molstar 3.1.0 → 3.2.0

package/lib/mol-model/structure/export/categories/atom_site.js

@@ -5,6 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { CifWriter } from '../../../../mol-io/writer/cif';
+import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
+import { SIFTSMapping } from '../../../../mol-model-props/sequence/sifts-mapping';
 import { StructureProperties as P } from '../../structure';
 var CifField = CifWriter.Field;
 var E = CifWriter.Encodings;
@@ -22,6 +24,61 @@ function atom_site_auth_asym_id(e) {
         return l;
     return l + suffix;
 }
+var atom_site_pdbx_label_index = {
+    shouldInclude: function (s) {
+        var _a;
+        return !!((_a = s.atom_site) === null || _a === void 0 ? void 0 : _a.pdbx_label_index.isDefined);
+    },
+    value: function (e, d) {
+        var srcIndex = d.sourceIndex.value(e.element);
+        return d.atom_site.pdbx_label_index.value(srcIndex);
+    },
+};
+var SIFTS = {
+    shouldInclude: function (s) {
+        return SIFTSMapping.isAvailable(s.structure.models[0]);
+    },
+    pdbx_sifts_xref_db_name: {
+        value: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_name.value(srcIndex);
+        },
+        valueKind: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_name.valueKind(srcIndex);
+        },
+    },
+    pdbx_sifts_xref_db_acc: {
+        value: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_acc.value(srcIndex);
+        },
+        valueKind: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_acc.valueKind(srcIndex);
+        },
+    },
+    pdbx_sifts_xref_db_num: {
+        value: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_num.value(srcIndex);
+        },
+        valueKind: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_num.valueKind(srcIndex);
+        },
+    },
+    pdbx_sifts_xref_db_res: {
+        value: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_res.value(srcIndex);
+        },
+        valueKind: function (e, d) {
+            var srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site.pdbx_sifts_xref_db_res.valueKind(srcIndex);
+        },
+    }
+};
 var atom_site_fields = function () { return CifWriter.fields()
     .str('group_PDB', P.residue.group_PDB)
     .index('id')
@@ -53,6 +110,12 @@ var atom_site_fields = function () { return CifWriter.fields()
     .int('auth_seq_id', P.residue.auth_seq_id, { encoder: E.deltaRLE })
     .str('auth_asym_id', atom_site_auth_asym_id)
     .int('pdbx_PDB_model_num', P.unit.model_num, { encoder: E.deltaRLE })
+    .int('pdbx_label_index', atom_site_pdbx_label_index.value, { shouldInclude: atom_site_pdbx_label_index.shouldInclude })
+    // SIFTS
+    .str('pdbx_sifts_xref_db_name', SIFTS.pdbx_sifts_xref_db_name.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_name.valueKind })
+    .str('pdbx_sifts_xref_db_acc', SIFTS.pdbx_sifts_xref_db_acc.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_acc.valueKind })
+    .str('pdbx_sifts_xref_db_num', SIFTS.pdbx_sifts_xref_db_num.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_num.valueKind })
+    .str('pdbx_sifts_xref_db_res', SIFTS.pdbx_sifts_xref_db_res.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_res.valueKind })
     // .str('operator_name', P.unit.operator_name, {
     //     shouldInclude: structure => structure.units.some(u => !u.conformation.operator.isIdentity)
     // })
@@ -64,7 +127,11 @@ export var _atom_site = {
         return {
             fields: atom_site_fields(),
             source: structures.map(function (s) { return ({
-                data: s,
+                data: {
+                    structure: s,
+                    sourceIndex: s.model.atomicHierarchy.atomSourceIndex,
+                    atom_site: MmcifFormat.is(s.model.sourceData) ? s.model.sourceData.data.db.atom_site : void 0
+                },
                 rowCount: s.elementCount,
                 keys: function () { return s.elementLocations(); }
             }); })

