molstar 3.0.0 → 3.0.1

package/lib/commonjs/mol-repr/structure/representation/cartoon.js

@@ -1,96 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2021 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.CartoonRepresentationProvider = exports.CartoonRepresentation = exports.getCartoonParams = exports.CartoonParams = void 0;
-var tslib_1 = require("tslib");
-var structure_1 = require("../../../mol-model/structure");
-var representation_1 = require("../../../mol-repr/representation");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var representation_2 = require("../representation");
-var units_representation_1 = require("../units-representation");
-var nucleotide_block_mesh_1 = require("../visual/nucleotide-block-mesh");
-var nucleotide_ring_mesh_1 = require("../visual/nucleotide-ring-mesh");
-var polymer_direction_wedge_1 = require("../visual/polymer-direction-wedge");
-var polymer_gap_cylinder_1 = require("../visual/polymer-gap-cylinder");
-var polymer_trace_mesh_1 = require("../visual/polymer-trace-mesh");
-var secondary_structure_1 = require("../../../mol-model-props/computed/secondary-structure");
-var helix_orientation_1 = require("../../../mol-model-props/computed/helix-orientation");
-var base_1 = require("../../../mol-geo/geometry/base");
-var CartoonVisuals = {
-    'polymer-trace': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer trace mesh', ctx, getParams, polymer_trace_mesh_1.PolymerTraceVisual); },
-    'polymer-gap': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer gap cylinder', ctx, getParams, polymer_gap_cylinder_1.PolymerGapVisual); },
-    'nucleotide-block': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Nucleotide block mesh', ctx, getParams, nucleotide_block_mesh_1.NucleotideBlockVisual); },
-    'nucleotide-ring': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Nucleotide ring mesh', ctx, getParams, nucleotide_ring_mesh_1.NucleotideRingVisual); },
-    'direction-wedge': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer direction wedge', ctx, getParams, polymer_direction_wedge_1.PolymerDirectionVisual); }
-};
-exports.CartoonParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, polymer_trace_mesh_1.PolymerTraceParams), polymer_gap_cylinder_1.PolymerGapParams), nucleotide_block_mesh_1.NucleotideBlockParams), nucleotide_ring_mesh_1.NucleotideRingParams), polymer_direction_wedge_1.PolymerDirectionParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-block'], param_definition_1.ParamDefinition.objectToOptions(CartoonVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
-function getCartoonParams(ctx, structure) {
-    var params = param_definition_1.ParamDefinition.clone(exports.CartoonParams);
-    var hasNucleotides = false;
-    var hasGaps = false;
-    structure.units.forEach(function (u) {
-        if (!hasNucleotides && structure_1.Unit.isAtomic(u) && u.nucleotideElements.length)
-            hasNucleotides = true;
-        if (!hasGaps && u.gapElements.length)
-            hasGaps = true;
-    });
-    params.visuals.defaultValue = ['polymer-trace'];
-    if (hasNucleotides)
-        params.visuals.defaultValue.push('nucleotide-block');
-    if (hasGaps)
-        params.visuals.defaultValue.push('polymer-gap');
-    return params;
-}
-exports.getCartoonParams = getCartoonParams;
-function CartoonRepresentation(ctx, getParams) {
-    return representation_1.Representation.createMulti('Cartoon', ctx, getParams, representation_2.StructureRepresentationStateBuilder, CartoonVisuals);
-}
-exports.CartoonRepresentation = CartoonRepresentation;
-exports.CartoonRepresentationProvider = (0, representation_2.StructureRepresentationProvider)({
-    name: 'cartoon',
-    label: 'Cartoon',
-    description: 'Displays ribbons, planks, tubes smoothly following the trace atoms of polymers.',
-    factory: CartoonRepresentation,
-    getParams: getCartoonParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.CartoonParams),
-    defaultColorTheme: { name: 'chain-id' },
-    defaultSizeTheme: { name: 'uniform' },
-    isApplicable: function (structure) { return structure.polymerResidueCount > 0; },
-    ensureCustomProperties: {
-        attach: function (ctx, structure) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-            var _i, _a, m;
-            return (0, tslib_1.__generator)(this, function (_b) {
-                switch (_b.label) {
-                    case 0: return [4 /*yield*/, secondary_structure_1.SecondaryStructureProvider.attach(ctx, structure, void 0, true)];
-                    case 1:
-                        _b.sent();
-                        _i = 0, _a = structure.models;
-                        _b.label = 2;
-                    case 2:
-                        if (!(_i < _a.length)) return [3 /*break*/, 5];
-                        m = _a[_i];
-                        return [4 /*yield*/, helix_orientation_1.HelixOrientationProvider.attach(ctx, m, void 0, true)];
-                    case 3:
-                        _b.sent();
-                        _b.label = 4;
-                    case 4:
-                        _i++;
-                        return [3 /*break*/, 2];
-                    case 5: return [2 /*return*/];
-                }
-            });
-        }); },
-        detach: function (data) {
-            secondary_structure_1.SecondaryStructureProvider.ref(data, false);
-            for (var _i = 0, _a = data.models; _i < _a.length; _i++) {
-                var m = _a[_i];
-                helix_orientation_1.HelixOrientationProvider.ref(m, false);
-            }
-        }
-    }
-});
-//# sourceMappingURL=cartoon.js.map

