rcsb-statistical-charts

RCSB Statistical Charts is an open-source library that includes different tools to plot statistics of RCSB PDB structure features.
RCSB Search API.

Node Module Installation

npm install @rcsb/rcsb-statistical-charts

Folder organization

• src module source code
  • StatsPlot React component for charting RCSB PDB data
  • StatsPlotInterface Configuration for charting distribution of RCSB PDB features
  • examples Charting examples
• test Unit tests

Testing

Different testing examples are available in the src/examples folder

• npm install
• npm run devServer

Go to:

• http://localhost:9000/ExplMethods.html
• http://localhost:9000/XrayMethod.html
• http://localhost:9000/OrganismXray.html
• http://localhost:9000/OrganismExplMethod.html
• http://localhost:9000/CathExplMethod.html
• http://localhost:9000/OrganismCath.html

Interfaces

• Main interface

interface StatsPlotInterface {
  /**Principal feature displayed in the chart defined as search Facet. It defines the magnitude associated to the domain axis*/
  firstDim: AttributeFacetType | FilterFacetType;
  /**Histogram, barplot or pie (display not implemented)*/
  chartType: ChartType;
  /**Granularity of the distribution: entry, polymer-entity, assembly, ...*/
  returnType: ReturnType;
  /**Second feature displayed in the chart defined as search Facet. It is displayed as stack bars*/
  secondDim?: AttributeFacetType | FilterFacetType;
  /**Search query to filter the structural data. Otherwise, the whole structural archive is used*/
  searchQuery?: SearchQueryType;
  /**Configuration for the chart*/
  chartConfig?: ChartConfigInterface;
}

• Main React component props: StatsPlotInterface

  <StatsPlot
    firstDim={{
        name: `FACET/${RcsbSearchMetadata.RcsbAccessionInfo.InitialReleaseDate.path}`,
        aggregation_type: AggregationType.DateHistogram,
        attribute: RcsbSearchMetadata.RcsbAccessionInfo.InitialReleaseDate.path,
        interval: Interval.Year,
        min_interval_population: 0
    }}
    secondDim={{
        name: `FACET/${RcsbSearchMetadata.Exptl.Method.path}`,
        aggregation_type: AggregationType.Terms,
        attribute: RcsbSearchMetadata.Exptl.Method.path
    }}
    chartType={ChartType.histogram}
    returnType={ReturnType.Entry}
/>

Contributing

All contributions are welcome. Please, make a pull request or open an issue.

License

The MIT License

Copyright (c) 2023 - 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.