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Jiang","email":"partridge@cpu.edu.cn"},"keywords":["chemistry","cheminformatics","chemoinformatics","molecule"],"description":"Open source JavaScript toolkit for chemoinformatics","contributors":[{"name":"Aaron Llanos","email":"aaronllanos93@gmail.com"},{"name":"Joshua Williams"}],"maintainers":[{"name":"partridge","email":"partridge@cpu.edu.cn"}],"readme":"# Kekule.js\r\n\r\nKekule.js is an open source JavaScript toolkit for chemoinformatics released under MIT license. \r\nIt can be used in both web applications and node applications to read, write, display and edit chemical objects (e.g. molecules) \r\nand to perform some chemical algorithms (e.g. molecule structure comparing, searching, aromatic detection).\r\n\r\nMore details about this project can be found in [Kekule.js website](http://partridgejiang.github.io/Kekule.js/). \r\n\r\n## Installation and import\r\n\r\nThe whole Kekule.js package can be installed with npm:\r\n\r\n```shell\r\nnpm install --save kekule\r\n```\r\n\r\nthen be imported to your project with ES module ``import`` or CommonJS ``require``:\r\n\r\n```javascript\r\nimport { Kekule } from 'kekule';\r\nimport 'kekule/theme/default';       // if Kekule widgets is used in browser, the theme CSS should be imported as well\r\nconsole.log(Kekule.VERSION);\r\n```\r\n\r\n```javascript\r\nlet Kekule = require('kekule').Kekule;\r\nrequire('kekule/theme/default');    // if Kekule widgets is used in browser, the theme CSS should be imported as well\r\nconsole.log(Kekule.VERSION);\r\n```\r\n\r\nFor web applications, Kekule.js can also be used in a traditional way by simply including it in the HTML page with `<script>` tag:\r\n\r\n```html\r\n<!-- from CDN -->\r\n<link rel=\"stylesheet\" type=\"text/css\" href=\"https://cdn.jsdelivr.net/npm/kekule/dist/themes/default/kekule.css\" />\r\n<script src=\"https://cdn.jsdelivr.net/npm/kekule/dist/kekule.min.js\"></script>\r\n```\r\n\r\n```html\r\n<!-- or from local file -->\r\n<link rel=\"stylesheet\" type=\"text/css\" href=\"./node_modules/dist/themes/default/kekule.css\" />\r\n<script src=\"./node_modules/kekule/dist/kekule.min.js\"></script>\r\n```\r\n\r\nAfter installation (in web or in node.js environment), you can run a small test to ensure that the toolkit works properly:\r\n\r\n```javascript\r\n// Create a simple CO2 molecule\r\nvar mol = new Kekule.Molecule();\r\nvar atomC = mol.appendAtom('C');\r\nvar atomO1 = mol.appendAtom('O');\r\nvar atomO2 = mol.appendAtom('O');\r\nmol.appendBond([atomC, atomO1], 2);\r\nmol.appendBond([atomC, atomO2], 2);\r\n\r\n// Get formula\r\nvar formula = mol.calcFormula();\r\nconsole.log('Formula: ', formula.getText());\r\n\r\n// Output SMILES\r\nvar smiles = Kekule.IO.saveFormatData(mol, 'smi');\r\nconsole.log('SMILES: ', smiles);\r\n\r\n// Output MOL2k\r\nvar mol2k = Kekule.IO.saveFormatData(mol, 'mol');\r\nconsole.log('MOL 2000: \\n', mol2k);\r\n```\r\n       \r\nThe [installation](http://partridgejiang.github.io/Kekule.js/documents/tutorial/content/installation.html) \r\nchapter of [Kekule.js tutorial](http://partridgejiang.github.io/Kekule.js/documents/tutorial/) provides more details\r\nof how to integrate Kekule.js into your own project.\r\n\r\n## Cheminformatics\r\n\r\nKekule.js implements many commonly-used cheminformatics tasks in JavaScript (in the other word, \r\nno need to communicate with a backend server). These include (but not limit to):\r\n\r\n### IO\r\n\r\n```javascript\r\n// load a molecule from JavaScript string\r\nlet cmlData = '<cml xmlns=\"http://www.xml-cml.org/schema\"><molecule id=\"m1\"><atomArray><atom id=\"a2\" elementType=\"C\" x2=\"7.493264658965051\" y2=\"35.58088907877604\"/><atom id=\"a3\" elementType=\"O\" x2=\"8.186084981992602\" y2=\"35.18088907877604\"/><atom id=\"a1\" elementType=\"C\" x2=\"6.800444335937501\" y2=\"35.18088907877604\"/></atomArray><bondArray><bond id=\"b2\" order=\"S\" atomRefs2=\"a2 a3\"/><bond id=\"b1\" order=\"S\" atomRefs2=\"a2 a1\"/></bondArray></molecule></cml>';\r\nlet molecule = Kekule.IO.loadFormatData(cmlData, 'cml');\r\n\r\n// load a spectrum from string\r\nlet jcampData = '##TITLE=CCH-4\\n##JCAMP-DX=4.24\\n##DATA TYPE=INFRARED SPECTRUM ...