drugflow-molstar 0.4.7 → 0.4.8

package/build/drugflow-molstar-plugin-0.4.8.js.LICENSE.txt

@@ -0,0 +1,39 @@
+/**
+ * @license React
+ * react-dom.production.min.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+
+/**
+ * @license React
+ * react-jsx-runtime.production.min.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+
+/**
+ * @license React
+ * react.production.min.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+
+/**
+ * @license React
+ * scheduler.production.min.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */

package/lib/alphafold-transparency.js

@@ -1,18 +1,21 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.clearStructureTransparency = exports.setStructureTransparency = exports.applyAFTransparency = void 0;
-const structure_1 = require("Molstar/mol-model/structure");
-const transforms_1 = require("Molstar/mol-plugin-state/transforms");
-const mol_state_1 = require("Molstar/mol-state");
-const loci_1 = require("Molstar/mol-model/loci");
-const transparency_1 = require("Molstar/mol-theme/transparency");
-const builder_1 = require("Molstar/mol-script/language/builder");
-const prop_1 = require("Molstar/extensions/model-archive/quality-assessment/prop");
-const compiler_1 = require("Molstar/mol-script/runtime/query/compiler");
-const structure_2 = require("Molstar/mol-model/structure");
-const TransparencyManagerTag = 'transparency-controls';
+exports.applyAFTransparency = applyAFTransparency;
+exports.setStructureTransparency = setStructureTransparency;
+exports.clearStructureTransparency = clearStructureTransparency;
+var tslib_1 = require("tslib");
+var structure_1 = require("Molstar/mol-model/structure");
+var transforms_1 = require("Molstar/mol-plugin-state/transforms");
+var mol_state_1 = require("Molstar/mol-state");
+var loci_1 = require("Molstar/mol-model/loci");
+var transparency_1 = require("Molstar/mol-theme/transparency");
+var builder_1 = require("Molstar/mol-script/language/builder");
+var prop_1 = require("Molstar/extensions/model-archive/quality-assessment/prop");
+var compiler_1 = require("Molstar/mol-script/runtime/query/compiler");
+var structure_2 = require("Molstar/mol-model/structure");
+var TransparencyManagerTag = 'transparency-controls';
 function getLociByPLDDT(score, contextData) {
-    const queryExp = builder_1.MolScriptBuilder.struct.modifier.union([
+    var queryExp = builder_1.MolScriptBuilder.struct.modifier.union([
         builder_1.MolScriptBuilder.struct.modifier.wholeResidues([
             builder_1.MolScriptBuilder.struct.modifier.union([
                 builder_1.MolScriptBuilder.struct.generator.atomGroups({
@@ -22,65 +25,157 @@ function getLociByPLDDT(score, contextData) {
             ])
         ])
     ]);
-    const query = (0, compiler_1.compile)(queryExp);
-    const sel = query(new structure_2.QueryContext(contextData));
+    var query = (0, compiler_1.compile)(queryExp);
+    var sel = query(new structure_2.QueryContext(contextData));
     return structure_2.StructureSelection.toLociWithSourceUnits(sel);
 }
-async function applyAFTransparency(plugin, structure, transparency, pLDDT = 70) {
-    return plugin.dataTransaction(async (ctx) => {
-        const loci = getLociByPLDDT(pLDDT, structure.cell.obj?.data);
-        await setStructureTransparency(plugin, structure.components, transparency, loci);
-    }, { canUndo: 'Apply Transparency' });
+function applyAFTransparency(plugin_1, structure_3, transparency_2) {
+    return tslib_1.__awaiter(this, arguments, void 0, function (plugin, structure, transparency, pLDDT) {
+        var _this = this;
+        if (pLDDT === void 0) { pLDDT = 70; }
+        return tslib_1.__generator(this, function (_a) {
+            return [2 /*return*/, plugin.dataTransaction(function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                    var loci;
+                    var _a;
+                    return tslib_1.__generator(this, function (_b) {
+                        switch (_b.label) {
+                            case 0:
+                                loci = getLociByPLDDT(pLDDT, (_a = structure.cell.obj) === null || _a === void 0 ? void 0 : _a.data);
+                                return [4 /*yield*/, setStructureTransparency(plugin, structure.components, transparency, loci)];
+                            case 1:
