molstar 3.3.1 → 3.4.0

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

@@ -0,0 +1,189 @@
+"use strict";
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.topologyFromTop = exports.TopFormat = void 0;
+var tslib_1 = require("tslib");
+var db_1 = require("../../mol-data/db");
+var types_1 = require("../../mol-model/structure/model/types");
+var topology_1 = require("../../mol-model/structure/topology/topology");
+var mol_task_1 = require("../../mol-task");
+var schema_1 = require("./basic/schema");
+var component_1 = require("./common/component");
+var entity_1 = require("./common/entity");
+var util_1 = require("./common/util");
+var util_2 = require("./util");
+function getBasic(top) {
+    var molecules = top.molecules, compounds = top.compounds;
+    var singleResidue = {};
+    var atomCount = 0;
+    for (var i = 0, il = molecules._rowCount; i < il; ++i) {
+        var mol = molecules.compound.value(i);
+        var count = molecules.molCount.value(i);
+        var atoms = compounds[mol].atoms;
+        db_1.Column.asArrayColumn(atoms.atom);
+        db_1.Column.asArrayColumn(atoms.resnr);
+        db_1.Column.asArrayColumn(atoms.residu);
+        atomCount += count * atoms._rowCount;
+        var prevResnr = atoms.resnr.value(0);
+        singleResidue[mol] = true;
+        for (var j = 1, jl = atoms._rowCount; j < jl; ++j) {
+            var resnr = atoms.resnr.value(j);
+            if (resnr !== prevResnr) {
+                singleResidue[mol] = false;
+                break;
+            }
+            prevResnr = resnr;
+        }
+    }
+    //
+    var atomNames = new Array(atomCount);
+    var residueIds = new Uint32Array(atomCount);
+    var residueNames = new Array(atomCount);
+    var k = 0;
+    for (var i = 0, il = molecules._rowCount; i < il; ++i) {
+        var mol = molecules.compound.value(i);
+        var count = molecules.molCount.value(i);
+        var atoms = compounds[mol].atoms;
+        var isSingleResidue = singleResidue[mol];
+        for (var j = 0; j < count; ++j) {
+            for (var l = 0, ll = atoms._rowCount; l < ll; ++l) {
+                atomNames[k] = atoms.atom.value(l);
+                residueIds[k] = atoms.resnr.value(l);
+                residueNames[k] = atoms.residu.value(l);
+                if (isSingleResidue)
+                    residueIds[k] += j;
+                k += 1;
+            }
+        }
+    }
+    var atomName = db_1.Column.ofStringArray(atomNames);
+    var residueId = db_1.Column.ofIntArray(residueIds);
+    var residueName = db_1.Column.ofStringArray(residueNames);
+    //
+    var entityIds = new Array(atomCount);
+    var asymIds = new Array(atomCount);
+    var seqIds = new Uint32Array(atomCount);
+    var ids = new Uint32Array(atomCount);
+    var entityBuilder = new entity_1.EntityBuilder();
+    var componentBuilder = new component_1.ComponentBuilder(residueId, atomName);
+    var currentEntityId = '';
+    var currentAsymIndex = 0;
+    var currentAsymId = '';
+    var currentSeqId = 0;
+    var prevMoleculeType = 0 /* Unknown */;
+    var prevResidueNumber = -1;
+    for (var i = 0, il = atomCount; i < il; ++i) {
+        var residueNumber = residueId.value(i);
+        if (residueNumber !== prevResidueNumber) {
+            var compId = residueName.value(i);
+            var moleculeType = (0, types_1.getMoleculeType)(componentBuilder.add(compId, i).type, compId);
+            if (moleculeType !== prevMoleculeType) {
+                currentAsymId = (0, util_1.getChainId)(currentAsymIndex);
+                currentAsymIndex += 1;
+                currentSeqId = 0;
+            }
+            currentEntityId = entityBuilder.getEntityId(compId, moleculeType, currentAsymId);
+            currentSeqId += 1;
+            prevResidueNumber = residueNumber;