package/lib/mol-model/structure/structure/util/superposition-sifts-mapping.d.ts

@@ -0,0 +1,21 @@
+/**
+ * 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>
+ */
+import { MinimizeRmsd } from '../../../../mol-math/linear-algebra/3d/minimize-rmsd';
+import { Structure } from '../structure';
+export interface AlignmentResultEntry {
+    transform: MinimizeRmsd.Result;
+    pivot: number;
+    other: number;
+}
+export interface AlignmentResult {
+    entries: AlignmentResultEntry[];
+    zeroOverlapPairs: [number, number][];
+    failedPairs: [number, number][];
+}
+export declare function alignAndSuperposeWithSIFTSMapping(structures: Structure[], options?: {
+    traceOnly?: boolean;
+}): AlignmentResult;

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

@@ -1,29 +1,41 @@
 /**
- * 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>
  */
 import { Segmentation } from '../../../../mol-data/int';
-import { Mat4 } from '../../../../mol-math/linear-algebra';
 import { MinimizeRmsd } from '../../../../mol-math/linear-algebra/3d/minimize-rmsd';
-import { BestDatabaseSequenceMapping } from '../../../../mol-model-props/sequence/best-database-mapping';
-export function alignAndSuperposeWithBestDatabaseMapping(structures) {
+import { SIFTSMapping } from '../../../../mol-model-props/sequence/sifts-mapping';
+export 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 = MinimizeRmsd.compute({ a: a, b: b });
-        console.log(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 = 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 };
 }
 function getPositionTables(index, pivot, other, N) {
     var xs = MinimizeRmsd.Positions.empty(N);
@@ -36,7 +48,6 @@ 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);
@@ -90,19 +101,20 @@ 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 = BestDatabaseSequenceMapping.Provider.get(model).value;
+        var map = SIFTSMapping.Provider.get(model).value;
         if (!map)
             return;
         var dbName = map.dbName, accession = map.accession, num = map.num;
         var chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
         var residuesIt = 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);
@@ -111,8 +123,17 @@ 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) });
@@ -126,6 +147,5 @@ function buildIndex(structure, index, sI) {
             }
         }
     }
-    console.log(index);
 }
-//# sourceMappingURL=superposition-db-mapping.js.map
+//# sourceMappingURL=superposition-sifts-mapping.js.map

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

@@ -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>
  */
 var FormatRegistry = /** @class */ (function () {
     function FormatRegistry() {
@@ -29,7 +30,7 @@ var FormatRegistry = /** @class */ (function () {
 export { FormatPropertyProvider };
 var FormatPropertyProvider;
 (function (FormatPropertyProvider) {
-    function create(descriptor) {
+    function create(descriptor, options) {
         var name = descriptor.name;
         var formatRegistry = new FormatRegistry();
         return {
@@ -39,22 +40,33 @@ 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/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/mol-model-formats/structure/property/bonds/index-pair.js

@@ -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 { __assign } from "tslib";
 import { IntAdjacencyGraph } from '../../../../mol-math/graph';
@@ -26,7 +27,7 @@ export var IndexPairBonds;
     IndexPairBonds.Descriptor = {
         name: 'index_pair_bonds',
     };
-    IndexPairBonds.Provider = FormatPropertyProvider.create(IndexPairBonds.Descriptor);
+    IndexPairBonds.Provider = FormatPropertyProvider.create(IndexPairBonds.Descriptor, { asDynamic: true });
     IndexPairBonds.DefaultProps = {
         /**
          * If negative, test using element-based threshold, otherwise distance in Angstrom.