+                                _b.sent();
+                                return [2 /*return*/];
+                        }
+                    });
+                }); }, { canUndo: 'Apply Transparency' })];
+        });
+    });
 }
-exports.applyAFTransparency = applyAFTransparency;
-async function setStructureTransparency(plugin, components, value, loci, types) {
-    await eachRepr(plugin, components, async (update, repr, transparencyCell) => {
-        if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
-            return;
-        const structure = repr.obj.data.sourceData;
-        if (loci_1.Loci.isEmpty(loci) || (0, loci_1.isEmptyLoci)(loci))
-            return;
-        const layer = {
-            bundle: structure_1.StructureElement.Bundle.fromLoci(loci),
-            value,
-        };
-        if (transparencyCell) {
-            const bundleLayers = [...transparencyCell.params.values.layers, layer];
-            const filtered = getFilteredBundle(bundleLayers, structure);
-            update.to(transparencyCell).update(transparency_1.Transparency.toBundle(filtered));
-        }
-        else {
-            const filtered = getFilteredBundle([layer], structure);
-            update.to(repr.transform.ref)
-                .apply(transforms_1.StateTransforms.Representation.TransparencyStructureRepresentation3DFromBundle, transparency_1.Transparency.toBundle(filtered), { tags: TransparencyManagerTag });
-        }
+function setStructureTransparency(plugin, components, value, loci, types) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var _this = this;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, eachRepr(plugin, components, function (update, repr, transparencyCell) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                        var structure, layer, bundleLayers, filtered, filtered;
+                        return tslib_1.__generator(this, function (_a) {
+                            if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
+                                return [2 /*return*/];
+                            structure = repr.obj.data.sourceData;
+                            if (loci_1.Loci.isEmpty(loci) || (0, loci_1.isEmptyLoci)(loci))
+                                return [2 /*return*/];
+                            layer = {
+                                bundle: structure_1.StructureElement.Bundle.fromLoci(loci),
+                                value: value,
+                            };
+                            if (transparencyCell) {
+                                bundleLayers = tslib_1.__spreadArray(tslib_1.__spreadArray([], tslib_1.__read(transparencyCell.params.values.layers), false), [layer], false);
+                                filtered = getFilteredBundle(bundleLayers, structure);
+                                update.to(transparencyCell).update(transparency_1.Transparency.toBundle(filtered));
+                            }
+                            else {
+                                filtered = getFilteredBundle([layer], structure);
+                                update.to(repr.transform.ref)
+                                    .apply(transforms_1.StateTransforms.Representation.TransparencyStructureRepresentation3DFromBundle, transparency_1.Transparency.toBundle(filtered), { tags: TransparencyManagerTag });
+                            }
+                            return [2 /*return*/];
+                        });
+                    }); })];
+                case 1:
+                    _a.sent();
+                    return [2 /*return*/];
+            }
+        });
     });
 }
-exports.setStructureTransparency = setStructureTransparency;
-async function clearStructureTransparency(plugin, components, types) {
-    await eachRepr(plugin, components, async (update, repr, transparencyCell) => {
-        if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
-            return;
-        if (transparencyCell) {
-            update.delete(transparencyCell.transform.ref);
-        }
+function clearStructureTransparency(plugin, components, types) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var _this = this;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, eachRepr(plugin, components, function (update, repr, transparencyCell) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+                        return tslib_1.__generator(this, function (_a) {
