Visualizes RNA secondary structures.
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.
- 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
Please refer to the examples, which show several possible ways of how you could embed DrawrnaJS into your page.
var Rna = ;var app =el: yourDivseq: "<your RNA sequence>"dotbr: "<your secondary structure>"/* ... */app;var defaults =layout: "naview" //the only layout that is currently supportedseqpanel: true //determines whether there is going to be a sqeuence paneloptspanel: true //determines whethere there is going to be an options panelresindex: true //determines whether residue indices are shown
Set sequence and structure
appstruct //get RNA sequenceappstruct //get structureappstruct //set new sequence
Get the cytoscape element
var cy = appviscy //location of the cytoscape element
Add new bonds
appstruct //creates a new bond between residues 12 and 23
Change the type of a bond
appvis //change the bond type of bond with//bond-id "1to7" to non-canonical
Add a new non-canonical bond without re-calculating the layout
appvis //creates a new bond between residues 12 and 23//without re-calculating the layout algorithm
Set Leontis-Westhof nomenclature for bond
appvis //sets Leontis-Westhof nomenclature//of non-canonical bond "2to7" to "sghgtrans"
The Leontis-Westhof nomenclature classes are formatted as follows
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).
All contributions are welcome.
If you have any problem or suggestion please open an issue here.
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.