molstar 3.1.0 → 3.2.0

package/lib/commonjs/mol-model/structure/structure/util/{superposition-db-mapping.js → superposition-sifts-mapping.js}

@@ -1,34 +1,46 @@
 "use strict";
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.alignAndSuperposeWithBestDatabaseMapping = void 0;
+exports.alignAndSuperposeWithSIFTSMapping = void 0;
 var int_1 = require("../../../../mol-data/int");
-var linear_algebra_1 = require("../../../../mol-math/linear-algebra");
 var minimize_rmsd_1 = require("../../../../mol-math/linear-algebra/3d/minimize-rmsd");
-var best_database_mapping_1 = require("../../../../mol-model-props/sequence/best-database-mapping");
-function alignAndSuperposeWithBestDatabaseMapping(structures) {
+var sifts_mapping_1 = require("../../../../mol-model-props/sequence/sifts-mapping");
+function alignAndSuperposeWithSIFTSMapping(structures, options) {
+    var _a;
     var indexMap = new Map();
     for (var i = 0; i < structures.length; i++) {
-        buildIndex(structures[i], indexMap, i);
+        buildIndex(structures[i], indexMap, i, (_a = options === null || options === void 0 ? void 0 : options.traceOnly) !== null && _a !== void 0 ? _a : true);
     }
     var index = Array.from(indexMap.values());
     // TODO: support non-first structure pivots
     var pairs = findPairs(structures.length, index);
-    var ret = [];
+    var zeroOverlapPairs = [];
+    var failedPairs = [];
+    var entries = [];
     for (var _i = 0, pairs_1 = pairs; _i < pairs_1.length; _i++) {
         var p = pairs_1[_i];
-        var _a = getPositionTables(index, p.i, p.j, p.count), a = _a[0], b = _a[1];
-        var transform = minimize_rmsd_1.MinimizeRmsd.compute({ a: a, b: b });
-        console.log(linear_algebra_1.Mat4.makeTable(transform.bTransform), transform.rmsd);
-        ret.push({ transform: transform, pivot: p.i, other: p.j });
+        if (p.count === 0) {
+            zeroOverlapPairs.push([p.i, p.j]);
+        }
+        else {
+            var _b = getPositionTables(index, p.i, p.j, p.count), a = _b[0], b = _b[1];
+            var transform = minimize_rmsd_1.MinimizeRmsd.compute({ a: a, b: b });
+            if (Number.isNaN(transform.rmsd)) {
+                failedPairs.push([p.i, p.j]);
+            }
+            else {
+                entries.push({ transform: transform, pivot: p.i, other: p.j });
+            }
+        }
     }
-    return ret;
+    return { entries: entries, zeroOverlapPairs: zeroOverlapPairs, failedPairs: failedPairs };
 }
-exports.alignAndSuperposeWithBestDatabaseMapping = alignAndSuperposeWithBestDatabaseMapping;
+exports.alignAndSuperposeWithSIFTSMapping = alignAndSuperposeWithSIFTSMapping;
 function getPositionTables(index, pivot, other, N) {
     var xs = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);
     var ys = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);
@@ -40,7 +52,6 @@ function getPositionTables(index, pivot, other, N) {
         if (!a || !b)
             continue;
         var l = Math.min(a[2] - a[1], b[2] - b[1]);
-        // TODO: allow to use just backbone atoms?
         // TODO: check if residue types match?
         for (var i = 0; i < l; i++) {
             var eI = (a[1] + i);
@@ -94,19 +105,20 @@ function findPairs(N, index) {
     // }
     return ret;
 }
-function buildIndex(structure, index, sI) {
+function buildIndex(structure, index, sI, traceOnly) {
     var _a;
     for (var _i = 0, _b = structure.units; _i < _b.length; _i++) {
         var unit = _b[_i];
         if (unit.kind !== 0 /* Atomic */)
             continue;
         var elements = unit.elements, model = unit.model;
-        var map = best_database_mapping_1.BestDatabaseSequenceMapping.Provider.get(model).value;
+        var map = sifts_mapping_1.SIFTSMapping.Provider.get(model).value;
         if (!map)
             return;
         var dbName = map.dbName, accession = map.accession, num = map.num;
         var chainsIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
         var residuesIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
+        var traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex;
         while (chainsIt.hasNext) {
             var chainSegment = chainsIt.move();
             residuesIt.setSegment(chainSegment);
@@ -115,8 +127,17 @@ function buildIndex(structure, index, sI) {
                 var rI = residueSegment.index;
                 if (!dbName[rI])
                     continue;
-                var start = elements[residueSegment.start];
-                var end = elements[residueSegment.end - 1] + 1;
+                var start = void 0, end = void 0;
+                if (traceOnly) {
+                    start = traceElementIndex[rI];
+                    if (start === -1)
+                        continue;
+                    end = start + 1;
+                }
+                else {
+                    start = elements[residueSegment.start];
+                    end = elements[residueSegment.end - 1] + 1;
+                }
                 var key = "".concat(dbName[rI], "-").concat(accession[rI], "-").concat(num[rI]);
                 if (!index.has(key)) {
                     index.set(key, { key: key, pivots: (_a = {}, _a[sI] = [unit, start, end], _a) });
@@ -130,6 +151,5 @@ function buildIndex(structure, index, sI) {
             }
         }
     }
-    console.log(index);
 }
-//# sourceMappingURL=superposition-db-mapping.js.map
+//# sourceMappingURL=superposition-sifts-mapping.js.map

