molstar 3.0.0 → 3.0.1

package/lib/commonjs/mol-repr/structure/complex-visual.js

@@ -1,325 +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.ComplexTextureMeshVisual = exports.ComplexTextureMeshParams = exports.ComplexDirectVolumeVisual = exports.ComplexDirectVolumeParams = exports.ComplexTextVisual = exports.ComplexTextParams = exports.ComplexLinesVisual = exports.ComplexLinesParams = exports.ComplexCylindersVisual = exports.ComplexCylindersParams = exports.ComplexMeshVisual = exports.ComplexMeshParams = exports.ComplexVisual = void 0;
-var tslib_1 = require("tslib");
-var visual_1 = require("../visual");
-var structure_1 = require("../../mol-model/structure");
-var geometry_1 = require("../../mol-geo/geometry/geometry");
-var theme_1 = require("../../mol-theme/theme");
-var transform_data_1 = require("../../mol-geo/geometry/transform-data");
-var render_object_1 = require("../../mol-gl/render-object");
-var loci_1 = require("../../mol-model/loci");
-var int_1 = require("../../mol-data/int");
-var util_1 = require("../util");
-var color_1 = require("../../mol-theme/color");
-var mol_util_1 = require("../../mol-util");
-var size_data_1 = require("../../mol-geo/geometry/size-data");
-var color_data_1 = require("../../mol-geo/geometry/color-data");
-var marker_action_1 = require("../../mol-util/marker-action");
-var mesh_1 = require("../../mol-geo/geometry/mesh/mesh");
-var cylinders_1 = require("../../mol-geo/geometry/cylinders/cylinders");
-var lines_1 = require("../../mol-geo/geometry/lines/lines");
-var text_1 = require("../../mol-geo/geometry/text/text");
-var size_1 = require("../../mol-theme/size");
-var direct_volume_1 = require("../../mol-geo/geometry/direct-volume/direct-volume");
-var marker_data_1 = require("../../mol-geo/geometry/marker-data");
-var params_1 = require("./params");
-var texture_mesh_1 = require("../../mol-geo/geometry/texture-mesh/texture-mesh");
-var type_helpers_1 = require("../../mol-util/type-helpers");
-function createComplexRenderObject(structure, geometry, locationIt, theme, props, materialId) {
-    var _a = geometry_1.Geometry.getUtils(geometry), createValues = _a.createValues, createRenderableState = _a.createRenderableState;
-    var transform = (0, transform_data_1.createIdentityTransform)();
-    var values = createValues(geometry, transform, locationIt, theme, props);
-    var state = createRenderableState(props);
-    return (0, render_object_1.createRenderObject)(geometry.kind, values, state, materialId);
-}
-function ComplexVisual(builder, materialId) {
-    var defaultProps = builder.defaultProps, createGeometry = builder.createGeometry, createLocationIterator = builder.createLocationIterator, getLoci = builder.getLoci, eachLocation = builder.eachLocation, setUpdateState = builder.setUpdateState, mustRecreate = builder.mustRecreate, processValues = builder.processValues, dispose = builder.dispose;
-    var _a = builder.geometryUtils, updateValues = _a.updateValues, updateBoundingSphere = _a.updateBoundingSphere, updateRenderableState = _a.updateRenderableState, createPositionIterator = _a.createPositionIterator;
-    var updateState = util_1.VisualUpdateState.create();
-    var previousMark = { loci: loci_1.EmptyLoci, action: marker_action_1.MarkerAction.None, status: -1 };
-    var renderObject;
-    var newProps;
-    var newTheme;
-    var newStructure;
-    var currentProps = Object.assign({}, defaultProps);
-    var currentTheme = theme_1.Theme.createEmpty();
-    var currentStructure;
-    var geometry;
-    var geometryVersion = -1;
-    var locationIt;
-    var positionIt;
-    function prepareUpdate(theme, props, structure) {
-        if (!structure && !currentStructure) {
-            throw new Error('missing structure');
-        }
-        newProps = Object.assign({}, currentProps, props);
-        newTheme = theme;
-        newStructure = structure;
-        util_1.VisualUpdateState.reset(updateState);
-        if (!renderObject || !currentStructure) {
-            updateState.createNew = true;
-            updateState.createGeometry = true;
-            return;
-        }
-        setUpdateState(updateState, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure);
-        if (!structure_1.Structure.areEquivalent(newStructure, currentStructure)) {
-            updateState.createGeometry = true;
-        }
-        if (!structure_1.Structure.areHierarchiesEqual(newStructure, currentStructure)) {
-            updateState.updateTransform = true;
-            updateState.createGeometry = true;
-        }
-        if (!color_1.ColorTheme.areEqual(theme.color, currentTheme.color)) {
