Packed Cell"), /*#__PURE__*/_react.default.createElement("label", null, /*#__PURE__*/_react.default.createElement("input", {
+      }), "Packed cell"), /*#__PURE__*/_react["default"].createElement("label", null, /*#__PURE__*/_react["default"].createElement("input", {
         className: "option-checkbox",
         type: "checkbox",
         checked: this.props.viewerParams.spaceFilling,
@@ -110,6 +111,6 @@ var ControlBox = /*#__PURE__*/function (_React$Component) {
     }
   }]);
   return ControlBox;
-}(_react.default.Component);
+}(_react["default"].Component);
 var _default = ControlBox;
-exports.default = _default;
+exports["default"] = _default;

package/dist/StructureWindow/3dmol/Visualizer3dmol.js

@@ -4,13 +4,14 @@ function _typeof(obj) { "@babel/helpers - typeof"; return _typeof = "function" =
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.default = void 0;
+exports["default"] = void 0;
 var _react = _interopRequireDefault(require("react"));
 var $3Dmol = _interopRequireWildcard(require("3dmol"));
 require("./Visualizer3dmol.css");
+var _utils = require("@testing-library/user-event/dist/utils");
 function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { "default": obj }; }
 function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
 function _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, _toPropertyKey(descriptor.key), descriptor); } }
 function _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); Object.defineProperty(Constructor, "prototype", { writable: false }); return Constructor; }
@@ -42,7 +43,7 @@ var Visualizer3dmol = /*#__PURE__*/function (_React$Component) {
     value: function componentDidMount() {
       // set up the viewer instance
       var config = {
-        backgroundColor: "mintcream",
+        backgroundColor: "white",
         orthographic: true
       };
       this.viewer = $3Dmol.createViewer(this.divId, config);
@@ -58,6 +59,7 @@ var Visualizer3dmol = /*#__PURE__*/function (_React$Component) {
   }, {
     key: "updateView",
     value: function updateView() {
+      var _this2 = this;
       this.viewer.removeAllModels();
       this.model = this.viewer.addModel(this.props.cifText, "cif");
       var style = {
@@ -80,7 +82,25 @@ var Visualizer3dmol = /*#__PURE__*/function (_React$Component) {
       var sc = this.props.viewerParams.supercell;
       this.viewer.replicateUnitCell(sc[0], sc[1], sc[2], this.model);
       this.model.assignBonds();
+      this.viewer.removeAllLabels();
+      if (this.props.viewerParams.atomLabels) {
+        this.model.atoms.forEach(function (atom) {
+          _this2.viewer.addLabel(atom.elem, {
+            position: {
+              x: atom.x,
+              y: atom.y,
+              z: atom.z
+            },
+            fontColor: atom.color,
+            fontSize: 18,
+            showBackground: false,
+            backgroundOpacity: 0.5,
+            inFront: false
+          }, null, true);
+        });
+      }
       this.viewer.zoomTo();
+      this.viewer.zoom(1.4);
       this.viewer.render();
     }
   }, {
@@ -98,18 +118,19 @@ var Visualizer3dmol = /*#__PURE__*/function (_React$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);
       }
     }
   }, {
     key: "render",
     value: function render() {
-      return /*#__PURE__*/_react.default.createElement("div", {
+      return /*#__PURE__*/_react["default"].createElement("div", {
         id: this.divId,
         className: "gldiv"
       }, "No data!");
     }
   }]);
   return Visualizer3dmol;
-}(_react.default.Component);
+}(_react["default"].Component);
 var _default = Visualizer3dmol;
-exports.default = _default;
+exports["default"] = _default;

package/dist/StructureWindow/index.css

@@ -7,7 +7,7 @@
   z-index: 2;
   height: 370px;
   width: 450px;
-  background: #f5fffa;
+  background: white;
   text-align: center;
   border: 1px solid #999;
   display: flex;
@@ -21,13 +21,23 @@
 }
 
