pdbe-molstar 3.6.0 → 3.7.0

package/lib/superposition.js

@@ -10,6 +10,7 @@ exports.transform = transform;
 const tslib_1 = require("tslib");
 const linear_algebra_1 = require("molstar/lib/mol-math/linear-algebra");
 const structure_1 = require("molstar/lib/mol-model/structure");
+const superposition_sifts_mapping_1 = require("molstar/lib/mol-model/structure/structure/util/superposition-sifts-mapping");
 const transforms_1 = require("molstar/lib/mol-plugin-state/transforms");
 const builder_1 = require("molstar/lib/mol-script/language/builder");
 const script_1 = require("molstar/lib/mol-script/script");
@@ -20,7 +21,6 @@ const lists_1 = require("molstar/lib/mol-util/color/lists");
 const alphafold_transparency_1 = require("./alphafold-transparency");
 const helpers_1 = require("./helpers");
 const plugin_custom_state_1 = require("./plugin-custom-state");
-const superposition_sifts_mapping_1 = require("./superposition-sifts-mapping");
 function combinedColorPalette(palettes) {
     return palettes.flatMap(paletteName => lists_1.ColorLists[paletteName].list);
 }
@@ -67,7 +67,6 @@ function initSuperposition(plugin, completeSubject) {
                     visibility: [],
                     transforms: [],
                     rmsds: [],
-                    coordinateSystems: [],
                 },
             };
             // Get segment and cluster information for the given uniprot accession
@@ -158,7 +157,7 @@ function loadAfStructure(plugin) {
         const { structure } = yield loadStructure(plugin, url, 'mmcif', isBinary);
         const strInstance = structure;
         if (!strInstance)
-            return false;
+            return undefined;
         // Store Refs in state
         const spState = customState.superpositionState;
         spState.alphafold.ref = strInstance === null || strInstance === void 0 ? void 0 : strInstance.ref;
@@ -170,79 +169,65 @@ function loadAfStructure(plugin) {
             yield plugin.builders.structure.representation.addRepresentation(chainSel, { type: 'putty', color: 'plddt-confidence', size: 'uniform', sizeParams: { value: 1.5 } }, { tag: `af-superposition-visual` });
             return strInstance === null || strInstance === void 0 ? void 0 : strInstance.ref;
         }
-        return false;
+        return undefined;
     });
 }
-function superposeAf(plugin, traceOnly, segmentIndex) {
+function superposeAf(plugin, traceOnly) {
     return tslib_1.__awaiter(this, void 0, void 0, function* () {
         const customState = (0, plugin_custom_state_1.PluginCustomState)(plugin);
         const spState = customState.superpositionState;
         if (!(spState === null || spState === void 0 ? void 0 : spState.segmentData))
-            return;
+            return false;
         // Load AF structure
-        const afStrRef = spState.alphafold.ref || (yield loadAfStructure(plugin));
-        if (!afStrRef)
-            return;
-        const afStr = plugin.managers.structure.hierarchy.current.refs.get(afStrRef);
-        const segmentNum = segmentIndex ? segmentIndex : spState.activeSegment - 1;
+        const afStructRefString = spState.alphafold.ref || (yield loadAfStructure(plugin));
+        if (!afStructRefString)
+            return false;
+        const afStructRef = plugin.managers.structure.hierarchy.current.refs.get(afStructRefString);
+        if ((afStructRef === null || afStructRef === void 0 ? void 0 : afStructRef.kind) !== 'structure')
+            return false;
+        const segmentNum = spState.activeSegment - 1;
         if (!spState.alphafold.transforms[segmentNum]) {
             // Create representative list
             const mappingResult = [];
-            const coordinateSystems = [];
-            const failedPairsResult = [];
-            const zeroOverlapPairsResult = [];
-            let minRmsd = 0;
+            let minRmsd = Infinity;
             let minIndex = 0;
             const rmsdList = [];
             const segmentClusters = spState.segmentData[segmentNum].clusters;
-            segmentClusters.forEach((cluster) => {
-                var _a, _b, _c;
-                const modelRef = spState.models[`${cluster[0].pdb_id}_${cluster[0].struct_asym_id}`];
-                if (modelRef) {
-                    const structHierarchy = plugin.managers.structure.hierarchy.current.refs.get(modelRef);
-                    if (structHierarchy) {
-                        const input = [structHierarchy.components[0], afStr];
-                        const structures = input.map(s => { var _a; return (_a = s.cell.obj) === null || _a === void 0 ? void 0 : _a.data; });
-                        let { entries, failedPairs, zeroOverlapPairs } = (0, superposition_sifts_mapping_1.alignAndSuperposeWithSIFTSMapping)(structures, {
-                            traceOnly,
-                            includeResidueTest: loc => structure_1.StructureProperties.atom.B_iso_or_equiv(loc) > 70,
-                            applyTestIndex: [1],
-                        });
-                        if (entries.length === 0 || (entries && entries[0] && entries[0].transform.rmsd.toFixed(1) === '0.0')) {
-                            const alignWithoutPlddt = (0, superposition_sifts_mapping_1.alignAndSuperposeWithSIFTSMapping)(structures, { traceOnly });
-                            entries = alignWithoutPlddt.entries;
-                        }
-                        if (entries && entries[0]) {
-                            mappingResult.push(entries[0]);
-                            coordinateSystems.push((_c = (_b = (_a = input[0]) === null || _a === void 0 ? void 0 : _a.transform) === null || _b === void 0 ? void 0 : _b.cell.obj) === null || _c === void 0 ? void 0 : _c.data.coordinateSystem);
