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drawrnajs

NPM version

Visualizes RNA secondary structures.

DrawrnaJS

To install the module, use: 'npm install drawrnajs'

DrawrnaJS visualises RNA secondary structures in Dot-bracket notation. It is heavily based on cytoscape.js. The algorithm used for layout determination is deterministic and will therefore always provide the same visualisation for a specific secondary structure.

Features

  • Deterministic layout
  • Residues can be coloured according to type
  • Precise selection and colouring via a lasso tool
  • Interactive mode for hydrogen bond adding
  • Export structure as PNG

Use DrawrnaJS

Full screen demo

Please refer to the examples, which show several possible ways of how you could embed DrawrnaJS into your page.

Initialisation

var Rna = require("drawrnajs");
 
var app = new Rna({
    el: yourDiv,
    seq: "<your RNA sequence>",
    dotbr: "<your secondary structure>",
    /* ... */
})
app.render();
 
var defaults = {
    layout: "naview", //the only layout that is currently supported 
    seqpanel: true, //determines whether there is going to be a sqeuence panel 
    optspanel: true, //determines whethere there is going to be an options panel 
    resindex: true //determines whether residue indices are shown 
}

Set sequence and structure

app.struct.get("seq") //get RNA sequence 
app.struct.get("dotbr") //get structure 
app.struct.set("seq", "ACGUACGAUCGUA") //set new sequence 

Get the cytoscape element

var cy = app.vis.cy //location of the cytoscape element 

Add new bonds

app.struct.get("links").newBond("12", "23") //creates a new bond between residues 12 and 23 

Change the type of a bond

app.vis.changeBondType("1to7", "non-canonical") //change the bond type of bond with  
                                                //bond-id "1to7" to non-canonical 

Add a new non-canonical bond without re-calculating the layout

app.vis.addNCBond(12, 23) //creates a new bond between residues 12 and 23  
                          //without re-calculating the layout algorithm 

Set Leontis-Westhof nomenclature for bond

app.vis.setLeontisWesthof("2to7", "sghgtrans") //sets Leontis-Westhof nomenclature 
                                               //of non-canonical bond "2to7" to "sghgtrans" 

The Leontis-Westhof nomenclature classes are formatted as follows

lwClasses = [
    "wcwccis",
    "wcwctrans",
    "sgsgcis",
    "sgsgtrans",
    "hghgcis",
    "hghgtrans",
    "sghgcis",
    "sghgtrans",
    "hgsgcis",
    "hgsgtrans"
    //etc. 
]

The 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).

Layouts

Currently the "naview" layout, which is a JavaScript port of VARNA's NAView layout, is used for all the example structures. We intend to implement other layouts in the future.

Contributing

All contributions are welcome.

Support

If you have any problem or suggestion please open an issue here.

License

The MIT License

Copyright (c) 2015, bene200

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.