Commit 329914a0 authored by Lukas Pravda's avatar Lukas Pravda
Browse files

Merge branch 'dev' -- release 1.0

parents 8dbb3078 f701abb1
Pipeline #176751 passed with stages
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## RELEASE 1.0 - 28 April 2021
* Support to display atom names
* Use `pdbeccdutils=0.6` data
* Minor bug fixes
## RELEASE 0.2 - 24 February 2020
Component rembranded to `pdb-ligand-env`
Component rebranded to `pdb-ligand-env`
### Features
......
# 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.
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, atom names, and binding site interactions.
## Step after cloning (use local server to see demo pages)
......@@ -133,6 +133,8 @@ let uiParams = {
help: false, // allow help option from the component menu
residueLabel: true, // show residue label
tooltip: true // show residue tooltip on mouse hover
menu: true // allow menu to be (not) available
names: true // allow ligand depiction with atom names
};
this.display = new Visualization(this, uiParams, environment);
......@@ -144,8 +146,8 @@ this.display.initCarbohydratePolymerInteractions('5e98', 'bm1','3');
// to display ligand interactions
this.display.initLigandInteractions('1cbs', 200, 'A');
// to display chemical component only
this.display.initLigandDisplay('HEM');
// to display chemical component with atom names only
this.display.initLigandDisplay('HEM', true);
````
## Parameters
......@@ -160,4 +162,5 @@ this.display.initLigandDisplay('HEM');
| 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. |
| names-on | boolean | No | Allow ligand depiction to be displayed with atom names. |
| environment | string | No | What data should be used: one of `production`, `development`, `internal` or a shorthand `prod`, `dev`, `int`. |
......@@ -14,7 +14,7 @@
<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="http://127.0.0.1:8080/pdb-ligand-env-component-0.3.0-min.js"></script>
<script type="module" src="http://127.0.0.1:8080/pdb-ligand-env-component-1.0.0-min.js"></script>
</head>
......@@ -37,7 +37,7 @@
<!--Mode C-->
<div style="position: relative; float: left;">
<div style="width: 500px; height: 500px; position: relative">
<pdb-ligand-env pdb-res-name="CLR" zoom-on></pdb-ligand-env>
<pdb-ligand-env pdb-res-name="CLR" zoom-on names-on></pdb-ligand-env>
</div>
</div>
......
......@@ -18,7 +18,7 @@
<script src="https://cdn.jsdelivr.net/npm/@webcomponents/webcomponentsjs/custom-elements-es5-adapter.js"
charset="utf-8"></script>
<script type="module" src="pdb-ligand-env-component-0.3.0-min.js"></script>
<script type="module" src="pdb-ligand-env-component-1.0.0-min.js"></script>
<script>
var renderBmInteractions = function (id, bmId) {
var int =
......@@ -126,9 +126,9 @@
<!--
Further use in the app for bound molecule interactions:
<pdb-ligand-env pdb-id="3d12" bound-molecule-id="bm1"></pdb-ligand-env>
for ligand interactions:
<pdb-ligand-env pdb-id="3d12" pdb-chain-id="A" pdb-res-id="200"></pdb-ligand-env>
-->
......
This diff is collapsed.
{
"name": "pdb-ligand-env",
"version": "0.3.0",
"version": "1.0.0",
"description": "",
"main": "app.js",
"dependencies": {
......
......@@ -17,6 +17,7 @@ class pdbLigandEnv extends LitElement {
substructureHighlight: { type: Array, attribute: 'substructure' },
substructureColor: { type: String, attribute: 'color' },
zoomOn: { type: Boolean, attribute: 'zoom-on' },
namesOn: { type: Boolean, attribute: 'names-on' },
env: { type: String, attribute: 'environment' },
};
}
......@@ -32,9 +33,9 @@ class pdbLigandEnv extends LitElement {
uiParams.menu = this.pdbId !== undefined;
let env = this.env === undefined ? "production" : this.env;
let names = this.namesOn === undefined ? false : this.namesOn;
this.display = new Visualization(this, uiParams, env);
if (this.pdbId) {
if (this.entityId) {
this.display.initCarbohydratePolymerInteractions(this.pdbId, this.bmId, this.entityId);
......@@ -47,7 +48,7 @@ class pdbLigandEnv extends LitElement {
}
}
else if (this.resName) {
this.display.initLigandDisplay(this.resName).then(() => this.display.centerScene());
this.display.initLigandDisplay(this.resName, names).then(() => this.display.centerScene());
}
}
......@@ -84,7 +85,11 @@ class pdbLigandEnv extends LitElement {
}
set zoom(data) {
if (this.display !== undefined) this.display.toogleZoom(data);
if (this.display !== undefined) this.display.toggleZoom(data);
}
set atomNames(data) {
this.display.toggleDepiction(data);
}
//#endregion properties
......
