molstar 3.0.0 → 3.2.0

package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -66,11 +66,12 @@ function createInterUnitInteractionCylinderMesh(ctx, structure, theme, props, me
                 if (!childUnitA)
                     return true;
                 var unitA = structure.unitMap.get(b.unitA);
-                var fA = unitsFeatures.get(b.unitA);
-                // TODO: check all members
-                var eA = unitA.elements[fA.members[fA.offsets[b.indexA]]];
-                if (!int_1.SortedArray.has(childUnitA.elements, eA))
-                    return true;
+                var _a = unitsFeatures.get(b.unitA), offsets = _a.offsets, members = _a.members;
+                for (var i = offsets[b.indexA], il = offsets[b.indexA + 1]; i < il; ++i) {
+                    var eA = unitA.elements[members[i]];
+                    if (!int_1.SortedArray.has(childUnitA.elements, eA))
+                        return true;
+                }
             }
             return false;
         }
@@ -119,8 +120,9 @@ function getInteractionLoci(pickingId, structure, id) {
     }
     return loci_1.EmptyLoci;
 }
+var __unitMap = new Map();
+var __contactIndicesSet = new Set();
 function eachInteraction(loci, structure, apply, isMarking) {
-    var _a;
     var changed = false;
     if (interactions_1.Interactions.isLoci(loci)) {
         if (!structure_1.Structure.areEquivalent(loci.data.structure, structure))
@@ -129,8 +131,8 @@ function eachInteraction(loci, structure, apply, isMarking) {
         if (loci.data.interactions !== interactions)
             return false;
         var contacts = interactions.contacts;
-        for (var _i = 0, _b = loci.elements; _i < _b.length; _i++) {
-            var c = _b[_i];
+        for (var _i = 0, _a = loci.elements; _i < _a.length; _i++) {
+            var c = _a[_i];
             var idx = contacts.getEdgeIndex(c.indexA, c.unitA.id, c.indexB, c.unitB.id);
             if (idx !== -1) {
                 if (apply(int_1.Interval.ofSingleton(idx)))
@@ -143,28 +145,52 @@ function eachInteraction(loci, structure, apply, isMarking) {
             return false;
         if (isMarking && loci.elements.length === 1)
             return false; // only a single unit
-        var contacts_1 = (_a = interactions_2.InteractionsProvider.get(structure).value) === null || _a === void 0 ? void 0 : _a.contacts;
-        if (!contacts_1)
+        var interactions = interactions_2.InteractionsProvider.get(structure).value;
+        if (!interactions)
             return false;
+        var contacts_1 = interactions.contacts, unitsFeatures_1 = interactions.unitsFeatures;
+        for (var _b = 0, _c = loci.elements; _b < _c.length; _b++) {
+            var e = _c[_b];
+            __unitMap.set(e.unit.id, e.indices);
+        }
         var _loop_1 = function (e) {
             var unit = e.unit;
             if (!structure_2.Unit.isAtomic(unit))
                 return "continue";
-            if (isMarking && int_1.OrderedSet.size(e.indices) === 1)
-                return "continue";
             int_1.OrderedSet.forEach(e.indices, function (v) {
                 for (var _i = 0, _a = contacts_1.getContactIndicesForElement(v, unit); _i < _a.length; _i++) {
                     var idx = _a[_i];
-                    if (apply(int_1.Interval.ofSingleton(idx)))
-                        changed = true;
+                    __contactIndicesSet.add(idx);
                 }
             });
         };
-        // TODO when isMarking, all elements of contact features need to be in the loci
-        for (var _c = 0, _d = loci.elements; _c < _d.length; _c++) {
-            var e = _d[_c];
+        for (var _d = 0, _e = loci.elements; _d < _e.length; _d++) {
+            var e = _e[_d];
             _loop_1(e);
         }
+        __contactIndicesSet.forEach(function (i) {
+            if (isMarking) {
+                var _a = contacts_1.edges[i], indexA = _a.indexA, unitA = _a.unitA, indexB = _a.indexB, unitB = _a.unitB;
+                var indicesA = __unitMap.get(unitA);
+                var indicesB = __unitMap.get(unitB);
+                if (!indicesA || !indicesB)
+                    return;
+                var _b = unitsFeatures_1.get(unitA), offsetsA = _b.offsets, membersA = _b.members;
+                for (var j = offsetsA[indexA], jl = offsetsA[indexA + 1]; j < jl; ++j) {
+                    if (!int_1.OrderedSet.has(indicesA, membersA[j]))
+                        return;
+                }
+                var _c = unitsFeatures_1.get(unitB), offsetsB = _c.offsets, membersB = _c.members;
+                for (var j = offsetsB[indexB], jl = offsetsB[indexB + 1]; j < jl; ++j) {
+                    if (!int_1.OrderedSet.has(indicesB, membersB[j]))
+                        return;
+                }
+            }
+            if (apply(int_1.Interval.ofSingleton(i)))
+                changed = true;
+        });
+        __unitMap.clear();
+        __contactIndicesSet.clear();
     }
     return changed;
 }

