PDBe-KB Polyproteins Section Component

This repository is for the codebase of a lightweight Angular v7 web component that displays all the processed proteins for a UniProt accession.

This web component is used on the PDBe-KB Aggregated Views of Proteins.

Note: This component uses the molstar-dialog web component available at https://github.com/PDBe-KB/component-molstar-dialog

Example:

Quick Start

Get the code and install dependencies

git clone https://github.com/PDBe-KB/component-polyprotein-section.git
cd component-polyprotein-section
npm i

Running the app

ng serve

Running tests

ng test

Dependencies

This web component embeds another PDBe-KB web component: https://github.com/PDBe-KB/component-molstar-dialog

In order to use all the features of this web component, retrieve the "molstar-dialog" component and replace the contents of the src/app/molstar-dialog folder with those files.

The main template (i.e. index.html by default) should also have the following CSS imports:

<link rel="stylesheet" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/css/ebi-global.css" type="text/css" media="all"/>
<link rel="stylesheet" href="https://ebi.emblstatic.net/web_guidelines/EBI-Icon-fonts/v1.3/fonts.css" type="text/css" media="all"/>
<link rel="stylesheet" href="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/css/theme-pdbe-green.css" type="text/css" media="all"/>

Basic usage

The component can be added to any Angular v7 apps.

1.) Import the component:

Import the component in app.module.ts by default.

import { BrowserModule } from '@angular/platform-browser';
import { NgModule } from '@angular/core';

import { AppComponent } from './app.component';
import { PolyproteinSectionComponent } from './polyprotein-section/polyprotein-section.component';
import { MolstarDialogComponent } from './molstar-dialog/molstar-dialog.component';
import {MatDialogModule} from '@angular/material';

@NgModule({
  declarations: [
    AppComponent,
    PolyproteinSectionComponent,
    MolstarDialogComponent
  ],
  imports: [
    BrowserModule,
    MatDialogModule
  ],
  providers: [],
  bootstrap: [AppComponent]
})
export class AppModule { }

2.) Add the component to a template:

<app-polyprotein-section [processedProteins]="processedProteins" [parentProtein]="proteinName"></app-polyprotein-section>

The data model for the input data is described in src/app/polyprotein-section/polyprotein-section.models.ts

Example input data

[
    {
      'id': 'PRO_0000449619',
      'name': 'Host translation inhibitor nsp1',
      'unp_length': 7096,
      'unp_start': 1,
      'unp_start_code': 'MET',
      'unp_end': 180,
      'unp_end_code': 'GLY',
      'summary_counts': {
        'pdbs': 16,
        'ligands': 5,
        'interactions': 3
      },
      'representative_pdb': {
        'pdb_id': '7k7p',
        'best_chain': 'A',
        'entity_id': 1,
        'unp_start': 10,
        'unp_end': 127
      }
    }
  ]

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

• Mihaly Varadi - Initial Implementation - mvaradi

See also the list of contributors who participated in this project.

License

This project is licensed under the EMBL-EBI License - see the LICENSE file for details

Acknowledgements

We would like to thank the PDBe team and the PDBe-KB partner resources for their feedback and contributions.