......@@ -70,6 +70,7 @@ namespace Config {
residueLabel: boolean;
tooltip: boolean;
menu: boolean;
names: boolean;
constructor() {
this.reinitialize = true;
......@@ -82,6 +83,7 @@ namespace Config {
this.residueLabel = true;
this.tooltip = true;
this.menu = true;
this.names = true;
}
}
}
\ No newline at end of file
......@@ -8,10 +8,10 @@
* @class Depiction
* @param {string} ccdId PDB CCD id.
* @param {Atom[]} atoms List of atoms.
* @param {Bond[]} bonds Visual representation of bonds.
* @param {Bond[]} bonds Visual representation of bonds.
* They do not correlate 1:1 with a number of bonds!
* @param {Vector2D} resolution x,y dimension of the image. Needs to be used
* for a scene shift, so it is centered.
* for a scene shift, so it is centered.
*/
class Depiction {
ccdId: string;
......@@ -39,7 +39,7 @@ class Depiction {
this.bonds = new Array<Bond>();
let bds = new Set<string>();
data.bonds.forEach(x => {
let atomA = this.atoms.find(e => e.name == x.bgn);
let atomB = this.atoms.find(e => e.name == x.end);
......@@ -58,14 +58,14 @@ class Depiction {
/**
* Returns an initial position of Residue node bound to a list of
* Returns an initial position of Residue node bound to a list of
* atom.
*
*
* Present implementation sorts all the partners based on the atom
* degree and then gets the one with the lovest degree and places
* degree and then gets the one with the lovest degree and places
* the initial residue position along the vector pointing from it.
*
* @param {string[]} atomNames list of atom names the bound residue
* @param {string[]} atomNames list of atom names the bound residue
* has a contact with.
* @returns {Vector2D} Returns an initial placement of the residue in contact.
* @memberof Depiction
......@@ -90,11 +90,13 @@ class Depiction {
return new Vector2D(x, y);
}
public draw() {
public draw(atomNames: boolean = false) {
this.structure.selectAll("*").remove();
this.appendBondVisuals();
this.appendTexts();
if (atomNames) this.appendAtomNames();
else this.appendLabels();
}
public highlightSubgraph(atoms: Array<string>, color: string = undefined) {
......@@ -145,39 +147,51 @@ class Depiction {
.attr('d', (y: Bond) => y.coords);
}
/**
* Append atom name labels to the visualization.
*
* @memberof Depiction
*/
private appendAtomNames() {
this.structure.selectAll()
.data(this.atoms)
.enter()
.append('text')
.attr('filter', "url(#solid-background)")
.attr('style', 'font-size:21px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;fill:#000000')
.attr('x', x => x.position.x)
.attr('y', x => x.position.y)
.attr('dominant-baseline', 'central')
.attr('text-anchor', 'middle')
.text(x => x.name);
}
/**
* Append depiction labels to the visualization. Because RDKIt places
* the labels slightly differently this information needs to be
* consumed too, because we cannot use just atom position directly.
* Also there are all sorts of colorful subscripts and superscripts,
* Also there are all sorts of colorful subscripts and superscripts,
* so it is much easier to use it this way.
*
* @memberof Depiction
*/
private appendTexts(): void {
private appendLabels() {
let data = this.atoms
.filter(x => x.labels.length > 0)
?.map(x => x.labels)
?.reduce((a, b) => a.concat(b));
.filter(x => x.labels.length > 0);
this.structure.selectAll()
.data(data)
.enter()
.append('text')
.attr('filter', "url(#solid-background)")
.attr('style', (x: any) => x.style)
.attr('x', (x: any) => x.x)
.attr('y', (x: any) => x.y)
.attr('dominant-baseline', (x: any) => x['dominant-baseline'])
.attr('text-anchor', (x: any) => x['text-anchor'])
.append('g')
.attr('filter', 'url(#solid-background)')
.each(function (x: any) {
for (var i = 0; i < x.tspans.length; i++) {
for (var i = 0; i < x.labels.length; i++) {
d3.select(this)
.append('tspan')
.attr('style', x.tspans[i].style)
.text(x.tspans[i].value);
.append('path')
.attr('d', x.labels[i].d)
.style("background-color", "white")
.attr('fill', x.labels[i].fill)
}
});
}
......@@ -243,7 +257,7 @@ class Atom {
}
/**
*
*
*
* @param {Atom} other
* @returns true if the atoms are equal
......@@ -310,7 +324,7 @@ class Vector2D {
/**
* Composes vectors to a single one. This is used in infering the
* Composes vectors to a single one. This is used in infering the
* original placement of the residue nodes.