+            prevMoleculeType = moleculeType;
+        }
+        entityIds[i] = currentEntityId;
+        asymIds[i] = currentAsymId;
+        seqIds[i] = currentSeqId;
+        ids[i] = i;
+    }
+    var id = db_1.Column.ofIntArray(ids);
+    var asym_id = db_1.Column.ofStringArray(asymIds);
+    //
+    var type_symbol = new Array(atomCount);
+    for (var i = 0; i < atomCount; ++i) {
+        type_symbol[i] = (0, util_2.guessElementSymbolString)(atomName.value(i), residueName.value(i));
+    }
+    var atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
+        auth_asym_id: asym_id,
+        auth_atom_id: db_1.Column.asArrayColumn(atomName),
+        auth_comp_id: residueName,
+        auth_seq_id: residueId,
+        id: db_1.Column.asArrayColumn(id),
+        label_asym_id: asym_id,
+        label_atom_id: db_1.Column.asArrayColumn(atomName),
+        label_comp_id: residueName,
+        label_seq_id: db_1.Column.ofIntArray(seqIds),
+        label_entity_id: db_1.Column.ofStringArray(entityIds),
+        occupancy: db_1.Column.ofConst(1, atomCount, db_1.Column.Schema.float),
+        type_symbol: db_1.Column.ofStringArray(type_symbol),
+        pdbx_PDB_model_num: db_1.Column.ofConst(1, atomCount, db_1.Column.Schema.int),
+    }, atomCount);
+    var basic = (0, schema_1.createBasic)({
+        entity: entityBuilder.getEntityTable(),
+        chem_comp: componentBuilder.getChemCompTable(),
+        atom_site: atom_site
+    });
+    return basic;
+}
+function getBonds(top) {
+    var molecules = top.molecules, compounds = top.compounds;
+    var indexA = [];
+    var indexB = [];
+    var atomOffset = 0;
+    for (var i = 0, il = molecules._rowCount; i < il; ++i) {
+        var mol = molecules.compound.value(i);
+        var count = molecules.molCount.value(i);
+        var _a = compounds[mol], atoms = _a.atoms, bonds = _a.bonds;
+        if (bonds) {
+            for (var j = 0; j < count; ++j) {
+                for (var l = 0, ll = bonds._rowCount; l < ll; ++l) {
+                    indexA.push(bonds.ai.value(l) - 1 + atomOffset);
+                    indexB.push(bonds.aj.value(l) - 1 + atomOffset);
+                }
+                atomOffset += atoms._rowCount;
+            }
+        }
+        else if (mol === 'TIP3') {
+            for (var j = 0; j < count; ++j) {
+                indexA.push(0 + atomOffset);
+                indexB.push(1 + atomOffset);
+                indexA.push(0 + atomOffset);
+                indexB.push(2 + atomOffset);
+                atomOffset += atoms._rowCount;
+            }
+        }
+        else {
+            atomOffset += count * atoms._rowCount;
+        }
+    }
+    return {
+        indexA: db_1.Column.ofIntArray(indexA),
+        indexB: db_1.Column.ofIntArray(indexB),
+        order: db_1.Column.ofConst(1, indexA.length, db_1.Column.Schema.int)
+    };
+}
+var TopFormat;
+(function (TopFormat) {
+    function is(x) {
+        return (x === null || x === void 0 ? void 0 : x.kind) === 'top';
+    }
+    TopFormat.is = is;
+    function fromTop(top) {
+        return { kind: 'top', name: top.system || 'TOP', data: top };
+    }
+    TopFormat.fromTop = fromTop;
+})(TopFormat || (TopFormat = {}));
+exports.TopFormat = TopFormat;
+function topologyFromTop(top) {
+    var _this = this;
+    return mol_task_1.Task.create('Parse TOP', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        var format, basic, bonds;
+        return tslib_1.__generator(this, function (_a) {
+            format = TopFormat.fromTop(top);
+            basic = getBasic(top);
+            bonds = getBonds(top);
+            return [2 /*return*/, topology_1.Topology.create(top.system || 'TOP', basic, bonds, format)];
+        });
+    }); });
+}
+exports.topologyFromTop = topologyFromTop;