-            updateState.updateColor = true;
-        }
-        if (!(0, mol_util_1.deepEqual)(newProps.unitKinds, currentProps.unitKinds)) {
-            updateState.createGeometry = true;
-        }
-        if (currentStructure.child !== newStructure.child) {
-            // console.log('new child');
-            updateState.createGeometry = true;
-        }
-        if (updateState.updateSize && !('uSize' in renderObject.values)) {
-            updateState.createGeometry = true;
-        }
-        if (updateState.createGeometry) {
-            updateState.updateColor = true;
-            updateState.updateSize = true;
-        }
-    }
-    function update(newGeometry) {
-        if (updateState.createNew) {
-            locationIt = createLocationIterator(newStructure);
-            if (newGeometry) {
-                renderObject = createComplexRenderObject(newStructure, newGeometry, locationIt, newTheme, newProps, materialId);
-                positionIt = createPositionIterator(newGeometry, renderObject.values);
-            }
-            else {
-                throw new Error('expected geometry to be given');
-            }
-        }
-        else {
-            if (!renderObject) {
-                throw new Error('expected renderObject to be available');
-            }
-            if (updateState.updateTransform) {
-                // console.log('update transform')
-                locationIt = createLocationIterator(newStructure);
-                var instanceCount = locationIt.instanceCount, groupCount = locationIt.groupCount;
-                (0, marker_data_1.createMarkers)(instanceCount * groupCount, renderObject.values);
-            }
-            if (updateState.createGeometry) {
-                if (newGeometry) {
-                    mol_util_1.ValueCell.updateIfChanged(renderObject.values.drawCount, geometry_1.Geometry.getDrawCount(newGeometry));
-                    mol_util_1.ValueCell.updateIfChanged(renderObject.values.uVertexCount, geometry_1.Geometry.getVertexCount(newGeometry));
-                }
-                else {
-                    throw new Error('expected geometry to be given');
-                }
-            }
-            if (updateState.updateTransform || updateState.createGeometry) {
-                updateBoundingSphere(renderObject.values, newGeometry || geometry);
-                positionIt = createPositionIterator(geometry, renderObject.values);
-            }
-            if (updateState.updateSize) {
-                // not all geometries have size data, so check here
-                if ('uSize' in renderObject.values) {
-                    (0, size_data_1.createSizes)(locationIt, newTheme.size, renderObject.values);
-                }
-            }
-            if (updateState.updateColor) {
-                (0, color_data_1.createColors)(locationIt, positionIt, newTheme.color, renderObject.values);
-            }
-            updateValues(renderObject.values, newProps);
-            updateRenderableState(renderObject.state, newProps);
-        }
-        currentProps = newProps;
-        currentTheme = newTheme;
-        currentStructure = newStructure;
-        if (newGeometry) {
-            geometry = newGeometry;
-            geometryVersion += 1;
-        }
-    }
-    function lociIsSuperset(loci) {
-        if ((0, loci_1.isEveryLoci)(loci))
-            return true;
-        if (structure_1.Structure.isLoci(loci) && structure_1.Structure.areRootsEquivalent(loci.structure, currentStructure))
-            return true;
-        if (structure_1.StructureElement.Loci.is(loci) && structure_1.Structure.areRootsEquivalent(loci.structure, currentStructure)) {
-            if (structure_1.StructureElement.Loci.isWholeStructure(loci))
-                return true;
-        }
-        return false;
-    }
-    function lociApply(loci, apply, isMarking) {
-        if (lociIsSuperset(loci)) {
-            return apply(int_1.Interval.ofBounds(0, locationIt.groupCount * locationIt.instanceCount));
-        }
-        else {
-            return eachLocation(loci, currentStructure, apply, isMarking);
-        }
-    }
-    function finalize(ctx) {
-        if (renderObject) {
-            processValues === null || processValues === void 0 ? void 0 : processValues(renderObject.values, geometry, currentProps, currentTheme, ctx.webgl);
-        }
-    }
-    return {
-        get groupCount() { return locationIt ? locationIt.count : 0; },
-        get renderObject() { return locationIt && locationIt.count ? renderObject : undefined; },
