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Commit e0b0db4e authored by Lukas Pravda's avatar Lukas Pravda
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Improve residue-level view 

Binding partners are placed along the vector of one of the bonds from the atom they are bound to.
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      CHANGELOG.md 0 → 100644
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      View file @ e0b0db4e
      # RELEASE 0.1 - 28 January 2019
      First release for public testing.
      ## Features
      * Bound molecule interactions view
      * Residue-level interactions view
      * Schematic view of glycans ([SNFG](https://www.ncbi.nlm.nih.gov/glycans/snfg.html)).
      * Download interactions in `JSON` format.
      * Save image in `SVG` format.
      * Basic help and controls.
      build/app.d.ts
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      View file @ e0b0db4e
      ......@@ -111,9 +111,10 @@ declare class Depiction {
      labels: any;
      constructor();
      load(id: string): Promise<this>;
      getInitalAtomPosition(atomName: string): number[];
      getInitalAtomPosition(atomNames: string[]): number[];
      appendBondVisualsTo(root: any): void;
      appendTextsTo(root: any): void;
      sortMap(map: Map<string, number>): Map<string, number>;
      }
      declare class Atom {
      name: string;
      ......
      build/app.js
      + 32
      − 6
      View file @ e0b0db4e
      ......@@ -29,10 +29,10 @@ var Models;
      if (['SER', 'SEP', 'THR', 'ASN', 'GLN', 'TPO'].includes(this.label_comp_id)) {
      return 'polar';
      }
      if (['ALA', 'VAL', 'ILE', 'LEU', 'MET', 'MSE'].includes(this.label_comp_id)) {
      if (['ALA', 'VAL', 'ILE', 'LEU', 'MET', 'PRO', 'MSE'].includes(this.label_comp_id)) {
      return 'aliphatic';
      }
      if (['TRP', 'TYR', 'PHE', 'HIS', 'PRO'].includes(this.label_comp_id)) {
      if (['TRP', 'TYR', 'PHE', 'HIS'].includes(this.label_comp_id)) {
      return 'aromatic';
      }
      return 'others';
      ......@@ -338,10 +338,23 @@ class Depiction {
      return this;
      });
      }
      getInitalAtomPosition(atomName) {
      let thisAtom = this.atoms.find(x => x.name === atomName);
      getInitalAtomPosition(atomNames) {
      if (this.atoms.length === 1) {
      return [this.atoms[0].x, this.atoms[0].y];
      }
      // ideally we want to find an atom which is part just a single bond to get nice initial position.
      // If there is no such atom any will do
      let searchStruct = new Map();
      this.bonds.forEach(x => {
      searchStruct.set(x.bgn.name, searchStruct.get(x.bgn.name) === undefined ? 1 : searchStruct.get(x.bgn.name) + 1);
      searchStruct.set(x.end.name, searchStruct.get(x.end.name) === undefined ? 1 : searchStruct.get(x.end.name) + 1);
      });
      searchStruct = this.sortMap(searchStruct); // ascending order so we hit the those with less partners sooner.
      let thisAtomName = [...searchStruct.keys()].find(x => atomNames.findIndex(y => y === x) !== -1);
      let thisAtom = this.atoms.find(x => x.name === thisAtomName);
      let bond = this.bonds.find(x => x.containsAtom(thisAtom));
      let otherAtom = bond.getOtherAtom(thisAtom);
      // to place the residue node a bond apart from the bondin atom
      let v = [otherAtom.x - (2 * (otherAtom.x - thisAtom.x)), otherAtom.y - 2 * ((otherAtom.y - thisAtom.y))];
      return v;
      }
      ......@@ -370,6 +383,19 @@ class Depiction {
      }
      });
      }
      sortMap(map) {
      let vals = [...map.values()].sort();
      let newMap = new Map();
      vals.forEach(x => {
      map.forEach((value, key) => {
      if (x === value) {
      newMap.set(key, x);
      return;
      }
      });
      });
      return newMap;
      }
      }
      class Atom {
      constructor(item) {
      ......@@ -588,8 +614,8 @@ class Visualization {
      visuals.nodes.forEach(x => {
      if (!(x instanceof Models.ResidueNode))
      return;
      let lnk = visuals.links.find(y => y.source.equals(x));
      let position = depiction.getInitalAtomPosition(lnk.target.atomName);
      let lnks = visuals.links.filter(y => y.source.equals(x)).map(x => x.target.atomName);
      let position = depiction.getInitalAtomPosition(lnks);
      x.x = position[0] + Math.random() * 50;
      x.y = position[1] + Math.random() * 50;
      });
      ......