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

@@ -0,0 +1,9 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { Task } from '../../mol-task';
+import { TrrFile } from '../../mol-io/reader/trr/parser';
+import { Coordinates } from '../../mol-model/structure/coordinates';
+export declare function coordinatesFromTrr(file: TrrFile): Task<Coordinates>;

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

@@ -0,0 +1,46 @@
+"use strict";
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.coordinatesFromTrr = void 0;
+var tslib_1 = require("tslib");
+var mol_task_1 = require("../../mol-task");
+var coordinates_1 = require("../../mol-model/structure/coordinates");
+var cell_1 = require("../../mol-math/geometry/spacegroup/cell");
+var linear_algebra_1 = require("../../mol-math/linear-algebra");
+function coordinatesFromTrr(file) {
+    var _this = this;
+    return mol_task_1.Task.create('Parse TRR', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        var deltaTime, offsetTime, frames, i, il, box, x, y, z;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, ctx.update('Converting to coordinates')];
+                case 1:
+                    _a.sent();
+                    deltaTime = (0, coordinates_1.Time)(file.deltaTime, 'step');
+                    offsetTime = (0, coordinates_1.Time)(file.timeOffset, deltaTime.unit);
+                    frames = [];
+                    for (i = 0, il = file.frames.length; i < il; ++i) {
+                        box = file.boxes[i];
+                        x = linear_algebra_1.Vec3.fromArray((0, linear_algebra_1.Vec3)(), box, 0);
+                        y = linear_algebra_1.Vec3.fromArray((0, linear_algebra_1.Vec3)(), box, 3);
+                        z = linear_algebra_1.Vec3.fromArray((0, linear_algebra_1.Vec3)(), box, 6);
+                        frames.push({
+                            elementCount: file.frames[i].count,
+                            cell: cell_1.Cell.fromBasis(x, y, z),
+                            x: file.frames[i].x,
+                            y: file.frames[i].y,
+                            z: file.frames[i].z,
+                            xyzOrdering: { isIdentity: true },
+                            time: (0, coordinates_1.Time)(offsetTime.value + deltaTime.value * i, deltaTime.unit)
+                        });
+                    }
+                    return [2 /*return*/, coordinates_1.Coordinates.create(frames, deltaTime, offsetTime)];
+            }
+        });
+    }); });
+}
+exports.coordinatesFromTrr = coordinatesFromTrr;

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

@@ -1,8 +1,8 @@
 /**
- * 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>
  */
 import { Tokens } from '../../mol-io/reader/common/text/tokenizer';
 export declare function guessElementSymbolTokens(tokens: Tokens, str: string, start: number, end: number): void;
-export declare function guessElementSymbolString(str: string): string;
+export declare function guessElementSymbolString(atomId: string, compId: string): string;

package/lib/commonjs/mol-model-formats/structure/util.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>
  */
@@ -44,35 +44,34 @@ function guessElementSymbolTokens(tokens, str, start, end) {
     tokenizer_1.TokenBuilder.add(tokens, s, s); // no reasonable guess, add empty token
 }
 exports.guessElementSymbolTokens = guessElementSymbolTokens;
+var TwoCharElementNames = new Set(['NA', 'CL', 'FE', 'SI', 'BR', 'AS']);
+var OneCharElementNames = new Set(['C', 'H', 'N', 'O', 'P', 'S']);
 var reTrimSpacesAndNumbers = /^[\s\d]+|[\s\d]+$/g;
-function guessElementSymbolString(str) {
+function guessElementSymbolString(atomId, compId) {
     // trim spaces and numbers, convert to upper case
-    str = str.replace(reTrimSpacesAndNumbers, '').toUpperCase();
-    var l = str.length;
+    atomId = atomId.replace(reTrimSpacesAndNumbers, '').toUpperCase();
+    var l = atomId.length;
     if (l === 0)
-        return str; // empty
+        return atomId; // empty
     if (l === 1)
-        return str; // one char
-    if (l === 2) { // two chars
-        if (str === 'NA' || str === 'CL' || str === 'FE' || str === 'SI' ||
-            str === 'BR' || str === 'AS')
-            return str;
-    }
-    if (l === 3) { // three chars
-        if (str === 'SOD')
+        return atomId; // one char
+    if (TwoCharElementNames.has(atomId))
+        return atomId; // two chars
+    // check for Charmm ion names where component and atom id are the same
+    if (l === 3 && compId === atomId) {
+        if (atomId === 'SOD')
             return 'NA';
-        if (str === 'POT')
+        if (atomId === 'POT')
             return 'K';
-        if (str === 'CES')
+        if (atomId === 'CES')
             return 'CS';
-        if (str === 'CAL')
+        if (atomId === 'CAL')
             return 'CA';
-        if (str === 'CLA')
+        if (atomId === 'CLA')
             return 'CL';
     }
-    var c = str[0];
-    if (c === 'C' || c === 'H' || c === 'N' || c === 'O' || c === 'P' || c === 'S')
-        return c;
+    if (OneCharElementNames.has(atomId[0]))
+        return atomId[0];
     return ''; // no reasonable guess, return empty string
 }
 exports.guessElementSymbolString = guessElementSymbolString;

