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",
seqpanel: true,
optspanel: true,
resindex: true
}
Set sequence and structure
app.struct.get("seq")
app.struct.get("dotbr")
app.struct.set("seq", "ACGUACGAUCGUA")
Get the cytoscape element
var cy = app.vis.cy
Add new bonds
app.struct.get("links").newBond("12", "23")
Change the type of a bond
app.vis.changeBondType("1to7", "non-canonical")
Add a new non-canonical bond without re-calculating the layout
app.vis.addNCBond(12, 23)
Set Leontis-Westhof nomenclature for bond
app.vis.setLeontisWesthof("2to7", "sghgtrans")
The Leontis-Westhof nomenclature classes are formatted as follows
lwClasses = [
"wcwccis",
"wcwctrans",
"sgsgcis",
"sgsgtrans",
"hghgcis",
"hghgtrans",
"sghgcis",
"sghgtrans",
"hgsgcis",
"hgsgtrans"
]
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,
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OTHER DEALINGS IN THE SOFTWARE.