molstar 4.2.0 → 4.4.0

package/lib/commonjs/mol-plugin-state/helpers/structure-component.js

@@ -5,7 +5,9 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.updateStructureComponent = exports.createStructureComponent = exports.StructureComponentParams = exports.StaticStructureComponentTypes = void 0;
+exports.StructureComponentParams = exports.StaticStructureComponentTypes = void 0;
+exports.createStructureComponent = createStructureComponent;
+exports.updateStructureComponent = updateStructureComponent;
 const param_definition_1 = require("../../mol-util/param-definition");
 const builder_1 = require("../../mol-script/language/builder");
 const structure_1 = require("../../mol-model/structure");
@@ -116,7 +118,6 @@ function createStructureComponent(a, params, cache) {
     const props = { label: `${params.label || label || 'Component'}`, description: structure_1.Structure.elementDescription(component) };
     return new objects_1.PluginStateObject.Molecule.Structure(component, props);
 }
-exports.createStructureComponent = createStructureComponent;
 function updateStructureComponent(a, b, oldParams, newParams, cache) {
     if (oldParams.type.name !== newParams.type.name)
         return mol_state_1.StateTransformer.UpdateResult.Recreate;
@@ -181,4 +182,3 @@ function updateStructureComponent(a, b, oldParams, newParams, cache) {
     }
     return updated ? mol_state_1.StateTransformer.UpdateResult.Updated : mol_state_1.StateTransformer.UpdateResult.Unchanged;
 }
-exports.updateStructureComponent = updateStructureComponent;

package/lib/commonjs/mol-plugin-state/helpers/structure-emissive.js

@@ -6,7 +6,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.clearStructureEmissive = exports.setStructureEmissive = void 0;
+exports.setStructureEmissive = setStructureEmissive;
+exports.clearStructureEmissive = clearStructureEmissive;
 const structure_1 = require("../../mol-model/structure");
 const transforms_1 = require("../transforms");
 const mol_state_1 = require("../../mol-state");
@@ -39,7 +40,6 @@ async function setStructureEmissive(plugin, components, value, lociGetter, types
         }
     });
 }
-exports.setStructureEmissive = setStructureEmissive;
 async function clearStructureEmissive(plugin, components, types) {
     await eachRepr(plugin, components, async (update, repr, emissiveCell) => {
         if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
@@ -49,7 +49,6 @@ async function clearStructureEmissive(plugin, components, types) {
         }
     });
 }
-exports.clearStructureEmissive = clearStructureEmissive;
 async function eachRepr(plugin, components, callback) {
     const state = plugin.state.data;
     const update = state.build();

package/lib/commonjs/mol-plugin-state/helpers/structure-overpaint.js

@@ -6,7 +6,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.clearStructureOverpaint = exports.setStructureOverpaint = void 0;
+exports.setStructureOverpaint = setStructureOverpaint;
+exports.clearStructureOverpaint = clearStructureOverpaint;
 const structure_1 = require("../../mol-model/structure");
 const transforms_1 = require("../../mol-plugin-state/transforms");
 const mol_state_1 = require("../../mol-state");
@@ -41,7 +42,6 @@ async function setStructureOverpaint(plugin, components, color, lociGetter, type
         }
     });
 }
-exports.setStructureOverpaint = setStructureOverpaint;
 async function clearStructureOverpaint(plugin, components, types) {
     await eachRepr(plugin, components, async (update, repr, overpaintCell) => {
         if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
@@ -51,7 +51,6 @@ async function clearStructureOverpaint(plugin, components, types) {
         }
     });
 }
-exports.clearStructureOverpaint = clearStructureOverpaint;
 async function eachRepr(plugin, components, callback) {
     const state = plugin.state.data;
     const update = state.build();

