molstar 3.0.0-dev.9 → 3.1.0

package/lib/commonjs/mol-model-formats/structure/basic/properties.js

@@ -6,11 +6,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getProperties = void 0;
+exports.getStructAsymMap = exports.getSaccharideComponentMap = exports.getChemicalComponentMap = exports.getMissingResidues = void 0;
+var db_1 = require("../../../mol-data/db");
 var types_1 = require("../../../mol-model/structure/model/types");
 var constants_1 = require("../../../mol-model/structure/structure/carbohydrates/constants");
 var memoize_1 = require("../../../mol-util/memoize");
-var db_1 = require("../../../mol-data/db");
 function getMissingResidues(data) {
     var map = new Map();
     var getKey = function (model_num, asym_id, seq_id) {
@@ -31,6 +31,7 @@ function getMissingResidues(data) {
         size: map.size
     };
 }
+exports.getMissingResidues = getMissingResidues;
 function getChemicalComponentMap(data) {
     var map = new Map();
     if (data.chem_comp._rowCount > 0) {
@@ -47,6 +48,7 @@ function getChemicalComponentMap(data) {
     }
     return map;
 }
+exports.getChemicalComponentMap = getChemicalComponentMap;
 function getSaccharideComponentMap(data) {
     var map = new Map();
     if (data.pdbx_chem_comp_identifier._rowCount > 0) {
@@ -93,6 +95,7 @@ function getSaccharideComponentMap(data) {
     }
     return map;
 }
+exports.getSaccharideComponentMap = getSaccharideComponentMap;
 var getUniqueComponentNames = (0, memoize_1.memoize1)(function (data) {
     var uniqueNames = new Set();
     var _a = data.atom_site, label_comp_id = _a.label_comp_id, auth_comp_id = _a.auth_comp_id;
@@ -102,20 +105,15 @@ var getUniqueComponentNames = (0, memoize_1.memoize1)(function (data) {
     }
     return uniqueNames;
 });
-function getStructAsymMap(data) {
+function getStructAsymMap(atomic, data) {
     var map = new Map();
-    var _a = data.atom_site, label_asym_id = _a.label_asym_id, auth_asym_id = _a.auth_asym_id, label_entity_id = _a.label_entity_id;
-    for (var i = 0, il = label_asym_id.rowCount; i < il; ++i) {
+    var _a = atomic.chains, auth_asym_id = _a.auth_asym_id, label_asym_id = _a.label_asym_id, label_entity_id = _a.label_entity_id;
+    for (var i = 0, _i = atomic.chains._rowCount; i < _i; i++) {
         var id = label_asym_id.value(i);
-        if (!map.has(id)) {
-            map.set(id, {
-                id: id,
-                auth_id: auth_asym_id.value(i),
-                entity_id: label_entity_id.value(i)
-            });
-        }
+        map.set(id, { id: id, auth_id: auth_asym_id.value(i), entity_id: label_entity_id.value(i) });
     }
-    if (data.struct_asym._rowCount > 0) {
+    // to get asym mapping for coarse/ihm data
+    if (data === null || data === void 0 ? void 0 : data.struct_asym._rowCount) {
         var _b = data.struct_asym, id = _b.id, entity_id = _b.entity_id;
         for (var i = 0, il = id.rowCount; i < il; ++i) {
             var _id = id.value(i);
@@ -130,13 +128,5 @@ function getStructAsymMap(data) {
     }
     return map;
 }
-function getProperties(data) {
-    return {
-        missingResidues: getMissingResidues(data),
-        chemicalComponentMap: getChemicalComponentMap(data),
-        saccharideComponentMap: getSaccharideComponentMap(data),
-        structAsymMap: getStructAsymMap(data)
-    };
-}
-exports.getProperties = getProperties;
+exports.getStructAsymMap = getStructAsymMap;
 //# sourceMappingURL=properties.js.map

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

@@ -1,8 +1,9 @@
 /**
- * Copyright (c) 2019-2020 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>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 import { MolFile } from '../../mol-io/reader/mol/parser';
 import { RuntimeContext, Task } from '../../mol-task';