+                            if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
+                                return [2 /*return*/];
+                            if (transparencyCell) {
+                                update.delete(transparencyCell.transform.ref);
+                            }
+                            return [2 /*return*/];
+                        });
+                    }); })];
+                case 1:
+                    _a.sent();
+                    return [2 /*return*/];
+            }
+        });
     });
 }
-exports.clearStructureTransparency = clearStructureTransparency;
-async function eachRepr(plugin, components, callback) {
-    const state = plugin.state.data;
-    const update = state.build();
-    for (const c of components) {
-        for (const r of c.representations) {
-            const transparency = state.select(mol_state_1.StateSelection.Generators.ofTransformer(transforms_1.StateTransforms.Representation.TransparencyStructureRepresentation3DFromBundle, r.cell.transform.ref).withTag(TransparencyManagerTag));
-            await callback(update, r.cell, transparency[0]);
-        }
-    }
-    return update.commit({ doNotUpdateCurrent: true });
+function eachRepr(plugin, components, callback) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var state, update, components_1, components_1_1, c, _a, _b, r, transparency, e_1_1, e_2_1;
+        var e_2, _c, e_1, _d;
+        return tslib_1.__generator(this, function (_e) {
+            switch (_e.label) {
+                case 0:
+                    state = plugin.state.data;
+                    update = state.build();
+                    _e.label = 1;
+                case 1:
+                    _e.trys.push([1, 12, 13, 14]);
+                    components_1 = tslib_1.__values(components), components_1_1 = components_1.next();
+                    _e.label = 2;
+                case 2:
+                    if (!!components_1_1.done) return [3 /*break*/, 11];
+                    c = components_1_1.value;
+                    _e.label = 3;
+                case 3:
+                    _e.trys.push([3, 8, 9, 10]);
+                    _a = (e_1 = void 0, tslib_1.__values(c.representations)), _b = _a.next();
+                    _e.label = 4;
+                case 4:
+                    if (!!_b.done) return [3 /*break*/, 7];
+                    r = _b.value;
+                    transparency = state.select(mol_state_1.StateSelection.Generators.ofTransformer(transforms_1.StateTransforms.Representation.TransparencyStructureRepresentation3DFromBundle, r.cell.transform.ref).withTag(TransparencyManagerTag));
+                    return [4 /*yield*/, callback(update, r.cell, transparency[0])];
+                case 5:
+                    _e.sent();
+                    _e.label = 6;
+                case 6:
+                    _b = _a.next();
+                    return [3 /*break*/, 4];
+                case 7: return [3 /*break*/, 10];
+                case 8:
+                    e_1_1 = _e.sent();
+                    e_1 = { error: e_1_1 };
+                    return [3 /*break*/, 10];
+                case 9:
+                    try {
+                        if (_b && !_b.done && (_d = _a.return)) _d.call(_a);
+                    }
+                    finally { if (e_1) throw e_1.error; }
+                    return [7 /*endfinally*/];
+                case 10:
+                    components_1_1 = components_1.next();
+                    return [3 /*break*/, 2];
+                case 11: return [3 /*break*/, 14];
+                case 12:
+                    e_2_1 = _e.sent();
+                    e_2 = { error: e_2_1 };
+                    return [3 /*break*/, 14];
+                case 13:
+                    try {
+                        if (components_1_1 && !components_1_1.done && (_c = components_1.return)) _c.call(components_1);
+                    }
+                    finally { if (e_2) throw e_2.error; }
+                    return [7 /*endfinally*/];
+                case 14: return [2 /*return*/, update.commit({ doNotUpdateCurrent: true })];
+            }
+        });
+    });
 }
 /** filter transparency layers for given structure */