{omitted}... ##END=';\r\nlet spectrum = Kekule.IO.loadMimeData(cmlData, 'chemical/x-jcamp-dx');\r\n\r\n// load from url\r\nlet url = './data/mol2D/quinone.mol';\r\nKekule.IO.loadUrlData(url, (mol, success) => {\r\n  if (success)\r\n    console.log('Load molecule successful', mol);\r\n});\r\n\r\n// load from file object\r\ndocument.getElementById('inputFile').addEventListener('change', () => {\r\n  let file = document.getElementById('inputFile').files[0];\r\n  if (file)\r\n  {\r\n    Kekule.IO.loadFileData(file, function(mol, success) {\r\n      if (success)\r\n      console.log('Load molecule successful', mol);\r\n    });\r\n  }\r\n});\r\n\r\n// save to string in SMILES format\r\nlet smiles = Kekule.IO.saveFormatData(spectrum, 'smi');\r\n// use mimetype to set the output format\r\nlet dataMol = Kekule.IO.saveMimeData(molecule, 'chemical/x-mdl-molfile');   \r\n```\r\n\r\n### Molecule information\r\n                                 \r\n```javascript\r\n// get all rings of molecule\r\nlet allRings = molecule.findAllRings();\r\n// get SSSR of molecule\r\nlet sssRings = molecule.findSSSR();\r\n// get aromatic of molecule\r\nlet aromaticRings = molecule.findAromaticRings();\r\n\r\n// find chiral atoms and stereo bonds in molecule\r\nlet chiralAtoms = molecule.perceiveChiralNodes();\r\nlet stereoBonds = molecule.perceiveStereoConnectors();\r\n```\r\n                        \r\n### Molecule comparison and sub-structure search\r\n\r\n```javascript\r\n// compare srcMol and targetMol, check if the structure is same\r\nlet isSame = srcMolecule.isSameStructureWith(targetMolecule);\r\n// search sub structure inside targetMolecule\r\nlet searchResult = targetMolecule.search(subStructure);\r\nif (!!searchResult)\r\n\tconsole.log('The sub structure is in target');\r\n```\r\n\r\n## Widget\r\n\r\nKekule.js shipped with a series of web widgets providing UIs to display / modify chemistry objects in web application. \r\nThese powerful widgets are probably the most commonly used parts of Kekule.js. \r\n\r\nThe widgets can be initialized automatically with simple HTML tag:\r\n\r\n```html\r\n<!-- a viewer widget to display the molecule -->\r\n<div id=\"chemViewer\" style=\"width:500px;height:400px\" data-widget=\"Kekule.ChemWidget.Viewer\" data-chem-obj=\"url(./data/mol2D/quinone.mol)\"></div>\r\n\r\n<!-- a composer widget to edit the molecule -->\r\n<div id=\"composer\" style=\"width:600px;height:400px\" data-widget=\"Kekule.Editor.Composer\" data-chem-obj=\"url(./data/mol2D/quinone.mol)\"></div>\r\n```\r\n```javascript\r\nKekule.X.domReady(() => {  // called after DOM ready and the widget been initialized\r\n  let viewer = Kekule.Widget.getWidgetById('chemViewer');\r\n  let composer = Kekule.Widget.getWidgetById('composer');\r\n});\r\n\r\n```\r\n\r\nor created with JavaScript code:\r\n\r\n```javascript\r\n// create a viewer widget and append it as child to #parent HTML element\r\nlet chemViewer = new Kekule.ChemWidget.Viewer(document);\r\nchemViewer.setDimension('500px', '400px');\r\nchemViewer\r\n  .appendToElem(document.getElementById('parent'))\r\n  .setChemObj(molecule);\r\n\r\n// create a composer widget directly on #div1\r\nlet composer = new Kekule.Editor.Composer(document.getElementById('div1'));\r\ncomposer.setDimension('600px', '400px');\r\ncomposer.setChemObj(molecule);\r\n```\r\n\r\n## Widget wrapper\r\n                                    \r\nIt is also possible to wrap a widget into standard [web components](https://developer.mozilla.org/en-US/docs/Web/Web_Components).\r\nDetails can be found at the web component chapter of [tutorial](http://partridgejiang.github.io/Kekule.js/documents/tutorial/content/webComponent.html).\r\n\r\nProject [Kekule-Vue](https://github.com/partridgejiang/Kekule-Vue) can be used to wrap Kekule widget into \r\n[Vue](https://github.com/vuejs/vue) components with vue props, models and events.\r\n\r\nProject [Kekule-React](https://github.com/partridgejiang/Kekule-React) can be used to wrap Kekule widget into\r\n[React](https://github.com/facebook/react) components with props and events.\r\n \r\n## Documentations and Demos\r\n\r\n[Tutorials](http://partridgejiang.github.io/Kekule.js/documents/tutorial/index.html) and \r\n[demos](http://partridgejiang.github.io/Kekule.js/demos/index.html) are built to explain the basic \r\noperations in Kekule.js (e.g. creating molecule, loading and saving chemical objects, getting molecule \r\ninformation and usage of chem widgets).\r\n \r\n## License\r\n\r\nThe toolkit is released under [MIT](https://github.com/partridgejiang/Kekule.js/blob/master/LICENSE) license.","readmeFilename":"README.md"}