package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts

@@ -125,6 +125,11 @@ export declare const BasicSchema: {
         pdbx_PDB_ins_code: import("../../../mol-data/db/column").Column.Schema.Str;
         pdbx_PDB_model_num: import("../../../mol-data/db/column").Column.Schema.Int;
         pdbx_formal_charge: import("../../../mol-data/db/column").Column.Schema.Int;
+        pdbx_label_index: import("../../../mol-data/db/column").Column.Schema.Int;
+        pdbx_sifts_xref_db_name: import("../../../mol-data/db/column").Column.Schema.Str;
+        pdbx_sifts_xref_db_acc: import("../../../mol-data/db/column").Column.Schema.Str;
+        pdbx_sifts_xref_db_num: import("../../../mol-data/db/column").Column.Schema.Str;
+        pdbx_sifts_xref_db_res: import("../../../mol-data/db/column").Column.Schema.Str;
         ihm_model_id: import("../../../mol-data/db/column").Column.Schema.Int;
     };
     ihm_sphere_obj_site: {

package/lib/commonjs/mol-model-formats/structure/common/property.d.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 import { Model } from '../../../mol-model/structure';
 import { ModelFormat } from '../../format';
@@ -24,5 +25,7 @@ interface FormatPropertyProvider<T> {
     delete(model: Model): void;
 }
 declare namespace FormatPropertyProvider {
-    function create<T>(descriptor: CustomPropertyDescriptor): FormatPropertyProvider<T>;
+    function create<T>(descriptor: CustomPropertyDescriptor, options?: {
+        asDynamic?: boolean;
+    }): FormatPropertyProvider<T>;
 }