package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-unit-cylinder.js

@@ -52,9 +52,19 @@ function createIntraUnitInteractionsCylinderMesh(ctx, unit, structure, theme, pr
                     var sizeB = theme.size.size(location);
                     return Math.min(sizeA, sizeB) * sizeFactor;
                 },
-                ignore: function (edgeIndex) { return (flag[edgeIndex] === 1 /* Filtered */ ||
-                    // TODO: check all members
-                    (!!childUnit && !int_1.SortedArray.has(childUnit.elements, unit.elements[members[offsets[a[edgeIndex]]]]))); }
+                ignore: function (edgeIndex) {
+                    if (flag[edgeIndex] === 1 /* Filtered */)
+                        return true;
+                    if (childUnit) {
+                        var f = a[edgeIndex];
+                        for (var i = offsets[f], jl = offsets[f + 1]; i < jl; ++i) {
+                            var e = unit.elements[members[offsets[i]]];
+                            if (!int_1.SortedArray.has(childUnit.elements, e))
+                                return true;
+                        }
+                    }
+                    return false;
+                }
             };
             m = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
             sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * sizeFactor);
@@ -147,7 +157,6 @@ function eachInteraction(loci, structureGroup, apply, isMarking) {
             var unitIdx = group.unitIndexMap.get(e.unit.id);
             if (unitIdx === undefined)
                 return "continue";
-            __contactIndicesSet.clear();
             int_1.OrderedSet.forEach(e.indices, function (v) {
                 for (var i = fOffsets_1[v], il = fOffsets_1[v + 1]; i < il; ++i) {
                     var fI = fIndices_1[i];
@@ -172,6 +181,7 @@ function eachInteraction(loci, structureGroup, apply, isMarking) {
                 if (apply(int_1.Interval.ofSingleton(unitIdx * groupCount_1 + i)))
                     changed = true;
             });
+            __contactIndicesSet.clear();
         };
         for (var _c = 0, _d = loci.elements; _c < _d.length; _c++) {
             var e = _d[_c];

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/representation.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/commonjs/mol-plugin/behavior/dynamic/representation.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -216,11 +216,16 @@ exports.DefaultLociLabelProvider = behavior_1.PluginBehavior.create({
             this.f = {
                 label: function (loci) {
                     var label = [];
-                    if (structure_1.StructureElement.Loci.is(loci) && loci.elements.length === 1) {
-                        var u = loci.elements[0].unit;
-                        var l = structure_1.StructureElement.Location.create(loci.structure, u, u.elements[0]);
-                        var name_1 = structure_1.StructureProperties.entity.pdbx_description(l).join(', ');
-                        label.push(name_1);
+                    if (structure_1.StructureElement.Loci.is(loci)) {
+                        var entityNames = new Set();
+                        for (var _i = 0, _a = loci.elements; _i < _a.length; _i++) {
+                            var u = _a[_i].unit;
+                            var l = structure_1.StructureElement.Location.create(loci.structure, u, u.elements[0]);
+                            var name_1 = structure_1.StructureProperties.entity.pdbx_description(l).join(', ');
+                            entityNames.add(name_1);
+                        }
+                        if (entityNames.size === 1)
+                            entityNames.forEach(function (name) { return label.push(name); });
                     }
                     label.push((0, label_1.lociLabel)(loci));
                     return label.filter(function (l) { return !!l; }).join('</br>');

package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -22,6 +22,7 @@ declare const StructureFocusRepresentationParams: (plugin: PluginContext) => {
     components: PD.MultiSelect<"target" | "surroundings" | "interactions">;
     excludeTargetFromSurroundings: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreLight: PD.BooleanParam;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;