package/lib/commonjs/mol-plugin-state/helpers/structure-representation-params.js

@@ -5,7 +5,10 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createStructureSizeThemeParams = exports.createStructureColorThemeParams = exports.getStructureThemeTypes = exports.createStructureRepresentationParams = void 0;
+exports.createStructureRepresentationParams = createStructureRepresentationParams;
+exports.getStructureThemeTypes = getStructureThemeTypes;
+exports.createStructureColorThemeParams = createStructureColorThemeParams;
+exports.createStructureSizeThemeParams = createStructureSizeThemeParams;
 const structure_1 = require("../../mol-model/structure");
 const param_definition_1 = require("../../mol-util/param-definition");
 function createStructureRepresentationParams(ctx, structure, props = {}) {
@@ -14,14 +17,12 @@ function createStructureRepresentationParams(ctx, structure, props = {}) {
         return createParamsByName(ctx, structure || structure_1.Structure.Empty, props);
     return createParamsProvider(ctx, structure || structure_1.Structure.Empty, props);
 }
-exports.createStructureRepresentationParams = createStructureRepresentationParams;
 function getStructureThemeTypes(ctx, structure) {
     const { themes: themeCtx } = ctx.representation.structure;
     if (!structure)
         return themeCtx.colorThemeRegistry.types;
     return themeCtx.colorThemeRegistry.getApplicableTypes({ structure });
 }
-exports.getStructureThemeTypes = getStructureThemeTypes;
 function createStructureColorThemeParams(ctx, structure, typeName, themeName, params) {
     const { registry, themes } = ctx.representation.structure;
     const repr = registry.get(typeName || registry.default.name);
@@ -31,7 +32,6 @@ function createStructureColorThemeParams(ctx, structure, typeName, themeName, pa
         Object.assign(colorDefaultParams, repr.defaultColorTheme.props);
     return { name: color.name, params: Object.assign(colorDefaultParams, params) };
 }
-exports.createStructureColorThemeParams = createStructureColorThemeParams;
 function createStructureSizeThemeParams(ctx, structure, typeName, themeName, params) {
     const { registry, themes } = ctx.representation.structure;
     const repr = registry.get(typeName || registry.default.name);
@@ -41,7 +41,6 @@ function createStructureSizeThemeParams(ctx, structure, typeName, themeName, par
         Object.assign(sizeDefaultParams, repr.defaultSizeTheme.props);
     return { name: size.name, params: Object.assign(sizeDefaultParams, params) };
 }
-exports.createStructureSizeThemeParams = createStructureSizeThemeParams;
 function createParamsByName(ctx, structure, props) {
     const typeProvider = (props.type && ctx.representation.structure.registry.get(props.type))
         || ctx.representation.structure.registry.default.provider;

package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js

@@ -6,7 +6,15 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.StructureSelectionQueryRegistry = exports.StructureSelectionQueries = exports.applyBuiltInSelection = exports.getPolymerAndBranchedEntityQueries = exports.getNonStandardResidueQueries = exports.getElementQueries = exports.EntityDescriptionQuery = exports.ElementSymbolQuery = exports.ResidueQuery = exports.StructureSelectionQuery = exports.StructureSelectionCategory = void 0;
+exports.StructureSelectionQueryRegistry = exports.StructureSelectionQueries = exports.StructureSelectionCategory = void 0;
+exports.StructureSelectionQuery = StructureSelectionQuery;
+exports.ResidueQuery = ResidueQuery;
+exports.ElementSymbolQuery = ElementSymbolQuery;
+exports.EntityDescriptionQuery = EntityDescriptionQuery;
+exports.getElementQueries = getElementQueries;
+exports.getNonStandardResidueQueries = getNonStandardResidueQueries;
+exports.getPolymerAndBranchedEntityQueries = getPolymerAndBranchedEntityQueries;
+exports.applyBuiltInSelection = applyBuiltInSelection;
 const structure_1 = require("../../mol-model/structure");
 const types_1 = require("../../mol-model/structure/model/types");
 const builder_1 = require("../../mol-script/language/builder");
@@ -58,7 +66,6 @@ function StructureSelectionQuery(label, expression, props = {}) {
         }
     };
 }
-exports.StructureSelectionQuery = StructureSelectionQuery;
 const all = StructureSelectionQuery('All', builder_1.MolScriptBuilder.struct.generator.all(), { category: '', priority: 1000 });
 const current = StructureSelectionQuery('Current Selection', builder_1.MolScriptBuilder.internal.generator.current(), { category: '', referencesCurrent: true });
 const polymer = StructureSelectionQuery('Polymer', builder_1.MolScriptBuilder.struct.modifier.union([
@@ -560,7 +567,6 @@ function ResidueQuery([names, label], category, priority = 0) {
         })
     ]), { category, priority, description });
 }
-exports.ResidueQuery = ResidueQuery;
 function ElementSymbolQuery([names, label], category, priority) {
     const description = `${label} (${names.join(', ')})`;
     return StructureSelectionQuery(description, builder_1.MolScriptBuilder.struct.modifier.union([
@@ -569,7 +575,6 @@ function ElementSymbolQuery([names, label], category, priority) {
         })
     ]), { category, priority, description });
 }
-exports.ElementSymbolQuery = ElementSymbolQuery;
 function EntityDescriptionQuery([names, label], category, priority) {
     const description = `${label}`;
     return StructureSelectionQuery(`${label}`, builder_1.MolScriptBuilder.struct.modifier.union([
@@ -578,7 +583,6 @@ function EntityDescriptionQuery([names, label], category, priority) {
         })
     ]), { category, priority, description });
 }
-exports.EntityDescriptionQuery = EntityDescriptionQuery;
 const StandardResidues = set_1.SetUtils.unionMany(types_1.AminoAcidNamesL, types_1.RnaBaseNames, types_1.DnaBaseNames, types_1.WaterNames);
 function getElementQueries(structures) {
     const uniqueElements = new Set();
@@ -592,7 +596,6 @@ function getElementQueries(structures) {
     });
     return queries;
 }
-exports.getElementQueries = getElementQueries;
 function getNonStandardResidueQueries(structures) {
     const residueLabels = new Map();
     const uniqueResidues = new Set();
@@ -613,7 +616,6 @@ function getNonStandardResidueQueries(structures) {
     });
     return queries;
 }
-exports.getNonStandardResidueQueries = getNonStandardResidueQueries;
 function getPolymerAndBranchedEntityQueries(structures) {
     const uniqueEntities = new Map();
     const l = structure_1.StructureElement.Location.create();
@@ -635,11 +637,9 @@ function getPolymerAndBranchedEntityQueries(structures) {
     });
     return queries;
 }
-exports.getPolymerAndBranchedEntityQueries = getPolymerAndBranchedEntityQueries;
 function applyBuiltInSelection(to, query, customTag) {
     return to.apply(transforms_1.StateTransforms.Model.StructureSelectionFromExpression, { expression: exports.StructureSelectionQueries[query].expression, label: exports.StructureSelectionQueries[query].label }, { tags: customTag ? [query, customTag] : [query] });
 }
-exports.applyBuiltInSelection = applyBuiltInSelection;
 exports.StructureSelectionQueries = {
     all,
     current,

package/lib/commonjs/mol-plugin-state/helpers/structure-substance.js

@@ -6,7 +6,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.clearStructureSubstance = exports.setStructureSubstance = void 0;
+exports.setStructureSubstance = setStructureSubstance;
+exports.clearStructureSubstance = clearStructureSubstance;
 const structure_1 = require("../../mol-model/structure");
 const transforms_1 = require("../../mol-plugin-state/transforms");
 const mol_state_1 = require("../../mol-state");
@@ -41,7 +42,6 @@ async function setStructureSubstance(plugin, components, material, lociGetter, t
         }
     });
 }
-exports.setStructureSubstance = setStructureSubstance;
 async function clearStructureSubstance(plugin, components, types) {
     await eachRepr(plugin, components, async (update, repr, substanceCell) => {
         if (types && types.length > 0 && !types.includes(repr.params.values.type.name))
@@ -51,7 +51,6 @@ async function clearStructureSubstance(plugin, components, types) {
         }
     });
 }
-exports.clearStructureSubstance = clearStructureSubstance;
 async function eachRepr(plugin, components, callback) {
     const state = plugin.state.data;
     const update = state.build();

package/lib/commonjs/mol-plugin-state/helpers/structure-transparency.js

@@ -6,7 +6,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.clearStructureTransparency = exports.setStructureTransparency = void 0;
+exports.setStructureTransparency = setStructureTransparency;
+exports.clearStructureTransparency = clearStructureTransparency;
 const structure_1 = require("../../mol-model/structure");
 const transforms_1 = require("../../mol-plugin-state/transforms");
 const mol_state_1 = require("../../mol-state");
@@ -39,7 +40,6 @@ async function setStructureTransparency(plugin, components, value, lociGetter, t
         }
     });
 }
-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))
@@ -49,7 +49,6 @@ async function clearStructureTransparency(plugin, components, types) {
         }
     });
 }
-exports.clearStructureTransparency = clearStructureTransparency;
 async function eachRepr(plugin, components, callback) {
     const state = plugin.state.data;
     const update = state.build();