package/lib/commonjs/mol-model-formats/structure/common/property.js

@@ -1,8 +1,9 @@
 "use strict";
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.FormatPropertyProvider = void 0;
@@ -31,7 +32,7 @@ var FormatRegistry = /** @class */ (function () {
 }());
 var FormatPropertyProvider;
 (function (FormatPropertyProvider) {
-    function create(descriptor) {
+    function create(descriptor, options) {
         var name = descriptor.name;
         var formatRegistry = new FormatRegistry();
         return {
@@ -41,22 +42,33 @@ var FormatPropertyProvider;
                 return formatRegistry.isApplicable(model);
             },
             get: function (model) {
-                if (model._staticPropertyData[name])
-                    return model._staticPropertyData[name];
+                var store = (options === null || options === void 0 ? void 0 : options.asDynamic) ? model._dynamicPropertyData : model._staticPropertyData;
+                if (store[name])
+                    return store[name];
                 if (model.customProperties.has(descriptor))
                     return;
                 var obtain = formatRegistry.get(model.sourceData.kind);
                 if (!obtain)
                     return;
-                model._staticPropertyData[name] = obtain(model);
+                store[name] = obtain(model);
                 model.customProperties.add(descriptor);
-                return model._staticPropertyData[name];
+                return store[name];
             },
             set: function (model, value) {
-                model._staticPropertyData[name] = value;
+                if (options === null || options === void 0 ? void 0 : options.asDynamic) {
+                    model._dynamicPropertyData[name] = value;
+                }
+                else {
+                    model._staticPropertyData[name] = value;
+                }
             },
             delete: function (model) {
-                delete model._staticPropertyData[name];
+                if (options === null || options === void 0 ? void 0 : options.asDynamic) {
+                    delete model._dynamicPropertyData[name];
+                }
+                else {
+                    delete model._staticPropertyData[name];
+                }
             }
         };
     }

package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.d.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2019-2022 Mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 import { CustomPropertyDescriptor } from '../../../../mol-model/custom-property';
 import { IntAdjacencyGraph } from '../../../../mol-math/graph';

package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js

@@ -3,6 +3,7 @@
  * Copyright (c) 2019-2022 Mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.IndexPairBonds = void 0;
@@ -29,7 +30,7 @@ var IndexPairBonds;
     IndexPairBonds.Descriptor = {
         name: 'index_pair_bonds',
     };
-    IndexPairBonds.Provider = property_1.FormatPropertyProvider.create(IndexPairBonds.Descriptor);
+    IndexPairBonds.Provider = property_1.FormatPropertyProvider.create(IndexPairBonds.Descriptor, { asDynamic: true });
     IndexPairBonds.DefaultProps = {
         /**
          * If negative, test using element-based threshold, otherwise distance in Angstrom.

package/lib/commonjs/mol-model-props/sequence/{best-database-mapping.d.ts → sifts-mapping.d.ts}

@@ -3,17 +3,19 @@
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
+import { Model } from '../../mol-model/structure';
 import { StructureElement } from '../../mol-model/structure/structure';
 import { CustomModelProperty } from '../common/custom-model-property';
-export { BestDatabaseSequenceMapping };
-interface BestDatabaseSequenceMapping {
+export { SIFTSMapping as SIFTSMapping };
+interface SIFTSMappingMapping {
     readonly dbName: string[];
     readonly accession: string[];
-    readonly num: number[];
+    readonly num: string[];
     readonly residue: string[];
 }
-declare namespace BestDatabaseSequenceMapping {
-    const Provider: CustomModelProperty.Provider<{}, BestDatabaseSequenceMapping>;
+declare namespace SIFTSMapping {
+    const Provider: CustomModelProperty.Provider<{}, SIFTSMappingMapping>;
+    function isAvailable(model: Model): boolean;
     function getKey(loc: StructureElement.Location): string;
     function getLabel(loc: StructureElement.Location): string | undefined;
 }

package/lib/commonjs/mol-model-props/sequence/{best-database-mapping.js → sifts-mapping.js}