-        get geometryVersion() { return geometryVersion; },
-        createOrUpdate: function (ctx, theme, props, structure) {
-            if (props === void 0) { props = {}; }
-            prepareUpdate(theme, props, structure || currentStructure);
-            if (updateState.createGeometry) {
-                var newGeometry = createGeometry(ctx, newStructure, newTheme, newProps, geometry);
-                if ((0, type_helpers_1.isPromiseLike)(newGeometry)) {
-                    return newGeometry.then(function (g) {
-                        update(g);
-                        finalize(ctx);
-                    });
-                }
-                update(newGeometry);
-            }
-            else {
-                update();
-            }
-            finalize(ctx);
-        },
-        getLoci: function (pickingId) {
-            return renderObject ? getLoci(pickingId, currentStructure, renderObject.id) : loci_1.EmptyLoci;
-        },
-        mark: function (loci, action) {
-            return visual_1.Visual.mark(renderObject, loci, action, lociApply, previousMark);
-        },
-        setVisibility: function (visible) {
-            visual_1.Visual.setVisibility(renderObject, visible);
-        },
-        setAlphaFactor: function (alphaFactor) {
-            visual_1.Visual.setAlphaFactor(renderObject, alphaFactor);
-        },
-        setPickable: function (pickable) {
-            visual_1.Visual.setPickable(renderObject, pickable);
-        },
-        setColorOnly: function (colorOnly) {
-            visual_1.Visual.setColorOnly(renderObject, colorOnly);
-        },
-        setTransform: function (matrix, instanceMatrices) {
-            visual_1.Visual.setTransform(renderObject, matrix, instanceMatrices);
-        },
-        setOverpaint: function (overpaint, webgl) {
-            var smoothing = { geometry: geometry, props: currentProps, webgl: webgl };
-            visual_1.Visual.setOverpaint(renderObject, overpaint, lociApply, true, smoothing);
-        },
-        setTransparency: function (transparency, webgl) {
-            var smoothing = { geometry: geometry, props: currentProps, webgl: webgl };
-            visual_1.Visual.setTransparency(renderObject, transparency, lociApply, true, smoothing);
-        },
-        setSubstance: function (substance, webgl) {
-            var smoothing = { geometry: geometry, props: currentProps, webgl: webgl };
-            visual_1.Visual.setSubstance(renderObject, substance, lociApply, true, smoothing);
-        },
-        setClipping: function (clipping) {
-            visual_1.Visual.setClipping(renderObject, clipping, lociApply, true);
-        },
-        destroy: function () {
-            dispose === null || dispose === void 0 ? void 0 : dispose(geometry);
-            if (renderObject) {
-                renderObject.state.disposed = true;
-                renderObject = undefined;
-            }
-        },
-        mustRecreate: mustRecreate
-    };
-}
-exports.ComplexVisual = ComplexVisual;
-// mesh
-exports.ComplexMeshParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params_1.StructureMeshParams), params_1.StructureParams);
-function ComplexMeshVisual(builder, materialId) {
-    return ComplexVisual((0, tslib_1.__assign)((0, tslib_1.__assign)({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {
-            builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure);
-            if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
-                state.createGeometry = true;
-        }, geometryUtils: mesh_1.Mesh.Utils }), materialId);
-}
-exports.ComplexMeshVisual = ComplexMeshVisual;
-// cylinders
-exports.ComplexCylindersParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params_1.StructureCylindersParams), params_1.StructureParams);
-function ComplexCylindersVisual(builder, materialId) {
-    return ComplexVisual((0, tslib_1.__assign)((0, tslib_1.__assign)({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {
-            builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure);
-            if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
-                state.updateSize = true;
-        }, geometryUtils: cylinders_1.Cylinders.Utils }), materialId);
-}
-exports.ComplexCylindersVisual = ComplexCylindersVisual;
-// lines
-exports.ComplexLinesParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params_1.StructureLinesParams), params_1.StructureParams);
-function ComplexLinesVisual(builder, materialId) {