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

@@ -14,9 +14,9 @@ var cell_1 = require("../../mol-math/geometry/spacegroup/cell");
 var linear_algebra_1 = require("../../mol-math/linear-algebra");
 function coordinatesFromXtc(file) {
     var _this = this;
-    return mol_task_1.Task.create('Parse XTC', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Parse XTC', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var deltaTime, offsetTime, frames, i, il, box, x, y, z;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, ctx.update('Converting to coordinates')];
                 case 1:

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

@@ -66,12 +66,12 @@ function getModels(mol, ctx) {
     var componentBuilder = new component_1.ComponentBuilder(seq_id, type_symbol);
     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
     componentBuilder.add('MOL', 0);
-    var basics = (0, schema_1.createBasic)({
+    var basic = (0, schema_1.createBasic)({
         entity: entityBuilder.getEntityTable(),
         chem_comp: componentBuilder.getChemCompTable(),
         atom_site: atom_site
     });
-    return (0, parser_1.createModels)(basics, XyzFormat.create(mol), ctx);
+    return (0, parser_1.createModels)(basic, XyzFormat.create(mol), ctx);
 }
 var XyzFormat;
 (function (XyzFormat) {

package/lib/commonjs/mol-model-formats/volume/ccp4.js

@@ -37,9 +37,9 @@ function getTypedArrayCtor(header) {
 }
 function volumeFromCcp4(source, params) {
     var _this = this;
-    return mol_task_1.Task.create('Create Volume', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Create Volume', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var header, values, size, angles, spacegroup, cell, axis_order_fast_to_slow, normalizeOrder, grid, extent, origin, gridOrigin, origin_frac, dimensions_frac, space, data, calcStats;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             header = source.header, values = source.values;
             size = linear_algebra_1.Vec3.create(header.xLength, header.yLength, header.zLength);
             if (params && params.voxelSize)

package/lib/commonjs/mol-model-formats/volume/cube.js

@@ -13,9 +13,9 @@ var array_1 = require("../../mol-util/array");
 var custom_property_1 = require("../../mol-model/custom-property");
 function volumeFromCube(source, params) {
     var _this = this;
-    return mol_task_1.Task.create('Create Volume', function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Create Volume', function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var header, sourceValues, space, values, _a, h, k, l, nth, o, s, u, v, w, data, matrix, basis;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             header = source.header, sourceValues = source.values;
             space = linear_algebra_1.Tensor.Space(header.dim, [0, 1, 2], Float64Array);
             if (header.dataSetIds.length === 0) {