      build/app.js.map
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      View file @ e0b0db4e
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      \ No newline at end of file
      src/Models.ts
      + 5
      − 5
      View file @ e0b0db4e
      ......@@ -186,7 +186,7 @@ namespace Models {
      ["hydrophobic", new Array<string>("hydrophobic")],
      ["aromatic", new Array<string>("aromatic")],
      ["metal", new Array<string>("metal_complex")],
      ["clashes", new Array<string>("clash", "vdw_clash")],
      ["clashes", new Array<string>("clash", "vdw_clash")],
      ["proximal", new Array<string>("proximal")],
      ]);
      let contacts = this.getTypes();
      ......@@ -240,7 +240,7 @@ namespace Models {
      ["hydrophobic", new Array<string>("hydrophobic")],
      ["aromatic", new Array<string>("aromatic")],
      ["metal", new Array<string>("metal_complex")],
      ["clashes", new Array<string>("clash", "vdw_clash")]
      ["clashes", new Array<string>("clash", "vdw_clash")]
      ]);
      ......@@ -296,9 +296,9 @@ namespace Models {
      let relevantContacts = this.contacts
      .filter(x => (x.partnerA.residue.equals(r) || x.partnerB.residue.equals(r)) && !x.isBoundMoleculePart); //
      relevantContacts.forEach(x => {
      let atomNode: AtomNode = undefined;
      let residueNode: ResidueNode = undefined;
      ......
      src/depictions.ts
      + 38
      − 8
      View file @ e0b0db4e
      ......@@ -25,15 +25,29 @@ class Depiction {
      return this;
      }
      public getInitalAtomPosition(atomName: string) {
      let thisAtom = this.atoms.find(x => x.name === atomName);
      public getInitalAtomPosition(atomNames: string[]) {
      if (this.atoms.length === 1) {
      return [this.atoms[0].x, this.atoms[0].y]
      }
      // ideally we want to find an atom which is part just a single bond to get nice initial position.
      // If there is no such atom any will do
      let searchStruct = new Map<string, number>();
      this.bonds.forEach(x => {
      searchStruct.set(x.bgn.name, searchStruct.get(x.bgn.name) === undefined ? 1 : searchStruct.get(x.bgn.name) + 1);
      searchStruct.set(x.end.name, searchStruct.get(x.end.name) === undefined ? 1 : searchStruct.get(x.end.name) + 1);
      });
      searchStruct = this.sortMap(searchStruct); // ascending order so we hit the those with less partners sooner.