-    return ComplexVisual((0, tslib_1.__assign)((0, tslib_1.__assign)({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {
-            builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure);
-            if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
-                state.updateSize = true;
-        }, geometryUtils: lines_1.Lines.Utils }), materialId);
-}
-exports.ComplexLinesVisual = ComplexLinesVisual;
-// text
-exports.ComplexTextParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params_1.StructureTextParams), params_1.StructureParams);
-function ComplexTextVisual(builder, materialId) {
-    return ComplexVisual((0, tslib_1.__assign)((0, tslib_1.__assign)({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {
-            builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure);
-            if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
-                state.updateSize = true;
-            if (newProps.background !== currentProps.background)
-                state.createGeometry = true;
-            if (newProps.backgroundMargin !== currentProps.backgroundMargin)
-                state.createGeometry = true;
-            if (newProps.tether !== currentProps.tether)
-                state.createGeometry = true;
-            if (newProps.tetherLength !== currentProps.tetherLength)
-                state.createGeometry = true;
-            if (newProps.tetherBaseWidth !== currentProps.tetherBaseWidth)
-                state.createGeometry = true;
-            if (newProps.attachment !== currentProps.attachment)
-                state.createGeometry = true;
-            if (newProps.fontFamily !== currentProps.fontFamily)
-                state.createGeometry = true;
-            if (newProps.fontQuality !== currentProps.fontQuality)
-                state.createGeometry = true;
-            if (newProps.fontStyle !== currentProps.fontStyle)
-                state.createGeometry = true;
-            if (newProps.fontVariant !== currentProps.fontVariant)
-                state.createGeometry = true;
-            if (newProps.fontWeight !== currentProps.fontWeight)
-                state.createGeometry = true;
-        }, geometryUtils: text_1.Text.Utils }), materialId);
-}
-exports.ComplexTextVisual = ComplexTextVisual;
-// direct-volume
-exports.ComplexDirectVolumeParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params_1.StructureDirectVolumeParams), params_1.StructureParams);
-function ComplexDirectVolumeVisual(builder, materialId) {
-    return ComplexVisual((0, tslib_1.__assign)((0, tslib_1.__assign)({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {
-            builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure);
-            if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
-                state.createGeometry = true;
-        }, geometryUtils: direct_volume_1.DirectVolume.Utils }), materialId);
-}
-exports.ComplexDirectVolumeVisual = ComplexDirectVolumeVisual;
-// texture-mesh
-exports.ComplexTextureMeshParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params_1.StructureTextureMeshParams), params_1.StructureParams);
-function ComplexTextureMeshVisual(builder, materialId) {
-    return ComplexVisual((0, tslib_1.__assign)((0, tslib_1.__assign)({}, builder), { setUpdateState: function (state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure) {
-            builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme, newStructure, currentStructure);
-            if (!size_1.SizeTheme.areEqual(newTheme.size, currentTheme.size))
-                state.createGeometry = true;
-        }, geometryUtils: texture_mesh_1.TextureMesh.Utils }), materialId);
-}
-exports.ComplexTextureMeshVisual = ComplexTextureMeshVisual;
-//# sourceMappingURL=complex-visual.js.map

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

@@ -1,37 +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.StructureTextureMeshParams = exports.StructureDirectVolumeParams = exports.StructureTextParams = exports.StructureLinesParams = exports.StructurePointsParams = exports.StructureCylindersParams = exports.StructureSpheresParams = exports.StructureMeshParams = exports.StructureParams = exports.getUnitKindsParam = void 0;
-var tslib_1 = require("tslib");
-var direct_volume_1 = require("../../mol-geo/geometry/direct-volume/direct-volume");
-var lines_1 = require("../../mol-geo/geometry/lines/lines");
-var mesh_1 = require("../../mol-geo/geometry/mesh/mesh");
-var points_1 = require("../../mol-geo/geometry/points/points");
-var spheres_1 = require("../../mol-geo/geometry/spheres/spheres");
