pdbe-molstar/build/pdbe-molstar-plugin.js

Molstar implementation for PDBe

/**
 * pdbe-molstar
 * @version 3.6.0
 * @link https://github.com/PDBeurope/pdbe-molstar
 * @license Apache 2.0
 */

/*! For license information please see pdbe-molstar-plugin.js.LICENSE.txt */
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d=o.PDBeMolstarPlugin.MAIN_STRUCTURE_ID;let B,h,f,p,I;if("pdb"===r.database)[B,h]=r.target.split("_");else{if("afdb50"!==r.database)throw new Error(`Unknown database: ${r.database}`);B=r.target,h="A"}if(r.tstructure)f=r.tstructure.url,p="cif"===r.tstructure.format||"bcif"===r.tstructure.format?"mmcif":r.tstructure.format,I=r.tstructure.binary;else{if("pdb"!==r.database)throw"afdb50"===r.database?new Error("tstructure must be provided when database==='afdb50'"):new Error(`Unknown database: ${r.database}`);f=(0,a.getStructureUrl)(e.initParams,{pdbId:B,queryType:"atoms",queryParams:{auth_asym_id:h}}),p="mmcif",I="bcif"===e.initParams.encoding}yield e.load({url:f,format:p,isBinary:I,id:t},!1);const m=null===(l=null===(A=e.getStructure(d))||void 0===A?void 0:A.cell.obj)||void 0===l?void 0:l.data,Q=null===(g=null===(u=e.getStructure(t))||void 0===u?void 0:u.cell.obj)||void 0===g?void 0:g.data;if(!m)throw new Error("Query structure not loaded");if(!Q)throw new Error("Target structure not loaded");const[E,C]=function(e,t,r,n){if(t.length!==n.length)throw new Error("Length of qaln and taln must be the same");const A=t.length;let i=e,o=r;const a=[],s=[];for(let e=0;e<A;e++)"-"===t[e]?o++:("-"===n[e]||(a.push(i),s.push(o),o++),i++);return[a,s]}(r.qstart-1,r.qaln,r.tstart-1,r.taln),y=function(e,t){const r=e.model.entities.data,n=r._rowCount,A=e.model.atomicHierarchy.chains,i=A._rowCount,o=new Set;for(let e=0;e<n;e++)"polymer"===r.type.value(e)&&o.add(r.id.value(e));for(let e=0;e<i;e++)if(A.auth_asym_id.value(e)===t&&o.has(A.label_entity_id.value(e)))return A.label_asym_id.value(e);throw new Error(`There is no polymer chain with auth_asym_id ${t}.`)}(Q,h),[v,b]=function(e,t){const r=e.x.length;if(t.x.length!==r)throw new Error("ValueError: Positions a and b must have the same length");const n=[];for(let A=0;A<r;A++)isNaN(e.x[A])||isNaN(t.x[A])||n.push(A);const A=n.length;if(A===r)return[e,t];{const r=i.MinimizeRmsd.Positions.empty(A),o=i.MinimizeRmsd.Positions.empty(A);for(let i=0;i<A;i++){const A=n[i];r.x[i]=e.x[A],r.y[i]=e.y[A],r.z[i]=e.z[A],o.x[i]=t.x[A],o.y[i]=t.y[A],o.z[i]=t.z[A]}return[r,o]}}(c(m,E,"A"),c(Q,C,y)),D=i.MinimizeRmsd.compute({a:v,b});return yield(0,s.transform)(e.plugin,e.getStructure(t).cell,D.bTransform),yield e.visual.select({data:[{color:n}],structureId:t}),yield e.visual.reset({camera:!0}),Object.assign(Object.assign({},D),{nAligned:v.x.length})}))},t.exportModels=function(e,t="cif"){return(0,A.exportHierarchy)(e.plugin,{format:t})};const n=r(31635),A=r(98567),i=r(17942),o=r(8509),a=r(50584),s=r(93901);function c(e,t,r){const n=function(e,t){const r=e.model.atomicHierarchy,n=Array.from(r.chains.label_asym_id.toArray()).indexOf(t),A=r.chainAtomSegments.offsets[n],i=r.chainAtomSegments.offsets[n+1];return{start:r.residueAtomSegments.index[A],end:r.residueAtomSegments.index[i-1]+1}}(e,r),A=t.map((e=>n.start+e));if(A[A.length-1]>=n.end)throw