*
* @static
......@@ -359,7 +373,7 @@ class Bond {
/**
* Get the other atom for a given bond.
*
* @param {Atom} other
* @param {Atom} other
* @returns {Atom} The other atom from the bond.
* @throws {Error} if the atom is not part of that bond at all.
* @memberof Bond
......
......@@ -17,7 +17,7 @@ class Visualization {
private links: any;
// #endregion
// #region data properties
// #region data properties
private environment: Model.Environment;
private pdbId: string;
private bindingSites: Model.BindingSite[];
......@@ -41,8 +41,9 @@ class Visualization {
this.visualsMapper = new VisualsMapper(this.environment);
this.rProvider = ResidueProvider.getInstance(this.environment);
this.fullScreen = false;
this.bindingSites = new Array<Model.BindingSite>();
this.fullScreen = false;
this.nodeDragged = false;
if (uiParameters === undefined) uiParameters = new Config.UIParameters();
......@@ -126,7 +127,6 @@ class Visualization {
});
this.links?.attr('opacity', 1);
this.nodes?.attr('opacity', 1);
}
private linkMouseOverEventHandler(x: Model.Link, i: number, g: any) {
......@@ -190,7 +190,7 @@ class Visualization {
/**
* Download bound molecule interactions data from PDBe Graph API end point
* /pdb/bound_molecule_interactions
*
*
* Correct parameters can be obtained using API call:
* /pdb/bound_molecules
*
......@@ -212,7 +212,7 @@ class Visualization {
/**
* Download carbohydrate interactions data from PDBe Graph API end point
* /pdb/carbohydrate_polymer_interactions
*
*
* Correct parameters can be obtained using API call:
* /pdb/bound_molecules
*
......@@ -235,40 +235,40 @@ class Visualization {
/**
* Download ligand interactions data from PDBe Graph API end point
* /pdb/bound_ligand_interactions.
*
*
* Correct parameters can be obtained using API call:
* /pdb/bound_molecules
*
*
* @param {string} pdbId pdb id
* @param {number} resId residue number aka: auth_seq_id
* @param {string} chainId chain id aka: auth_asym_id
* @memberof Visualization
*/
public initLigandInteractions(pdbId: string, resId: number, chainId: string) {
public initLigandInteractions(pdbId: string, resId: number, chainId: string, withNames: boolean = false) {
this.pdbId = pdbId;
let url = Resources.ligandInteractionsAPI(pdbId, chainId, resId, this.environment);
d3.json(url)
.catch(e => this.processError(e, 'No interactions data are available.'))
.then((data: any) => this.addLigandInteractions(data))
.then((data: any) => this.addLigandInteractions(data, withNames))
.then(() => new Promise(resolve => setTimeout(resolve, 1500)))
.then(() => this.centerScene());
}
/**
* Download ligand structure given the anotation generated by the
* Download ligand structure given the anotation generated by the
* PDBeChem process.
*
* @param {string} ligandId
* @returns
* @memberof Visualization
*/
public async initLigandDisplay(ligandId: string) {
public async initLigandDisplay(ligandId: string, withNames: boolean = false) {
const ligandUrl = Resources.ligandAnnotationAPI(ligandId, this.environment);
return d3.json(ligandUrl)
.catch(e => this.processError(e, `Component ${ligandId} was not found.`))
.then((d: any) => this.addDepiction(d))
.then((d: any) => this.addDepiction(d, withNames))
.then(() => this.centerScene());
}
......@@ -280,9 +280,26 @@ class Visualization {
* the PDBeChem process.