package/lib/commonjs/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -27,11 +27,19 @@ var StructureFocusRepresentationParams = function (plugin) {
         expandRadius: param_definition_1.ParamDefinition.Numeric(5, { min: 1, max: 10, step: 1 }),
         targetParams: param_definition_1.ParamDefinition.Group(reprParams, {
             label: 'Target',
-            customDefault: (0, structure_representation_params_1.createStructureRepresentationParams)(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.26, alpha: 0.51, adjustCylinderLength: true } })
+            customDefault: (0, structure_representation_params_1.createStructureRepresentationParams)(plugin, void 0, {
+                type: 'ball-and-stick',
+                size: 'physical',
+                typeParams: { sizeFactor: 0.22, sizeAspectRatio: 0.73, adjustCylinderLength: true, xrayShaded: true, aromaticBonds: false, multipleBonds: 'off', excludeTypes: ['hydrogen-bond', 'metal-coordination'] },
+            })
         }),
         surroundingsParams: param_definition_1.ParamDefinition.Group(reprParams, {
             label: 'Surroundings',
-            customDefault: (0, structure_representation_params_1.createStructureRepresentationParams)(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.16 } })
+            customDefault: (0, structure_representation_params_1.createStructureRepresentationParams)(plugin, void 0, {
+                type: 'ball-and-stick',
+                size: 'physical',
+                typeParams: { sizeFactor: 0.16, excludeTypes: ['hydrogen-bond', 'metal-coordination'] }
+            })
         }),
         nciParams: param_definition_1.ParamDefinition.Group(reprParams, {
             label: 'Non-covalent Int.',
@@ -44,6 +52,7 @@ var StructureFocusRepresentationParams = function (plugin) {
         components: param_definition_1.ParamDefinition.MultiSelect(FocusComponents, param_definition_1.ParamDefinition.arrayToOptions(FocusComponents)),
         excludeTargetFromSurroundings: param_definition_1.ParamDefinition.Boolean(false, { label: 'Exclude Target', description: 'Exclude the focus "target" from the surroudings component.' }),
         ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false),
+        ignoreLight: param_definition_1.ParamDefinition.Boolean(false),
         material: material_1.Material.getParam(),
         clip: param_definition_1.ParamDefinition.Group(clip_1.Clip.Params),
     };
@@ -71,9 +80,9 @@ var StructureFocusRepresentationBehavior = /** @class */ (function (_super) {
         configurable: true
     });
     StructureFocusRepresentationBehavior.prototype.getReprParams = function (reprParams) {
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.params.targetParams), { type: {
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, reprParams), { type: {
                 name: reprParams.type.name,
-                params: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, reprParams.type.params), { ignoreHydrogens: this.params.ignoreHydrogens, material: this.params.material, clip: this.params.clip })
+                params: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, reprParams.type.params), { ignoreHydrogens: this.params.ignoreHydrogens, ignoreLight: this.params.ignoreLight, material: this.params.material, clip: this.params.clip })
             } });
     };
     StructureFocusRepresentationBehavior.prototype.ensureShape = function (cell) {
@@ -107,7 +116,7 @@ var StructureFocusRepresentationBehavior = /** @class */ (function (_super) {
         if (components.indexOf('interactions') >= 0 && !refs[StructureFocusRepresentationTags.SurrNciRepr] && cell.obj && interactions_1.InteractionsRepresentationProvider.isApplicable((_a = cell.obj) === null || _a === void 0 ? void 0 : _a.data)) {
             refs[StructureFocusRepresentationTags.SurrNciRepr] = builder
                 .to(refs[StructureFocusRepresentationTags.SurrSel])
-                .apply(transforms_1.StateTransforms.Representation.StructureRepresentation3D, this.params.nciParams, { tags: StructureFocusRepresentationTags.SurrNciRepr }).ref;
+                .apply(transforms_1.StateTransforms.Representation.StructureRepresentation3D, this.getReprParams(this.params.nciParams), { tags: StructureFocusRepresentationTags.SurrNciRepr }).ref;
         }
         return { state: state, builder: builder, refs: refs };
     };
@@ -217,7 +226,7 @@ var StructureFocusRepresentationBehavior = /** @class */ (function (_super) {
                             if (!hasComponent)
                                 builder.delete(repr.transform.ref);
                             else
-                                builder.to(repr).update(this.params.nciParams);
+                                builder.to(repr).update(this.getReprParams(this.params.nciParams));
                         }
                         return [4 /*yield*/, commands_1.PluginCommands.State.Update(this.plugin, { state: state, tree: builder, options: { doNotLogTiming: true, doNotUpdateCurrent: true } })];
                     case 1: