Newer
Older
# PDB ligand environment component
This is a web-component to display ligand structure in 2D along with its interactions. Ligand can be perceived as a set of covalently linked pdb residues (refered to as bound molecule) or a single pdb residue. This depiction can be enriched with a substructure highlight and binding site interactions.
## Step after cloning (use local server to see demo pages)
```shell
npm run install
npm run build
npm run start
open any of the *.html pages in the demo directory
* Mode A: Display bound molecule and its interactions
* Mode B: Display ligand and its interactions
* Mode C: Display ligand (chemical component) only
| <img src="https://www.ebi.ac.uk/~lpravda/imgs/1cbs_REA_200_A.png"/>| <img src="https://www.ebi.ac.uk/~lpravda/imgs/3d12_bm1.png"/> | <img src="https://www.ebi.ac.uk/pdbe-srv/pdbechem/image/showNew?code=VIA&size=500"/> |
| [1cbs REA 200 A](https://www.ebi.ac.uk/pdbe/entry/pdb/1cbs/bound/REA) | 3D12 bm1 (`2xGLC-2xBGC-LXZ-NGA-GL0`)| [wwPDB CCD - VIA](https://pdbe.org/chem/VIA)
The component can be inserted into the pages by two different ways. Either as a `web-component` using html tag, or directly by using javascript as a `plugin`.
Interactions data displayed by the component can come from three different environments `Production`, `Development`, `Internal`. If no environment is specified `Production` is used as default..
A few files needs to be imported in the page before the component is attempted to be loaded:
<!-- D3 -->
<script src="https://d3js.org/d3.v5.min.js"></script>
<!-- CSS style to be used for scene drawing (required for saving SVGs.) -->
<link rel="stylesheet" href="pdb-ligand-env-svg.css" />
<!-- CSS style to be used for the component UI -->
<link rel="stylesheet" href="pdb-ligand-env.css" />
<link rel="stylesheet" href="https://ebi.emblstatic.net/web_guidelines/EBI-Icon-fonts/v1.3/fonts.css" />
<!-- Web component polyfill (only loads what it needs) -->
<script src="https://cdn.jsdelivr.net/npm/@webcomponents/webcomponentsjs/webcomponents-lite.js" charset="utf-8"></script>
<script src="https://cdn.jsdelivr.net/npm/@webcomponents/webcomponentsjs/custom-elements-es5-adapter.js"
charset="utf-8"></script>
<!--PDBe interactions component-->
<script type="module" src="pdb-ligand-env-component-0.3.0-min.js"></script>
<pdb-ligand-env pdb-id="1cbs" pdb-res-id="200" pdb-chain-id="A" environment="development"></pdb-ligand-env>
<pdb-ligand-env pdb-id="3d12" bound-molecule-id="bm1"></pdb-ligand-env>
<pdb-ligand-env pdb-res-name="CLR" zoom-on ></pdb-ligand-env>
The component contains a number of properties that can be set, in order to change data that are being displayed. First you need to define a component on the page:
<pdb-ligand-env id='SIA-component'></pdb-ligand-env>
```javascript
let chemUrl = `https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/SIA/annotation`;
let interactionsURL = "https://wwwdev.ebi.ac.uk/pdbe/graph-api/pdb/bound_ligand_interactions/4yy1/A/604";
let component = document.getElementById('SIA-component');
const depiction = await (await fetch(chemUrl)).json();
const interactionsData = await (await fetch(interactionsURL)).json();
const atomsToHighlight = ['C10', 'C11', 'O10'];
component.depiction = depiction;
component.ligandHighlight = atomsToHighlight;
component.interactions = interactionsData;
```
### Plugin
The component can be also added to DOM directly from JavaScript. There are some requirements
```html
<!-- D3 -->
<script src="https://d3js.org/d3.v5.min.js"></script>
<!-- CSS style to be used for scene drawing (required for saving SVGs.) -->
<link rel="stylesheet" href="pdb-ligand-env-svg.css" />
<!-- UI icons -->
<link rel="stylesheet" href="https://ebi.emblstatic.net/web_guidelines/EBI-Icon-fonts/v1.3/fonts.css" />
<!--PDB ligand environment plugin-->
<script src="pdb-ligand-env-plugin-min.js"></script>
<link rel="stylesheet" href="pdb-ligand-env.css" />
```
and then the component can be instantiated as simply as:
```javascript
let component = document.getElementById('SIA-component');
let uiParams = {
reinitialize: true, // allow reinitialize option in the component menu
zoom: true, // allow scene zoom
fullScreen: true, // allow allow full screen option in the component menu
downloadImage: true, // allow image download from the component menu
downloadData: true, // allow interactions data download from compoment menu
center: true, // allow scene centering option from the component menu
help: false, // allow help option from the component menu
residueLabel: true, // show residue label
tooltip: true // show residue tooltip on mouse hover
};
this.display = new Visualization(this, uiParams, environment);
this.display.initBoundMoleculeInteractions('3d12', 'bm1');
// to display carbohydrate polymer interactions
this.display.initCarbohydratePolymerInteractions('5e98', 'bm1','3');
// to display ligand interactions
this.display.initLigandInteractions('1cbs', 200, 'A');
// to display chemical component only
## Parameters
| Parametr | Type | Required | Description |
|-------------------- | --------- | -------- | ------- |
| pdb-id | string | No | PDB id of a protein to retrieve interactions from. `(mode A and B only)` |
| bound-molecule-id | string | No | PDB bound molecule id `(mode A only)` |
| pdb-res-name | string | No | PDB residue name aka: *auth_comp_id* `(mode C only)`
| pdb-res-id | number | No | PDB residue id aka: *auth_seq_id* `(mode B only)`
| pdb-chain-id | string | No | PDB residue chain aka: *auth_asym_id* `(mode B only)`|
| substructure | string[] | No | List of atom names to be highlighted on the ligand structure |
| color | string | No | HEX representation of the color highlight. `(Default: #D3D3D3)` |
| zoom-on | boolean | No | Allow zoom functionality on the component level. |
| environment | string | No | What data should be used: one of `production`, `development`, `internal` or a shorthand `prod`, `dev`, `int`. |