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

@@ -7,38 +7,45 @@ import { __awaiter, __generator } from "tslib";
 import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
 import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 import { CustomModelProperty } from '../common/custom-model-property';
-export { BestDatabaseSequenceMapping };
-var BestDatabaseSequenceMapping;
-(function (BestDatabaseSequenceMapping) {
+export { SIFTSMapping as SIFTSMapping };
+var SIFTSMapping;
+(function (SIFTSMapping) {
     var _this = this;
-    BestDatabaseSequenceMapping.Provider = CustomModelProperty.createProvider({
-        label: 'Best Database Sequence Mapping',
+    SIFTSMapping.Provider = CustomModelProperty.createProvider({
+        label: 'SIFTS Mapping',
         descriptor: CustomPropertyDescriptor({
-            name: 'molstar_best_database_sequence_mapping'
+            name: 'sifts_sequence_mapping'
         }),
         type: 'static',
         defaultParams: {},
         getParams: function () { return ({}); },
-        isApplicable: function (data) { var _a, _b; return 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 __awaiter(_this, void 0, void 0, function () {
             return __generator(this, function (_a) {
                 return [2 /*return*/, { value: fromCif(data) }];
             });
         }); }
     });
+    function isAvailable(model) {
+        if (!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];
@@ -48,19 +55,15 @@ 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 (!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);
@@ -70,16 +73,16 @@ 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 = {}));
-//# sourceMappingURL=best-database-mapping.js.map
+})(SIFTSMapping || (SIFTSMapping = {}));
+//# sourceMappingURL=sifts-mapping.js.map

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

@@ -8,21 +8,21 @@ import { Bond, StructureElement, Unit } from '../../../mol-model/structure';
 import { Color } from '../../../mol-util/color';
 import { getPalette, getPaletteParams } from '../../../mol-util/color/palette';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { BestDatabaseSequenceMapping } from '../best-database-mapping';
+import { SIFTSMapping } from '../sifts-mapping';
 var DefaultColor = 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();
-export var BestDatabaseSequenceMappingColorThemeParams = __assign({}, getPaletteParams({ type: 'colors', colorList: 'set-1' }));
-export function getBestDatabaseSequenceMappingColorThemeParams(ctx) {
-    return BestDatabaseSequenceMappingColorThemeParams; // TODO return copy
+export var SIFTSMappingColorThemeParams = __assign({}, getPaletteParams({ type: 'colors', colorList: 'set-1' }));
+export function getSIFTSMappingColorThemeParams(ctx) {
+    return SIFTSMappingColorThemeParams; // TODO return copy
 }
-export function BestDatabaseSequenceMappingColorTheme(ctx, props) {
+export 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 = BestDatabaseSequenceMapping.Provider.get(m).value;
+            var mapping = SIFTSMapping.Provider.get(m).value;
             if (!mapping)
                 continue;
             for (var _b = 0, _c = mapping.accession; _b < _c.length; _b++) {
@@ -36,7 +36,7 @@ export function BestDatabaseSequenceMappingColorTheme(ctx, props) {
         var 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 = BestDatabaseSequenceMapping.getKey(location);
+            var key = SIFTSMapping.getKey(location);
             if (!key)
                 return DefaultColor;
             if (colorMap_1.has(key))
@@ -61,7 +61,7 @@ export function BestDatabaseSequenceMappingColorTheme(ctx, props) {
         color = function () { return DefaultColor; };
     }
     return {
-        factory: BestDatabaseSequenceMappingColorTheme,
+        factory: SIFTSMappingColorTheme,
         granularity: 'group',
         preferSmoothing: true,
         color: color,
@@ -69,14 +69,14 @@ export function BestDatabaseSequenceMappingColorTheme(ctx, props) {
         description: Description,
     };
 }
-export var BestDatabaseSequenceMappingColorThemeProvider = {
-    name: 'best-sequence-database-mapping',
-    label: 'Best Database Sequence Mapping',
+export var SIFTSMappingColorThemeProvider = {
+    name: 'sifts-mapping',
+    label: 'SIFTS Mapping',
     category: "Residue Property" /* Residue */,
-    factory: BestDatabaseSequenceMappingColorTheme,
-    getParams: getBestDatabaseSequenceMappingColorThemeParams,
-    defaultValues: PD.getDefaultValues(BestDatabaseSequenceMappingColorThemeParams),
-    isApplicable: function (ctx) { var _a; return !!((_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models.some(function (m) { return BestDatabaseSequenceMapping.Provider.isApplicable(m); })); },
+    factory: SIFTSMappingColorTheme,
+    getParams: getSIFTSMappingColorThemeParams,
+    defaultValues: PD.getDefaultValues(SIFTSMappingColorThemeParams),
+    isApplicable: function (ctx) { var _a; return !!((_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models.some(function (m) { return SIFTSMapping.Provider.isApplicable(m); })); },
     ensureCustomProperties: {
         attach: function (ctx, data) { return __awaiter(void 0, void 0, void 0, function () {
             var _i, _a, m;
@@ -90,7 +90,7 @@ export var BestDatabaseSequenceMappingColorThemeProvider = {
                     case 1:
                         if (!(_i < _a.length)) return [3 /*break*/, 4];
                         m = _a[_i];
-                        return [4 /*yield*/, BestDatabaseSequenceMapping.Provider.attach(ctx, m, void 0, true)];
+                        return [4 /*yield*/, SIFTSMapping.Provider.attach(ctx, m, void 0, true)];
                     case 2:
                         _b.sent();
                         _b.label = 3;
@@ -106,9 +106,9 @@ export var BestDatabaseSequenceMappingColorThemeProvider = {
                 return;
             for (var _i = 0, _a = data.structure.models; _i < _a.length; _i++) {
                 var m = _a[_i];
-                BestDatabaseSequenceMapping.Provider.ref(m, false);
+                SIFTSMapping.Provider.ref(m, false);
             }
         }
     }
 };
-//# sourceMappingURL=best-database-mapping.js.map
+//# sourceMappingURL=sifts-mapping.js.map