-                            const totalMappings = mappingResult.length;
-                            if (totalMappings === 1 || entries[0].transform.rmsd < minRmsd) {
-                                minRmsd = entries[0].transform.rmsd;
-                                minIndex = totalMappings === 1 ? 0 : mappingResult.length - 1;
-                            }
-                            rmsdList.push(`${cluster[0].pdb_id} chain ${cluster[0].struct_asym_id}:${entries[0].transform.rmsd.toFixed(2)}`);
-                        }
-                        else {
-                            if (failedPairs.length > 0)
-                                failedPairsResult.push(failedPairs);
-                            if (zeroOverlapPairs.length > 0)
-                                zeroOverlapPairsResult.push(zeroOverlapPairs);
-                            // rmsdList.push(`${cluster[0].pdb_id} ${cluster[0].struct_asym_id}:-`)
-                        }
+            for (const cluster of segmentClusters) {
+                const representative = cluster[0];
+                const structRefString = spState.models[`${representative.pdb_id}_${representative.struct_asym_id}`];
+                if (!structRefString)
+                    continue;
+                const structRef = plugin.managers.structure.hierarchy.current.refs.get(structRefString);
+                if ((structRef === null || structRef === void 0 ? void 0 : structRef.kind) !== 'structure')
+                    continue;
+                const structComponentRef = structRef.components[0];
+                const structures = [structComponentRef.cell.obj.data, afStructRef.cell.obj.data];
+                let { entries } = (0, superposition_sifts_mapping_1.alignAndSuperposeWithSIFTSMapping)(structures, {
+                    traceOnly,
+                    includeResidueTest: loc => !(loc.structure === structures[1] && structure_1.StructureProperties.atom.B_iso_or_equiv(loc) <= 70), // exclude AlphaFold residues with pLDDT <= 70
+                });
+                if (entries.length === 0 || (entries[0] && entries[0].transform.rmsd.toFixed(1) === '0.0')) {
+                    const alignWithoutPlddt = (0, superposition_sifts_mapping_1.alignAndSuperposeWithSIFTSMapping)(structures, { traceOnly });
+                    entries = alignWithoutPlddt.entries;
+                }
+                if (entries[0]) {
+                    mappingResult.push(entries[0]);
+                    if (entries[0].transform.rmsd < minRmsd) {
+                        minRmsd = entries[0].transform.rmsd;
+                        minIndex = mappingResult.length - 1;
                     }
+                    rmsdList.push(`${representative.pdb_id} chain ${representative.struct_asym_id}:${entries[0].transform.rmsd.toFixed(2)}`);
                 }
-            });
-            // console.log(failedPairsResult);
-            // console.log(zeroOverlapPairsResult);
+            }
             if (mappingResult.length > 0) {
                 spState.alphafold.visibility[segmentNum] = true;
                 spState.alphafold.transforms[segmentNum] = mappingResult[minIndex].transform.bTransform;
-                spState.alphafold.coordinateSystems[segmentNum] = coordinateSystems[minIndex];
                 spState.alphafold.rmsds[segmentNum] = rmsdList.sort((a, b) => parseFloat(a.split(':')[1]) - parseFloat(b.split(':')[1]));
             }
         }
-        yield afTransform(plugin, afStr.cell, spState.alphafold.transforms[segmentNum], spState.alphafold.coordinateSystems[segmentNum]);
-        (0, alphafold_transparency_1.applyAFTransparency)(plugin, afStr, 0.8, 70);
+        yield afTransform(plugin, afStructRef.cell, spState.alphafold.transforms[segmentNum]);
+        yield (0, alphafold_transparency_1.applyAFTransparency)(plugin, afStructRef, 0.8, 70);
         return true;
     });
 }
@@ -325,10 +310,6 @@ function renderSuperposition(plugin, segmentIndex, entryList) {
                         yield plugin.builders.structure.representation.addRepresentation(chainSel, { type: 'putty', color: 'uniform', colorParams: { value: uniformColor2 }, size: 'uniform' }, { tag: `superposition-visual` });
                         spState.refMaps[chainSel.ref] = `${s.pdb_id}_${s.struct_asym_id}`;
                     }
-                    // // const addTooltipUpdate = plugin.state.behaviors.build().to(BestDatabaseSequenceMapping.id).update(BestDatabaseSequenceMapping, (old: any) => { old.showTooltip = true; });
-                    // // await plugin.runTask(plugin.state.behaviors.updateTree(addTooltipUpdate));
-                    // BestDatabaseSequenceMapping
-                    // console.log(plugin.state.data.select(modelRef)[0])
                 }
                 let invalidStruct = chainSel ? false : true;
                 if (superpositionParams && superpositionParams.ligandView) {
@@ -391,7 +372,7 @@ function renderSuperposition(plugin, segmentIndex, entryList) {
                                 0: polymerChainWithSurroundings,
                                 by: carbEntityChain,
                             });
-                            const data = (plugin.state.data.select(strInstance.ref)[0].obj).data;
+                            const data = plugin.state.data.select(strInstance.ref)[0].obj.data;
                             const carbChainSel = script_1.Script.getStructureSelection(carbEntityChainInVicinity, data);
                             if (carbChainSel && carbChainSel.kind === 'sequence') {
                                 // console.log(carbEntityChainId + ' chain present in 5 A radius');

