pdbe-molstar 3.2.0-beta.4 → 3.2.1-beta.1

package/build/pdbe-molstar-plugin.js.LICENSE.txt

@@ -1,6 +1,6 @@
 /**
  * pdbe-molstar
- * @version 3.2.0-beta.4
+ * @version 3.2.1-beta.1
  * @link https://github.com/PDBeurope/pdbe-molstar
  * @license Apache 2.0
  */

package/build/pdbe-molstar.css

@@ -1,9 +1,9 @@
 /**
  * pdbe-molstar
- * @version 3.2.0-beta.4
+ * @version 3.2.1-beta.1
  * @link https://github.com/PDBeurope/pdbe-molstar
  * @license Apache 2.0
  */
 
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.msp-plugin-content{color:#ccd4e0}.msp-plugin .msp-plugin-init-error{white-space:pre;margin:10px}
-.pdbemolstar-overlay{z-index:1000;position:fixed;top:0px;bottom:0px;left:0px;right:0px;display:flex;justify-content:center;align-items:center;pointer-events:none}.pdbemolstar-overlay-box{width:25%;height:25%}svg.pdbe-animated-logo{background-color:rgba(0,0,0,0);width:100%;height:100%;opacity:80%}svg.pdbe-animated-logo .path-fg{stroke-dasharray:1812 250;stroke-dashoffset:-250;animation:dash linear normal infinite;animation-duration:5s;animation-delay:1s}@keyframes dash{0%{stroke-dashoffset:1812}80%{stroke-dashoffset:-250}100%{stroke-dashoffset:-250}}
+.pdbemolstar-overlay{z-index:1000;position:fixed;top:0px;bottom:0px;left:0px;right:0px;display:flex;justify-content:center;align-items:center;pointer-events:none}.pdbemolstar-overlay-box{width:25%;height:25%}svg.pdbe-animated-logo{background-color:rgba(0,0,0,0);width:100%;height:100%;opacity:80%}svg.pdbe-animated-logo .path-fg{stroke-dasharray:1812 250;stroke-dashoffset:-250;animation:dash linear normal infinite;animation-duration:5s;animation-delay:1s}@keyframes dash{0%{stroke-dashoffset:1812}80%{stroke-dashoffset:-250}100%{stroke-dashoffset:-250}}.msp-plugin ::-webkit-scrollbar-thumb{background-color:rgba(128,128,128,.5019607843);border-radius:10px;border:solid 1px rgba(0,0,0,0);background-clip:content-box}

package/lib/extensions/foldseek.d.ts

@@ -0,0 +1,23 @@
+/** Helper functions to allow visualizing Foldseek results and superposing them on the query structure */
+import { Mat4 } from 'Molstar/mol-math/linear-algebra';
+import { PDBeMolstarPlugin } from '..';
+export interface FoldseekApiData {
+    query: string;
+    target: string;
+    qstart: number;
+    qend: number;
+    tstart: number;
+    tend: number;
+    qaln: string;
+    taln: string;
+    database: 'pdb' | 'afdb';
+}
+/** Load target structure as defined by `apiData`
+ * and superpose it on the already loaded query structure. */
+export declare function loadFoldseekSuperposition(viewer: PDBeMolstarPlugin, targetStructId: string, apiData: FoldseekApiData, targetColor?: string): Promise<{
+    rmsd: number;
+    nAligned: number;
+    bTransform: Mat4;
+}>;
+/** Export currently loaded models in mmCIF (or BCIF). Pack in a ZIP if there is more then 1 model. */
+export declare function exportModels(viewer: PDBeMolstarPlugin, format?: 'cif' | 'bcif'): Promise<void>;