@@ -5,42 +5,49 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.BestDatabaseSequenceMapping = void 0;
+exports.SIFTSMapping = void 0;
 var tslib_1 = require("tslib");
 var mmcif_1 = require("../../mol-model-formats/structure/mmcif");
 var custom_property_1 = require("../../mol-model/custom-property");
 var custom_model_property_1 = require("../common/custom-model-property");
-var BestDatabaseSequenceMapping;
-(function (BestDatabaseSequenceMapping) {
+var SIFTSMapping;
+(function (SIFTSMapping) {
     var _this = this;
-    BestDatabaseSequenceMapping.Provider = custom_model_property_1.CustomModelProperty.createProvider({
-        label: 'Best Database Sequence Mapping',
+    SIFTSMapping.Provider = custom_model_property_1.CustomModelProperty.createProvider({
+        label: 'SIFTS Mapping',
         descriptor: (0, custom_property_1.CustomPropertyDescriptor)({
-            name: 'molstar_best_database_sequence_mapping'
+            name: 'sifts_sequence_mapping'
         }),
         type: 'static',
         defaultParams: {},
         getParams: function () { return ({}); },
-        isApplicable: function (data) { var _a, _b; return mmcif_1.MmcifFormat.is(data.sourceData) && ((_b = (_a = data.sourceData.data.frame.categories) === null || _a === void 0 ? void 0 : _a.atom_site) === null || _b === void 0 ? void 0 : _b.fieldNames.indexOf('pdbx_sifts_xref_db_name')) >= 0; },
+        isApplicable: function (data) { return isAvailable(data); },
         obtain: function (ctx, data) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
             return (0, tslib_1.__generator)(this, function (_a) {
                 return [2 /*return*/, { value: fromCif(data) }];
             });
         }); }
     });
+    function isAvailable(model) {
+        if (!mmcif_1.MmcifFormat.is(model.sourceData))
+            return false;
+        var _a = model.sourceData.data.db.atom_site, db_name = _a.pdbx_sifts_xref_db_name, db_acc = _a.pdbx_sifts_xref_db_acc, db_num = _a.pdbx_sifts_xref_db_num, db_res = _a.pdbx_sifts_xref_db_res;
+        return db_name.isDefined && db_acc.isDefined && db_num.isDefined && db_res.isDefined;
+    }
+    SIFTSMapping.isAvailable = isAvailable;
     function getKey(loc) {
         var model = loc.unit.model;
-        var data = BestDatabaseSequenceMapping.Provider.get(model).value;
+        var data = SIFTSMapping.Provider.get(model).value;
         if (!data)
             return '';
         var eI = loc.unit.elements[loc.element];
         var rI = model.atomicHierarchy.residueAtomSegments.index[eI];
         return data.accession[rI];
     }
-    BestDatabaseSequenceMapping.getKey = getKey;
+    SIFTSMapping.getKey = getKey;
     function getLabel(loc) {
         var model = loc.unit.model;
-        var data = BestDatabaseSequenceMapping.Provider.get(model).value;
+        var data = SIFTSMapping.Provider.get(model).value;
         if (!data)
             return;
         var eI = loc.unit.elements[loc.element];
@@ -50,19 +57,15 @@ var BestDatabaseSequenceMapping;
             return;
         return "".concat(dbName, " ").concat(data.accession[rI], " ").concat(data.num[rI], " ").concat(data.residue[rI]);
     }
-    BestDatabaseSequenceMapping.getLabel = getLabel;
+    SIFTSMapping.getLabel = getLabel;
     function fromCif(model) {
         if (!mmcif_1.MmcifFormat.is(model.sourceData))
             return;
-        var atom_site = model.sourceData.data.frame.categories.atom_site;
-        var db_name = atom_site.getField('pdbx_sifts_xref_db_name');
-        var db_acc = atom_site.getField('pdbx_sifts_xref_db_acc');
-        var db_num = atom_site.getField('pdbx_sifts_xref_db_num');
-        var db_res = atom_site.getField('pdbx_sifts_xref_db_res');
-        if (!db_name || !db_acc || !db_num || !db_res)
+        var _a = model.sourceData.data.db.atom_site, db_name = _a.pdbx_sifts_xref_db_name, db_acc = _a.pdbx_sifts_xref_db_acc, db_num = _a.pdbx_sifts_xref_db_num, db_res = _a.pdbx_sifts_xref_db_res;
+        if (!db_name.isDefined || !db_acc.isDefined || !db_num.isDefined || !db_res.isDefined)
             return;
         var atomSourceIndex = model.atomicHierarchy.atomSourceIndex;
-        var _a = model.atomicHierarchy.residueAtomSegments, count = _a.count, residueOffsets = _a.offsets;
+        var _b = model.atomicHierarchy.residueAtomSegments, count = _b.count, residueOffsets = _b.offsets;
         var dbName = new Array(count);
         var accession = new Array(count);
         var num = new Array(count);
@@ -72,17 +75,17 @@ var BestDatabaseSequenceMapping;
             if (db_name.valueKind(row) !== 0 /* Present */) {
                 dbName[i] = '';
                 accession[i] = '';
-                num[i] = 0;
+                num[i] = '';
                 residue[i] = '';
                 continue;
             }
-            dbName[i] = db_name.str(row);
-            accession[i] = db_acc.str(row);
-            num[i] = db_num.int(row);
-            residue[i] = db_res.str(row);
+            dbName[i] = db_name.value(row);
+            accession[i] = db_acc.value(row);
+            num[i] = db_num.value(row);
+            residue[i] = db_res.value(row);
         }
         return { dbName: dbName, accession: accession, num: num, residue: residue };
     }
-})(BestDatabaseSequenceMapping || (BestDatabaseSequenceMapping = {}));
-exports.BestDatabaseSequenceMapping = BestDatabaseSequenceMapping;
-//# sourceMappingURL=best-database-mapping.js.map
+})(SIFTSMapping || (SIFTSMapping = {}));
+exports.SIFTSMapping = SIFTSMapping;
+//# sourceMappingURL=sifts-mapping.js.map