-var cylinders_1 = require("../../mol-geo/geometry/cylinders/cylinders");
-var text_1 = require("../../mol-geo/geometry/text/text");
-var texture_mesh_1 = require("../../mol-geo/geometry/texture-mesh/texture-mesh");
-var param_definition_1 = require("../../mol-util/param-definition");
-var common_1 = require("./visual/util/common");
-function getUnitKindsParam(defaultValue) {
-    return param_definition_1.ParamDefinition.MultiSelect(defaultValue, common_1.UnitKindOptions, { description: 'For which kinds of units/chains to show the representation visuals.' });
-}
-exports.getUnitKindsParam = getUnitKindsParam;
-exports.StructureParams = {
-    unitKinds: getUnitKindsParam(['atomic', 'spheres']),
-    includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }),
-};
-exports.StructureMeshParams = (0, tslib_1.__assign)({}, mesh_1.Mesh.Params);
-exports.StructureSpheresParams = (0, tslib_1.__assign)({}, spheres_1.Spheres.Params);
-exports.StructureCylindersParams = (0, tslib_1.__assign)({}, cylinders_1.Cylinders.Params);
-exports.StructurePointsParams = (0, tslib_1.__assign)({}, points_1.Points.Params);
-exports.StructureLinesParams = (0, tslib_1.__assign)({}, lines_1.Lines.Params);
-exports.StructureTextParams = (0, tslib_1.__assign)({}, text_1.Text.Params);
-exports.StructureDirectVolumeParams = (0, tslib_1.__assign)({}, direct_volume_1.DirectVolume.Params);
-exports.StructureTextureMeshParams = (0, tslib_1.__assign)({}, texture_mesh_1.TextureMesh.Params);
-//# sourceMappingURL=params.js.map

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

@@ -1,59 +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.StructureRepresentationRegistry = void 0;
-var tslib_1 = require("tslib");
-var object_1 = require("../../mol-util/object");
-var representation_1 = require("../representation");
-var ball_and_stick_1 = require("./representation/ball-and-stick");
-var carbohydrate_1 = require("./representation/carbohydrate");
-var cartoon_1 = require("./representation/cartoon");
-var ellipsoid_1 = require("./representation/ellipsoid");
-var gaussian_surface_1 = require("./representation/gaussian-surface");
-var label_1 = require("./representation/label");
-var molecular_surface_1 = require("./representation/molecular-surface");
-var orientation_1 = require("./representation/orientation");
-var point_1 = require("./representation/point");
-var putty_1 = require("./representation/putty");
-var spacefill_1 = require("./representation/spacefill");
-var line_1 = require("./representation/line");
-var gaussian_volume_1 = require("./representation/gaussian-volume");
-var backbone_1 = require("./representation/backbone");
-var StructureRepresentationRegistry = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(StructureRepresentationRegistry, _super);
-    function StructureRepresentationRegistry() {
-        var _this = _super.call(this) || this;
-        (0, object_1.objectForEach)(StructureRepresentationRegistry.BuiltIn, function (p, k) {
-            if (p.name !== k)
-                throw new Error("Fix BuiltInStructureRepresentations to have matching names. ".concat(p.name, " ").concat(k));
-            _this.add(p);
-        });
-        return _this;
-    }
-    return StructureRepresentationRegistry;
-}(representation_1.RepresentationRegistry));
-exports.StructureRepresentationRegistry = StructureRepresentationRegistry;
-(function (StructureRepresentationRegistry) {
-    StructureRepresentationRegistry.BuiltIn = {
-        'cartoon': cartoon_1.CartoonRepresentationProvider,
-        'backbone': backbone_1.BackboneRepresentationProvider,
-        'ball-and-stick': ball_and_stick_1.BallAndStickRepresentationProvider,
-        'carbohydrate': carbohydrate_1.CarbohydrateRepresentationProvider,
-        'ellipsoid': ellipsoid_1.EllipsoidRepresentationProvider,
-        'gaussian-surface': gaussian_surface_1.GaussianSurfaceRepresentationProvider,
-        'gaussian-volume': gaussian_volume_1.GaussianVolumeRepresentationProvider,
-        'label': label_1.LabelRepresentationProvider,
-        'line': line_1.LineRepresentationProvider,
-        'molecular-surface': molecular_surface_1.MolecularSurfaceRepresentationProvider,
-        'orientation': orientation_1.OrientationRepresentationProvider,
-        'point': point_1.PointRepresentationProvider,
-        'putty': putty_1.PuttyRepresentationProvider,
-        'spacefill': spacefill_1.SpacefillRepresentationProvider,
-    };
-})(StructureRepresentationRegistry = exports.StructureRepresentationRegistry || (exports.StructureRepresentationRegistry = {}));
-exports.StructureRepresentationRegistry = StructureRepresentationRegistry;