new Error("Residues out of range");const o=function(e,t){const r=e.model.atomicHierarchy,n=e.model.atomicConformation,A=t.length,o=i.MinimizeRmsd.Positions.empty(A);for(let i=0;i<A;i++){const A=t[i],a=r.residueAtomSegments.offsets[A],s=r.residueAtomSegments.offsets[A+1];let c=-1;for(let e=a;e<s;e++)if("CA"===r.atoms.label_atom_id.value(e)){c=e;break}if(c>=0)o.x[i]=n.x[c],o.y[i]=n.y[c],o.z[i]=n.z[c];else{const t=r.residues.label_seq_id.value(A);console.warn(`Foldseek extension: C alpha not found for residue ${t} in ${e.model.entry}. Ignoring this residue.`),o.x[i]=NaN,o.y[i]=NaN,o.z[i]=NaN}}return o}(e,A);return o}},14628:(e,t,r)=>{"use strict";Object.defineProperty(t,"__esModule",{value:!0}),t.loadInteractions_example=function(e,t){return h(e,Object.assign(Object.assign({},t),{interactions:f}))},t.loadInteractions=h,t.clearInteractions=function(e){return n.__awaiter(this,void 0,void 0,(function*(){const t=l(e.plugin).visuals;if(t){for(const e of t)yield e.delete();t.length=0}}))};const n=r(31635),A=r(72658),i=r(72010),o=r(48311),a=r(15883),s=r(8509),c=r(50584),l=r(58640).ExtensionCustomState.getter("pdbe-custom-interactions"),u="white",g=.075,d=.1,B=1;function h(e,t){return n.__awaiter(this,void 0,void 0,(function*(){var r,n,h;const f=null!==(r=t.structureId)&&void 0!==r?r:s.PDBeMolstarPlugin.MAIN_STRUCTURE_ID,p=e.getStructure(f);if(!p)throw new Error(`Did not find structure with ID "${f}"`);const I=function(e){var t,r,n,A,o,a,s;const l=i.MVSData.createBuilder(),h=l.primitives({opacity:null!==(t=e.opacity)&&void 0!==t?t:B,color:null!==(r=e.color)&&void 0!==r?r:u});for(const t of e.interactions)h.tube({start:{expressions:(0,c.queryParamsToMvsComponentExpressions)([t.start])},end:{expressions:(0,c.queryParamsToMvsComponentExpressions)([t.end])},radius:null!==(A=null!==(n=t.radius)&&void 0!==n?n:e.radius)&&void 0!==A?A:g,dash_length:null!==(a=null!==(o=t.dash_length)&&void 0!==o?o:e.dash_length)&&void 0!==a?a:d,color:t.color,tooltip:t.tooltip});const f=null===(s=l.getState().root.children)||void 0===s?void 0:s.find((e=>"primitives"===e.kind));if(!f)throw new Error('AssertionError: Failed to create MVS "primitives" subtree.');return f}(t),m=e.plugin.build(),Q=m.to(p.cell).apply(A.MVSInlinePrimitiveData,{node:I},{tags:["custom-interactions-data"]});Q.apply(A.MVSBuildPrimitiveShape,{kind:"mesh"}).apply(o.ShapeRepresentation3D,{},{tags:["custom-interactions-mesh"]}),Q.apply(A.MVSBuildPrimitiveShape,{kind:"lines"}).apply(o.ShapeRepresentation3D,{},{tags:["custom-interactions-lines"]}),Q.apply(A.MVSBuildPrimitiveShape,{kind:"labels"}).apply(o.ShapeRepresentation3D,{},{tags:["custom-interactions-labels"]}),yield m.commit();const E={ref:Q.ref,setVisibility:t=>(0,a.setSubtreeVisibility)(e.plugin.state.data,Q.ref,!t),delete:()=>e.plugin.build().delete(Q.ref).commit()};return(null!==(n=(h=l(e.plugin)).visuals)&&void 0!