molstar 3.0.0-dev.6 → 3.0.0

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-formats/structure/mol2.d.ts

@@ -1,5 +1,5 @@
 /**
- * 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>
  */

package/lib/commonjs/mol-model-formats/structure/mol2.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -17,9 +17,12 @@ var index_pair_1 = require("./property/bonds/index-pair");
 var partial_charge_1 = require("./property/partial-charge");
 var structure_1 = require("../../mol-model/structure");
 var util_1 = require("./util");
+var symmetry_1 = require("./property/symmetry");
+var geometry_1 = require("../../mol-math/geometry");
+var linear_algebra_1 = require("../../mol-math/linear-algebra");
 function getModels(mol2, ctx) {
     return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var models, i, il, _a, atoms, bonds, molecule, A, type_symbol, i_1, atom_site, entityBuilder, componentBuilder, i_2, il_1, basics, _models, indexA, indexB, order, flag, pairBonds, first;
+        var models, i, il, _a, molecule, atoms, bonds, crysin, A, type_symbol, hasAtomType, i_1, i_2, atom_site, entityBuilder, componentBuilder, i_3, il_1, basics, _models, indexA, indexB, key, order, flag, pairBonds, first, symmetry;
         return (0, tslib_1.__generator)(this, function (_b) {
             switch (_b.label) {
                 case 0:
@@ -28,11 +31,20 @@ function getModels(mol2, ctx) {
                     _b.label = 1;
                 case 1:
                     if (!(i < il)) return [3 /*break*/, 4];
-                    _a = mol2.structures[i], atoms = _a.atoms, bonds = _a.bonds, molecule = _a.molecule;
+                    _a = mol2.structures[i], molecule = _a.molecule, atoms = _a.atoms, bonds = _a.bonds, crysin = _a.crysin;
                     A = db_1.Column.ofConst('A', atoms.count, db_1.Column.Schema.str);
                     type_symbol = new Array(atoms.count);
+                    hasAtomType = false;
                     for (i_1 = 0; i_1 < atoms.count; ++i_1) {
-                        type_symbol[i_1] = (0, util_1.guessElementSymbolString)(atoms.atom_name.value(i_1));
+                        if (atoms.atom_type.value(i_1).includes('.')) {
+                            hasAtomType = true;
+                            break;
+                        }
+                    }
+                    for (i_2 = 0; i_2 < atoms.count; ++i_2) {
+                        type_symbol[i_2] = hasAtomType
+                            ? atoms.atom_type.value(i_2).split('.')[0].toUpperCase()
+                            : (0, util_1.guessElementSymbolString)(atoms.atom_name.value(i_2));
                     }
                     atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
                         auth_asym_id: A,
@@ -56,8 +68,8 @@ function getModels(mol2, ctx) {
                     entityBuilder.setNames([['MOL', molecule.mol_name || 'Unknown Entity']]);
                     entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
                     componentBuilder = new component_1.ComponentBuilder(atoms.subst_id, atoms.atom_name);
-                    for (i_2 = 0, il_1 = atoms.subst_name.rowCount; i_2 < il_1; ++i_2) {
-                        componentBuilder.add(atoms.subst_name.value(i_2), i_2);
+                    for (i_3 = 0, il_1 = atoms.subst_name.rowCount; i_3 < il_1; ++i_3) {
+                        componentBuilder.add(atoms.subst_name.value(i_3), i_3);
                     }
                     basics = (0, schema_1.createBasic)({
                         entity: entityBuilder.getEntityTable(),
@@ -70,6 +82,7 @@ function getModels(mol2, ctx) {
                     if (_models.frameCount > 0) {
                         indexA = db_1.Column.ofIntArray(db_1.Column.mapToArray(bonds.origin_atom_id, function (x) { return x - 1; }, Int32Array));
                         indexB = db_1.Column.ofIntArray(db_1.Column.mapToArray(bonds.target_atom_id, function (x) { return x - 1; }, Int32Array));
+                        key = bonds.bond_id;
                         order = db_1.Column.ofIntArray(db_1.Column.mapToArray(bonds.bond_type, function (x) {
                             switch (x) {
                                 case 'ar': // aromatic
@@ -96,13 +109,18 @@ function getModels(mol2, ctx) {
                                     return 1 /* Covalent */;
                             }
                         }, Int8Array));
-                        pairBonds = index_pair_1.IndexPairBonds.fromData({ pairs: { indexA: indexA, indexB: indexB, order: order, flag: flag }, count: atoms.count });
+                        pairBonds = index_pair_1.IndexPairBonds.fromData({ pairs: { key: key, indexA: indexA, indexB: indexB, order: order, flag: flag }, count: atoms.count });
                         first = _models.representative;
                         index_pair_1.IndexPairBonds.Provider.set(first, pairBonds);
                         partial_charge_1.AtomPartialCharge.Provider.set(first, {
                             data: atoms.charge,
                             type: molecule.charge_type
                         });
+                        if (crysin) {
+                            symmetry = getSymmetry(crysin);
+                            if (symmetry)
+                                symmetry_1.ModelSymmetry.Provider.set(first, symmetry);
+                        }
                         models.push(first);
                     }
                     _b.label = 3;
@@ -114,6 +132,18 @@ function getModels(mol2, ctx) {
         });
     });
 }
+function getSymmetry(crysin) {
+    // TODO handle `crysin.setting`
+    if (crysin.setting !== 1)
+        return;
+    var spaceCell = geometry_1.SpacegroupCell.create(crysin.spaceGroup, linear_algebra_1.Vec3.create(crysin.a, crysin.b, crysin.c), linear_algebra_1.Vec3.scale((0, linear_algebra_1.Vec3)(), linear_algebra_1.Vec3.create(crysin.alpha, crysin.beta, crysin.gamma), Math.PI / 180));
+    return {
+        spacegroup: geometry_1.Spacegroup.create(spaceCell),
+        assemblies: [],
+        isNonStandardCrystalFrame: false,
+        ncsOperators: []
+    };
+}
 var Mol2Format;
 (function (Mol2Format) {
     function is(x) {