package/lib/{mol-model-props/sequence/themes/best-database-mapping.d.ts → commonjs/mol-model-props/sequence/themes/sifts-mapping.d.ts}

@@ -6,7 +6,7 @@
 import { ColorTheme } from '../../../mol-theme/color';
 import { ThemeDataContext } from '../../../mol-theme/theme';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-export declare const BestDatabaseSequenceMappingColorThemeParams: {
+export declare const SIFTSMappingColorThemeParams: {
     palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
         maxCount: number;
         hue: [number, number];
@@ -21,8 +21,8 @@ export declare const BestDatabaseSequenceMappingColorThemeParams: {
         };
     }>, "colors">>;
 };
-export declare type BestDatabaseSequenceMappingColorThemeParams = typeof BestDatabaseSequenceMappingColorThemeParams;
-export declare function getBestDatabaseSequenceMappingColorThemeParams(ctx: ThemeDataContext): {
+export declare type SIFTSMappingColorThemeParams = typeof SIFTSMappingColorThemeParams;
+export declare function getSIFTSMappingColorThemeParams(ctx: ThemeDataContext): {
     palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
         maxCount: number;
         hue: [number, number];
@@ -37,5 +37,5 @@ export declare function getBestDatabaseSequenceMappingColorThemeParams(ctx: Them
         };
     }>, "colors">>;
 };
-export declare function BestDatabaseSequenceMappingColorTheme(ctx: ThemeDataContext, props: PD.Values<BestDatabaseSequenceMappingColorThemeParams>): ColorTheme<BestDatabaseSequenceMappingColorThemeParams>;
-export declare const BestDatabaseSequenceMappingColorThemeProvider: ColorTheme.Provider<BestDatabaseSequenceMappingColorThemeParams, 'best-sequence-database-mapping'>;
+export declare function SIFTSMappingColorTheme(ctx: ThemeDataContext, props: PD.Values<SIFTSMappingColorThemeParams>): ColorTheme<SIFTSMappingColorThemeParams>;
+export declare const SIFTSMappingColorThemeProvider: ColorTheme.Provider<SIFTSMappingColorThemeParams, 'sifts-mapping'>;

package/lib/commonjs/mol-model-props/sequence/themes/{best-database-mapping.js → sifts-mapping.js}