      let thisAtomName = [...searchStruct.keys()].find(x => atomNames.findIndex(y => y === x) !== -1)
      let thisAtom = this.atoms.find(x => x.name === thisAtomName);
      let bond = this.bonds.find(x => x.containsAtom(thisAtom));
      let otherAtom = bond.getOtherAtom(thisAtom);
      let v = [otherAtom.x - (2* (otherAtom.x - thisAtom.x)) , otherAtom.y - 2*((otherAtom.y - thisAtom.y))];
      return v;
      let otherAtom = bond.getOtherAtom(thisAtom);
      // to place the residue node a bond apart from the bondin atom
      let v = [otherAtom.x - (2 * (otherAtom.x - thisAtom.x)), otherAtom.y - 2 * ((otherAtom.y - thisAtom.y))];
      return v;
      }
      ......@@ -63,6 +77,22 @@ class Depiction {
      }
      });
      }
      public sortMap(map: Map<string, number>) {
      let vals = [...map.values()].sort();
      let newMap = new Map<string, number>();
      vals.forEach(x => {
      map.forEach((value, key) => {
      if (x === value) {
      newMap.set(key, x);
      return;
      }
      })
      });
      return newMap;
      }
      }
      ......@@ -95,11 +125,11 @@ class Bond {
      public getOtherAtom(other: Atom) {
      if (!this.bgn.equals(other) && !this.end.equals(other)) throw new Error(`Atom ${other.name} is not a part of the bond.`);
      return this.bgn.equals(other) ? this.end : this.bgn;
      }
      public containsAtom(other: Atom) {
      public containsAtom(other: Atom) {
      return this.bgn.equals(other) || this.end.equals(other);
      }
      }
      ......
      src/visualization.ts
      + 63
      − 63
      View file @ e0b0db4e
      ......@@ -15,7 +15,7 @@ class Visualization {
      private nodes: any;
      private links: any
      // #endregion
      // #region ui properties
      private screenshotBtn: d3.Selection<d3.BaseType, {}, HTMLElement, any>;
      private centerBtn: d3.Selection<d3.BaseType, {}, HTMLElement, any>;
      ......@@ -28,7 +28,7 @@ class Visualization {
      // #region data properties
      private pdbId: string;
      private glycanMapper: GlycanMapper;
      private selectedBindingSite: Models.BindingSite;
      private selectedBindingSite: Models.BindingSite;
      // #endregion
      // #region handlers
      ......@@ -72,10 +72,10 @@ class Visualization {
      .append('svg')
      .attr('xmlns', 'http://www.w3.org/2000/svg')
      .attr('width', () => this.width)
      .attr('height', () => this.height);
      .attr('height', () => this.height);
      this.visualization = this.svg.append('g').attr('id', 'vis-root');
      this.glycanMapper = new GlycanMapper('het_mapping.json', 'glycans.xml');
      this.visualization = this.svg.append('g').attr('id', 'vis-root');
      this.glycanMapper = new GlycanMapper('het_mapping.json', 'glycans.xml');
      }
      ......@@ -89,14 +89,14 @@ class Visualization {
      d3.json(`${this.pdbId}.json`)
      .catch(e => { throw e; })
      .then((data: any) => {
      this.selectedBindingSite = new Models.BindingSite(data.boundMolecules[i]);
      .then((data: any) => {
      this.selectedBindingSite = new Models.BindingSite(data.boundMolecules[i]);
      this.setupScene();
      });
      }
      private saveSvg(ctx: Visualization) {
      private saveSvg(ctx: Visualization) {
      d3.text('svgstyles.css').then(x => {
      let svgToDl = d3.select('#int-canvas');
      svgToDl.select('svg')
      ......@@ -116,11 +116,11 @@ class Visualization {
      });
      }
      private downloadInteractionsData(ctx: Visualization): void {
      let downloadLink = document.createElement('a');
      let dataBlob = new Blob([JSON.stringify(ctx.selectedBindingSite.rawData, null, 4)], { type: 'application/json' });
      let dataBlob = new Blob([JSON.stringify(ctx.selectedBindingSite.rawData, null, 4)], { type: 'application/json' });