package/lib/commonjs/mol-repr/structure/representation/ellipsoid.js

@@ -1,50 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019-2021 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.EllipsoidRepresentationProvider = exports.EllipsoidRepresentation = exports.getEllipsoidParams = exports.EllipsoidParams = void 0;
-var tslib_1 = require("tslib");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var representation_1 = require("../../../mol-repr/representation");
-var representation_2 = require("../../../mol-repr/structure/representation");
-var ellipsoid_mesh_1 = require("../visual/ellipsoid-mesh");
-var anisotropic_1 = require("../../../mol-model-formats/structure/property/anisotropic");
-var bond_intra_unit_cylinder_1 = require("../visual/bond-intra-unit-cylinder");
-var bond_inter_unit_cylinder_1 = require("../visual/bond-inter-unit-cylinder");
-var params_1 = require("../params");
-var base_1 = require("../../../mol-geo/geometry/base");
-var EllipsoidVisuals = {
-    'ellipsoid-mesh': function (ctx, getParams) { return (0, representation_2.UnitsRepresentation)('Ellipsoid Mesh', ctx, getParams, ellipsoid_mesh_1.EllipsoidMeshVisual); },
-    'intra-bond': function (ctx, getParams) { return (0, representation_2.UnitsRepresentation)('Intra-unit bond cylinder', ctx, getParams, bond_intra_unit_cylinder_1.IntraUnitBondCylinderVisual); },
-    'inter-bond': function (ctx, getParams) { return (0, representation_2.ComplexRepresentation)('Inter-unit bond cylinder', ctx, getParams, bond_inter_unit_cylinder_1.InterUnitBondCylinderVisual); },
-};
-exports.EllipsoidParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, ellipsoid_mesh_1.EllipsoidMeshParams), bond_intra_unit_cylinder_1.IntraUnitBondCylinderParams), bond_inter_unit_cylinder_1.InterUnitBondCylinderParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false), adjustCylinderLength: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0.01, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(0.1, { min: 0.01, max: 3, step: 0.01 }), linkCap: param_definition_1.ParamDefinition.Boolean(true), visuals: param_definition_1.ParamDefinition.MultiSelect(['ellipsoid-mesh', 'intra-bond', 'inter-bond'], param_definition_1.ParamDefinition.objectToOptions(EllipsoidVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
-function getEllipsoidParams(ctx, structure) {
-    return param_definition_1.ParamDefinition.clone(exports.EllipsoidParams);
-}
-exports.getEllipsoidParams = getEllipsoidParams;
-function EllipsoidRepresentation(ctx, getParams) {
-    return representation_1.Representation.createMulti('Ellipsoid', ctx, getParams, representation_2.StructureRepresentationStateBuilder, EllipsoidVisuals);
-}
-exports.EllipsoidRepresentation = EllipsoidRepresentation;
-exports.EllipsoidRepresentationProvider = (0, representation_2.StructureRepresentationProvider)({
-    name: 'ellipsoid',
-    label: 'Ellipsoid',
-    description: 'Displays anisotropic displacement ellipsoids of atomic elements plus bonds as cylinders.',
-    factory: EllipsoidRepresentation,
-    getParams: getEllipsoidParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.EllipsoidParams),
-    defaultColorTheme: { name: 'element-symbol' },
-    defaultSizeTheme: { name: 'uniform' },
-    isApplicable: function (structure) { return structure.elementCount > 0 && structure.models.some(function (m) { return anisotropic_1.AtomSiteAnisotrop.Provider.isApplicable(m); }); },
-    getData: function (structure, props) {
-        return props.includeParent ? structure.asParent() : structure;
-    },
-    mustRecreate: function (oldProps, newProps) {
-        return oldProps.includeParent !== newProps.includeParent;
-    }
-});
-//# sourceMappingURL=ellipsoid.js.map