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

@@ -1,31 +1,44 @@
 "use strict";
 /**
- * Copyright (c) 2019-2020 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>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.trajectoryFromMol = exports.MolFormat = exports.getMolModels = void 0;
 var tslib_1 = require("tslib");
 var db_1 = require("../../mol-data/db");
+var parser_1 = require("../../mol-io/reader/mol/parser");
 var mol_task_1 = require("../../mol-task");
-var parser_1 = require("./basic/parser");
+var parser_2 = require("./basic/parser");
 var schema_1 = require("./basic/schema");
 var component_1 = require("./common/component");
 var entity_1 = require("./common/entity");
 var index_pair_1 = require("./property/bonds/index-pair");
 function getMolModels(mol, format, ctx) {
     return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var atoms, bonds, MOL, A, type_symbol, seq_id, atom_site, entityBuilder, componentBuilder, basics, models, indexA, indexB, order, pairBonds;
+        var atoms, bonds, formalCharges, MOL, A, type_symbol, seq_id, computedFormalCharges, i, i, atom_site, entityBuilder, componentBuilder, basics, models, indexA, indexB, order, pairBonds;
         return (0, tslib_1.__generator)(this, function (_a) {
             switch (_a.label) {
                 case 0:
-                    atoms = mol.atoms, bonds = mol.bonds;
+                    atoms = mol.atoms, bonds = mol.bonds, formalCharges = mol.formalCharges;
                     MOL = db_1.Column.ofConst('MOL', mol.atoms.count, db_1.Column.Schema.str);
                     A = db_1.Column.ofConst('A', mol.atoms.count, db_1.Column.Schema.str);
                     type_symbol = db_1.Column.asArrayColumn(atoms.type_symbol);
                     seq_id = db_1.Column.ofConst(1, atoms.count, db_1.Column.Schema.int);
+                    computedFormalCharges = new Int32Array(mol.atoms.count);
+                    if (formalCharges.atomIdx.rowCount > 0) {
+                        for (i = 0; i < formalCharges.atomIdx.rowCount; i++) {
+                            computedFormalCharges[formalCharges.atomIdx.value(i) - 1] = formalCharges.charge.value(i);
+                        }
+                    }
+                    else {
+                        for (i = 0; i < mol.atoms.count; i++) {
+                            computedFormalCharges[i] = (0, parser_1.formalChargeMapper)(atoms.formal_charge.value(i));
+                        }
+                    }
                     atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
                         auth_asym_id: A,
                         auth_atom_id: type_symbol,
@@ -43,6 +56,7 @@ function getMolModels(mol, format, ctx) {
                         occupancy: db_1.Column.ofConst(1, atoms.count, db_1.Column.Schema.float),
                         type_symbol: type_symbol,
                         pdbx_PDB_model_num: db_1.Column.ofConst(1, atoms.count, db_1.Column.Schema.int),
+                        pdbx_formal_charge: db_1.Column.ofIntArray(computedFormalCharges)
                     }, atoms.count);
                     entityBuilder = new entity_1.EntityBuilder();
                     entityBuilder.setNames([['MOL', 'Unknown Entity']]);
@@ -55,7 +69,7 @@ function getMolModels(mol, format, ctx) {
                         chem_comp: componentBuilder.getChemCompTable(),
                         atom_site: atom_site
                     });
-                    return [4 /*yield*/, (0, parser_1.createModels)(basics, format !== null && format !== void 0 ? format : MolFormat.create(mol), ctx)];
+                    return [4 /*yield*/, (0, parser_2.createModels)(basics, format !== null && format !== void 0 ? format : MolFormat.create(mol), ctx)];
                 case 1:
                     models = _a.sent();
                     if (models.frameCount > 0) {

package/lib/commonjs/mol-model-props/common/custom-property.d.ts

@@ -47,7 +47,7 @@ declare namespace CustomProperty {
             }>>;
         };
         setDefaultAutoAttach(name: string, value: boolean): void;
-        get(name: string): Provider<Data, any, any>;
+        get(name: string): Provider<Data, any, any> | undefined;
         register(provider: Provider<Data, any, any>, defaultAutoAttach: boolean): void;
         unregister(name: string): void;
     }

package/lib/commonjs/mol-model-props/computed/interactions/common.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 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>
  */

