RCSB Saguaro 1D Feature Viewer is an open-source TypeScript library used to display protein and genomic sequence annotations over the web. The project is developed and maintained at RCSB PDB and it is currently used to display protein features on its web site. The package offers multiple types of data displays and a rich set of options to customize feature visualization.
When using rcsb-saguaro, please cite:
Joan Segura, Yana Rose, John Westbrook, Stephen K Burley, Jose M Duarte. RCSB Protein Data Bank 1D tools and services, Bioinformatics, 2020; https://doi.org/10.1093/bioinformatics/btaa1012
npm install @rcsb/rcsb-saguaro
Different testing example are available in the src/examples
folder
git clone git@github.com:rcsb/rcsb-saguaro.git
cd rcsb-saguaro
npm install
npm run devServer
Go to:
http://localhost:9000/MultipleTracks.html
http://localhost:9000/MultipleAlignment.html
<script src="https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro@3.0.3/build/rcsb-saguaro.min.js" type="text/javascript"></script>
TypeScript full classes documentation can be found here.
These are the most important elements if you are only interested in using RCSB Saguaro to visualise protein annotations
Main feature viewer board object configuration defines the coordinate range, track and title width and axis display. The full set of attributes is defined in RcsbFvBoardConfigInterface interface.
Main Board Configuration properties are:
const boardConfig = {
range: {
min: 20,
max: 110
},
trackWidth: 940,
rowTitleWidth: 260,
includeAxis: true
};
Row configuration object defines format and content of feature viewer rows. The full set of board row configuration attributes is defined in RcsbFvRowConfigInterface.
Main Row Configuration properties are:
const sequence = "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQ"+
"EEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAA"+
"RTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMS"
const sequenceTrack = {
trackHeight: 20,
trackColor: "#F9F9F9",
displayType: "sequence",
rowTitle: "SEQUENCE",
trackData: [{
begin: 1,
label: sequence
}]
}
const blockTrack= {
trackId: "blockTrack",
trackHeight: 20,
trackColor: "#F9F9F9",
displayType: "block",
displayColor: "#FF0000",
rowTitle: "BLOCK",
trackData: [{
begin: 30,
end: 60,
gaps:[{
begin:40,
end:50
}]
},{
begin: 80,
end: 90,
openEnd: true
}]
}
const pfv = new RcsbFv.Create({
boardConfigData: boardConfig,
rowConfigData: [sequenceTrack, blockTrack],
elementId: "htmlElementId"
});
See this expanded example online here
The full collection of examples can be edited and modified at CODEPEN
We also provide a library (rcsb-saguaro-app) to build preconfigured 1D Protein Feature Views of RCSB PDB and UniProtKB annotations.
All contributions are welcome. Please, make a pull request or open an issue.
The MIT License
Copyright (c) 2019 - now, RCSB PDB and contributors
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.
Generated using TypeDoc