package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.js

@@ -1,42 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2021 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.GaussianSurfaceRepresentationProvider = exports.GaussianSurfaceRepresentation = exports.getGaussianSurfaceParams = exports.GaussianSurfaceParams = void 0;
-var tslib_1 = require("tslib");
-var gaussian_surface_mesh_1 = require("../visual/gaussian-surface-mesh");
-var units_representation_1 = require("../units-representation");
-var gaussian_surface_wireframe_1 = require("../visual/gaussian-surface-wireframe");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var representation_1 = require("../representation");
-var representation_2 = require("../../../mol-repr/representation");
-var base_1 = require("../../../mol-geo/geometry/base");
-var GaussianSurfaceVisuals = {
-    'gaussian-surface-mesh': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Gaussian surface mesh', ctx, getParams, gaussian_surface_mesh_1.GaussianSurfaceVisual); },
-    'structure-gaussian-surface-mesh': function (ctx, getParams) { return (0, representation_1.ComplexRepresentation)('Structure-Gaussian surface mesh', ctx, getParams, gaussian_surface_mesh_1.StructureGaussianSurfaceVisual); },
-    'gaussian-surface-wireframe': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Gaussian surface wireframe', ctx, getParams, gaussian_surface_wireframe_1.GaussianWireframeVisual); },
-};
-exports.GaussianSurfaceParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, gaussian_surface_mesh_1.GaussianSurfaceMeshParams), gaussian_surface_wireframe_1.GaussianWireframeParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['gaussian-surface-mesh'], param_definition_1.ParamDefinition.objectToOptions(GaussianSurfaceVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
-function getGaussianSurfaceParams(ctx, structure) {
-    return param_definition_1.ParamDefinition.clone(exports.GaussianSurfaceParams);
-}
-exports.getGaussianSurfaceParams = getGaussianSurfaceParams;
-function GaussianSurfaceRepresentation(ctx, getParams) {
-    return representation_2.Representation.createMulti('Gaussian Surface', ctx, getParams, representation_1.StructureRepresentationStateBuilder, GaussianSurfaceVisuals);
-}
-exports.GaussianSurfaceRepresentation = GaussianSurfaceRepresentation;
-exports.GaussianSurfaceRepresentationProvider = (0, representation_1.StructureRepresentationProvider)({
-    name: 'gaussian-surface',
-    label: 'Gaussian Surface',
-    description: 'Displays a gaussian molecular surface.',
-    factory: GaussianSurfaceRepresentation,
-    getParams: getGaussianSurfaceParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.GaussianSurfaceParams),
-    defaultColorTheme: { name: 'chain-id' },
-    defaultSizeTheme: { name: 'physical' },
-    isApplicable: function (structure) { return structure.elementCount > 0; }
-});
-//# sourceMappingURL=gaussian-surface.js.map

package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.js

@@ -1,40 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2021 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.GaussianVolumeRepresentationProvider = exports.GaussianVolumeRepresentation = exports.getGaussianVolumeParams = exports.GaussianVolumeParams = void 0;
-var tslib_1 = require("tslib");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var gaussian_density_volume_1 = require("../visual/gaussian-density-volume");
-var representation_1 = require("../representation");
-var representation_2 = require("../../../mol-repr/representation");
-var GaussianVolumeVisuals = {
-    'gaussian-volume': function (ctx, getParams) { return (0, representation_1.ComplexRepresentation)('Gaussian volume', ctx, getParams, gaussian_density_volume_1.GaussianDensityVolumeVisual); },
-    'units-gaussian-volume': function (ctx, getParams) { return (0, representation_1.UnitsRepresentation)('Units-Gaussian volume', ctx, getParams, gaussian_density_volume_1.UnitsGaussianDensityVolumeVisual); }
-};
-exports.GaussianVolumeParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, gaussian_density_volume_1.GaussianDensityVolumeParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['gaussian-volume'], param_definition_1.ParamDefinition.objectToOptions(GaussianVolumeVisuals)) });
-function getGaussianVolumeParams(ctx, structure) {
-    var p = param_definition_1.ParamDefinition.clone(exports.GaussianVolumeParams);
-    p.jumpLength = param_definition_1.ParamDefinition.Numeric(4, { min: 0, max: 20, step: 0.1 });
-    return p;
-}
-exports.getGaussianVolumeParams = getGaussianVolumeParams;
-function GaussianVolumeRepresentation(ctx, getParams) {
-    return representation_2.Representation.createMulti('Gaussian Volume', ctx, getParams, representation_1.StructureRepresentationStateBuilder, GaussianVolumeVisuals);
-}
-exports.GaussianVolumeRepresentation = GaussianVolumeRepresentation;
-exports.GaussianVolumeRepresentationProvider = (0, representation_1.StructureRepresentationProvider)({
-    name: 'gaussian-volume',
-    label: 'Gaussian Volume',
-    description: 'Displays a gaussian molecular density using direct volume rendering.',
-    factory: GaussianVolumeRepresentation,
-    getParams: getGaussianVolumeParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.GaussianVolumeParams),
-    defaultColorTheme: { name: 'chain-id' },
-    defaultSizeTheme: { name: 'physical' },
-    isApplicable: function (structure) { return structure.elementCount > 0; }
-});
-//# sourceMappingURL=gaussian-volume.js.map

package/lib/commonjs/mol-repr/structure/representation/label.js

@@ -1,40 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019 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.LabelRepresentationProvider = exports.LabelRepresentation = exports.getLabelParams = exports.LabelParams = void 0;
-var tslib_1 = require("tslib");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var representation_1 = require("../representation");
-var representation_2 = require("../../../mol-repr/representation");
-var label_text_1 = require("../visual/label-text");
-var marker_action_1 = require("../../../mol-util/marker-action");
-var LabelVisuals = {
-    'label-text': function (ctx, getParams) { return (0, representation_1.ComplexRepresentation)('Label text', ctx, getParams, label_text_1.LabelTextVisual); },
-};
-exports.LabelParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, label_text_1.LabelTextParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['label-text'], param_definition_1.ParamDefinition.objectToOptions(LabelVisuals)) });
-function getLabelParams(ctx, structure) {
-    return param_definition_1.ParamDefinition.clone(exports.LabelParams);
-}
-exports.getLabelParams = getLabelParams;
-function LabelRepresentation(ctx, getParams) {
-    var repr = representation_2.Representation.createMulti('Label', ctx, getParams, representation_1.StructureRepresentationStateBuilder, LabelVisuals);
-    repr.setState({ pickable: false, markerActions: marker_action_1.MarkerAction.None });
-    return repr;
-}
-exports.LabelRepresentation = LabelRepresentation;
-exports.LabelRepresentationProvider = (0, representation_1.StructureRepresentationProvider)({
-    name: 'label',
-    label: 'Label',
-    description: 'Displays labels.',
-    factory: LabelRepresentation,
-    getParams: getLabelParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.LabelParams),
-    defaultColorTheme: { name: 'uniform' },
-    defaultSizeTheme: { name: 'physical' },
-    isApplicable: function (structure) { return structure.elementCount > 0; }
-});
-//# sourceMappingURL=label.js.map