==n?n:h.visuals=[]).push(E),E}))}const f=[{start:{auth_asym_id:"C",auth_seq_id:143,atoms:["CBC"]},end:{auth_asym_id:"C",auth_seq_id:32,atoms:["CE"]},color:"yellow",tooltip:"<strong>Hydrophobic interaction</strong><br>HEM 143 | CBC — MET 32 | CE"},{start:{auth_asym_id:"C",auth_seq_id:143,atoms:["CBC"]},end:{auth_asym_id:"C",auth_seq_id:32,atoms:["SD"]},color:"yellow",tooltip:"<strong>Hydrophobic interaction</strong><br>HEM 143 | CBC — MET 32 | SD"},{start:{auth_asym_id:"C",auth_seq_id:143,atoms:["CMD"]},end:{auth_asym_id:"C",auth_seq_id:42,atoms:["O"]},color:"gray",tooltip:"<strong>Mixed interaction</strong><br>Vdw, Weak polar<br>HEM 143 | CMD — TYR 42 | O"},{start:{auth_asym_id:"C",auth_seq_id:143,atoms:["C1B","C2B","C3B","C4B","NB"]},end:{auth_asym_id:"C",auth_seq_id:136,atoms:["CD1"]},color:"magenta",tooltip:"<strong>CARBONPI interaction</strong><br>HEM 143 | C1B, C2B, C3B, C4B, NB — LEU 136 | CD1"}]},487:(e,t,r)=>{"use strict";Object.defineProperty(t,"__esModule",{value:!0}),t.StateGalleryExtensionFunctions=t.StateGallery=t.StateGalleryCustomState=t.StateGalleryExtensionName=void 0;const n=r(79668),A=r(51142),i=r(9422),o=r(79364),a=r(58640),s=r(94334),c=r(12039);t.StateGalleryExtensionName="pdbe-state-gallery",t.StateGalleryCustomState=a.ExtensionCustomState.getter(t.StateGalleryExtensionName),t.StateGallery=n.PluginBehavior.create({name:t.StateGalleryExtensionName,category:"misc",display:{name:"3D State Gallery",description:"Browse pre-computed 3D states for a PDB entry"},ctor:class extends n.PluginBehavior.Handler{register(){(0,t.StateGalleryCustomState)(this.ctx).requestedImage=new o.BehaviorSubject(void 0),(0,t.StateGalleryCustomState)(this.ctx).manager=new o.BehaviorSubject(void 0),(0,t.StateGalleryCustomState)(this.ctx).status=new o.BehaviorSubject("ready"),this.toggleStructureControls(this.params.showControls),this.toggleTitleBox(this.params.showTitleBox)}update(e){return!(0,A.shallowEqual)(e,this.params)&&(this.toggleStructureControls(e.showControls),this.toggleTitleBox(e.showTitleBox),this.params=e,!0)}unregister(){this.toggleStructureControls(!1),this.toggleTitleBox(!1),a.ExtensionCustomState.clear(this.ctx,t.StateGalleryExtensionName)}toggleStructureControls(e){a.PluginCustomControls.toggle(this.ctx,"structure-tools",t.StateGalleryExtensionName,c.StateGalleryControls,e)}toggleTitleBox(e){a.PluginCustomControls.toggle(this.ctx,"viewport-top-center",t.StateGalleryExtensionName,c.StateGalleryTitleBox,e)}},params:()=>({showControls:i.ParamDefinition.Boolean(!0,{description:'Show "3D State Gallery" section in Structure Tools controls'}),showTitleBox:i.ParamDefinition.Boolean(!0,{description:"Show a box in viewport with state title and arrows to move between states"})})}),t.StateGalleryExtensionFunctions={StateGalleryManager:s.StateGalleryManager,StateGalleryCustomState:t.StateGalleryCustomState,UI:{StateGalleryControls:c.StateGalleryControls}}},44735:(e,t,r)=>{"use strict";Object.defineProperty(t,"__esModule",{value:!0}),t.StateGalleryConfig=t.StateGalleryConfigDefaults=void 0,t.getStateGalleryConfig=function(e){return A.PluginConfigUtils.getConfigValues(e,t.StateGalleryConfig,t.StateGalleryConfigDefaults)};const