 .mouse-disabled-note {
-  background-color: #fafafa;
+  background-color: #fff1f1;
   border: 1px solid black;
   color: #353434;
-  padding: 5px;
+  padding: 2px 6px;
   border-radius: 5px;
   position: absolute;
-  top: 15px;
-  left: 170px;
+  top: 10px;
+  left: 10px;
   z-index: 3;
+  cursor: pointer;
+  user-select: none;
+}
+
+.on {
+  background-color: #e9ffe7;
+}
+
+.mouse-disabled-note:hover {
+  filter: brightness(90%);
 }

package/dist/StructureWindow/index.js

@@ -4,11 +4,11 @@ function _typeof(obj) { "@babel/helpers - typeof"; return _typeof = "function" =
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.default = void 0;
+exports["default"] = void 0;
 var _react = _interopRequireDefault(require("react"));
 var _Visualizer3dmol = _interopRequireDefault(require("./3dmol/Visualizer3dmol"));
 require("./index.css");
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
+function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { "default": obj }; }
 function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
 function _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, _toPropertyKey(descriptor.key), descriptor); } }
 function _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); Object.defineProperty(Constructor, "prototype", { writable: false }); return Constructor; }
@@ -34,23 +34,32 @@ var StructureWindow = /*#__PURE__*/function (_React$Component) {
       var _this = this;
       var swClassName = "structure-window";
       if (!this.props.mouseEnabled) swClassName += " disable-mouse";
-      return /*#__PURE__*/_react.default.createElement("div", {
+      var mouseNoteText = "Interaction off";
+      var mouseNoteClass = "mouse-disabled-note";
+      if (this.props.mouseEnabled) {
+        mouseNoteText = "Interaction on";
+        mouseNoteClass = "mouse-disabled-note on";
+      }
+      return /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement("div", {
         className: "structure-window-outer",
         onClick: function onClick() {
-          return _this.props.setMouseEnabled();
+          return _this.props.setMouseEnabledState(true);
         }
-      }, /*#__PURE__*/_react.default.createElement("div", {
+      }, /*#__PURE__*/_react["default"].createElement("div", {
         className: swClassName
-      }, /*#__PURE__*/_react.default.createElement(_Visualizer3dmol.default, {
+      }, /*#__PURE__*/_react["default"].createElement(_Visualizer3dmol["default"], {
         ref: this.props.visualizerRef,
         viewerParams: this.props.viewerParams,
         cifText: this.props.cifText
-      })), !this.props.mouseEnabled && /*#__PURE__*/_react.default.createElement("div", {
-        className: "mouse-disabled-note"
-      }, "Click to interact!"));
+      }))), /*#__PURE__*/_react["default"].createElement("div", {
+        className: mouseNoteClass,
+        onClick: function onClick() {
+          return _this.props.setMouseEnabledState(!_this.props.mouseEnabled);
+        }
+      }, mouseNoteText));
     }
   }]);
   return StructureWindow;
-}(_react.default.Component);
+}(_react["default"].Component);
 var _default = StructureWindow;
-exports.default = _default;
+exports["default"] = _default;

package/dist/index.js

@@ -4,12 +4,12 @@ function _typeof(obj) { "@babel/helpers - typeof"; return _typeof = "function" =
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.default = void 0;
+exports["default"] = void 0;
 var _react = _interopRequireDefault(require("react"));
 var _ControlBox = _interopRequireDefault(require("./ControlBox"));
 var _StructureWindow = _interopRequireDefault(require("./StructureWindow"));
 require("./index.css");
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
+function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { "default": obj }; }
 function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
 function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { _defineProperty(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
 function _defineProperty(obj, key, value) { key = _toPropertyKey(key); if (key in obj) { Object.defineProperty(obj, key, { value: value, enumerable: true, configurable: true, writable: true }); } else { obj[key] = value; } return obj; }
@@ -44,14 +44,14 @@ var StructureVisualizer = /*#__PURE__*/function (_React$Component) {
     };
 
     // use Ref to send events to the visualizer backend
-    _this.visualizerRef = /*#__PURE__*/_react.default.createRef();
+    _this.visualizerRef = /*#__PURE__*/_react["default"].createRef();
 