package/lib/commonjs/mol-repr/structure/representation/line.js

@@ -1,54 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2020-2021 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.LineRepresentationProvider = exports.LineRepresentation = exports.getLineParams = exports.LineParams = void 0;
-var tslib_1 = require("tslib");
-var bond_intra_unit_line_1 = require("../visual/bond-intra-unit-line");
-var bond_inter_unit_line_1 = require("../visual/bond-inter-unit-line");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var units_representation_1 = require("../units-representation");
-var complex_representation_1 = require("../complex-representation");
-var representation_1 = require("../representation");
-var representation_2 = require("../../../mol-repr/representation");
-var params_1 = require("../params");
-var element_point_1 = require("../visual/element-point");
-var element_cross_1 = require("../visual/element-cross");
-var LineVisuals = {
-    'intra-bond': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Intra-unit bond line', ctx, getParams, bond_intra_unit_line_1.IntraUnitBondLineVisual); },
-    'inter-bond': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Inter-unit bond line', ctx, getParams, bond_inter_unit_line_1.InterUnitBondLineVisual); },
-    'element-point': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Points', ctx, getParams, element_point_1.ElementPointVisual); },
-    'element-cross': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Crosses', ctx, getParams, element_cross_1.ElementCrossVisual); },
-};
-exports.LineParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, bond_intra_unit_line_1.IntraUnitBondLineParams), bond_inter_unit_line_1.InterUnitBondLineParams), element_point_1.ElementPointParams), element_cross_1.ElementCrossParams), { multipleBonds: param_definition_1.ParamDefinition.Select('offset', param_definition_1.ParamDefinition.arrayToOptions(['off', 'symmetric', 'offset'])), includeParent: param_definition_1.ParamDefinition.Boolean(false), sizeFactor: param_definition_1.ParamDefinition.Numeric(3, { min: 0.01, max: 10, step: 0.01 }), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), visuals: param_definition_1.ParamDefinition.MultiSelect(['intra-bond', 'inter-bond', 'element-point', 'element-cross'], param_definition_1.ParamDefinition.objectToOptions(LineVisuals)) });
-function getLineParams(ctx, structure) {
-    var params = param_definition_1.ParamDefinition.clone(exports.LineParams);
-    params.pointStyle.defaultValue = 'circle';
-    return params;
-}
-exports.getLineParams = getLineParams;
-function LineRepresentation(ctx, getParams) {
-    return representation_2.Representation.createMulti('Line', ctx, getParams, representation_1.StructureRepresentationStateBuilder, LineVisuals);
-}
-exports.LineRepresentation = LineRepresentation;
-exports.LineRepresentationProvider = (0, representation_1.StructureRepresentationProvider)({
-    name: 'line',
-    label: 'Line',
-    description: 'Displays bonds as lines and atoms as points or croses.',
-    factory: LineRepresentation,
-    getParams: getLineParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.LineParams),
-    defaultColorTheme: { name: 'element-symbol' },
-    defaultSizeTheme: { name: 'uniform' },
-    isApplicable: function (structure) { return structure.elementCount > 0; },
-    getData: function (structure, props) {
-        return props.includeParent ? structure.asParent() : structure;
-    },
-    mustRecreate: function (oldProps, newProps) {
-        return oldProps.includeParent !== newProps.includeParent;
-    }
-});
-//# sourceMappingURL=line.js.map