 function getFilteredBundle(layers, structure) {
-    const transparency = transparency_1.Transparency.ofBundle(layers, structure.root);
-    const merged = transparency_1.Transparency.merge(transparency);
+    var transparency = transparency_1.Transparency.ofBundle(layers, structure.root);
+    var merged = transparency_1.Transparency.merge(transparency);
     return transparency_1.Transparency.filter(merged, structure);
 }

package/lib/contact.d.ts

@@ -24,12 +24,12 @@ export declare const ContactParams: {
     tether: PD.BooleanParam;
     tetherLength: PD.Numeric;
     tetherBaseWidth: PD.Numeric;
-    attachment: PD.Select<"middle-center" | "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-right" | "top-left" | "top-center" | "top-right">;
-    fontFamily: PD.Select<import("molstar/lib/mol-geo/geometry/text/font-atlas").FontFamily>;
+    attachment: PD.Select<"bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right">;
+    fontFamily: PD.Select<import("Molstar/mol-geo/geometry/text/font-atlas").FontFamily>;
     fontQuality: PD.Select<number>;
-    fontStyle: PD.Select<import("molstar/lib/mol-geo/geometry/text/font-atlas").FontStyle>;
-    fontVariant: PD.Select<import("molstar/lib/mol-geo/geometry/text/font-atlas").FontVariant>;
-    fontWeight: PD.Select<import("molstar/lib/mol-geo/geometry/text/font-atlas").FontWeight>;
+    fontStyle: PD.Select<import("Molstar/mol-geo/geometry/text/font-atlas").FontStyle>;
+    fontVariant: PD.Select<import("Molstar/mol-geo/geometry/text/font-atlas").FontVariant>;
+    fontWeight: PD.Select<import("Molstar/mol-geo/geometry/text/font-atlas").FontWeight>;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
@@ -38,22 +38,16 @@ export declare const ContactParams: {
         bumpiness: number;
     }>>;
     clip: PD.Group<PD.Normalize<{
-        variant: import("molstar/lib/mol-util/clip").Clip.Variant;
+        variant: import("Molstar/mol-util/clip").Clip.Variant;
         objects: PD.Normalize<{
             type: any;
             invert: any;
             position: any;
             rotation: any;
             scale: any;
-            transform: any;
         }>[];
     }>>;
-    emissive: PD.Numeric;
-    density: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
-    lod: PD.Vec3;
-    cellSize: PD.Numeric;
-    batchSize: PD.Numeric;
     lineSizeAttenuation: PD.BooleanParam;
     linesSize: PD.Numeric;
     dashLength: PD.Numeric;
@@ -62,9 +56,8 @@ export declare const ContactParams: {
     sizeAspectRatio: PD.Numeric;
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
-    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<"off" | "on" | "opaque">;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     solidInterior: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;

package/lib/contact.js

@@ -1,59 +1,52 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ContactRepresentation = exports.contactLabel = exports.ContactParams = void 0;
+exports.ContactParams = void 0;
+exports.contactLabel = contactLabel;
+exports.ContactRepresentation = ContactRepresentation;
+var tslib_1 = require("tslib");
 // contact.ts
-const loci_1 = require("molstar/lib/mol-model/loci");
-const text_1 = require("molstar/lib/mol-geo/geometry/text/text");
-const param_definition_1 = require("molstar/lib/mol-util/param-definition");
-const names_1 = require("molstar/lib/mol-util/color/names");
-const representation_1 = require("molstar/lib/mol-repr/shape/representation");
-const representation_2 = require("molstar/lib/mol-repr/representation");
-const shape_1 = require("molstar/lib/mol-model/shape");
-const text_builder_1 = require("molstar/lib/mol-geo/geometry/text/text-builder");
-const linear_algebra_1 = require("molstar/lib/mol-math/linear-algebra");
-const marker_action_1 = require("molstar/lib/mol-util/marker-action");
-const label_1 = require("molstar/lib/mol-theme/label");
-const common_1 = require("molstar/lib/mol-repr/shape/loci/common");
-const geometry_1 = require("molstar/lib/mol-math/geometry");
-const cylinders_builder_1 = require("molstar/lib/mol-geo/geometry/cylinders/cylinders-builder");
-const cylinders_1 = require("molstar/lib/mol-geo/geometry/cylinders/cylinders");
-const label_2 = require("molstar/lib/mol-theme/label");
-const SharedParams = {
+var loci_1 = require("molstar/lib/mol-model/loci");