package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.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>
  */
@@ -10,6 +10,7 @@ import { FormatPropertyProvider } from '../../common/property';
 import { BondType } from '../../../../mol-model/structure/model/types';
 import { ElementIndex } from '../../../../mol-model/structure';
 export declare type IndexPairsProps = {
+    readonly key: ArrayLike<number>;
     readonly order: ArrayLike<number>;
     readonly distance: ArrayLike<number>;
     readonly flag: ArrayLike<BondType.Flag>;
@@ -26,13 +27,29 @@ export declare namespace IndexPairBonds {
         pairs: {
             indexA: Column<number>;
             indexB: Column<number>;
+            key?: Column<number>;
             order?: Column<number>;
+            /**
+             * Useful for bonds in periodic cells. That is, only bonds within the given
+             * distance are added. This allows for bond between periodic image but
+             * avoids unwanted bonds with wrong distances. If negative, test using the
+             * `maxDistance` option from `Props`.
+             */
             distance?: Column<number>;
             flag?: Column<BondType.Flag>;
         };
         count: number;
     };
     const DefaultProps: {
+        /**
+         * If negative, test using element-based threshold, otherwise distance in Angstrom.
+         *
+         * This option exists to handle bonds in periodic cells. For systems that are
+         * made from beads (as opposed to atomic elements), set to a specific distance.
+         *
+         * Note that `Data` has a `distance` field which allows specifying a distance
+         * for each bond individually which takes precedence over this option.
+         */
         maxDistance: number;
     };
     type Props = typeof DefaultProps;