package/lib/commonjs/mol-model-formats/volume/density-server.js

@@ -13,9 +13,9 @@ var linear_algebra_1 = require("../../mol-math/linear-algebra");
 var custom_property_1 = require("../../mol-model/custom-property");
 function volumeFromDensityServerData(source, params) {
     var _this = this;
-    return mol_task_1.Task.create('Create Volume', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Create Volume', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var info, values, cell, axis_order_fast_to_slow, normalizeOrder, sample_count, tensorSpace, data, origin, dimensions;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             info = source.volume_data_3d_info, values = source.volume_data_3d;
             cell = geometry_1.SpacegroupCell.create(info.spacegroup_number.value(0), linear_algebra_1.Vec3.ofArray(info.spacegroup_cell_size.value(0)), linear_algebra_1.Vec3.scale(linear_algebra_1.Vec3.zero(), linear_algebra_1.Vec3.ofArray(info.spacegroup_cell_angles.value(0)), Math.PI / 180));
             axis_order_fast_to_slow = info.axis_order.value(0);

package/lib/commonjs/mol-model-formats/volume/dsn6.js

@@ -15,9 +15,9 @@ var array_1 = require("../../mol-util/array");
 var custom_property_1 = require("../../mol-model/custom-property");
 function volumeFromDsn6(source, params) {
     var _this = this;
-    return mol_task_1.Task.create('Create Volume', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Create Volume', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var header, values, size, angles, cell, grid, extent, gridOrigin, origin_frac, dimensions_frac, space, data;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             header = source.header, values = source.values;
             size = linear_algebra_1.Vec3.create(header.xlen, header.ylen, header.zlen);
             if (params && params.voxelSize)

package/lib/commonjs/mol-model-formats/volume/dx.js

@@ -13,9 +13,9 @@ var array_1 = require("../../mol-util/array");
 var custom_property_1 = require("../../mol-model/custom-property");
 function volumeFromDx(source, params) {
     var _this = this;
-    return mol_task_1.Task.create('Create Volume', function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Create Volume', function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var header, values, space, data, matrix, basis;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             header = source.header, values = source.values;
             space = linear_algebra_1.Tensor.Space(header.dim, [0, 1, 2], Float64Array);
             data = linear_algebra_1.Tensor.create(space, linear_algebra_1.Tensor.Data1(values));

package/lib/commonjs/mol-model-props/common/custom-element-property.js

@@ -35,8 +35,8 @@ var CustomElementProperty;
             defaultParams: {},
             getParams: function (data) { return ({}); },
             isApplicable: function (data) { return !builder.isApplicable || !!builder.isApplicable(data); },
-            obtain: function (ctx, data) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                return (0, tslib_1.__generator)(this, function (_a) {
+            obtain: function (ctx, data) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                return tslib_1.__generator(this, function (_a) {
                     switch (_a.label) {
                         case 0: return [4 /*yield*/, builder.getData(data, ctx)];
                         case 1: return [2 /*return*/, _a.sent()];

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

@@ -20,7 +20,7 @@ var CustomModelProperty;
         var get = function (data) {
             if (!(descriptorName in data[propertyDataName])) {
                 data[propertyDataName][descriptorName] = {
-                    props: (0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(builder.getParams(data))),
+                    props: tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(builder.getParams(data))),
                     data: mol_util_1.ValueBox.create(undefined)
                 };
             }
@@ -46,9 +46,9 @@ var CustomModelProperty;
             isApplicable: builder.isApplicable,
             attach: function (ctx, data, props, addRef) {
                 if (props === void 0) { props = {}; }
-                return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+                return tslib_1.__awaiter(_this, void 0, void 0, function () {
                     var property, p, _a, value, assets;
-                    return (0, tslib_1.__generator)(this, function (_b) {
+                    return tslib_1.__generator(this, function (_b) {
                         switch (_b.label) {
                             case 0:
                                 if (addRef)
@@ -96,9 +96,9 @@ var CustomModelProperty;
             defaultParams: defaultParams,
             getParams: function () { return ({ value: param_definition_1.ParamDefinition.Value(defaultValue, { isHidden: true }) }); },
             isApplicable: function () { return true; },
-            obtain: function (ctx, data, props) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+            obtain: function (ctx, data, props) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                 var _a;
-                return (0, tslib_1.__generator)(this, function (_b) {
+                return tslib_1.__generator(this, function (_b) {
                     return [2 /*return*/, { value: (_a = props.value) !== null && _a !== void 0 ? _a : defaultValue }];
                 });
             }); }