      downloadLink.href = URL.createObjectURL(dataBlob);
      downloadLink.download = `${ctx.pdbId}_interactions_data.json`;
      ......@@ -160,9 +160,9 @@ class Visualization {
      //https://stackoverflow.com/questions/40722344/understanding-d3-with-an-example-mouseover-mouseup-with-multiple-arguments
      private nodeMouseOver(x: Models.ResidueNode, i: number, g: any) {
      private nodeMouseOver(x: Models.ResidueNode, i: number, g: any) {
      x.scale = 1.5;
      d3.select(g[i])
      .attr('transform', () => `translate(${x.x},${x.y}) scale(${x.scale})`)
      ......@@ -186,19 +186,19 @@ class Visualization {
      // #region Labels
      private resize(ctx: Visualization, isBoundMolecule: boolean) {
      private resize(ctx: Visualization, isBoundMolecule: boolean) {
      ctx.width = document.getElementById('int-canvas').clientWidth;
      ctx.height = window.innerHeight;
      ctx.svg.attr('width', ctx.width).attr('height', ctx.height);
      if (isBoundMolecule) {
      ctx.simulation.force('center', d3.forceCenter(ctx.width / 2, ctx.height / 2))
      .restart();
      } else {
      } else {
      ctx.simulation.restart();
      }
      ctx.zoom_handler(ctx.svg);
      }
      ......@@ -234,12 +234,12 @@ class Visualization {
      this.nodeMouseOut(n, i, g);
      this.showLabel(n);
      let depiction = await new Depiction().load(n.residue.label_comp_id);
      let depiction = await new Depiction().load(n.residue.label_comp_id);
      let xShift = (this.width / 2) - (depiction.x / 2);
      let yShift = (this.height / 2) - (depiction.y / 2);
      let visuals = this.selectedBindingSite.getResidueInteractions(n.residue, depiction.atoms);
      let visuals = this.selectedBindingSite.getResidueInteractions(n.residue, depiction.atoms);
      this.visualization = this.svg.append('g')
      .attr('id', 'vis-root')
      ......@@ -256,36 +256,36 @@ class Visualization {
      this.tooltip.transition()
      .duration(500)
      .style('opacity', 0);
      });
      });
      depiction.appendBondVisualsTo(this.visualization);
      depiction.appendTextsTo(this.visualization);
      depiction.appendTextsTo(this.visualization);
      visuals.nodes.forEach(x => {
      if (!(x instanceof Models.ResidueNode)) return;
      let lnk = visuals.links.find(y => y.source.equals(x));
      let position = depiction.getInitalAtomPosition(lnk.target.atomName);
      let lnks = visuals.links.filter(y => y.source.equals(x)).map(x => x.target.atomName);
      let position = depiction.getInitalAtomPosition(lnks);
      x.x = position[0] + Math.random() * 50;
      x.y = position[1]+ Math.random() * 50;
      x.y = position[1] + Math.random() * 50;
      });
      //# region copy-paste
      //setup nodes
      this.nodes = this.visualization.append('g')
      .selectAll()
      .data(visuals.nodes)
      .enter().append('g');
      this.nodes.filter(x => x instanceof Models.ResidueNode)
      .enter().append('g');
      this.nodes.filter(x => x instanceof Models.ResidueNode)
      .attr('class', (e: Models.ResidueNode) => `svg-node svg-${e.residue.getResidueType()}-res`)
      .on('mouseover', (x: Models.ResidueNode, i: number, g: any) => this.nodeMouseOver(x, i, g))
      .on('mouseout', (x: Models.ResidueNode, i: number, g: any) => context.nodeMouseOut(x, i, g));
      // draw glycans
      this.nodes.filter(x => x instanceof Models.ResidueNode)
      .filter((x: Models.ResidueNode) => this.glycanMapper.mapping.has(x.residue.label_comp_id))
      ......@@ -296,7 +296,7 @@ class Visualization {
      .filter(x => x instanceof Models.ResidueNode)
      .filter(x => !this.glycanMapper.mapping.has(x.residue.label_comp_id))
      .append('circle')
      .attr('r', '25');
      .attr('r', '25');
      this.nodes