package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.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>
  */
@@ -9,19 +9,20 @@ exports.IndexPairBonds = void 0;
 var tslib_1 = require("tslib");
 var graph_1 = require("../../../../mol-math/graph");
 var property_1 = require("../../common/property");
-var common_1 = require("../../../../mol-model/structure/structure/unit/bonds/common");
 function getGraph(indexA, indexB, props, count) {
     var builder = new graph_1.IntAdjacencyGraph.EdgeBuilder(count, indexA, indexB);
+    var key = new Int32Array(builder.slotCount);
     var order = new Int8Array(builder.slotCount);
     var distance = new Array(builder.slotCount);
     var flag = new Array(builder.slotCount);
     for (var i = 0, _i = builder.edgeCount; i < _i; i++) {
         builder.addNextEdge();
+        builder.assignProperty(key, props.key ? props.key[i] : -1);
         builder.assignProperty(order, props.order ? props.order[i] : 1);
         builder.assignProperty(distance, props.distance ? props.distance[i] : -1);
         builder.assignProperty(flag, props.flag ? props.flag[i] : 1 /* Covalent */);
     }
-    return builder.createGraph({ order: order, distance: distance, flag: flag });
+    return builder.createGraph({ key: key, order: order, distance: distance, flag: flag });
 }
 var IndexPairBonds;
 (function (IndexPairBonds) {
@@ -29,18 +30,30 @@ var IndexPairBonds;
         name: 'index_pair_bonds',
     };
     IndexPairBonds.Provider = property_1.FormatPropertyProvider.create(IndexPairBonds.Descriptor);
-    IndexPairBonds.DefaultProps = { maxDistance: common_1.DefaultBondMaxRadius };
+    IndexPairBonds.DefaultProps = {
+        /**
+         * If negative, test using element-based threshold, otherwise distance in Angstrom.
+         *
+         * This option exists to handle bonds in periodic cells. For systems that are
+         * made from beads (as opposed to atomic elements), set to a specific distance.
+         *
+         * Note that `Data` has a `distance` field which allows specifying a distance
+         * for each bond individually which takes precedence over this option.
+         */
+        maxDistance: -1
+    };
     function fromData(data, props) {
         if (props === void 0) { props = {}; }
         var p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, IndexPairBonds.DefaultProps), props);
         var pairs = data.pairs, count = data.count;
         var indexA = pairs.indexA.toArray();
         var indexB = pairs.indexB.toArray();
+        var key = pairs.key && pairs.key.toArray();
         var order = pairs.order && pairs.order.toArray();
         var distance = pairs.distance && pairs.distance.toArray();
         var flag = pairs.flag && pairs.flag.toArray();
         return {
-            bonds: getGraph(indexA, indexB, { order: order, distance: distance, flag: flag }, count),
+            bonds: getGraph(indexA, indexB, { key: key, order: order, distance: distance, flag: flag }, count),
             maxDistance: p.maxDistance
         };
     }

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/representations/interactions-inter-unit-cylinder.d.ts

@@ -34,6 +34,16 @@ export declare const InteractionsInterUnitParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type InteractionsInterUnitParams = typeof InteractionsInterUnitParams;
 export declare function InteractionsInterUnitVisual(materialId: number): ComplexVisual<InteractionsInterUnitParams>;

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>
  */
@@ -34,6 +34,16 @@ export declare const InteractionsIntraUnitParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type InteractionsIntraUnitParams = typeof InteractionsIntraUnitParams;
 export declare function InteractionsIntraUnitVisual(materialId: number): UnitsVisual<InteractionsIntraUnitParams>;

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>
  */
@@ -102,6 +102,7 @@ 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 +137,42 @@ 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";
+            __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];
                     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;
             });
         };
-        // 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/computed/representations/interactions.d.ts

