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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 {
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+ StructureRepresentationPresetProvider
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+} from "molstar/lib/mol-plugin-state/builder/structure/representation-preset";
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+import {PluginContext} from "molstar/lib/mol-plugin/context";
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+import {PluginStateObject} from "molstar/lib/mol-plugin-state/objects";
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+import {StateObjectRef} from "molstar/lib/mol-state";
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+import {Structure, StructureElement, StructureProperties as SP, Unit} from "molstar/lib/mol-model/structure";
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+import {MolScriptBuilder as MS} from "molstar/lib/mol-script/language/builder";
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+import reprBuilder = StructureRepresentationPresetProvider.reprBuilder;
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+import uniqid from "uniqid";
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+import {PLDDTConfidenceColorThemeProvider} from "molstar/lib/extensions/model-archive/quality-assessment/color/plddt";
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+import {ColorTheme} from "molstar/lib/mol-theme/color";
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+import {createSelectionExpressions} from "@rcsb/rcsb-molstar/build/src/viewer/helpers/selection";
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+import {ParamDefinition as PD} from "molstar/lib/mol-util/param-definition";
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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 {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 {StateTransforms} from "molstar/lib/mol-plugin-state/transforms";
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+
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+export const AlignmentRepresentationPresetProvider = StructureRepresentationPresetProvider<{ref?:{entryId:string;entityId:string;};pdb?:{entryId:string;entityId:string;};},any>({
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+ id: 'alignment-to-reference',
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+ display: {
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+ name: 'Alignemnt to Reference'
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+ },
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+ isApplicable: (structureRef: PluginStateObject.Molecule.Structure, plugin: PluginContext): boolean => true,
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+ params: (structureRef: PluginStateObject.Molecule.Structure | undefined, plugin: PluginContext) => ({
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+ ref: PD.Value<{entryId:string;entityId:string;}|undefined>(undefined),
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+ pdb: PD.Value<{entryId:string;entityId:string;}|undefined>(undefined)
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+ }),
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+ apply: async (structureRef: StateObjectRef<PluginStateObject.Molecule.Structure>, params: {ref?:{entryId:string;entityId:string;};pdb?:{entryId:string;entityId:string;};}, plugin: PluginContext) => {
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+ const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, structureRef);
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+ if (!structureCell) return;
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+ const structure = structureCell.obj!.data;
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+ if(params.ref && params.pdb){
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+ await structuralAlignment(plugin, params.ref, params.pdb, structure);
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+ }
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+ const entryId = structure.model.entryId;
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+ const l = StructureElement.Location.create(structure);
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+ const asymObserved: {[key:string]:boolean} = {};
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+ for(const unit of structure.units) {
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+ StructureElement.Location.set(l, structure, unit, unit.elements[0]);
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+ const asymId = SP.chain.label_asym_id(l);
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+ if(asymObserved[asymId])
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+ continue;
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+ asymObserved[asymId] = true;
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+ const operators = SP.unit.pdbx_struct_oper_list_ids(l);
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+ const type = SP.entity.type(l);
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+ if (type == "polymer") {
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+ const comp = await plugin.builders.structure.tryCreateComponentFromExpression(
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+ structureCell,
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+ MS.struct.generator.atomGroups({
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+ 'chain-test': MS.core.rel.eq([MS.ammp('label_asym_id'), asymId])
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+ }),
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+ uniqid(`${entryId}_${asymId}_${operators.join(",")}`),
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+ {
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+ label: `${entryId}.${asymId}-${operators.join(",")}`
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+ }
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+ );
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+ //TODO This needs to be called after tryCreateComponentFromExpression
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+ const { update, builder } = reprBuilder(plugin, {
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+ ignoreHydrogens: true,
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+ ignoreLight: false,
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+ quality: "auto"
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+ });
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+ builder.buildRepresentation(update, comp, {
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+ color: PLDDTConfidenceColorThemeProvider.isApplicable({ structure }) ? PLDDTConfidenceColorThemeProvider.name as ColorTheme.BuiltIn : "chain-id",
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+ type: "cartoon"
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+ })
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+ await update.commit({ revertOnError: false });
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+ }
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+ }
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+ for(const expression of createSelectionExpressions(entryId)){
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+ if(expression.tag == "polymer")
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+ continue;
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+ const comp = await plugin.builders.structure.tryCreateComponentFromExpression(
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+ structureCell,
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+ expression.expression,
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+ uniqid(`${entryId}_${expression.tag}`),
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+ {
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+ label: expression.label
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+ });
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+ //TODO This needs to be called after tryCreateComponentFromExpression
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+ const { update, builder } = reprBuilder(plugin, {
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+ ignoreHydrogens: true,
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+ ignoreLight: false,
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+ quality: "auto"
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+ });
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+ builder.buildRepresentation(update, comp, {
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+ type: expression.type
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+ });
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+ await update.commit({ revertOnError: false });
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+ }
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+
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+ }
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+ });
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+
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+let refData: Structure|undefined = undefined;
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+async function structuralAlignment(plugin: PluginContext, ref:{entryId:string;entityId:string;}, pdb:{entryId:string;entityId:string;}, structure: Structure): Promise<void> {
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+ if(ref.entryId == pdb.entryId){
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+ refData = structure;
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+ }else{
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+ const pdbData: Structure = structure;
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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 transform(plugin, plugin.helpers.substructureParent.get(pdbData)!, bTransform, coordinateSystem);
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+ }
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+ }
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+ }
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+}
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+
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+const SuperpositionTag = 'SuperpositionTransform';
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+async function transform(plugin:PluginContext, s: StateObjectRef<PluginStateObject.Molecule.Structure>, matrix: Mat4, coordinateSystem?: SymmetryOperator): Promise<void>{
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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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