@@ -5,28 +5,28 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.BestDatabaseSequenceMappingColorThemeProvider = exports.BestDatabaseSequenceMappingColorTheme = exports.getBestDatabaseSequenceMappingColorThemeParams = exports.BestDatabaseSequenceMappingColorThemeParams = void 0;
+exports.SIFTSMappingColorThemeProvider = exports.SIFTSMappingColorTheme = exports.getSIFTSMappingColorThemeParams = exports.SIFTSMappingColorThemeParams = void 0;
 var tslib_1 = require("tslib");
 var structure_1 = require("../../../mol-model/structure");
 var color_1 = require("../../../mol-util/color");
 var palette_1 = require("../../../mol-util/color/palette");
 var param_definition_1 = require("../../../mol-util/param-definition");
-var best_database_mapping_1 = require("../best-database-mapping");
+var sifts_mapping_1 = require("../sifts-mapping");
 var DefaultColor = (0, color_1.Color)(0xFAFAFA);
-var Description = 'Assigns a color based on best dababase sequence mapping.';
+var Description = 'Assigns a color based on SIFTS mapping.';
 // same colors for same accessions
 var globalAccessionMap = new Map();
-exports.BestDatabaseSequenceMappingColorThemeParams = (0, tslib_1.__assign)({}, (0, palette_1.getPaletteParams)({ type: 'colors', colorList: 'set-1' }));
-function getBestDatabaseSequenceMappingColorThemeParams(ctx) {
-    return exports.BestDatabaseSequenceMappingColorThemeParams; // TODO return copy
+exports.SIFTSMappingColorThemeParams = (0, tslib_1.__assign)({}, (0, palette_1.getPaletteParams)({ type: 'colors', colorList: 'set-1' }));
+function getSIFTSMappingColorThemeParams(ctx) {
+    return exports.SIFTSMappingColorThemeParams; // TODO return copy
 }
-exports.getBestDatabaseSequenceMappingColorThemeParams = getBestDatabaseSequenceMappingColorThemeParams;
-function BestDatabaseSequenceMappingColorTheme(ctx, props) {
+exports.getSIFTSMappingColorThemeParams = getSIFTSMappingColorThemeParams;
+function SIFTSMappingColorTheme(ctx, props) {
     var color;
     if (ctx.structure) {
         for (var _i = 0, _a = ctx.structure.models; _i < _a.length; _i++) {
             var m = _a[_i];
-            var mapping = best_database_mapping_1.BestDatabaseSequenceMapping.Provider.get(m).value;
+            var mapping = sifts_mapping_1.SIFTSMapping.Provider.get(m).value;
             if (!mapping)
                 continue;
             for (var _b = 0, _c = mapping.accession; _b < _c.length; _b++) {
@@ -40,7 +40,7 @@ function BestDatabaseSequenceMappingColorTheme(ctx, props) {
         var palette_2 = (0, palette_1.getPalette)(globalAccessionMap.size + 1, props, { valueLabel: function (i) { return "".concat(i); } });
         var colorMap_1 = new Map();
         var getColor_1 = function (location) {
-            var key = best_database_mapping_1.BestDatabaseSequenceMapping.getKey(location);
+            var key = sifts_mapping_1.SIFTSMapping.getKey(location);
             if (!key)
                 return DefaultColor;
             if (colorMap_1.has(key))
@@ -65,7 +65,7 @@ function BestDatabaseSequenceMappingColorTheme(ctx, props) {
         color = function () { return DefaultColor; };
     }
     return {
-        factory: BestDatabaseSequenceMappingColorTheme,
+        factory: SIFTSMappingColorTheme,
         granularity: 'group',
         preferSmoothing: true,
         color: color,
@@ -73,15 +73,15 @@ function BestDatabaseSequenceMappingColorTheme(ctx, props) {
         description: Description,
     };
 }
-exports.BestDatabaseSequenceMappingColorTheme = BestDatabaseSequenceMappingColorTheme;
-exports.BestDatabaseSequenceMappingColorThemeProvider = {
-    name: 'best-sequence-database-mapping',
-    label: 'Best Database Sequence Mapping',
+exports.SIFTSMappingColorTheme = SIFTSMappingColorTheme;
+exports.SIFTSMappingColorThemeProvider = {
+    name: 'sifts-mapping',
+    label: 'SIFTS Mapping',
     category: "Residue Property" /* Residue */,
-    factory: BestDatabaseSequenceMappingColorTheme,
-    getParams: getBestDatabaseSequenceMappingColorThemeParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.BestDatabaseSequenceMappingColorThemeParams),
-    isApplicable: function (ctx) { var _a; return !!((_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models.some(function (m) { return best_database_mapping_1.BestDatabaseSequenceMapping.Provider.isApplicable(m); })); },
+    factory: SIFTSMappingColorTheme,
+    getParams: getSIFTSMappingColorThemeParams,
+    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.SIFTSMappingColorThemeParams),
+    isApplicable: function (ctx) { var _a; return !!((_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models.some(function (m) { return sifts_mapping_1.SIFTSMapping.Provider.isApplicable(m); })); },
     ensureCustomProperties: {
         attach: function (ctx, data) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
             var _i, _a, m;
@@ -95,7 +95,7 @@ exports.BestDatabaseSequenceMappingColorThemeProvider = {
                     case 1:
                         if (!(_i < _a.length)) return [3 /*break*/, 4];
                         m = _a[_i];
-                        return [4 /*yield*/, best_database_mapping_1.BestDatabaseSequenceMapping.Provider.attach(ctx, m, void 0, true)];
+                        return [4 /*yield*/, sifts_mapping_1.SIFTSMapping.Provider.attach(ctx, m, void 0, true)];
                     case 2:
                         _b.sent();
                         _b.label = 3;
@@ -111,9 +111,9 @@ exports.BestDatabaseSequenceMappingColorThemeProvider = {
                 return;
             for (var _i = 0, _a = data.structure.models; _i < _a.length; _i++) {
                 var m = _a[_i];
-                best_database_mapping_1.BestDatabaseSequenceMapping.Provider.ref(m, false);
+                sifts_mapping_1.SIFTSMapping.Provider.ref(m, false);
             }
         }
     }
 };
-//# sourceMappingURL=best-database-mapping.js.map
+//# sourceMappingURL=sifts-mapping.js.map