     // Ref to detect click outside
-    _this.wrapperRef = /*#__PURE__*/_react.default.createRef();
+    _this.wrapperRef = /*#__PURE__*/_react["default"].createRef();
     _this.handleClickOutside = _this.handleClickOutside.bind(_assertThisInitialized(_this));
     _this.handleViewerParamChange = _this.handleViewerParamChange.bind(_assertThisInitialized(_this));
     _this.handleViewerEvent = _this.handleViewerEvent.bind(_assertThisInitialized(_this));
-    _this.setMouseEnabled = _this.setMouseEnabled.bind(_assertThisInitialized(_this));
+    _this.setMouseEnabledState = _this.setMouseEnabledState.bind(_assertThisInitialized(_this));
     return _this;
   }
   _createClass(StructureVisualizer, [{
@@ -74,10 +74,10 @@ var StructureVisualizer = /*#__PURE__*/function (_React$Component) {
       }
     }
   }, {
-    key: "setMouseEnabled",
-    value: function setMouseEnabled() {
+    key: "setMouseEnabledState",
+    value: function setMouseEnabledState(state) {
       this.setState({
-        mouseEnabled: true
+        mouseEnabled: state
       });
     }
   }, {
@@ -95,16 +95,16 @@ var StructureVisualizer = /*#__PURE__*/function (_React$Component) {
   }, {
     key: "render",
     value: function render() {
-      return /*#__PURE__*/_react.default.createElement("div", {
+      return /*#__PURE__*/_react["default"].createElement("div", {
         ref: this.wrapperRef,
         className: "structure-visualizer"
-      }, /*#__PURE__*/_react.default.createElement(_StructureWindow.default, {
+      }, /*#__PURE__*/_react["default"].createElement(_StructureWindow["default"], {
         visualizerRef: this.visualizerRef,
         viewerParams: this.state.viewerParams,
         cifText: this.props.cifText,
         mouseEnabled: this.state.mouseEnabled,
-        setMouseEnabled: this.setMouseEnabled
-      }), /*#__PURE__*/_react.default.createElement(_ControlBox.default, {
+        setMouseEnabledState: this.setMouseEnabledState
+      }), /*#__PURE__*/_react["default"].createElement(_ControlBox["default"], {
         viewerParams: this.state.viewerParams,
         onViewerParamChange: this.handleViewerParamChange,
         onViewerEvent: this.handleViewerEvent
@@ -112,6 +112,6 @@ var StructureVisualizer = /*#__PURE__*/function (_React$Component) {
     }
   }]);
   return StructureVisualizer;
-}(_react.default.Component);
+}(_react["default"].Component);
 var _default = StructureVisualizer;
-exports.default = _default;
+exports["default"] = _default;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "mc-react-structure-visualizer",
-  "version": "0.4.0",
+  "version": "0.4.1",
   "author": "Kristjan Eimre <kristjan.eimre@epfl.ch>",
   "main": "dist/index.js",
   "module": "dist/index.js",
@@ -24,7 +24,8 @@
   },
   "scripts": {
     "start": "react-scripts start",
-    "build": "SET NODE_ENV=production && rm -rf dist && npx babel src/StructureVisualizer --out-dir dist --copy-files",
+    "prebuild": "rimraf dist",
+    "build": "SET NODE_ENV=production && npx babel src/StructureVisualizer --out-dir dist --copy-files",
     "test": "react-scripts test",
     "eject": "react-scripts eject"
   },
@@ -51,6 +52,7 @@
     "@babel/core": "^7.20.12",
     "@babel/preset-env": "^7.20.2",
     "@babel/preset-react": "^7.18.6",
-    "babel-loader": "^9.1.2"
+    "babel-loader": "^9.1.2",
+    "rimraf": "^4.1.2"
   }
 }

package/public/index.html

@@ -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

@@ -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

@@ -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

@@ -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/StructureVisualizer/ControlBox/index.css