package/lib/extensions/foldseek.js

@@ -0,0 +1,163 @@
+"use strict";
+/** Helper functions to allow visualizing Foldseek results and superposing them on the query structure */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.exportModels = exports.loadFoldseekSuperposition = void 0;
+var tslib_1 = require("tslib");
+var export_1 = require("Molstar/extensions/model-export/export");
+var minimize_rmsd_1 = require("Molstar/mol-math/linear-algebra/3d/minimize-rmsd");
+var superposition_1 = require("../superposition");
+/** Load target structure as defined by `apiData`
+ * and superpose it on the already loaded query structure. */
+function loadFoldseekSuperposition(viewer, targetStructId, apiData, targetColor) {
+    var _a, _b, _c, _d;
+    if (targetColor === void 0) { targetColor = '#00ff00'; }
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var Q_STRUCT_ID, tEntryId, tAuthAsymId, pdbeUrl, url, qStructure, tStructure, _e, qMatchedIndicesInChain, tMatchedIndicesInChain, qLabelAsymId, tLabelAsymId, qCoords, tCoords, superposition;
+        var _f;
+        return tslib_1.__generator(this, function (_g) {
+            switch (_g.label) {
+                case 0:
+                    Q_STRUCT_ID = 'main';
+                    if (!(apiData.database === 'pdb')) return [3 /*break*/, 2];
+                    _f = apiData.target.split('_'), tEntryId = _f[0], tAuthAsymId = _f[1];
+                    pdbeUrl = viewer.initParams.pdbeUrl.replace(/\/$/, '');
+                    url = "".concat(pdbeUrl, "/model-server/v1/").concat(tEntryId, "/atoms?auth_asym_id=").concat(tAuthAsymId);
+                    return [4 /*yield*/, viewer.load({ url: url, format: 'mmcif', isBinary: false, id: targetStructId }, false)];
+                case 1:
+                    _g.sent();
+                    return [3 /*break*/, 3];
+                case 2:
+                    if (apiData.database === 'afdb') {
+                        // TODO assign tEntryId, tAuthAsymId and download structure from AFDB
+                        throw new Error('NotImplementedError');
+                    }
+                    else {
+                        throw new Error("Unknown database: ".concat(apiData.database));
+                    }
+                    _g.label = 3;
+                case 3:
+                    qStructure = (_b = (_a = viewer.getStructure(Q_STRUCT_ID)) === null || _a === void 0 ? void 0 : _a.cell.obj) === null || _b === void 0 ? void 0 : _b.data;
+                    tStructure = (_d = (_c = viewer.getStructure(targetStructId)) === null || _c === void 0 ? void 0 : _c.cell.obj) === null || _d === void 0 ? void 0 : _d.data;
+                    if (!qStructure)
+                        throw new Error('Query structure not loaded');
+                    if (!tStructure)
+                        throw new Error('Target structure not loaded');
+                    _e = getMatchedResidues(apiData.qstart - 1, apiData.qaln, apiData.tstart - 1, apiData.taln), qMatchedIndicesInChain = _e[0], tMatchedIndicesInChain = _e[1];
+                    qLabelAsymId = 'A';
+                    tLabelAsymId = auth_asym_id_to_label_asym_id(tStructure, tAuthAsymId);
+                    qCoords = getCoordsForResiduesInChain(qStructure, qMatchedIndicesInChain, qLabelAsymId);
+                    tCoords = getCoordsForResiduesInChain(tStructure, tMatchedIndicesInChain, tLabelAsymId);
+                    superposition = minimize_rmsd_1.MinimizeRmsd.compute({ a: qCoords, b: tCoords });
+                    // Transform, color, focus
+                    return [4 /*yield*/, (0, superposition_1.transform)(viewer.plugin, viewer.getStructure(targetStructId).cell, superposition.bTransform)];
+                case 4:
+                    // Transform, color, focus
+                    _g.sent();
+                    return [4 /*yield*/, viewer.visual.select({ data: [{ color: targetColor }], structureId: targetStructId })];
+                case 5:
+                    _g.sent(); // color target
+                    return [4 /*yield*/, viewer.visual.reset({ camera: true })];
+                case 6:
+                    _g.sent();
+                    return [2 /*return*/, tslib_1.__assign(tslib_1.__assign({}, superposition), { nAligned: qMatchedIndicesInChain.length })];
+            }
+        });
+    });
+}
+exports.loadFoldseekSuperposition = loadFoldseekSuperposition;
+function getMatchedResidues(qstart, qaln, tstart, taln) {
+    if (qaln.length !== taln.length) {
+        throw new Error('Length of qaln and taln must be the same');
+    }
+    var n = qaln.length;
+    var q = qstart;
+    var t = tstart;
+    var qResis = [];
+    var tResis = [];
+    for (var i = 0; i < n; i++) {
+        if (qaln[i] === '-') {
+            // gap in query
+            t++;
+        }
+        else if (taln[i] === '-') {
+            // gap in target
+            q++;
+        }
+        else {
+            // match
+            qResis.push(q);
+            tResis.push(t);
+            t++;
+            q++;
+        }
+    }
+    return [qResis, tResis];
+}
+function getCoordsForResiduesInChain(structure, residueIndicesInChain, label_asym_id) {
+    var resRangeForChain = residueIndexRangeForChain(structure, label_asym_id);
+    var residueIndices = residueIndicesInChain.map(function (i) { return resRangeForChain.start + i; });
+    if (residueIndices[residueIndices.length - 1] >= resRangeForChain.end)
+        throw new Error('Residues out of range');
+    var coords = getCACoordsForResidues(structure, residueIndices);
+    return coords;
+}
+function residueIndexRangeForChain(struct, label_asym_id) {
+    var h = struct.model.atomicHierarchy;
+    var iChain = Array.from(h.chains.label_asym_id.toArray()).indexOf(label_asym_id);
+    var fromAtom = h.chainAtomSegments.offsets[iChain];
+    var toAtom = h.chainAtomSegments.offsets[iChain + 1];
+    var fromResidue = h.residueAtomSegments.index[fromAtom];
+    var toResidue = h.residueAtomSegments.index[toAtom - 1] + 1;
+    return { start: fromResidue, end: toResidue };
+}
+function auth_asym_id_to_label_asym_id(struct, auth_asym_id) {
+    var entities = struct.model.entities.data;
+    var nEntities = entities._rowCount;
+    var chains = struct.model.atomicHierarchy.chains;
+    var nChains = chains._rowCount;
+    var polymerEntityIds = new Set();
+    for (var i = 0; i < nEntities; i++) {
+        if (entities.type.value(i) === 'polymer') {
+            polymerEntityIds.add(entities.id.value(i));
+        }
+    }
+    for (var i = 0; i < nChains; i++) {
+        if (chains.auth_asym_id.value(i) === auth_asym_id && polymerEntityIds.has(chains.label_entity_id.value(i))) {
+            return chains.label_asym_id.value(i);
+        }
+    }
+    throw new Error("There is no polymer chain with auth_asym_id ".concat(auth_asym_id, "."));
+}
+function getCACoordsForResidues(struct, residueIndices) {
+    var hier = struct.model.atomicHierarchy;
+    var conf = struct.model.atomicConformation;
+    var n = residueIndices.length;
+    var coords = minimize_rmsd_1.MinimizeRmsd.Positions.empty(n);
+    for (var i = 0; i < n; i++) {
+        var iRes = residueIndices[i];
+        var fromAtom = hier.residueAtomSegments.offsets[iRes];
+        var toAtom = hier.residueAtomSegments.offsets[iRes + 1];
+        var theAtom = -1;
+        for (var iAtom = fromAtom; iAtom < toAtom; iAtom++) {
+            var atomName = hier.atoms.label_atom_id.value(iAtom);
+            if (atomName === 'CA') {
+                theAtom = iAtom;
+                break;
+            }
+        }
+        if (theAtom === -1) {
+            var label_seq_id = hier.residues.label_seq_id.value(iRes);
+            throw new Error("C alpha not found for residue ".concat(label_seq_id, "."));
+        }
+        coords.x[i] = conf.x[theAtom];
+        coords.y[i] = conf.y[theAtom];
+        coords.z[i] = conf.z[theAtom];
+    }
+    return coords;
+}
+/** Export currently loaded models in mmCIF (or BCIF). Pack in a ZIP if there is more then 1 model. */
+function exportModels(viewer, format) {
+    if (format === void 0) { format = 'cif'; }
+    return (0, export_1.exportHierarchy)(viewer.plugin, { format: format });
+}
+exports.exportModels = exportModels;