package/lib/ui/alphafold-superposition.js

@@ -148,10 +148,10 @@ class AfSuperpositionControls extends base_1.PurePluginUIComponent {
         return (0, plugin_custom_state_1.PluginCustomState)(this.plugin);
     }
     superposeByDbMapping() {
-        return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsx)(common_1.Button, { icon: icons_1.SuperposeChainsSvg, title: 'Superpose AlphaFold structure using intersection of residues from SIFTS UNIPROT mapping.', className: 'msp-btn msp-btn-block', onClick: this.superposeDb, style: { marginTop: '1px', textAlign: 'left' }, disabled: this.state.isBusy, children: "Load AlphaFold structure" }) });
+        return (0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsx)(common_1.Button, { icon: icons_1.AddSvg, title: 'Superpose AlphaFold structure using intersection of residues from SIFTS UNIPROT mapping.', className: 'msp-btn msp-btn-block', onClick: this.superposeDb, style: { marginTop: '1px', textAlign: 'left' }, disabled: this.state.isBusy, children: "Load AlphaFold structure" }) });
     }
     render() {
-        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", { style: { backgroundColor: '#dce54e', fontWeight: 500, padding: '5px 12px' }, children: "New Feature!" }), (0, jsx_runtime_1.jsx)("div", { className: 'msp-help-text', style: { margin: '2px 0' }, children: (0, jsx_runtime_1.jsxs)("div", { className: 'msp-help-description', children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_2.InfoIconSvg, inline: true }), "Load and superpose AlphaFold structure against representative chains."] }) }), (0, jsx_runtime_1.jsxs)("div", { className: 'msp-flex-row', children: [this.state.canUseDb && this.superposeByDbMapping(), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.TuneSvg, label: '', title: 'Options', toggle: this.toggleOptions, isSelected: this.state.action === 'options', disabled: this.state.isBusy, style: { flex: '0 0 40px', padding: 0 } })] }), this.state.action === 'options' && (0, jsx_runtime_1.jsx)("div", { className: 'msp-control-offset', children: (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: exports.AlphafoldSuperpositionParams, values: this.state.options, onChangeValues: this.setOptions, isDisabled: this.state.isBusy }) })] });
+        return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", { className: 'msp-help-text', style: { margin: '2px 0' }, children: (0, jsx_runtime_1.jsxs)("div", { className: 'msp-help-description', children: [(0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: icons_2.InfoIconSvg, inline: true }), "Load and superpose AlphaFold structure against representative chains."] }) }), (0, jsx_runtime_1.jsxs)("div", { className: 'msp-flex-row', children: [this.state.canUseDb && this.superposeByDbMapping(), (0, jsx_runtime_1.jsx)(common_1.ToggleButton, { icon: icons_1.TuneSvg, label: '', title: 'Options', toggle: this.toggleOptions, isSelected: this.state.action === 'options', disabled: this.state.isBusy, style: { flex: '0 0 40px', padding: 0 } })] }), this.state.action === 'options' && (0, jsx_runtime_1.jsx)("div", { className: 'msp-control-offset', children: (0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: exports.AlphafoldSuperpositionParams, values: this.state.options, onChangeValues: this.setOptions, isDisabled: this.state.isBusy }) })] });
     }
 }
 exports.AfSuperpositionControls = AfSuperpositionControls;