+var text_1 = require("molstar/lib/mol-geo/geometry/text/text");
+var param_definition_1 = require("molstar/lib/mol-util/param-definition");
+var names_1 = require("molstar/lib/mol-util/color/names");
+var representation_1 = require("molstar/lib/mol-repr/shape/representation");
+var representation_2 = require("molstar/lib/mol-repr/representation");
+var shape_1 = require("molstar/lib/mol-model/shape");
+var text_builder_1 = require("molstar/lib/mol-geo/geometry/text/text-builder");
+var linear_algebra_1 = require("molstar/lib/mol-math/linear-algebra");
+var marker_action_1 = require("molstar/lib/mol-util/marker-action");
+var label_1 = require("molstar/lib/mol-theme/label");
+var common_1 = require("molstar/lib/mol-repr/shape/loci/common");
+var geometry_1 = require("molstar/lib/mol-math/geometry");
+var cylinders_builder_1 = require("molstar/lib/mol-geo/geometry/cylinders/cylinders-builder");
+var cylinders_1 = require("molstar/lib/mol-geo/geometry/cylinders/cylinders");
+var label_2 = require("molstar/lib/mol-theme/label");
+var SharedParams = {
     unitLabel: param_definition_1.ParamDefinition.Text('\u212B', { isEssential: true }),
 };
-const CylinderParams = {
-    ...cylinders_1.Cylinders.Params,
-    ...SharedParams,
-    lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(true),
-    linesSize: param_definition_1.ParamDefinition.Numeric(0.075, { min: 0.01, max: 5, step: 0.01 }),
-    dashLength: param_definition_1.ParamDefinition.Numeric(0.12, { min: 0.01, max: 0.2, step: 0.01 }),
-    interactionType: param_definition_1.ParamDefinition.Text('', { isEssential: true }),
-    cylinderColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.lightgreen, { isEssential: true }),
-};
-const TextParams = {
-    ...common_1.LociLabelTextParams,
-    ...SharedParams,
-};
-const ContactVisuals = {
-    cylinder: (ctx, getParams) => (0, representation_1.ShapeRepresentation)(getCylindersShape, cylinders_1.Cylinders.Utils, {
-        modifyState: (s) => ({ ...s, markerActions: marker_action_1.MarkerActions.Highlighting }),
-    }),
-    text: (ctx, getParams) => (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, {
-        modifyState: (s) => ({ ...s, markerActions: marker_action_1.MarkerAction.None }),
-    }),
-};
-exports.ContactParams = {
-    ...CylinderParams,
-    ...TextParams,
-    visuals: param_definition_1.ParamDefinition.MultiSelect(['cylinder', 'text'], param_definition_1.ParamDefinition.objectToOptions(ContactVisuals)),
+var CylinderParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, cylinders_1.Cylinders.Params), SharedParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(true), linesSize: param_definition_1.ParamDefinition.Numeric(0.075, { min: 0.01, max: 5, step: 0.01 }), dashLength: param_definition_1.ParamDefinition.Numeric(0.12, { min: 0.01, max: 0.2, step: 0.01 }), interactionType: param_definition_1.ParamDefinition.Text('', { isEssential: true }), cylinderColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.lightgreen, { isEssential: true }) });
+var TextParams = tslib_1.__assign(tslib_1.__assign({}, common_1.LociLabelTextParams), SharedParams);
+var ContactVisuals = {
+    cylinder: function (ctx, getParams) {
+        return (0, representation_1.ShapeRepresentation)(getCylindersShape, cylinders_1.Cylinders.Utils, {
+            modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerActions.Highlighting })); },
+        });
+    },
+    text: function (ctx, getParams) {
+        return (0, representation_1.ShapeRepresentation)(getTextShape, text_1.Text.Utils, {
+            modifyState: function (s) { return (tslib_1.__assign(tslib_1.__assign({}, s), { markerActions: marker_action_1.MarkerAction.None })); },
+        });
+    },
 };
+exports.ContactParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, CylinderParams), TextParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['cylinder', 'text'], param_definition_1.ParamDefinition.objectToOptions(ContactVisuals)) });
 //
-function contactLabel(pair, options = {}) {
-    const o = { ...label_2.DefaultLabelOptions, ...options };
-    const label = (0, label_2.bundleLabel)(pair, o);
-    return `${o?.interactionType ?? 'Distance'}</br>${label}`;
+function contactLabel(pair, options) {
+    var _a;
+    if (options === void 0) { options = {}; }