@@ -38,6 +38,16 @@ export declare const InteractionsParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type InteractionsParams = typeof InteractionsParams;
 export declare function getInteractionParams(ctx: ThemeRegistryContext, structure: Structure): {
@@ -70,6 +80,16 @@ export declare function getInteractionParams(ctx: ThemeRegistryContext, structur
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type InteractionRepresentation = StructureRepresentation<InteractionsParams>;
 export declare function InteractionRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, InteractionsParams>): InteractionRepresentation;
@@ -103,4 +123,14 @@ export declare const InteractionsRepresentationProvider: StructureRepresentation
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }, "interactions">;

package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/representation.d.ts

@@ -39,6 +39,16 @@ export declare const CrossLinkRestraintCylinderParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type CrossLinkRestraintCylinderParams = typeof CrossLinkRestraintCylinderParams;
 export declare function CrossLinkRestraintVisual(materialId: number): ComplexVisual<CrossLinkRestraintCylinderParams>;
@@ -71,6 +81,16 @@ export declare const CrossLinkRestraintParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type CrossLinkRestraintParams = typeof CrossLinkRestraintParams;
 export declare function getCrossLinkRestraintParams(ctx: ThemeRegistryContext, structure: Structure): {
@@ -102,6 +122,16 @@ export declare function getCrossLinkRestraintParams(ctx: ThemeRegistryContext, s
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type CrossLinkRestraintRepresentation = StructureRepresentation<CrossLinkRestraintParams>;
 export declare function CrossLinkRestraintRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, CrossLinkRestraintParams>): CrossLinkRestraintRepresentation;
@@ -134,4 +164,14 @@ export declare const CrossLinkRestraintRepresentationProvider: StructureRepresen
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }, CrossLinkRestraint.Tag>;

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.js

@@ -56,12 +56,11 @@ exports.HighlightLoci = behavior_1.PluginBehavior.create({
         class_1.prototype.register = function () {
             var _this = this;
             this.subscribeObservable(this.ctx.behaviors.interaction.hover, function (_a) {
-                var _b;
                 var current = _a.current, buttons = _a.buttons, modifiers = _a.modifiers;
                 if (!_this.ctx.canvas3d || _this.ctx.isBusy)
                     return;
                 var loci = _this.getLoci(current.loci);
-                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(loci.kind)) >= 0) {
+                if (_this.params.ignore.includes(loci.kind)) {
                     _this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci: loci_1.EmptyLoci });
                     return;
                 }
@@ -159,16 +158,15 @@ exports.SelectLoci = behavior_1.PluginBehavior.create({
                 return l - k;
             });
             this.subscribeObservable(this.ctx.behaviors.interaction.click, function (_a) {
-                var _b;
                 var current = _a.current, button = _a.button, modifiers = _a.modifiers;
                 if (!_this.ctx.canvas3d || _this.ctx.isBusy || !_this.ctx.selectionMode)
                     return;
                 var loci = _this.getLoci(current.loci);
-                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(loci.kind)) >= 0)
+                if (_this.params.ignore.includes(loci.kind))
                     return;
                 // only trigger the 1st action that matches
                 for (var _i = 0, actions_1 = actions; _i < actions_1.length; _i++) {
-                    var _c = actions_1[_i], binding = _c[0], action = _c[1], condition = _c[2];
+                    var _b = actions_1[_i], binding = _b[0], action = _b[1], condition = _b[2];
                     if (binding_1.Binding.match(_this.params.bindings[binding], button, modifiers) && (!condition || condition(loci))) {
                         action({ repr: current.repr, loci: loci });
                         break;
@@ -192,7 +190,7 @@ exports.SelectLoci = behavior_1.PluginBehavior.create({
                         structure_1.Structure.areEquivalent(structure, oldStructure) &&
                         structure_1.Structure.areHierarchiesEqual(structure, oldStructure))
                         return;
-                    var reprs = _this.ctx.state.data.select(mol_state_1.StateSelection.Generators.ofType(objects_1.PluginStateObject.Molecule.Structure.Representation3D, ref));
+                    var reprs = _this.ctx.state.data.select(mol_state_1.StateSelection.children(ref).ofType(objects_1.PluginStateObject.Molecule.Structure.Representation3D));
                     for (var _i = 0, reprs_1 = reprs; _i < reprs_1.length; _i++) {
                         var repr = reprs_1[_i];
                         _this.applySelectMark(repr.transform.ref, true);