n=r(31517),A=r(50584);t.StateGalleryConfigDefaults={ServerUrl:"https://www.ebi.ac.uk/pdbe/static/entry",LoadCanvasProps:!1,LoadCameraOrientation:!0,CameraPreTransitionMs:100,CameraTransitionMs:400},t.StateGalleryConfig={ServerUrl:new n.PluginConfigItem("pdbe-state-gallery.server-url",t.StateGalleryConfigDefaults.ServerUrl),LoadCanvasProps:new n.PluginConfigItem("pdbe-state-gallery.load-canvas-props",t.StateGalleryConfigDefaults.LoadCanvasProps),LoadCameraOrientation:new n.PluginConfigItem("pdbe-state-gallery.load-camera-orientation",t.StateGalleryConfigDefaults.LoadCameraOrientation),CameraPreTransitionMs:new n.PluginConfigItem("pdbe-state-gallery.camera-pre-transition-ms",t.StateGalleryConfigDefaults.CameraPreTransitionMs),CameraTransitionMs:new n.PluginConfigItem("pdbe-state-gallery.camera-transition-ms",t.StateGalleryConfigDefaults.CameraTransitionMs)}},94334:(e,t,r)=>{"use strict";Object.defineProperty(t,"__esModule",{value:!0}),t.StateGalleryManager=t.ImageCategory=void 0;const n=r(31635),A=r(2906),i=r(73868),o=r(17e3),a=r(35332),s=r(39872),c=r(79364),l=r(50584),u=r(487),g=r(44735),d=r(73666),B=r(94830);function h(e,t){if((0,a.isPlainObject)(t))for(const r in t){const n=t[r];"image"===r&&Array.isArray(n)?e.push(...n):h(e,n)}return e}t.ImageCategory=["Entry","Assemblies","Entities","Ligands","Modified 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null!==(g=null===(u=null===(c=null==e?void 0:e.entry)||void 0===c?void 0:c.bfactor)||void 0===u?void 0:u.image)&&void 0!==g?g:[])t.push(Object.assign(Object.assign(Object.assign({},r),{category:"Entry"}),d.ImageTitles.bfactor(r)));const C=null==e?void 0:e.assembly;for(const e in C)for(const r of null!==(B=C[e].image)&&void 0!==B?B:[])t.push(Object.assign(Object.assign(Object.assign({},r),{category:"Assemblies"}),d.ImageTitles.assembly(r,{assemblyId:e})));const y=null==e?void 0:e.entity;for(const e in y)for(const r of null!==(f=y[e].image)&&void 0!==f?f:[])t.push(Object.assign(Object.assign(Object.assign({},r),{category:"Entities"}),d.ImageTitles.entity(r,{entityId:e})));const v=null===(p=null==e?void 0:e.entry)||void 0===p?void 0:p.ligands;for(const e in v)for(const r of null!==(I=v[e].image)&&void 0!==I?I:[])t.push(Object.assign(Object.assign(Object.assign({},r),{category:"Ligands"}),d.ImageTitles.ligand(r,{compId:e})));const b=null===(m=null==e?void 0:e.entry)||void 0===m?void 0:m.mod_res;for(const e in b)for(const r of null!==(Q=b[e].image)&&void 0!==Q?Q:[])t.push(Object.assign(Object.assign(Object.assign({},r),{category:"Modified residues"}),d.ImageTitles.modres(r,{compId:e})));for(const e in y){const r=y[e].database;for(const n in r){const A=r[n];for(const r in A)for(const i of null!==(E=A[r].image)&&void 0!==E?E:[])t.push(Object.assign(Object.assign(Object.assign({},i),{category:"Domains"}),d.ImageTitles.domain(i,{db:n,familyId:r,entityId:e})))}}return h(t,e),(0,l.distinct)(t,(e=>e.filename))}return h([],e)}(r,!0);var i;this.images=(i=["_side","_top"],A.filter((e=>!i.some((t=>e.filename.endsWith(t)))))),this.filenameIndex=(0,l.createIndex)(this.images.map((e=>e.filename))),this.events.status.subscribe((e=>{var t,r,n;const A=(0,u.StateGalleryCustomState)(this.plugin);null===(t=A.status)||void 0===t||t.next(e),(null===(r=A.manager)||void 0===r?void 0:r.value)!