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install the module, use: 'npm install drawrnajs'\n\nDrawrnaJS visualises RNA secondary structures in [Dot-bracket notation](http://ultrastudio.org/en/Dot-Bracket_Notation). It is heavily based on [cytoscape.js](http://biojs.io/d/cytoscape). The algorithm used for layout determination is deterministic and will therefore always provide the same visualisation for a specific secondary structure.\n\n####  Features\n* Deterministic layout\n* Residues can be coloured according to type\n* Precise selection and colouring via a lasso tool\n* Interactive mode for hydrogen bond adding\n* Export structure as PNG\n\n## Use DrawrnaJS\n\n[Full screen demo](http://workmen.biojs.net/demo/drawrnajs/simple)\n\nPlease refer to the examples, which show several possible ways of how you could embed DrawrnaJS into your page.\n\n#### Initialisation\n\n```javascript\nvar Rna = require(\"drawrnajs\");\n\nvar app = new Rna({\n    el: yourDiv,\n    seq: \"<your RNA sequence>\",\n    dotbr: \"<your secondary structure>\",\n    /* ... */\n})\napp.render();\n\nvar defaults = {\n    layout: \"naview\", //the only layout that is currently supported\n    seqpanel: true, //determines whether there is going to be a sqeuence panel\n    optspanel: true, //determines whethere there is going to be an options panel\n    resindex: true //determines whether residue indices are shown\n}\n```\n#### Set sequence and structure\n\n```javascript\napp.struct.get(\"seq\") //get RNA sequence\napp.struct.get(\"dotbr\") //get structure\napp.struct.set(\"seq\", \"ACGUACGAUCGUA\") //set new sequence\n```\n\n#### Get the cytoscape element\n\n```javascript\nvar cy = app.vis.cy //location of the cytoscape element\n```\n\n#### Add new bonds\n\n```javascript\napp.struct.get(\"links\").newBond(\"12\", \"23\") //creates a new bond between residues 12 and 23\n```\n\n#### Change the type of a bond\n\n```javascript\napp.vis.changeBondType(\"1to7\", \"non-canonical\") //change the bond type of bond with \n                                                //bond-id \"1to7\" to non-canonical\n```\n\n#### Add a new non-canonical bond without re-calculating the layout\n\n```javascript\napp.vis.addNCBond(12, 23) //creates a new bond between residues 12 and 23 \n                          //without re-calculating the layout algorithm\n```\n\n#### Set Leontis-Westhof nomenclature for bond\n\n```javascript\napp.vis.setLeontisWesthof(\"2to7\", \"sghgtrans\") //sets Leontis-Westhof nomenclature\n                                               //of non-canonical bond \"2to7\" to \"sghgtrans\"\n```\n\nThe Leontis-Westhof nomenclature classes are formatted as follows\n\n```javascript\nlwClasses = [\n    \"wcwccis\",\n    \"wcwctrans\",\n    \"sgsgcis\",\n    \"sgsgtrans\",\n    \"hghgcis\",\n    \"hghgtrans\",\n    \"sghgcis\",\n    \"sghgtrans\",\n    \"hgsgcis\",\n    \"hgsgtrans\"\n    //etc.\n]\n```\nThe first two charcters define the bond edge of residue 1, the second two characters define the ond edge of residue 2 and the rest of the class labels is either cis or trans. Bond edges are one of the following: wc (Watson-Crick), hg (Hoogsteen) or sg (Sugar).\n\n#### Layouts\n\nCurrently the \"naview\" layout, which is a JavaScript port of [VARNA](http://varna.lri.fr/)'s NAView layout, is used for all the example structures. \nWe intend to implement other layouts in the future.\n\n## Contributing\n\nAll contributions are welcome.\n\n## Support\n\nIf you have any problem or suggestion please open an issue [here](https://github.com/bene200/drawrnajs/issues).\n\n## License\n\nThe MIT License\n\nCopyright (c) 2015, bene200\n\nPermission is hereby granted, free of charge, to any person\nobtaining a copy of this software and associated documentation\nfiles (the \"Software\"), to deal in the Software without\nrestriction, including without limitation the rights to use,\ncopy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the\nSoftware is furnished to do so, subject to the following\nconditions:\n\nThe above copyright notice and this permission notice shall be\nincluded in all copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND,\nEXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES\nOF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND\nNONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT\nHOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,\nWHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\nFROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR\nOTHER DEALINGS IN THE SOFTWARE.\n","maintainers":[{"name":"bene200","email":"berau90@web.de"}],"time":{"modified":"2022-06-15T23:58:20.283Z","created":"2015-01-03T15:58:54.988Z","0.1.0":"2015-01-03T15:58:54.988Z","0.2.0":"2015-01-13T23:31:14.222Z","0.2.1":"2015-01-13T23:34:06.090Z","0.2.2":"2015-01-23T11:54:55.373Z","0.2.3":"2015-01-23T12:06:51.955Z","0.2.4":"2015-01-23T12:13:17.689Z","0.2.5":"2015-01-23T12:15:20.491Z","0.2.6":"2015-01-23T12:18:44.576Z","0.2.7":"2015-01-23T12:28:31.311Z","0.3.0":"2015-03-24T11:03:58.432Z","0.3.1":"2015-03-24T11:31:39.643Z","0.3.2":"2015-04-13T10:37:29.223Z","0.3.3":"2015-05-18T16:23:49.734Z","0.3.4":"2015-05-18T16:43:04.736Z","0.3.5":"2015-07-15T20:00:02.496Z","1.0.0":"2015-08-20T17:11:31.724Z","1.0.1":"2015-08-20T17:14:57.208Z","1.0.2":"2015-08-20T17:26:35.536Z","1.0.3":"2015-08-20T17:34:53.177Z","1.1.0":"2015-08-21T16:01:47.706Z","1.1.1":"2015-08-21T16:09:06.417Z","1.1.2":"2015-08-21T16:14:13.608Z","1.1.3":"2015-08-21T16:16:22.795Z","1.1.4":"2015-08-21T20:54:47.156Z","1.2.0":"2015-08-27T14:24:20.393Z","1.2.1":"2015-09-10T13:50:06.875Z","1.2.2":"2015-09-14T09:57:11.297Z","1.2.3":"2015-10-01T09:37:13.676Z","1.2.4":"2015-10-02T13:22:06.680Z","1.2.5":"2015-10-11T17:53:50.339Z","1.2.6":"2015-11-17T13:49:43.800Z"},"homepage":"https://github.com/bene200/drawrnajs","keywords":["rna","secondary structure","biojs","galaxy-vis"],"repository":{"type":"git","url":"git://github.com/bene200/drawrnajs.git"},"author":{"name":"bene200","email":"berau90@web.de"},"bugs":{"url":"https://github.com/bene200/drawrnajs/issues"},"readmeFilename":"README.md"}