* @memberof Visualization
*/
public addDepiction(depiction: any) {
public addDepiction(depiction: any, withNames: boolean) {
this.depiction = new Depiction(this.depictionRoot, depiction);
this.depiction.draw();
this.depiction.draw(withNames);
}
/**
* Show depiction with/without atom names
*
* @param {boolean} withNames Controls atom labels to be displayed
* @memberof Visualization
*/
public toggleDepiction(withNames: boolean) {
if (!this.depiction) return;
this.depiction.draw(withNames);
}
public toggleZoom(active: boolean) {
this.zoomHandler = active ? this.getZoomHandler() : undefined;
}
......@@ -310,25 +327,20 @@ class Visualization {
}
public toogleZoom(active: boolean) {
this.zoomHandler = active ? this.getZoomHandler() : undefined;
}
/**
* Add ligand interactions to the canvas
*
* @param {*} data Data content of the API end point
* @param {*} data Data content of the API end point
* /pdb/bound_ligand_interactions
* @memberof Visualization
*/
public addLigandInteractions(data: any) {
public addLigandInteractions(data: any, withNames: boolean = false) {
let key = Object.keys(data)[0];
let body = data[key][0];
this.interactionsData = data;
if (this.depiction === undefined || this.depiction.ccdId !== body.ligand.chem_comp_id) {
this.initLigandDisplay(body.ligand.chem_comp_id).then(() => {
this.initLigandDisplay(body.ligand.chem_comp_id, withNames).then(() => {
this.presentBindingSite = new Model.BindingSite().fromLigand(key, body, this.depiction);
this.bindingSites.push(this.presentBindingSite);
this.setupLigandScene();
......@@ -344,7 +356,7 @@ class Visualization {
/**
* Add bound molecule interactions to the canvas.
*
* @param {*} data Data content of the API end point
* @param {*} data Data content of the API end point
* /pdb/bound_molecule_interactions
* @param {string} bmId Bound molecule id
* @memberof Visualization
......@@ -472,8 +484,8 @@ class Visualization {
private computeBoundingBox(minX: number, maxX: number, minY: number, maxY: number) {
// The width and the height of the graph
let molWidth = (maxX - minX) + 1; // +1 to avoid 0 division
let molHeight = (maxY - minY) + 1;
let molWidth = Math.max((maxX - minX), this.parent.offsetWidth);
let molHeight = Math.max((maxY - minY), this.parent.offsetHeight);
// how much larger the drawing area is than the width and the height
let widthRatio = this.parent.offsetWidth / molWidth;
......@@ -495,8 +507,7 @@ class Visualization {
this.canvas.attr('transform', `translate(${xTrans}, ${yTrans}) scale(${minRatio})`);
// tell the zoomer what we did so that next we zoom, it uses the
// transformation we entered here
// transformation we entered here
let translation = d3.zoomIdentity.translate(xTrans, yTrans).scale(minRatio);
this.zoomHandler?.transform(this.svg, translation);
}
......@@ -761,7 +772,7 @@ class Visualization {
this.simulation = d3.forceSimulation(this.presentBindingSite.interactionNodes)
.force('link', forceLink)
.force('charge', charge) //strength
.force('charge', charge) //strength
.force('collision', collision)
.on('tick', () => this.simulationStep());
......@@ -771,7 +782,7 @@ class Visualization {
/**
* Setup display of interactions for bound molecule.
* Setup display of interactions for bound molecule.
* * This includes: setup of links, nodes, simulation and subscribing to relevant events.
* No depiction is required for this step.
*
......@@ -818,7 +829,7 @@ class Visualization {
this.simulation = d3.forceSimulation(this.presentBindingSite.interactionNodes)
.force('link', forceLink)
.force('charge', charge) //strength
.force('charge', charge) //strength
.force('collision', collision)
.force('center', center)
.on('tick', () => this.simulationStep());
......
......@@ -234,6 +234,15 @@ class UI {
.attr('class', 'icon icon-common icon-sync-alt')
.on('click', () => this.reinitialize());
}
if (p.names) {
dynamicPanel.append('i')
.attr('id', 'pdb-lig-env-names-btn')
.attr('title', 'Show/hide atom names')
.attr('class', 'icon icon-common icon-font')
.classed('active', false)
.on('click', () => this.showNames());
}
}
if (p.tooltip) {
......@@ -299,6 +308,21 @@ class UI {
}
}
private showNames() {
let btn = d3.select(this.parent).select('#pdb-lig-env-names-btn');
let isActive = btn.classed('active');
if (isActive) {
this.display.toggleDepiction(false);
btn.style('color', '#637ca0');
btn.classed('active', false);
} else {
this.display.toggleDepiction(true);
btn.style('color', '');
btn.classed('active', true);
}
}
private showHelp() {
let el = d3.select(this.parent).select('#pdb-lig-env-help-container');
let btn = d3.select(this.parent).select('#pdb-lig-env-help-btn');
......
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