package/lib/commonjs/mol-repr/structure/representation/molecular-surface.js

@@ -1,41 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2019 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.MolecularSurfaceRepresentationProvider = exports.MolecularSurfaceRepresentation = exports.getMolecularSurfaceParams = exports.MolecularSurfaceParams = void 0;
-var tslib_1 = require("tslib");
-var molecular_surface_mesh_1 = require("../visual/molecular-surface-mesh");
-var units_representation_1 = require("../units-representation");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var representation_1 = require("../representation");
-var representation_2 = require("../../../mol-repr/representation");
-var molecular_surface_wireframe_1 = require("../visual/molecular-surface-wireframe");
-var base_1 = require("../../../mol-geo/geometry/base");
-var MolecularSurfaceVisuals = {
-    'molecular-surface-mesh': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Molecular surface mesh', ctx, getParams, molecular_surface_mesh_1.MolecularSurfaceMeshVisual); },
-    'molecular-surface-wireframe': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Molecular surface wireframe', ctx, getParams, molecular_surface_wireframe_1.MolecularSurfaceWireframeVisual); },
-};
-exports.MolecularSurfaceParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, molecular_surface_mesh_1.MolecularSurfaceMeshParams), molecular_surface_wireframe_1.MolecularSurfaceWireframeParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['molecular-surface-mesh'], param_definition_1.ParamDefinition.objectToOptions(MolecularSurfaceVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
-function getMolecularSurfaceParams(ctx, structure) {
-    return param_definition_1.ParamDefinition.clone(exports.MolecularSurfaceParams);
-}
-exports.getMolecularSurfaceParams = getMolecularSurfaceParams;
-function MolecularSurfaceRepresentation(ctx, getParams) {
-    return representation_2.Representation.createMulti('Molecular Surface', ctx, getParams, representation_1.StructureRepresentationStateBuilder, MolecularSurfaceVisuals);
-}
-exports.MolecularSurfaceRepresentation = MolecularSurfaceRepresentation;
-exports.MolecularSurfaceRepresentationProvider = (0, representation_1.StructureRepresentationProvider)({
-    name: 'molecular-surface',
-    label: 'Molecular Surface',
-    description: 'Displays a molecular surface.',
-    factory: MolecularSurfaceRepresentation,
-    getParams: getMolecularSurfaceParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.MolecularSurfaceParams),
-    defaultColorTheme: { name: 'chain-id' },
-    defaultSizeTheme: { name: 'physical' },
-    isApplicable: function (structure) { return structure.elementCount > 0; }
-});
-//# sourceMappingURL=molecular-surface.js.map

package/lib/commonjs/mol-repr/structure/representation/orientation.js

@@ -1,39 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019 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.OrientationRepresentationProvider = exports.OrientationRepresentation = exports.getOrientationParams = exports.OrientationParams = void 0;
-var tslib_1 = require("tslib");
-var units_representation_1 = require("../units-representation");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var representation_1 = require("../representation");
-var representation_2 = require("../../../mol-repr/representation");
-var orientation_ellipsoid_mesh_1 = require("../visual/orientation-ellipsoid-mesh");
-var base_1 = require("../../../mol-geo/geometry/base");
-var OrientationVisuals = {
-    'orientation-ellipsoid-mesh': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Orientation ellipsoid mesh', ctx, getParams, orientation_ellipsoid_mesh_1.OrientationEllipsoidMeshVisual); },
-};
-exports.OrientationParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, orientation_ellipsoid_mesh_1.OrientationEllipsoidMeshParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['orientation-ellipsoid-mesh'], param_definition_1.ParamDefinition.objectToOptions(OrientationVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
-function getOrientationParams(ctx, structure) {
-    return param_definition_1.ParamDefinition.clone(exports.OrientationParams);
-}
-exports.getOrientationParams = getOrientationParams;
-function OrientationRepresentation(ctx, getParams) {
-    return representation_2.Representation.createMulti('Orientation', ctx, getParams, representation_1.StructureRepresentationStateBuilder, OrientationVisuals);
-}
-exports.OrientationRepresentation = OrientationRepresentation;
-exports.OrientationRepresentationProvider = (0, representation_1.StructureRepresentationProvider)({
-    name: 'orientation',
-    label: 'Orientation',
-    description: 'Displays orientation ellipsoids for polymer chains.',
-    factory: OrientationRepresentation,
-    getParams: getOrientationParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.OrientationParams),
-    defaultColorTheme: { name: 'chain-id' },
-    defaultSizeTheme: { name: 'uniform' },
-    isApplicable: function (structure) { return structure.elementCount > 0; }
-});
-//# sourceMappingURL=orientation.js.map