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

@@ -36,7 +36,7 @@ var CustomProperty;
                             autoAttachDefault.push(provider.descriptor.name);
                         }
                     }
-                    propertiesParams[provider.descriptor.name] = param_definition_1.ParamDefinition.Group((0, tslib_1.__assign)({}, provider.getParams(data)), { label: provider.label, isHidden: provider.isHidden });
+                    propertiesParams[provider.descriptor.name] = param_definition_1.ParamDefinition.Group(tslib_1.__assign({}, provider.getParams(data)), { label: provider.label, isHidden: provider.isHidden });
                 }
             }
             return {

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

@@ -20,7 +20,7 @@ var CustomStructureProperty;
         var get = function (data) {
             if (!(descriptorName in data[propertyDataName])) {
                 data[propertyDataName][descriptorName] = {
-                    props: (0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(builder.getParams(data))),
+                    props: tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(builder.getParams(data))),
                     data: mol_util_1.ValueBox.create(undefined)
                 };
             }
@@ -46,9 +46,9 @@ var CustomStructureProperty;
             isApplicable: builder.isApplicable,
             attach: function (ctx, data, props, addRef) {
                 if (props === void 0) { props = {}; }
-                return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+                return tslib_1.__awaiter(_this, void 0, void 0, function () {
                     var rootProps, property, p, _a, value, assets;
-                    return (0, tslib_1.__generator)(this, function (_b) {
+                    return tslib_1.__generator(this, function (_b) {
                         switch (_b.label) {
                             case 0:
                                 if (addRef)
@@ -101,9 +101,9 @@ var CustomStructureProperty;
             defaultParams: defaultParams,
             getParams: function () { return ({ value: param_definition_1.ParamDefinition.Value(defaultValue, { isHidden: true }) }); },
             isApplicable: function () { return true; },
-            obtain: function (ctx, data, props) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                return (0, tslib_1.__generator)(this, function (_a) {
-                    return [2 /*return*/, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(defaultParams)), props)];
+            obtain: function (ctx, data, props) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                return tslib_1.__generator(this, function (_a) {
+                    return [2 /*return*/, tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(defaultParams)), props)];
                 });
             }); }
         });

package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/area.js

@@ -16,9 +16,9 @@ var common_1 = require("./common");
 // - factor serialResidueIndex out
 var updateChunk = 5000;
 function computeArea(runtime, ctx) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var atomRadius, i;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     atomRadius = ctx.atomRadiusType;

package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley.js

@@ -33,9 +33,9 @@ var AccessibleSurfaceArea;
     function compute(structure, props) {
         var _this = this;
         if (props === void 0) { props = {}; }
-        var p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(exports.ShrakeRupleyComputationParams)), props);
-        return mol_task_1.Task.create('Compute Accessible Surface Area', function (runtime) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-            return (0, tslib_1.__generator)(this, function (_a) {
+        var p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.ShrakeRupleyComputationParams)), props);
+        return mol_task_1.Task.create('Compute Accessible Surface Area', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, calculate(runtime, structure, p)];
                     case 1: return [2 /*return*/, _a.sent()];
@@ -45,9 +45,9 @@ var AccessibleSurfaceArea;
     }
     AccessibleSurfaceArea.compute = compute;
     function calculate(runtime, structure, props) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var ctx, area, serialResidueIndex;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         ctx = initialize(structure, props);