package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/sequence/{best-database-mapping.d.ts → sifts-mapping.d.ts}

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 import { PluginBehavior } from '../../../behavior';
-export declare const BestDatabaseSequenceMapping: import("../../../../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
+export declare const SIFTSMapping: import("../../../../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
     autoAttach: boolean;
     showTooltip: boolean;
 }>;

package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/sequence/{best-database-mapping.js → sifts-mapping.js}

@@ -5,23 +5,23 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.BestDatabaseSequenceMapping = void 0;
+exports.SIFTSMapping = void 0;
 var tslib_1 = require("tslib");
 var int_1 = require("../../../../../mol-data/int");
-var best_database_mapping_1 = require("../../../../../mol-model-props/sequence/best-database-mapping");
-var best_database_mapping_2 = require("../../../../../mol-model-props/sequence/themes/best-database-mapping");
+var sifts_mapping_1 = require("../../../../../mol-model-props/sequence/sifts-mapping");
+var sifts_mapping_2 = require("../../../../../mol-model-props/sequence/themes/sifts-mapping");
 var structure_1 = require("../../../../../mol-model/structure");
 var param_definition_1 = require("../../../../../mol-util/param-definition");
 var behavior_1 = require("../../../behavior");
-exports.BestDatabaseSequenceMapping = behavior_1.PluginBehavior.create({
-    name: 'best-sequence-database-mapping-prop',
+exports.SIFTSMapping = behavior_1.PluginBehavior.create({
+    name: 'sifts-mapping-prop',
     category: 'custom-props',
-    display: { name: 'Best Database Sequence Mapping' },
+    display: { name: 'SIFTS Mapping' },
     ctor: /** @class */ (function (_super) {
         (0, tslib_1.__extends)(class_1, _super);
         function class_1() {
             var _this = _super !== null && _super.apply(this, arguments) || this;
-            _this.provider = best_database_mapping_1.BestDatabaseSequenceMapping.Provider;
+            _this.provider = sifts_mapping_1.SIFTSMapping.Provider;
             _this.labelProvider = {
                 label: function (loci) {
                     if (!_this.params.showTooltip)
@@ -41,12 +41,12 @@ exports.BestDatabaseSequenceMapping = behavior_1.PluginBehavior.create({
         };
         class_1.prototype.register = function () {
             this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
-            this.ctx.representation.structure.themes.colorThemeRegistry.add(best_database_mapping_2.BestDatabaseSequenceMappingColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(sifts_mapping_2.SIFTSMappingColorThemeProvider);
             this.ctx.managers.lociLabels.addProvider(this.labelProvider);
         };
         class_1.prototype.unregister = function () {
             this.ctx.customModelProperties.unregister(this.provider.descriptor.name);
-            this.ctx.representation.structure.themes.colorThemeRegistry.remove(best_database_mapping_2.BestDatabaseSequenceMappingColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(sifts_mapping_2.SIFTSMappingColorThemeProvider);
             this.ctx.managers.lociLabels.removeProvider(this.labelProvider);
         };
         return class_1;
@@ -64,7 +64,7 @@ function bestDatabaseSequenceMappingLabel(loci) {
         var e = loci.elements[0];
         var u = e.unit;
         var se = structure_1.StructureElement.Location.create(loci.structure, u, u.elements[int_1.OrderedSet.getAt(e.indices, 0)]);
-        return best_database_mapping_1.BestDatabaseSequenceMapping.getLabel(se);
+        return sifts_mapping_1.SIFTSMapping.getLabel(se);
     }
 }
-//# sourceMappingURL=best-database-mapping.js.map
+//# sourceMappingURL=sifts-mapping.js.map

