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+/*
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+* Copyright (c) 2021 RCSB PDB and contributors, licensed under MIT, See LICENSE file for more info.
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+* @author Joan Segura Mora <joan.segura@rcsb.org>
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+*/
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+
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+import {StructureLoaderInterface} from "./StructureLoaderInterface";
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+import {ViewerActionManagerInterface, ViewerCallbackManagerInterface} from "../StructureViewerInterface";
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+import {StructureRef} from "molstar/lib/mol-plugin-state/manager/structure/hierarchy-state";
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+import {Loci} from "molstar/lib/mol-model/loci";
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+import {alignAndSuperpose} from "molstar/lib/mol-model/structure/structure/util/superposition";
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+import {Structure, StructureElement, Unit} from "molstar/lib/mol-model/structure";
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+import {PluginContext} from "molstar/lib/mol-plugin/context";
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+import {StateObjectRef} from "molstar/lib/mol-state";
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+import {Mat4} from "molstar/lib/mol-math/linear-algebra";
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+import {SymmetryOperator} from "molstar/lib/mol-math/geometry/symmetry-operator";
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+import {PluginStateObject} from "molstar/lib/mol-plugin-state/objects";
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+import {StateTransforms} from "molstar/lib/mol-plugin-state/transforms";
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+import {PluginCommands} from "molstar/lib/mol-plugin/commands";
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+import {LoadMethod, LoadMolstarInterface} from "../StructureViewers/MolstarViewer/MolstarActionManager";
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+import {TagDelimiter} from "@rcsb/rcsb-saguaro-app";
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+
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+const SuperpositionTag = 'SuperpositionTransform';
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+export class MolstarAlignmentLoader implements StructureLoaderInterface<[ViewerCallbackManagerInterface & ViewerActionManagerInterface <LoadMolstarInterface>,{entryId:string;entityId:string;},{entryId:string;entityId:string;}]> {
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+
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+ private readonly structureMap: Map<string,string|undefined> = new Map<string,string|undefined>();
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+
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+ async load(structureViewer: ViewerCallbackManagerInterface & ViewerActionManagerInterface <LoadMolstarInterface>, ref: {entryId:string;entityId:string;}, pdb:{entryId:string;entityId:string;}): Promise<void> {
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+ const structureId: string = `${pdb.entryId}${TagDelimiter.entity}${pdb.entityId}`;
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+ if(!this.structureMap.has(structureId)){
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+ await structureViewer.load({
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+ loadMethod: LoadMethod.loadPdbId,
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+ loadParams:{
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+ pdbId:pdb.entryId
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+ }
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+ });
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+ structureViewer.pluginCall(async (plugin)=>{
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+ this.structureMap.set(
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+ structureId,
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+ plugin.managers.structure.hierarchy.current.structures[ plugin.managers.structure.hierarchy.current.structures.length -1].properties?.cell?.obj?.data?.units[0]?.model?.id
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+ );
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+
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+ });
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+
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+ } else {
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+ structureViewer.pluginCall(async (plugin)=>{
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+ const pdbStr: StructureRef|undefined = plugin.managers.structure.hierarchy.current.structures.find(s=>s.properties?.cell?.obj?.data?.units[0]?.model?.id == this.structureMap.get(structureId));
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+ if(pdbStr) {
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+ plugin.managers.structure.hierarchy.remove([pdbStr]);
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+ this.structureMap.delete(structureId);
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+ await PluginCommands.Camera.Reset(plugin);
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+ }
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+ });
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+ return;
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+ }
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+ if(ref.entryId != pdb.entryId)
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+ structureViewer.pluginCall(async (plugin)=>{
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+ const pdbId: string = `${pdb.entryId}${TagDelimiter.entity}${pdb.entityId}`;
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+ const refId: string = `${ref.entryId}${TagDelimiter.entity}${ref.entityId}`;
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+ const refStr: StructureRef|undefined = plugin.managers.structure.hierarchy.current.structures.find(s=>s.properties?.cell?.obj?.data?.units[0]?.model?.id == this.structureMap.get(refId));
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+ const pdbStr: StructureRef|undefined = plugin.managers.structure.hierarchy.current.structures.find(s=>s.properties?.cell?.obj?.data?.units[0]?.model?.id == this.structureMap.get(pdbId));
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+ if(refStr && pdbStr){
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+ const refData: Structure|undefined = refStr.properties?.cell.obj?.data;
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+ const pdbData: Structure|undefined = pdbStr.properties?.cell.obj?.data;
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+ const pdbUnit:Unit|undefined = pdbData?.units.find((u,n)=>u.model.atomicHierarchy.chains.label_entity_id.value(n) === pdb.entityId);
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+ const refUnit:Unit|undefined = refData?.units.find((u,n)=>u.model.atomicHierarchy.chains.label_entity_id.value(n) === ref.entityId);
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+ if(pdbData && pdbUnit && refData && refUnit){
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+ const refLoci: Loci = Structure.toStructureElementLoci(Structure.create([refUnit]));
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+ const pdbLoci: Loci = Structure.toStructureElementLoci(Structure.create([pdbUnit]));
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+ if(StructureElement.Loci.is(refLoci) && StructureElement.Loci.is(pdbLoci)) {
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+ const pivot = plugin.managers.structure.hierarchy.findStructure(refLoci.structure);
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+ const coordinateSystem = pivot?.transform?.cell.obj?.data.coordinateSystem;
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+ const transforms = alignAndSuperpose([refLoci, pdbLoci]);
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+ const { bTransform } = transforms[0];
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+ await this.transform(plugin, plugin.helpers.substructureParent.get(pdbData)!, bTransform, coordinateSystem);
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+ await PluginCommands.Camera.Reset(plugin);
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+ }
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+ }
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+ }
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+ });
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+ }
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+
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+ private async transform(plugin:PluginContext, s: StateObjectRef<PluginStateObject.Molecule.Structure>, matrix: Mat4, coordinateSystem?: SymmetryOperator) {
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+ const r = StateObjectRef.resolveAndCheck(plugin.state.data, s);
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+ if (!r) return;
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+ const o = plugin.state.data.selectQ(q => q.byRef(r.transform.ref).subtree().withTransformer(StateTransforms.Model.TransformStructureConformation))[0];
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+
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+ const transform = coordinateSystem && !Mat4.isIdentity(coordinateSystem.matrix)
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+ ? Mat4.mul(Mat4(), coordinateSystem.matrix, matrix)
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+ : matrix;
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+
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+ const params = {
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+ transform: {
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+ name: 'matrix' as const,
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+ params: { data: transform, transpose: false }
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+ }
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+ };
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+ const b = o
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+ ? plugin.state.data.build().to(o).update(params)
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+ : plugin.state.data.build().to(s)
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+ .insert(StateTransforms.Model.TransformStructureConformation, params, { tags: SuperpositionTag });
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+ await plugin.runTask(plugin.state.data.updateTree(b));
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+ }
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+
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+}
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bioinsilico