==this&&(null===(n=A.manager)||void 0===n||n.next(this))})),this.events.requestedImage.subscribe((e=>{var t,r,n;const A=(0,u.StateGalleryCustomState)(this.plugin);null===(t=A.requestedImage)||void 0===t||t.next(e),(null===(r=A.manager)||void 0===r?void 0:r.value)!==this&&(null===(n=A.manager)||void 0===n||n.next(this))}))}static create(e,t,r){return n.__awaiter(this,void 0,void 0,(function*(){const A=Object.assign(Object.assign({},(0,g.getStateGalleryConfig)(e)),r),i=yield function(e,t,r){return n.__awaiter(this,void 0,void 0,(function*(){const n=(0,l.combineUrl)(t,r+".json");try{const t=yield e.runTask(e.fetch(n));return JSON.parse(t)[r]}catch(e){return}}))}(e,A.ServerUrl,t);return void 0===i&&console.error(`StateGalleryManager failed to get data for entry ${t}`),new this(e,t,i,A)}))}_load(e){return n.__awaiter(this,void 0,void 0,(function*(){if(!this.plugin.canvas3d)throw new Error("plugin.canvas3d is not defined");let t=yield this.getSnapshot(e);const r=(n=this.plugin).canvas3d?(n.canvas3d.commit(),n.canvas3d.camera.getSnapshot()):A.Camera.createDefaultSnapshot();var n;const a=function(e){var t,r,n,A;const i=JSON.parse(e);return null===(A=null===(n=null===(r=null===(t=null==i?void 0:i.entries)||void 0===t?void 0:t[0])||void 0===r?void 0:r.snapshot)||void 0===n?void 0:n.camera)||void 0===A?void 0:A.current}(t),c=Object.assign(Object.assign({},r),function(e,t){if(void 0===t)return;const r=i.Vec3.sub((0,i.Vec3)(),t.target,t.position);return e.getInvariantFocus(t.target,t.radius,t.up,r)}(this.plugin.canvas3d.camera,a));t=function(e,t){var r;const n=JSON.parse(e);for(const e of null!==(r=n.entries)&&void 0!==r?r:[])if(e.snapshot&&(t.removeCanvasProps&&e.snapshot.canvas3d&&delete e.snapshot.canvas3d.props,t.replaceCamera)){const{camera:r,transitionDurationInMs:n}=t.replaceCamera;e.snapshot.camera={current:r,transitionStyle:n>0?"animate":"instant",transitionDurationInMs:n>0?n:void 0}}return JSON.stringify(n)}(t,{removeCanvasProps:!this.options.LoadCanvasProps,replaceCamera:{camera:this.options.LoadCameraOrientation&&!this.firstLoaded?c:r,transitionDurationInMs:0}}),yield this.plugin.managers.snapshot.setStateSnapshot(JSON.parse(t)),yield(0,s.sleep)(this.firstLoaded?this.options.CameraPreTransitionMs:0),yield o.PluginCommands.Camera.Reset(this.plugin,{snapshot:this.options.LoadCameraOrientation?c:void 0,durationMs:this.firstLoaded?this.options.CameraTransitionMs:0}),this.firstLoaded=!0}))}load(e){return n.__awaiter(this,void 0,void 0,(function*(){var t;let r;"string"==typeof e&&(e=null!==(t=this.getImageByFilename(e))&&void 0!==t?t:{filename:e}),this.events.requestedImage.next(e),this.events.loadedImage.next(void 0),this.events.status.next("loading");try{return r=yield this.loader.requestRun(e.filename),r}finally{"completed"===(null==r?void 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this.fetchSnapshot(e)}))}getImageByFilename(e){const t=this.filenameIndex.get(e);if(void 0!==t)return this.images[t]}}},73666:(e,t)=>{"use strict";function r(e){const t=(null!