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

@@ -5,15 +5,15 @@
  */
 import { __extends } from "tslib";
 import { OrderedSet } from '../../../../../mol-data/int';
-import { BestDatabaseSequenceMapping as BestDatabaseSequenceMappingProp } from '../../../../../mol-model-props/sequence/best-database-mapping';
-import { BestDatabaseSequenceMappingColorThemeProvider } from '../../../../../mol-model-props/sequence/themes/best-database-mapping';
+import { SIFTSMapping as BestDatabaseSequenceMappingProp } from '../../../../../mol-model-props/sequence/sifts-mapping';
+import { SIFTSMappingColorThemeProvider } from '../../../../../mol-model-props/sequence/themes/sifts-mapping';
 import { StructureElement } from '../../../../../mol-model/structure';
 import { ParamDefinition as PD } from '../../../../../mol-util/param-definition';
 import { PluginBehavior } from '../../../behavior';
-export var BestDatabaseSequenceMapping = PluginBehavior.create({
-    name: 'best-sequence-database-mapping-prop',
+export var SIFTSMapping = PluginBehavior.create({
+    name: 'sifts-mapping-prop',
     category: 'custom-props',
-    display: { name: 'Best Database Sequence Mapping' },
+    display: { name: 'SIFTS Mapping' },
     ctor: /** @class */ (function (_super) {
         __extends(class_1, _super);
         function class_1() {
@@ -38,12 +38,12 @@ export var BestDatabaseSequenceMapping = PluginBehavior.create({
         };
         class_1.prototype.register = function () {
             this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
-            this.ctx.representation.structure.themes.colorThemeRegistry.add(BestDatabaseSequenceMappingColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(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(BestDatabaseSequenceMappingColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(SIFTSMappingColorThemeProvider);
             this.ctx.managers.lociLabels.removeProvider(this.labelProvider);
         };
         return class_1;
@@ -64,4 +64,4 @@ function bestDatabaseSequenceMappingLabel(loci) {
         return BestDatabaseSequenceMappingProp.getLabel(se);
     }
 }
-//# sourceMappingURL=best-database-mapping.js.map
+//# sourceMappingURL=sifts-mapping.js.map