package/lib/commonjs/mol-model-props/computed/interactions/common.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2020 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>
  */
@@ -64,29 +64,21 @@ var InteractionsInterContacts = /** @class */ (function (_super) {
     (0, tslib_1.__extends)(InteractionsInterContacts, _super);
     function InteractionsInterContacts(map, unitsFeatures) {
         var _this = _super.call(this, map) || this;
-        var count = 0;
-        var elementKeyIndex = new Map();
-        var add = function (index, unitId) {
-            var vertexKey = _this.getElementKey(index, unitId);
-            var e = elementKeyIndex.get(vertexKey);
-            if (e === undefined)
-                elementKeyIndex.set(vertexKey, [count]);
-            else
-                e.push(count);
-        };
-        _this.map.forEach(function (pairEdgesArray) {
-            pairEdgesArray.forEach(function (_a) {
-                var unitA = _a.unitA, connectedIndices = _a.connectedIndices;
-                connectedIndices.forEach(function (indexA) {
-                    var _a = unitsFeatures.get(unitA), offsetsA = _a.offsets, membersA = _a.members;
-                    for (var j = offsetsA[indexA], jl = offsetsA[indexA + 1]; j < jl; ++j) {
-                        add(membersA[j], unitA);
-                    }
-                    count += 1;
-                });
-            });
-        });
-        _this.elementKeyIndex = elementKeyIndex;
+        _this.elementKeyIndex = new Map();
+        for (var i = 0, il = _this.edges.length; i < il; ++i) {
+            var _a = _this.edges[i], unitA = _a.unitA, indexA = _a.indexA;
+            var _b = unitsFeatures.get(unitA), offsets = _b.offsets, members = _b.members;
+            for (var j = offsets[indexA], jl = offsets[indexA + 1]; j < jl; ++j) {
+                var vertexKey = _this.getElementKey(members[j], unitA);
+                var e = _this.elementKeyIndex.get(vertexKey);
+                if (e === undefined) {
+                    _this.elementKeyIndex.set(vertexKey, [i]);
+                }
+                else {
+                    e.push(i);
+                }
+            }
+        }
         return _this;
     }
     InteractionsInterContacts.prototype.getContactIndicesForElement = function (index, unit) {

package/lib/commonjs/mol-model-props/computed/representations/interactions-inter-unit-cylinder.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 Alexander Rose <alexander.rose@weirdbyte.de>
  */

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.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 Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/mol-model-props/computed/representations/interactions-intra-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>
  */
@@ -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);
@@ -102,6 +112,7 @@ function getInteractionLoci(pickingId, structureGroup, id) {
     }
     return loci_1.EmptyLoci;
 }
+var __contactIndicesSet = new Set();
 function eachInteraction(loci, structureGroup, apply, isMarking) {
     var changed = false;
     if (interactions_2.Interactions.isLoci(loci)) {
@@ -136,28 +147,42 @@ function eachInteraction(loci, structureGroup, apply, isMarking) {
         if (!interactions)
             return false;
         var unit = group.units[0];
-        var contacts = interactions.unitsContacts.get(unit.id);
+        var contacts_1 = interactions.unitsContacts.get(unit.id);
         var features = interactions.unitsFeatures.get(unit.id);
-        var groupCount_1 = contacts.edgeCount * 2;
-        var offset_1 = contacts.offset;
+        var groupCount_1 = contacts_1.edgeCount * 2;
+        var offset_1 = contacts_1.offset;
         var _b = features.elementsIndex, fOffsets_1 = _b.offsets, fIndices_1 = _b.indices;
+        var members_1 = features.members, offsets_1 = features.offsets;
         var _loop_1 = function (e) {
             var unitIdx = group.unitIndexMap.get(e.unit.id);
-            if (unitIdx !== undefined)
-                return "continue";
-            if (isMarking && int_1.OrderedSet.size(e.indices) === 1)
+            if (unitIdx === undefined)
                 return "continue";
             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];
                     for (var j = offset_1[fI], jl = offset_1[fI + 1]; j < jl; ++j) {
-                        if (apply(int_1.Interval.ofSingleton(unitIdx * groupCount_1 + j)))
-                            changed = true;
+                        __contactIndicesSet.add(j);
+                    }
+                }
+            });
+            __contactIndicesSet.forEach(function (i) {
+                if (isMarking) {
+                    var fA = contacts_1.a[i];
+                    for (var j = offsets_1[fA], jl = offsets_1[fA + 1]; j < jl; ++j) {
+                        if (!int_1.OrderedSet.has(e.indices, members_1[j]))
+                            return;
+                    }
+                    var fB = contacts_1.b[i];
+                    for (var j = offsets_1[fB], jl = offsets_1[fB + 1]; j < jl; ++j) {
+                        if (!int_1.OrderedSet.has(e.indices, members_1[j]))
+                            return;
                     }
                 }
+                if (apply(int_1.Interval.ofSingleton(unitIdx * groupCount_1 + i)))
+                    changed = true;
             });
+            __contactIndicesSet.clear();
         };
-        // 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];
             _loop_1(e);