package/lib/commonjs/mol-model-props/computed/accessible-surface-area.js

@@ -16,7 +16,7 @@ var compiler_1 = require("../../mol-script/runtime/query/compiler");
 var symbol_1 = require("../../mol-script/language/symbol");
 var type_1 = require("../../mol-script/language/type");
 var custom_property_1 = require("../../mol-model/custom-property");
-exports.AccessibleSurfaceAreaParams = (0, tslib_1.__assign)({}, shrake_rupley_1.ShrakeRupleyComputationParams);
+exports.AccessibleSurfaceAreaParams = tslib_1.__assign({}, shrake_rupley_1.ShrakeRupleyComputationParams);
 exports.AccessibleSurfaceAreaSymbols = {
     isBuried: compiler_1.QuerySymbolRuntime.Dynamic((0, symbol_1.CustomPropSymbol)('computed', 'accessible-surface-area.is-buried', type_1.Type.Bool), function (ctx) {
         if (!structure_1.Unit.isAtomic(ctx.element.unit))
@@ -46,13 +46,13 @@ exports.AccessibleSurfaceAreaProvider = custom_structure_property_1.CustomStruct
     defaultParams: exports.AccessibleSurfaceAreaParams,
     getParams: function (data) { return exports.AccessibleSurfaceAreaParams; },
     isApplicable: function (data) { return true; },
-    obtain: function (ctx, data, props) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+    obtain: function (ctx, data, props) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var p;
         var _a;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
-                    p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(exports.AccessibleSurfaceAreaParams)), props);
+                    p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.AccessibleSurfaceAreaParams)), props);
                     _a = {};
                     return [4 /*yield*/, shrake_rupley_1.AccessibleSurfaceArea.compute(data, p).runInContext(ctx.runtime)];
                 case 1: return [2 /*return*/, (_a.value = _b.sent(), _a)];

package/lib/commonjs/mol-model-props/computed/chemistry/valence-model.js

@@ -306,10 +306,10 @@ exports.ValenceModelParams = {
     assignH: param_definition_1.ParamDefinition.Select('auto', [['always', 'always'], ['auto', 'auto'], ['never', 'never']]),
 };
 function calcValenceModel(ctx, structure, props) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var p, map, i, il, u, valenceModel;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, param_definition_1.ParamDefinition.getDefaultValues(exports.ValenceModelParams)), props);
+        return tslib_1.__generator(this, function (_a) {
+            p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.ValenceModelParams)), props);
             map = new Map();
             for (i = 0, il = structure.units.length; i < il; ++i) {
                 u = structure.units[i];

package/lib/commonjs/mol-model-props/computed/helix-orientation.js

@@ -20,8 +20,8 @@ exports.HelixOrientationProvider = custom_model_property_1.CustomModelProperty.c
     defaultParams: {},
     getParams: function () { return ({}); },
     isApplicable: function (data) { return true; },
-    obtain: function (ctx, data) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    obtain: function (ctx, data) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             return [2 /*return*/, { value: (0, helix_orientation_1.calcHelixOrientation)(data) }];
         });
     }); }

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

@@ -61,7 +61,7 @@ var InteractionsIntraContacts;
 })(InteractionsIntraContacts || (InteractionsIntraContacts = {}));
 exports.InteractionsIntraContacts = InteractionsIntraContacts;
 var InteractionsInterContacts = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(InteractionsInterContacts, _super);
+    tslib_1.__extends(InteractionsInterContacts, _super);
     function InteractionsInterContacts(map, unitsFeatures) {
         var _this = _super.call(this, map) || this;
         _this.elementKeyIndex = new Map();

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

@@ -107,7 +107,7 @@ function _addUnitContacts(structure, unit, features, builder, tester, props) {
     var x = features.x, y = features.y, z = features.z;
     var _a = features.subset(tester.requiredFeatures), lookup3d = _a.lookup3d, subsetIndices = _a.indices;
     var infoA = features_1.Features.Info(structure, unit, features);
-    var infoB = (0, tslib_1.__assign)({}, infoA);
+    var infoB = tslib_1.__assign({}, infoA);
     var distFactor = props.lineOfSightDistFactor;
     for (var t = 0, tl = int_1.OrderedSet.size(subsetIndices); t < tl; ++t) {
         var i = int_1.OrderedSet.getAt(subsetIndices, t);

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

@@ -49,7 +49,7 @@ var Features;
     function create(elementsCount, data) {
         var lookup3d;
         var elementsIndex;
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, data), { get lookup3d() {
+        return tslib_1.__assign(tslib_1.__assign({}, data), { get lookup3d() {
                 if (!lookup3d) {
                     var position_1 = { x: data.x, y: data.y, z: data.z, indices: int_1.OrderedSet.ofBounds(0, data.count) };
                     lookup3d = (0, geometry_1.GridLookup3D)(position_1, (0, boundary_1.getBoundary)(position_1));