Commit 3cc4c357 authored by Lukas Pravda's avatar Lukas Pravda
Browse files

allow atom names to be displayed

parent d323cd99
......@@ -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(atom_names: boolean = false) {
this.structure.selectAll("*").remove();
this.appendBondVisuals();
this.appendTexts();
if (atom_names) this.appendAtomNames();
else this.appendLabels();
}
public highlightSubgraph(atoms: Array<string>, color: string = undefined) {
......@@ -145,17 +147,35 @@ 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)
......@@ -172,7 +192,6 @@ class Depiction {
.attr('dominant-baseline', (x: any) => x['dominant-baseline'])
.attr('text-anchor', (x: any) => x['text-anchor'])
.each(function (x: any) {
for (var i = 0; i < x.tspans.length; i++) {
d3.select(this)
.append('tspan')
......@@ -243,7 +262,7 @@ class Atom {
}
/**
*
*
*
* @param {Atom} other
* @returns true if the atoms are equal
......@@ -310,7 +329,7 @@ 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 +378,7 @@ 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[];
......@@ -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
*
......@@ -235,10 +235,10 @@ 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
......@@ -256,7 +256,7 @@ class Visualization {
}
/**
* Download ligand structure given the anotation generated by the
* Download ligand structure given the anotation generated by the
* PDBeChem process.
*
* @param {string} ligandId
......@@ -285,6 +285,10 @@ class Visualization {
this.depiction.draw();
}
public toggleDepiction(atomNames: boolean) {
this.depiction.draw(atomNames);
}
/**
* Add atom highlight to the ligand structure. The previous highlight
......@@ -318,7 +322,7 @@ class Visualization {
/**
* 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
*/
......@@ -344,7 +348,7 @@ 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 +476,8 @@ 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 +499,7 @@ 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 +764,7 @@ 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 +774,7 @@ 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 +821,7 @@ 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.reinitialize) {
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(true);
btn.style('color', '#637ca0');
btn.classed('active', false);
} else {
this.display.toggleDepiction(false);
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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