package/lib/commonjs/mol-model-props/sequence/best-database-mapping.js

@@ -21,7 +21,7 @@ var BestDatabaseSequenceMapping;
         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('db_name')) >= 0; },
+        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; },
         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) }];
@@ -34,7 +34,7 @@ var BestDatabaseSequenceMapping;
         if (!data)
             return '';
         var eI = loc.unit.elements[loc.element];
-        var rI = model.atomicHierarchy.residueAtomSegments.offsets[eI];
+        var rI = model.atomicHierarchy.residueAtomSegments.index[eI];
         return data.accession[rI];
     }
     BestDatabaseSequenceMapping.getKey = getKey;
@@ -44,7 +44,7 @@ var BestDatabaseSequenceMapping;
         if (!data)
             return;
         var eI = loc.unit.elements[loc.element];
-        var rI = model.atomicHierarchy.residueAtomSegments.offsets[eI];
+        var rI = model.atomicHierarchy.residueAtomSegments.index[eI];
         var dbName = data.dbName[rI];
         if (!dbName)
             return;
@@ -55,10 +55,10 @@ var BestDatabaseSequenceMapping;
         if (!mmcif_1.MmcifFormat.is(model.sourceData))
             return;
         var atom_site = model.sourceData.data.frame.categories.atom_site;
-        var db_name = atom_site.getField('db_name');
-        var db_acc = atom_site.getField('db_acc');
-        var db_num = atom_site.getField('db_num');
-        var db_res = atom_site.getField('db_res');
+        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)
             return;
         var atomSourceIndex = model.atomicHierarchy.atomSourceIndex;
@@ -70,16 +70,16 @@ var BestDatabaseSequenceMapping;
         for (var i = 0; i < count; i++) {
             var row = atomSourceIndex.value(residueOffsets[i]);
             if (db_name.valueKind(row) !== 0 /* Present */) {
-                dbName[row] = '';
-                accession[row] = '';
-                num[row] = 0;
-                residue[row] = '';
+                dbName[i] = '';
+                accession[i] = '';
+                num[i] = 0;
+                residue[i] = '';
                 continue;
             }
-            dbName[row] = db_name.str(row);
-            accession[row] = db_acc.str(row);
-            num[row] = db_num.int(row);
-            residue[row] = db_res.str(row);
+            dbName[i] = db_name.str(row);
+            accession[i] = db_acc.str(row);
+            num[i] = db_num.int(row);
+            residue[i] = db_res.str(row);
         }
         return { dbName: dbName, accession: accession, num: num, residue: residue };
     }

package/lib/commonjs/mol-plugin/animation-loop.d.ts

@@ -4,6 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 import { PluginContext } from './context';
+import { PluginAnimationManager } from '../mol-plugin-state/manager/animation';
 export declare class PluginAnimationLoop {
     private plugin;
     private currentFrame;
@@ -12,6 +13,7 @@ export declare class PluginAnimationLoop {
     tick(t: number, options?: {
         isSynchronous?: boolean;
         manualDraw?: boolean;
+        animation?: PluginAnimationManager.AnimationInfo;
     }): Promise<void>;
     private frame;
     resetTime(t?: number): void;

package/lib/commonjs/mol-plugin/animation-loop.js

@@ -33,7 +33,7 @@ var PluginAnimationLoop = /** @class */ (function () {
         return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
             return (0, tslib_1.__generator)(this, function (_b) {
                 switch (_b.label) {
-                    case 0: return [4 /*yield*/, this.plugin.managers.animation.tick(t, options === null || options === void 0 ? void 0 : options.isSynchronous)];
+                    case 0: return [4 /*yield*/, this.plugin.managers.animation.tick(t, options === null || options === void 0 ? void 0 : options.isSynchronous, options === null || options === void 0 ? void 0 : options.animation)];
                     case 1:
                         _b.sent();
                         (_a = this.plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.tick(t, options);

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;