=e?e:"").matchAll(/<span [^>]*>([^<]*)<\/span>/g);return Array.from(t).map((e=>e[1]))}function n(e){var t;return null===(t=null==e?void 0:e.match(/\((.*)\)/))||void 0===t?void 0:t[1]}Object.defineProperty(t,"__esModule",{value:!0}),t.ImageTitles=void 0,t.ImageTitles={entry:e=>e.filename.includes("_chemically_distinct_molecules")?{title:"Deposited model (color by entity)"}:e.filename.includes("_chain")?{title:"Deposited model (color by chain)"}:{},validation:e=>({title:"Geometry validation"}),bfactor:e=>({title:"B-factor"}),assembly:(e,t)=>e.filename.includes("_chemically_distinct_molecules")?{title:`Assembly ${t.assemblyId} (color by entity)`}:e.filename.includes("_chain")?{title:`Assembly ${t.assemblyId} (color by chain)`}:{},entity(e,t){const n=r(e.description)[1];return{title:`Entity 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i.Mat4.identity();case"back":return[-1,0,0,0,0,1,0,0,0,0,-1,0,0,0,0,1];case"right":return[0,0,-1,0,0,1,0,0,1,0,0,0,0,0,0,1];case"left":return[0,0,1,0,0,1,0,0,-1,0,0,0,0,0,0,1];case"top":return[1,0,0,0,0,0,-1,0,0,1,0,0,0,0,0,1];case"bottom":return[1,0,0,0,0,0,1,0,0,-1,0,0,0,0,0,1];default:{const t=i.Mat4.fromMat3((0,i.Mat4)(),e);return t[15]=1,t}}};const n=r(31635),A=r(38685),i=r(73868),o=r(28243),a=r(12313),s=r(18842),c=r(459),l=r(17e3),u=r(44804),g=r(13636),d=r(1366),B=r(66139),h=r(24832),f=r(78739),p=r(23391),I=r(39872),m=r(61165);var Q,E,C,y,v,b;function D(e,t){var r;const n=Object.assign({},e);for(const e in t)null!==(r=n[e])&&void 0!==r||(n[e]=t[e]);return n}!function(e){e.mapParams=function(e,t,r){const n=Object.assign({},e);n.options.behaviorRef="volume-streaming"+Math.floor(Math.random()*Math.floor(100)),n.options.emContourProvider="pdbe",n.options.serverUrl="https://www.ebi.ac.uk/pdbe/volume-server";const A={opacity:.49,wireframe:!1},i={opacity:.3,wireframe:!0};return n.options.channelParams.em=D(null==t?void 0:t.em,A),n.options.channelParams["2fo-fc"]=D(null==t?void 0:t["2fo-fc"],A),n.options.channelParams["fo-fc(+ve)"]=D(null==t?void 0:t["fo-fc(+ve)"],i),n.options.channelParams["fo-fc(-ve)"]=D(null==t?void 0:t["fo-fc(-ve)"],i),n},e.displayUsibilityMessage=function(e){l.PluginCommands.Toast.Show(e,{title:"Volume",message:"Streaming enabled, click on a residue or an atom to view the data.",key:"toast-1",timeoutMs:7e3})},e.toggle=function(e){const t=e.state.data,r=t.select(B.StateSelection.Generators.ofTransformer(c.CreateVolumeStreamingInfo))[0];r&&l.PluginCommands.State.ToggleVisibility(e,{state:t,ref:r.transform.ref})}}(Q||(t.PDBeVolumes=Q={})),function(e){e.getLociByPLDDT=function(e,t){const r=g.MolScriptBuilder.struct.modifier.union([g.MolScriptBuilder.struct.modifier.wholeResidues([g.MolScriptBuilder.struct.modifier.union([g.MolScriptBuilder.struct.generator.atomGroups({"chain-test":g.MolScriptBuilder.core.rel.eq([g.MolScriptBuilder.ammp("objectPrimitive"),"atomistic"]),"residue-test":g.MolScriptBuilder.core.rel.gr([A.QualityAssessment.symbols.pLDDT.symbol(),e])})])])]),n=(0,d.compile)(r)(new o.QueryContext(t));return o.StructureSelection.toLociWithSourceUnits(n)}}(E||(t.AlphafoldView=E