@@ -27,8 +27,14 @@
 }
 
 .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 {
@@ -55,6 +61,7 @@
 }
 
 .control-box-row .camera-controls {
-  margin: 0px 30px;
+  margin-left: auto;
+  margin-right: auto;
   display: inline;
 }

package/src/StructureVisualizer/ControlBox/index.js

@@ -25,19 +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"
-              min="1"
-              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>
@@ -61,9 +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
@@ -73,7 +74,7 @@ class ControlBox extends React.Component {
               onChange={() => this.handleOptionChange("packedCell")}
               disabled={true}
             />
-            Packed Cell
+            Packed cell
           </label>
           <label>
             <input

package/src/StructureVisualizer/StructureWindow/3dmol/Visualizer3dmol.js

@@ -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) {
@@ -17,7 +18,7 @@ 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();
@@ -51,9 +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();
 
+    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();
   }
 
@@ -70,6 +92,7 @@ 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);
     }
   }
 

package/src/StructureVisualizer/StructureWindow/index.css

@@ -7,7 +7,7 @@
   z-index: 2;
   height: 370px;
   width: 450px;
-  background: #f5fffa;
+  background: white;
   text-align: center;
   border: 1px solid #999;
   display: flex;
@@ -21,13 +21,23 @@
 }
 
 .mouse-disabled-note {
-  background-color: #fafafa;
+  background-color: #fff1f1;
   border: 1px solid black;
   color: #353434;
-  padding: 5px;
+  padding: 2px 6px;
   border-radius: 5px;
   position: absolute;
-  top: 15px;
-  left: 170px;
+  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

@@ -12,21 +12,35 @@ class StructureWindow extends React.Component {
   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
-        className="structure-window-outer"
-        onClick={() => this.props.setMouseEnabled()}
-      >
-        <div className={swClassName}>
-          <Visualizer3dmol
-            ref={this.props.visualizerRef}
-            viewerParams={this.props.viewerParams}
-            cifText={this.props.cifText}
-          />
+      <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>
-        {!this.props.mouseEnabled && (
-          <div className="mouse-disabled-note">Click to interact!</div>
-        )}
       </div>
     );
   }

package/src/StructureVisualizer/index.js

@@ -30,7 +30,7 @@ class StructureVisualizer extends React.Component {
 
     this.handleViewerParamChange = this.handleViewerParamChange.bind(this);
     this.handleViewerEvent = this.handleViewerEvent.bind(this);
-    this.setMouseEnabled = this.setMouseEnabled.bind(this);
+    this.setMouseEnabledState = this.setMouseEnabledState.bind(this);
   }
 
   componentDidMount() {
@@ -47,8 +47,8 @@ class StructureVisualizer extends React.Component {
     }
   }
 
-  setMouseEnabled() {
-    this.setState({ mouseEnabled: true });
+  setMouseEnabledState(state) {
+    this.setState({ mouseEnabled: state });
   }
 
   handleViewerParamChange(param, value) {
@@ -72,7 +72,7 @@ class StructureVisualizer extends React.Component {
           viewerParams={this.state.viewerParams}
           cifText={this.props.cifText}
           mouseEnabled={this.state.mouseEnabled}
-          setMouseEnabled={this.setMouseEnabled}
+          setMouseEnabledState={this.setMouseEnabledState}
         />
         <ControlBox
           viewerParams={this.state.viewerParams}

package/src/index.css

@@ -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

@@ -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();

package/src/reportWebVitals.js

@@ -1,13 +1,13 @@
-const reportWebVitals = onPerfEntry => {
-  if (onPerfEntry && onPerfEntry instanceof Function) {
-    import('web-vitals').then(({ getCLS, getFID, getFCP, getLCP, getTTFB }) => {
-      getCLS(onPerfEntry);
-      getFID(onPerfEntry);
-      getFCP(onPerfEntry);
-      getLCP(onPerfEntry);
-      getTTFB(onPerfEntry);
-    });
-  }
-};
-
-export default reportWebVitals;
+const reportWebVitals = onPerfEntry => {
+  if (onPerfEntry && onPerfEntry instanceof Function) {
+    import('web-vitals').then(({ getCLS, getFID, getFCP, getLCP, getTTFB }) => {
+      getCLS(onPerfEntry);
+      getFID(onPerfEntry);
+      getFCP(onPerfEntry);
+      getLCP(onPerfEntry);
+      getTTFB(onPerfEntry);
+    });
+  }
+};
+
+export default reportWebVitals;