package/lib/viewer.js

@@ -776,7 +776,7 @@ class PDBeMolstarPlugin {
                             return;
                         const asm = this.state.select(this.assemblyRef)[0].obj;
                         const defaultMapParams = transformers_1.InitVolumeStreaming.createDefaultParams(asm, this.plugin);
-                        const pdbeMapParams = helpers_1.PDBeVolumes.mapParams(defaultMapParams, this.initParams.mapSettings, '');
+                        const pdbeMapParams = helpers_1.PDBeVolumes.mapParams(defaultMapParams, this.initParams.mapSettings);
                         if (pdbeMapParams) {
                             yield this.plugin.runTask(this.state.applyAction(transformers_1.InitVolumeStreaming, pdbeMapParams, this.assemblyRef));
                             if (pdbeMapParams.method !== 'em' && !this.initParams.ligandView)

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "pdbe-molstar",
-  "version": "3.6.0",
+  "version": "3.7.0",
   "description": "Molstar implementation for PDBe",
   "main": "index.js",
   "scripts": {

package/lib/superposition-sifts-mapping.d.ts

@@ -1,22 +0,0 @@
-import { MinimizeRmsd } from 'molstar/lib/mol-math/linear-algebra/3d/minimize-rmsd';
-import { Structure } from 'molstar/lib/mol-model/structure';
-import { ElementIndex, ResidueIndex } from 'molstar/lib/mol-model/structure/model/indexing';
-import { StructureElement } from 'molstar/lib/mol-model/structure/structure/element';
-import { Unit } from 'molstar/lib/mol-model/structure/structure/unit';
-export interface AlignmentResultEntry {
-    transform: MinimizeRmsd.Result;
-    pivot: number;
-    other: number;
-}
-export interface AlignmentResult {
-    entries: AlignmentResultEntry[];
-    zeroOverlapPairs: [number, number][];
-    failedPairs: [number, number][];
-}
-type IncludeResidueTest = (traceElementOrFirstAtom: StructureElement.Location<Unit.Atomic>, residueIndex: ResidueIndex, startIndex: ElementIndex, endIndex: ElementIndex) => boolean;
-export declare function alignAndSuperposeWithSIFTSMapping(structures: Structure[], options?: {
-    traceOnly?: boolean;
-    includeResidueTest?: IncludeResidueTest;
-    applyTestIndex?: number[];
-}): AlignmentResult;
-export {};