package/lib/helpers.d.ts

@@ -13,6 +13,8 @@ export type LoadParams = {
     isHetView?: boolean;
     isBinary?: boolean;
     progressMessage?: string;
+    /** Arbitrary string identifier to refer to this structure later */
+    id?: string;
 };
 export type MapParams = {
     'em'?: MapStyle;
@@ -108,4 +110,19 @@ export declare function addDefaults<T extends {}>(object: Partial<T> | undefined
 /** Apply overpaint to every representation of every component in a structure.
  * Excludes representations created as "added representations" by `PDBeMolstarPlugin.visual.select`. */
 export declare function applyOverpaint(plugin: PluginContext, structRef: StructureRef, overpaintLayers: Overpaint.BundleLayer[]): Promise<void>;
+export declare const Tags: {
+    /** Tag needed for `clearStructureOverpaint`; defined in src/mol-plugin-state/helpers/structure-overpaint.ts but private */
+    readonly Overpaint: "overpaint-controls";
+    /** Marks structure components added by `select` */
+    readonly AddedComponent: "pdbe-molstar.added-component";
+};
+export declare const StructureComponentTags: {
+    polymer: string[];
+    het: string[];
+    water: string[];
+    carbs: string[];
+    nonStandard: string[];
+    coarse: string[];
+    maps: string[];
+};
 export {};

package/lib/helpers.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.applyOverpaint = exports.addDefaults = exports.getStructureUrl = exports.runWithProgressMessage = exports.ModelInfo = exports.QueryHelper = exports.LigandView = exports.AlphafoldView = exports.PDBeVolumes = void 0;
+exports.StructureComponentTags = exports.Tags = exports.applyOverpaint = exports.addDefaults = exports.getStructureUrl = exports.runWithProgressMessage = exports.ModelInfo = exports.QueryHelper = exports.LigandView = exports.AlphafoldView = exports.PDBeVolumes = void 0;
 var tslib_1 = require("tslib");
 var prop_1 = require("Molstar/extensions/model-archive/quality-assessment/prop");
 var structure_1 = require("Molstar/mol-model/structure");
@@ -12,7 +12,6 @@ var builder_1 = require("Molstar/mol-script/language/builder");
 var compiler_1 = require("Molstar/mol-script/runtime/query/compiler");
 var mol_state_1 = require("Molstar/mol-state");
 var mol_task_1 = require("Molstar/mol-task");
-var index_1 = require("./index");
 var sifts_mapping_1 = require("./sifts-mapping");
 var PDBeVolumes;
 (function (PDBeVolumes) {
@@ -356,16 +355,16 @@ function applyOverpaint(plugin, structRef, overpaintLayers) {
                     update = plugin.build();
                     for (_i = 0, _b = structRef.components; _i < _b.length; _i++) {
                         component = _b[_i];
-                        if ((_a = component.cell.transform.tags) === null || _a === void 0 ? void 0 : _a.includes(index_1.Tags.AddedComponent))
+                        if ((_a = component.cell.transform.tags) === null || _a === void 0 ? void 0 : _a.includes(exports.Tags.AddedComponent))
                             continue;
                         for (_c = 0, _d = component.representations; _c < _d.length; _c++) {
                             repr = _d[_c];
                             currentOverpaint = plugin.state.data.select(mol_state_1.StateSelection.Generators
                                 .ofTransformer(transforms_1.StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle, repr.cell.transform.ref)
-                                .withTag(index_1.Tags.Overpaint));
+                                .withTag(exports.Tags.Overpaint));
                             if (currentOverpaint.length === 0) {
                                 // Create a new overpaint
-                                update.to(repr.cell.transform.ref).apply(transforms_1.StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle, { layers: overpaintLayers }, { tags: index_1.Tags.Overpaint });
+                                update.to(repr.cell.transform.ref).apply(transforms_1.StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle, { layers: overpaintLayers }, { tags: exports.Tags.Overpaint });
                             }
                             else {
                                 // Add layers to existing overpaint
@@ -382,3 +381,18 @@ function applyOverpaint(plugin, structRef, overpaintLayers) {
     });
 }
 exports.applyOverpaint = applyOverpaint;
+exports.Tags = {
+    /** Tag needed for `clearStructureOverpaint`; defined in src/mol-plugin-state/helpers/structure-overpaint.ts but private */
+    Overpaint: 'overpaint-controls',
+    /** Marks structure components added by `select` */
+    AddedComponent: 'pdbe-molstar.added-component',
+};
+exports.StructureComponentTags = {
+    polymer: ['structure-component-static-polymer'],
+    het: ['structure-component-static-ligand', 'structure-component-static-ion'],
+    water: ['structure-component-static-water'],
+    carbs: ['structure-component-static-branched'],
+    nonStandard: ['structure-component-static-non-standard'],
+    coarse: ['structure-component-static-coarse'],
+    maps: ['volume-streaming-info'],
+};