package/lib/commonjs/mol-repr/structure/representation/point.js

@@ -1,38 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018 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.PointRepresentationProvider = exports.PointRepresentation = exports.getPointParams = exports.PointParams = void 0;
-var tslib_1 = require("tslib");
-var element_point_1 = require("../visual/element-point");
-var units_representation_1 = require("../units-representation");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var representation_1 = require("../representation");
-var representation_2 = require("../../../mol-repr/representation");
-var PointVisuals = {
-    'element-point': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Points', ctx, getParams, element_point_1.ElementPointVisual); },
-};
-exports.PointParams = (0, tslib_1.__assign)({}, element_point_1.ElementPointParams);
-function getPointParams(ctx, structure) {
-    return param_definition_1.ParamDefinition.clone(exports.PointParams);
-}
-exports.getPointParams = getPointParams;
-function PointRepresentation(ctx, getParams) {
-    return representation_2.Representation.createMulti('Point', ctx, getParams, representation_1.StructureRepresentationStateBuilder, PointVisuals);
-}
-exports.PointRepresentation = PointRepresentation;
-exports.PointRepresentationProvider = (0, representation_1.StructureRepresentationProvider)({
-    name: 'point',
-    label: 'Point',
-    description: 'Displays elements (atoms, coarse spheres) as points.',
-    factory: PointRepresentation,
-    getParams: getPointParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.PointParams),
-    defaultColorTheme: { name: 'element-symbol' },
-    defaultSizeTheme: { name: 'uniform' },
-    isApplicable: function (structure) { return structure.elementCount > 0; }
-});
-//# sourceMappingURL=point.js.map

package/lib/commonjs/mol-repr/structure/representation/putty.js

@@ -1,54 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019-2020 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.PuttyRepresentationProvider = exports.PuttyRepresentation = exports.getPuttyParams = exports.PuttyParams = void 0;
-var tslib_1 = require("tslib");
-var polymer_tube_mesh_1 = require("../visual/polymer-tube-mesh");
-var polymer_gap_cylinder_1 = require("../visual/polymer-gap-cylinder");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var units_representation_1 = require("../units-representation");
-var representation_1 = require("../representation");
-var representation_2 = require("../../../mol-repr/representation");
-var structure_1 = require("../../../mol-model/structure");
-var base_1 = require("../../../mol-geo/geometry/base");
-var PuttyVisuals = {
-    'polymer-tube': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer tube mesh', ctx, getParams, polymer_tube_mesh_1.PolymerTubeVisual); },
-    'polymer-gap': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer gap cylinder', ctx, getParams, polymer_gap_cylinder_1.PolymerGapVisual); },
-};
-exports.PuttyParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, polymer_tube_mesh_1.PolymerTubeParams), polymer_gap_cylinder_1.PolymerGapParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-tube', 'polymer-gap'], param_definition_1.ParamDefinition.objectToOptions(PuttyVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
-function getPuttyParams(ctx, structure) {
-    var params = param_definition_1.ParamDefinition.clone(exports.PuttyParams);
-    var hasNucleotides = false;
-    var hasGaps = false;
-    structure.units.forEach(function (u) {
-        if (!hasNucleotides && structure_1.Unit.isAtomic(u) && u.nucleotideElements.length)
-            hasNucleotides = true;
-        if (!hasGaps && u.gapElements.length)
-            hasGaps = true;
-    });
-    params.visuals.defaultValue = ['polymer-tube'];
-    if (hasGaps)
-        params.visuals.defaultValue.push('polymer-gap');
-    return params;
-}
-exports.getPuttyParams = getPuttyParams;
-function PuttyRepresentation(ctx, getParams) {
-    return representation_2.Representation.createMulti('Putty', ctx, getParams, representation_1.StructureRepresentationStateBuilder, PuttyVisuals);
-}
-exports.PuttyRepresentation = PuttyRepresentation;
-exports.PuttyRepresentationProvider = (0, representation_1.StructureRepresentationProvider)({
-    name: 'putty',
-    label: 'Putty',
-    description: 'Displays a tube smoothly following the trace atoms of polymers.',
-    factory: PuttyRepresentation,
-    getParams: getPuttyParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.PuttyParams),
-    defaultColorTheme: { name: 'chain-id' },
-    defaultSizeTheme: { name: 'uncertainty' },
-    isApplicable: function (structure) { return structure.polymerResidueCount > 0; },
-});
-//# sourceMappingURL=putty.js.map