+    var o = tslib_1.__assign(tslib_1.__assign({}, label_2.DefaultLabelOptions), options);
+    var label = (0, label_2.bundleLabel)(pair, o);
+    return "".concat((_a = o === null || o === void 0 ? void 0 : o.interactionType) !== null && _a !== void 0 ? _a : 'Distance', "</br>").concat(label);
 }
-exports.contactLabel = contactLabel;
 function getContactState() {
     return {
         sphereA: (0, geometry_1.Sphere3D)(),
@@ -63,8 +56,8 @@ function getContactState() {
     };
 }
 function setContactState(pair, state) {
-    const { sphereA, sphereB, center } = state;
-    const [lociA, lociB] = pair.loci;
+    var sphereA = state.sphereA, sphereB = state.sphereB, center = state.center;
+    var _a = tslib_1.__read(pair.loci, 2), lociA = _a[0], lociB = _a[1];
     loci_1.Loci.getBoundingSphere(lociA, sphereA);
     loci_1.Loci.getBoundingSphere(lociB, sphereB);
     linear_algebra_1.Vec3.add(center, sphereA.center, sphereB.center);
@@ -72,19 +65,19 @@ function setContactState(pair, state) {
     state.distance = linear_algebra_1.Vec3.distance(sphereA.center, sphereB.center);
     return state;
 }
-const tmpState = getContactState();
+var tmpState = getContactState();
 function getContactName(data, unitLabel) {
     return data.pairs.length === 1
-        ? `Contact ${(0, label_1.distanceLabel)(data.pairs[0], {
-            unitLabel,
+        ? "Contact ".concat((0, label_1.distanceLabel)(data.pairs[0], {
+            unitLabel: unitLabel,
             measureOnly: true,
-        })}`
-        : `${data.pairs.length} Contacts`;
+        }))
+        : "".concat(data.pairs.length, " Contacts");
 }
 //
 function buildCylinders(data, props, cylinders) {
-    const builder = cylinders_builder_1.CylindersBuilder.create(128, 64, cylinders);
-    for (let i = 0, il = data.pairs.length; i < il; ++i) {
+    var builder = cylinders_builder_1.CylindersBuilder.create(128, 64, cylinders);
+    for (var i = 0, il = data.pairs.length; i < il; ++i) {
         setContactState(data.pairs[i], tmpState);
         // TODO: radiusScale: number, topCap: boolean, bottomCap: boolean
         builder.addFixedLengthDashes(tmpState.sphereA.center, tmpState.sphereB.center, props.dashLength, 1, true, true, false, // interpolate parameter
@@ -93,31 +86,34 @@ function buildCylinders(data, props, cylinders) {
     return builder.getCylinders();
 }
 function getCylindersShape(ctx, data, props, shape) {
-    const cylinders = buildCylinders(data, props, shape && shape.geometry);
-    const name = getContactName(data, props.unitLabel);
-    const getLabel = (groupId) => contactLabel(data.pairs[groupId], props);
-    return shape_1.Shape.create(name, data, cylinders, () => props.cylinderColor, () => props.linesSize, getLabel);
+    var cylinders = buildCylinders(data, props, shape && shape.geometry);
+    var name = getContactName(data, props.unitLabel);
+    var getLabel = function (groupId) {
+        return contactLabel(data.pairs[groupId], props);
+    };
+    return shape_1.Shape.create(name, data, cylinders, function () { return props.cylinderColor; }, function () { return props.linesSize; }, getLabel);
 }
 //
 function buildText(data, props, text) {
-    const builder = text_builder_1.TextBuilder.create(props, 128, 64, text);
-    for (let i = 0, il = data.pairs.length; i < il; ++i) {
+    var builder = text_builder_1.TextBuilder.create(props, 128, 64, text);
+    for (var i = 0, il = data.pairs.length; i < il; ++i) {
         setContactState(data.pairs[i], tmpState);
-        const { center, distance, sphereA, sphereB } = tmpState;
-        const label = props.customText || `${distance.toFixed(2)} ${props.unitLabel}`;
-        const radius = Math.max(2, sphereA.radius, sphereB.radius);
-        const scale = radius / 2;
+        var center = tmpState.center, distance = tmpState.distance, sphereA = tmpState.sphereA, sphereB = tmpState.sphereB;
+        var label = props.customText || "".concat(distance.toFixed(2), " ").concat(props.unitLabel);
+        var radius = Math.max(2, sphereA.radius, sphereB.radius);
+        var scale = radius / 2;
         builder.add(label, center[0], center[1], center[2], 1, scale, i);
     }
     return builder.getText();
 }
 function getTextShape(ctx, data, props, shape) {
-    const text = buildText(data, props, shape && shape.geometry);
-    const name = getContactName(data, props.unitLabel);