package/lib/superposition-sifts-mapping.js

@@ -1,153 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.alignAndSuperposeWithSIFTSMapping = alignAndSuperposeWithSIFTSMapping;
-const int_1 = require("molstar/lib/mol-data/int");
-const minimize_rmsd_1 = require("molstar/lib/mol-math/linear-algebra/3d/minimize-rmsd");
-const element_1 = require("molstar/lib/mol-model/structure/structure/element");
-const sifts_mapping_1 = require("./sifts-mapping");
-function alignAndSuperposeWithSIFTSMapping(structures, options) {
-    var _a, _b;
-    const indexMap = new Map();
-    for (let i = 0; i < structures.length; i++) {
-        let includeResidueTest = (_a = options === null || options === void 0 ? void 0 : options.includeResidueTest) !== null && _a !== void 0 ? _a : _includeAllResidues;
-        if ((options === null || options === void 0 ? void 0 : options.applyTestIndex) && !options.applyTestIndex.includes(i))
-            includeResidueTest = _includeAllResidues;
-        buildIndex(structures[i], indexMap, i, (_b = options === null || options === void 0 ? void 0 : options.traceOnly) !== null && _b !== void 0 ? _b : true, includeResidueTest);
-    }
-    const index = Array.from(indexMap.values());
-    // TODO: support non-first structure pivots
-    const pairs = findPairs(structures.length, index);
-    const zeroOverlapPairs = [];
-    const failedPairs = [];
-    const entries = [];
-    for (const p of pairs) {
-        if (p.count === 0) {
-            zeroOverlapPairs.push([p.i, p.j]);
-        }
-        else {
-            const [a, b] = getPositionTables(index, p.i, p.j, p.count);
-            const transform = minimize_rmsd_1.MinimizeRmsd.compute({ a, b });
-            if (Number.isNaN(transform.rmsd)) {
-                failedPairs.push([p.i, p.j]);
-            }
-            else {
-                entries.push({ transform, pivot: p.i, other: p.j });
-            }
-        }
-    }
-    return { entries, zeroOverlapPairs, failedPairs };
-}
-function getPositionTables(index, pivot, other, N) {
-    const xs = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);
-    const ys = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);
-    let o = 0;
-    for (const { pivots } of index) {
-        const a = pivots[pivot];
-        const b = pivots[other];
-        if (!a || !b)
-            continue;
-        const l = Math.min(a[2] - a[1], b[2] - b[1]);
-        // TODO: check if residue types match?
-        for (let i = 0; i < l; i++) {
-            let eI = (a[1] + i);
-            xs.x[o] = a[0].conformation.x(eI);
-            xs.y[o] = a[0].conformation.y(eI);
-            xs.z[o] = a[0].conformation.z(eI);
-            eI = (b[1] + i);
-            ys.x[o] = b[0].conformation.x(eI);
-            ys.y[o] = b[0].conformation.y(eI);
-            ys.z[o] = b[0].conformation.z(eI);
-            o++;
-        }
-    }
-    return [xs, ys];
-}
-function findPairs(N, index) {
-    const pairwiseCounts = [];
-    for (let i = 0; i < N; i++) {
-        pairwiseCounts[i] = [];
-        for (let j = 0; j < N; j++)
-            pairwiseCounts[i][j] = 0;
-    }
-    for (const { pivots } of index) {
-        for (let i = 0; i < N; i++) {
-            if (!pivots[i])
-                continue;
-            const lI = pivots[i][2] - pivots[i][1];
-            for (let j = i + 1; j < N; j++) {
-                if (!pivots[j])
-                    continue;
-                const lJ = pivots[j][2] - pivots[j][1];
-                pairwiseCounts[i][j] = pairwiseCounts[i][j] + Math.min(lI, lJ);
-            }
-        }
-    }
-    const ret = [];
-    for (let j = 1; j < N; j++) {
-        ret[j - 1] = { i: 0, j, count: pairwiseCounts[0][j] };
-    }
-    // TODO: support non-first structure pivots
-    // for (let i = 0; i < N - 1; i++) {
-    //     let max = 0, maxJ = i;
-    //     for (let j = i + 1; j < N; j++) {
-    //         if (pairwiseCounts[i][j] > max) {
-    //             maxJ = j;
-    //             max = pairwiseCounts[i][j];
-    //         }
-    //     }
-    //     ret[i] = { i, j: maxJ, count: max };
-    // }
-    return ret;
-}
-function _includeAllResidues() { return true; }
-function buildIndex(structure, index, sI, traceOnly, includeTest) {
-    const loc = element_1.StructureElement.Location.create(structure);
-    for (const unit of structure.units) {
-        if (unit.kind !== 0 /* Unit.Kind.Atomic */)
-            continue;
-        const { elements, model } = unit;
-        loc.unit = unit;
-        const map = sifts_mapping_1.SIFTSMapping.Provider.get(model).value;
-        if (!map)
-            return;
-        const { dbName, accession, num } = map;
-        const chainsIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
-        const residuesIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
-        const traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex;
-        while (chainsIt.hasNext) {
-            const chainSegment = chainsIt.move();
-            residuesIt.setSegment(chainSegment);
-            while (residuesIt.hasNext) {
-                const residueSegment = residuesIt.move();
-                const rI = residueSegment.index;
-                if (!dbName[rI])
-                    continue;
-                const traceElement = traceElementIndex[rI];
-                let start, end;
-                if (traceOnly) {
-                    start = traceElement;
-                    if (start === -1)
-                        continue;
-                    end = start + 1;
-                }
-                else {
-                    start = elements[residueSegment.start];
-                    end = elements[residueSegment.end - 1] + 1;
-                }
-                loc.element = (traceElement >= 0 ? traceElement : start);
-                if (!includeTest(loc, rI, start, end))
-                    continue;
-                const key = `${dbName[rI]}-${accession[rI].split('-')[0]}-${num[rI]}`;
-                if (!index.has(key)) {
-                    index.set(key, { key, pivots: { [sI]: [unit, start, end] } });
-                }
-                else {
-                    const entry = index.get(key);
-                    if (!entry.pivots[sI]) {
-                        entry.pivots[sI] = [unit, start, end];
-                    }
-                }
-            }
-        }
-    }
-}