      .filter(x => x instanceof Models.ResidueNode)
      ......@@ -313,28 +313,28 @@ class Visualization {
      .text(labels[i]);
      }
      });
      // let forceLink = d3.forceLink()
      // .links(visuals.links)
      // .distance(150)
      // .strength(0.5);
      // let forceLink = d3.forceLink()
      // .links(visuals.links)
      // .distance(150)
      // .strength(0.5);
      //let charge = d3.forceManyBody().strength(-1000).distanceMin(50).distanceMax(150);
      let collision = d3.forceCollide().radius(50)
      //let center = d3.forceCenter(xShift, yShift);
      this.simulation = d3.forceSimulation(visuals.nodes)
      // .force('link', forceLink)
      // .force('charge', charge) //strength
      // .force('link', forceLink)
      // .force('charge', charge) //strength
      .force('collision', collision)
      // .force('center', center)
      .on('tick', () => this.simulationStep(this));
      // .force('center', center)
      .on('tick', () => this.simulationStep(this));
      this.drag_handler(this.nodes);
      this.zoom_handler(this.svg);
      //#endregion
      d3.select(window).on('resize', () => this.resize(context, false));
      d3.select(window).on('resize', () => this.resize(context, false));
      }
      ......@@ -367,9 +367,9 @@ class Visualization {
      let pivot = visuals.nodes.filter((x: Models.ResidueNode) => x.residue.isLigand)[0];
      this.selectLigand(pivot, 0, this.nodes);
      }
      this.nodes.filter((n: Models.ResidueNode) =>
      this.glycanMapper.mapping.has(n.residue.label_comp_id))
      .html((e: Models.ResidueNode) => this.glycanMapper.getGlycanImage(e.residue.label_comp_id));
      ......@@ -400,7 +400,7 @@ class Visualization {
      let charge = d3.forceManyBody().strength(-1000).distanceMin(55).distanceMax(250);
      let collision = d3.forceCollide(45);
      let center = d3.forceCenter(this.width / 2, this.height / 2);
      this.simulation = d3.forceSimulation(visuals.nodes)
      .force('link', forceLink)
      .force('charge', charge) //strength
      ......@@ -410,10 +410,10 @@ class Visualization {
      this.drag_handler(this.nodes);
      this.zoom_handler(this.svg);
      d3.select(window).on('resize', () => this.resize(context, true));
      d3.select(window).on('resize', () => this.resize(context, true));
      }
      private simulationStep(ctx: Visualization) {
      ctx.nodes.attr('transform', (d) => `translate(${d.x},${d.y}) scale(${d.scale})`);
      ctx.links.attr('x1', (x: any) => x.source.x)
      ......@@ -422,10 +422,10 @@ class Visualization {
      .attr('y2', (x: any) => x.target.y);
      }
      private centerScene(ctx: Visualization){
      private centerScene(ctx: Visualization) {
      if (ctx.nodes.length === 0)
      return;
      return;
      // Get the bounding box
      let minX: any = d3.min(ctx.nodes.data().map((x) => x.x));
      let minY: any = d3.min(ctx.nodes.data().map((x) => x.y));
      ......@@ -433,7 +433,7 @@ class Visualization {
      let maxX: any = d3.max(ctx.nodes.data().map((x) => x.x));
      let maxY: any = d3.max(ctx.nodes.data().map((x) => x.y));
      // The width and the height of the graph
      let molWidth = maxX - minX;
      let molHeight = maxY - minY;
      ......@@ -458,8 +458,8 @@ class Visualization {
      // do the actual moving
      ctx.visualization.attr("transform", `translate(${x_trans}, ${y_trans}) scale(${min_ratio})`);
      // tell the zoomer what we did so that next we zoom, it uses the
      // transformation we entered here
      // tell the zoomer what we did so that next we zoom, it uses the
      // transformation we entered here
      //ctx.zoom_handler.(ctx.svg, x_trans, y_trans);
      //ctx.zoom_handler.scaleTo(ctx.svg, min_ratio);
      ......
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