-    const getLabel = (groupId) => (0, label_1.distanceLabel)(data.pairs[groupId], props);
-    return shape_1.Shape.create(name, data, text, () => props.textColor, () => props.textSize, getLabel);
+    var text = buildText(data, props, shape && shape.geometry);
+    var name = getContactName(data, props.unitLabel);
+    var getLabel = function (groupId) {
+        return (0, label_1.distanceLabel)(data.pairs[groupId], props);
+    };
+    return shape_1.Shape.create(name, data, text, function () { return props.textColor; }, function () { return props.textSize; }, getLabel);
 }
 function ContactRepresentation(ctx, getParams) {
     return representation_2.Representation.createMulti('Contact', ctx, getParams, representation_2.Representation.StateBuilder, ContactVisuals);
 }
-exports.ContactRepresentation = ContactRepresentation;

package/lib/custom-events.js

@@ -1,25 +1,25 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.CustomEvents = void 0;
-const loci_details_1 = require("./loci-details");
-const operators_1 = require("rxjs/operators");
+var loci_details_1 = require("./loci-details");
+var operators_1 = require("rxjs/operators");
 var CustomEvents;
 (function (CustomEvents) {
     function create(eventTypeArr) {
-        let eventObj = {};
-        for (let ei = 0, el = eventTypeArr.length; ei < el; ei++) {
-            let eventType = eventTypeArr[ei];
-            let event;
+        var eventObj = {};
+        for (var ei = 0, el = eventTypeArr.length; ei < el; ei++) {
+            var eventType = eventTypeArr[ei];
+            var event_1 = void 0;
             if (typeof MouseEvent == 'function') {
                 // current standard
-                event = new MouseEvent(eventType, { 'view': window, 'bubbles': true, 'cancelable': true });
+                event_1 = new MouseEvent(eventType, { 'view': window, 'bubbles': true, 'cancelable': true });
             }
             else if (typeof document.createEvent == 'function') {
                 // older standard
-                event = document.createEvent('MouseEvents');
-                event.initEvent(eventType, true /* bubbles */, true /* cancelable */);
+                event_1 = document.createEvent('MouseEvents');
+                event_1.initEvent(eventType, true /* bubbles */, true /* cancelable */);
             }
-            eventObj[eventType] = event;
+            eventObj[eventType] = event_1;
         }
         ;
         return eventObj;
@@ -33,17 +33,17 @@ var CustomEvents;
         }
     }
     function add(plugin, targetElement) {
-        const pdbevents = create(['PDB.molstar.click', 'PDB.molstar.mouseover', 'PDB.molstar.mouseout']);
-        plugin.behaviors.interaction.click.subscribe((e) => {
+        var pdbevents = create(['PDB.molstar.click', 'PDB.molstar.mouseover', 'PDB.molstar.mouseout']);
+        plugin.behaviors.interaction.click.subscribe(function (e) {
             if (e.button === 1 && e.current && e.current.loci.kind !== 'empty-loci') {
-                const evData = (0, loci_details_1.lociDetails)(e.current.loci);
+                var evData = (0, loci_details_1.lociDetails)(e.current.loci);
                 if (evData)
                     dispatchCustomEvent(pdbevents['PDB.molstar.click'], evData, targetElement);
             }
         });
-        plugin.behaviors.interaction.hover.pipe((0, operators_1.debounceTime)(100)).subscribe((e) => {
+        plugin.behaviors.interaction.hover.pipe((0, operators_1.debounceTime)(100)).subscribe(function (e) {
             if (e.current && e.current.loci && e.current.loci.kind !== 'empty-loci') {
-                const evData = (0, loci_details_1.lociDetails)(e.current.loci);
+                var evData = (0, loci_details_1.lociDetails)(e.current.loci);
                 if (evData)
                     dispatchCustomEvent(pdbevents['PDB.molstar.mouseover'], evData, targetElement);
             }

package/lib/domain-annotations/behavior.d.ts

@@ -1,5 +1,5 @@
 import { PluginBehavior } from 'Molstar/mol-plugin/behavior';
-export declare const PDBeDomainAnnotations: import("molstar/lib/mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
+export declare const PDBeDomainAnnotations: import("Molstar/mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
     autoAttach: boolean;
     showTooltip: boolean;
 }>;