package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props.d.ts

@@ -9,5 +9,5 @@ export { AccessibleSurfaceArea } from './custom-props/computed/accessible-surfac
 export { Interactions } from './custom-props/computed/interactions';
 export { SecondaryStructure } from './custom-props/computed/secondary-structure';
 export { ValenceModel } from './custom-props/computed/valence-model';
-export { BestDatabaseSequenceMapping } from './custom-props/sequence/best-database-mapping';
+export { SIFTSMapping as BestDatabaseSequenceMapping } from './custom-props/sequence/sifts-mapping';
 export { CrossLinkRestraint } from './custom-props/integrative/cross-link-restraint';

package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props.js

@@ -17,8 +17,8 @@ var secondary_structure_1 = require("./custom-props/computed/secondary-structure
 Object.defineProperty(exports, "SecondaryStructure", { enumerable: true, get: function () { return secondary_structure_1.SecondaryStructure; } });
 var valence_model_1 = require("./custom-props/computed/valence-model");
 Object.defineProperty(exports, "ValenceModel", { enumerable: true, get: function () { return valence_model_1.ValenceModel; } });
-var best_database_mapping_1 = require("./custom-props/sequence/best-database-mapping");
-Object.defineProperty(exports, "BestDatabaseSequenceMapping", { enumerable: true, get: function () { return best_database_mapping_1.BestDatabaseSequenceMapping; } });
+var sifts_mapping_1 = require("./custom-props/sequence/sifts-mapping");
+Object.defineProperty(exports, "BestDatabaseSequenceMapping", { enumerable: true, get: function () { return sifts_mapping_1.SIFTSMapping; } });
 var cross_link_restraint_1 = require("./custom-props/integrative/cross-link-restraint");
 Object.defineProperty(exports, "CrossLinkRestraint", { enumerable: true, get: function () { return cross_link_restraint_1.CrossLinkRestraint; } });
 //# sourceMappingURL=custom-props.js.map

package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts

@@ -9,12 +9,12 @@ import { Volume } from '../../../../mol-model/volume';
 import { Structure } from '../../../../mol-model/structure';
 declare const VolumeServerInfo_base: {
     new (data: VolumeServerInfo.Data, props?: {
-        label: string; /** Precision data the server can show. */
+        /** Precision data the server can show. */
+        label: string;
         description?: string | undefined;
     } | undefined): {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
-        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;
@@ -23,7 +23,6 @@ declare const VolumeServerInfo_base: {
     is(obj?: import("../../../../mol-state/object").StateObject<any, import("../../../../mol-state/object").StateObject.Type<any>> | undefined): obj is {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
-        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;