package/lib/commonjs/mol-repr/structure/representation/spacefill.js

@@ -1,43 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2021 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.SpacefillRepresentationProvider = exports.SpacefillRepresentation = exports.getSpacefillParams = exports.SpacefillParams = void 0;
-var tslib_1 = require("tslib");
-var element_sphere_1 = require("../visual/element-sphere");
-var units_representation_1 = require("../units-representation");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var representation_1 = require("../representation");
-var representation_2 = require("../../../mol-repr/representation");
-var base_1 = require("../../../mol-geo/geometry/base");
-var SpacefillVisuals = {
-    'element-sphere': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Sphere mesh', ctx, getParams, element_sphere_1.ElementSphereVisual); },
-};
-exports.SpacefillParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, element_sphere_1.ElementSphereParams), { bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
-function getSpacefillParams(ctx, structure) {
-    var params = param_definition_1.ParamDefinition.clone(exports.SpacefillParams);
-    if (structure.isCoarseGrained) {
-        params.sizeFactor.defaultValue = 2;
-    }
-    return params;
-}
-exports.getSpacefillParams = getSpacefillParams;
-function SpacefillRepresentation(ctx, getParams) {
-    return representation_2.Representation.createMulti('Spacefill', ctx, getParams, representation_1.StructureRepresentationStateBuilder, SpacefillVisuals);
-}
-exports.SpacefillRepresentation = SpacefillRepresentation;
-exports.SpacefillRepresentationProvider = (0, representation_1.StructureRepresentationProvider)({
-    name: 'spacefill',
-    label: 'Spacefill',
-    description: 'Displays atomic/coarse elements as spheres.',
-    factory: SpacefillRepresentation,
-    getParams: getSpacefillParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.SpacefillParams),
-    defaultColorTheme: { name: 'element-symbol' },
-    defaultSizeTheme: { name: 'physical' },
-    isApplicable: function (structure) { return structure.elementCount > 0; }
-});
-//# sourceMappingURL=spacefill.js.map

package/lib/commonjs/mol-repr/structure/representation.js

@@ -1,33 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.UnitsVisual = exports.UnitsRepresentation = exports.ComplexVisual = exports.ComplexRepresentation = exports.StructureRepresentationProvider = exports.StructureRepresentationStateBuilder = void 0;
-var tslib_1 = require("tslib");
-var representation_1 = require("../representation");
-exports.StructureRepresentationStateBuilder = {
-    create: function () {
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, representation_1.Representation.createState()), { unitTransforms: null, unitTransformsVersion: -1 });
-    },
-    update: function (state, update) {
-        representation_1.Representation.updateState(state, update);
-        if (update.unitTransforms !== undefined)
-            state.unitTransforms = update.unitTransforms;
-    }
-};
-function StructureRepresentationProvider(p) { return p; }
-exports.StructureRepresentationProvider = StructureRepresentationProvider;
-//
-var complex_representation_1 = require("./complex-representation");
-Object.defineProperty(exports, "ComplexRepresentation", { enumerable: true, get: function () { return complex_representation_1.ComplexRepresentation; } });
-var complex_visual_1 = require("./complex-visual");
-Object.defineProperty(exports, "ComplexVisual", { enumerable: true, get: function () { return complex_visual_1.ComplexVisual; } });
-var units_representation_1 = require("./units-representation");
-Object.defineProperty(exports, "UnitsRepresentation", { enumerable: true, get: function () { return units_representation_1.UnitsRepresentation; } });
-var units_visual_1 = require("./units-visual");
-Object.defineProperty(exports, "UnitsVisual", { enumerable: true, get: function () { return units_visual_1.UnitsVisual; } });
-//# sourceMappingURL=representation.js.map