-//# sourceMappingURL=registry.js.map

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

@@ -1,52 +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.BackboneRepresentationProvider = exports.BackboneRepresentation = exports.getBackboneParams = exports.BackboneParams = void 0;
-var tslib_1 = require("tslib");
-var polymer_backbone_cylinder_1 = require("../visual/polymer-backbone-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 polymer_backbone_sphere_1 = require("../visual/polymer-backbone-sphere");
-var polymer_gap_cylinder_1 = require("../visual/polymer-gap-cylinder");
-var base_1 = require("../../../mol-geo/geometry/base");
-var BackboneVisuals = {
-    'polymer-backbone-cylinder': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer backbone cylinder', ctx, getParams, polymer_backbone_cylinder_1.PolymerBackboneCylinderVisual); },
-    'polymer-backbone-sphere': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer backbone sphere', ctx, getParams, polymer_backbone_sphere_1.PolymerBackboneSphereVisual); },
-    'polymer-gap': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer gap cylinder', ctx, getParams, polymer_gap_cylinder_1.PolymerGapVisual); },
-};
-exports.BackboneParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, polymer_backbone_sphere_1.PolymerBackboneSphereParams), polymer_backbone_cylinder_1.PolymerBackboneCylinderParams), polymer_gap_cylinder_1.PolymerGapParams), { sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(1, { min: 0.1, max: 3, step: 0.1 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-backbone-cylinder', 'polymer-backbone-sphere', 'polymer-gap'], param_definition_1.ParamDefinition.objectToOptions(BackboneVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
-function getBackboneParams(ctx, structure) {
-    var params = param_definition_1.ParamDefinition.clone(exports.BackboneParams);
-    var hasGaps = false;
-    structure.units.forEach(function (u) {
-        if (!hasGaps && u.gapElements.length)
-            hasGaps = true;
-    });
-    params.visuals.defaultValue = ['polymer-backbone-cylinder', 'polymer-backbone-sphere'];
-    if (hasGaps)
-        params.visuals.defaultValue.push('polymer-gap');
-    return params;
-}
-exports.getBackboneParams = getBackboneParams;
-function BackboneRepresentation(ctx, getParams) {
-    return representation_2.Representation.createMulti('Backbone', ctx, getParams, representation_1.StructureRepresentationStateBuilder, BackboneVisuals);
-}
-exports.BackboneRepresentation = BackboneRepresentation;
-exports.BackboneRepresentationProvider = (0, representation_1.StructureRepresentationProvider)({
-    name: 'backbone',
-    label: 'Backbone',
-    description: 'Displays polymer backbone with cylinders and spheres.',
-    factory: BackboneRepresentation,
-    getParams: getBackboneParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.BackboneParams),
-    defaultColorTheme: { name: 'chain-id' },
-    defaultSizeTheme: { name: 'uniform' },
-    isApplicable: function (structure) { return structure.polymerResidueCount > 0; },
-});
-//# sourceMappingURL=backbone.js.map

package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.js

@@ -1,51 +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.BallAndStickRepresentationProvider = exports.BallAndStickRepresentation = exports.getBallAndStickParams = exports.BallAndStickParams = void 0;
-var tslib_1 = require("tslib");
-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 element_sphere_1 = require("../visual/element-sphere");
-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 base_1 = require("../../../mol-geo/geometry/base");
-var BallAndStickVisuals = {
-    'element-sphere': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Element sphere', ctx, getParams, element_sphere_1.ElementSphereVisual); },
-    'intra-bond': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Intra-unit bond cylinder', ctx, getParams, bond_intra_unit_cylinder_1.IntraUnitBondCylinderVisual); },
-    'inter-bond': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Inter-unit bond cylinder', ctx, getParams, bond_inter_unit_cylinder_1.InterUnitBondCylinderVisual); },
-};
-exports.BallAndStickParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, element_sphere_1.ElementSphereParams), { traceOnly: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) }), bond_intra_unit_cylinder_1.IntraUnitBondCylinderParams), bond_inter_unit_cylinder_1.InterUnitBondCylinderParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), sizeFactor: param_definition_1.ParamDefinition.Numeric(0.15, { min: 0.01, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(2 / 3, { min: 0.01, max: 3, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['element-sphere', 'intra-bond', 'inter-bond'], param_definition_1.ParamDefinition.objectToOptions(BallAndStickVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
-function getBallAndStickParams(ctx, structure) {
-    return param_definition_1.ParamDefinition.clone(exports.BallAndStickParams);
-}
-exports.getBallAndStickParams = getBallAndStickParams;
-function BallAndStickRepresentation(ctx, getParams) {
-    return representation_2.Representation.createMulti('Ball & Stick', ctx, getParams, representation_1.StructureRepresentationStateBuilder, BallAndStickVisuals);
-}
-exports.BallAndStickRepresentation = BallAndStickRepresentation;
-exports.BallAndStickRepresentationProvider = (0, representation_1.StructureRepresentationProvider)({
-    name: 'ball-and-stick',
-    label: 'Ball & Stick',
-    description: 'Displays atoms as spheres and bonds as cylinders.',
-    factory: BallAndStickRepresentation,
-    getParams: getBallAndStickParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.BallAndStickParams),
-    defaultColorTheme: { name: 'element-symbol' },
-    defaultSizeTheme: { name: 'physical' },
-    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=ball-and-stick.js.map

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

@@ -1,46 +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.CarbohydrateRepresentationProvider = exports.CarbohydrateRepresentation = exports.getCarbohydrateParams = exports.CarbohydrateParams = void 0;
-var tslib_1 = require("tslib");
-var base_1 = require("../../../mol-geo/geometry/base");
-var structure_1 = require("../../../mol-model/structure");
-var representation_1 = require("../../../mol-repr/representation");
-var param_definition_1 = require("../../../mol-util/param-definition");
-var complex_representation_1 = require("../complex-representation");
-var representation_2 = require("../representation");
-var carbohydrate_link_cylinder_1 = require("../visual/carbohydrate-link-cylinder");
-var carbohydrate_symbol_mesh_1 = require("../visual/carbohydrate-symbol-mesh");
-var carbohydrate_terminal_link_cylinder_1 = require("../visual/carbohydrate-terminal-link-cylinder");
-var CarbohydrateVisuals = {
-    'carbohydrate-symbol': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Carbohydrate symbol mesh', ctx, getParams, carbohydrate_symbol_mesh_1.CarbohydrateSymbolVisual); },
-    'carbohydrate-link': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Carbohydrate link cylinder', ctx, getParams, carbohydrate_link_cylinder_1.CarbohydrateLinkVisual); },
-    'carbohydrate-terminal-link': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Carbohydrate terminal link cylinder', ctx, getParams, carbohydrate_terminal_link_cylinder_1.CarbohydrateTerminalLinkVisual); },
-};
-exports.CarbohydrateParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, carbohydrate_symbol_mesh_1.CarbohydrateSymbolParams), carbohydrate_link_cylinder_1.CarbohydrateLinkParams), carbohydrate_terminal_link_cylinder_1.CarbohydrateTerminalLinkParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['carbohydrate-symbol', 'carbohydrate-link', 'carbohydrate-terminal-link'], param_definition_1.ParamDefinition.objectToOptions(CarbohydrateVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
-function getCarbohydrateParams(ctx, structure) {
-    return param_definition_1.ParamDefinition.clone(exports.CarbohydrateParams);
-}
-exports.getCarbohydrateParams = getCarbohydrateParams;
-function CarbohydrateRepresentation(ctx, getParams) {
-    return representation_1.Representation.createMulti('Carbohydrate', ctx, getParams, representation_2.StructureRepresentationStateBuilder, CarbohydrateVisuals);
-}
-exports.CarbohydrateRepresentation = CarbohydrateRepresentation;
-exports.CarbohydrateRepresentationProvider = (0, representation_2.StructureRepresentationProvider)({
-    name: 'carbohydrate',
-    label: 'Carbohydrate',
-    description: 'Displays carbohydrate symbols (3D SNFG).',
-    factory: CarbohydrateRepresentation,
-    getParams: getCarbohydrateParams,
-    defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.CarbohydrateParams),
-    defaultColorTheme: { name: 'carbohydrate-symbol' },
-    defaultSizeTheme: { name: 'uniform' },
-    isApplicable: function (structure) {
-        return structure.models.some(function (m) { return structure_1.Model.hasCarbohydrate(m); });
-    }
-});
-//# sourceMappingURL=carbohydrate.js.map