package/lib/commonjs/mol-plugin-state/helpers/volume-representation-params.js

@@ -5,7 +5,10 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createVolumeSizeThemeParams = exports.createVolumeColorThemeParams = exports.getVolumeThemeTypes = exports.createVolumeRepresentationParams = void 0;
+exports.createVolumeRepresentationParams = createVolumeRepresentationParams;
+exports.getVolumeThemeTypes = getVolumeThemeTypes;
+exports.createVolumeColorThemeParams = createVolumeColorThemeParams;
+exports.createVolumeSizeThemeParams = createVolumeSizeThemeParams;
 const volume_1 = require("../../mol-model/volume");
 const param_definition_1 = require("../../mol-util/param-definition");
 function createVolumeRepresentationParams(ctx, volume, props = {}) {
@@ -14,14 +17,12 @@ function createVolumeRepresentationParams(ctx, volume, props = {}) {
         return createParamsByName(ctx, volume || volume_1.Volume.One, props);
     return createParamsProvider(ctx, volume || volume_1.Volume.One, props);
 }
-exports.createVolumeRepresentationParams = createVolumeRepresentationParams;
 function getVolumeThemeTypes(ctx, volume) {
     const { themes: themeCtx } = ctx.representation.volume;
     if (!volume)
         return themeCtx.colorThemeRegistry.types;
     return themeCtx.colorThemeRegistry.getApplicableTypes({ volume });
 }
-exports.getVolumeThemeTypes = getVolumeThemeTypes;
 function createVolumeColorThemeParams(ctx, volume, typeName, themeName, params) {
     const { registry, themes } = ctx.representation.volume;
     const repr = registry.get(typeName || registry.default.name);
@@ -31,7 +32,6 @@ function createVolumeColorThemeParams(ctx, volume, typeName, themeName, params)
         Object.assign(colorDefaultParams, repr.defaultColorTheme.props);
     return { name: color.name, params: Object.assign(colorDefaultParams, params) };
 }
-exports.createVolumeColorThemeParams = createVolumeColorThemeParams;
 function createVolumeSizeThemeParams(ctx, volume, typeName, themeName, params) {
     const { registry, themes } = ctx.representation.volume;
     const repr = registry.get(typeName || registry.default.name);
@@ -41,7 +41,6 @@ function createVolumeSizeThemeParams(ctx, volume, typeName, themeName, params) {
         Object.assign(sizeDefaultParams, repr.defaultSizeTheme.props);
     return { name: size.name, params: Object.assign(sizeDefaultParams, params) };
 }
-exports.createVolumeSizeThemeParams = createVolumeSizeThemeParams;
 function createParamsByName(ctx, volume, props) {
     const typeProvider = (props.type && ctx.representation.volume.registry.get(props.type))
         || ctx.representation.volume.registry.default.provider;

package/lib/commonjs/mol-plugin-state/manager/focus-camera/focus-first-residue.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getPcaTransform = exports.pcaFocus = void 0;
+exports.pcaFocus = pcaFocus;
+exports.getPcaTransform = getPcaTransform;
 const vec3_1 = require("../../..//mol-math/linear-algebra/3d/vec3");
 const principal_axes_1 = require("../../../mol-math/linear-algebra/matrix/principal-axes");
 const camera_1 = require("../../../mol-canvas3d/camera");
@@ -97,7 +98,6 @@ function pcaFocus(plugin, radius, options) {
     }
     return plugin.canvas3d.camera.getFocus(origin, radius, up, dir, camera_1.Camera.createDefaultSnapshot());
 }
-exports.pcaFocus = pcaFocus;
 function getPcaTransform(group) {
     var _a;
     const structure = (_a = group[0].cell.obj) === null || _a === void 0 ? void 0 : _a.data;
@@ -119,4 +119,3 @@ function getPcaTransform(group) {
     structure.currentPropertyData._pcaTransformData = pcaTransfromData;
     return pcaTransfromData;
 }
-exports.getPcaTransform = getPcaTransform;

package/lib/commonjs/mol-plugin-state/manager/focus-camera/orient-axes.js

@@ -5,7 +5,10 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.changeCameraRotation = exports.layingTransform = exports.structureLayingTransform = exports.ROTATION_MATRICES = void 0;
+exports.ROTATION_MATRICES = void 0;
+exports.structureLayingTransform = structureLayingTransform;
+exports.layingTransform = layingTransform;
+exports.changeCameraRotation = changeCameraRotation;
 const linear_algebra_1 = require("../../../mol-math/linear-algebra");
 const principal_axes_1 = require("../../../mol-math/linear-algebra/matrix/principal-axes");
 const structure_1 = require("../../../mol-model/structure");
@@ -38,7 +41,6 @@ function structureLayingTransform(structures, referenceRotation) {
     const coords = smartSelectCoords(structures, MIN_ATOMS_FOR_PCA);
     return layingTransform(coords, referenceRotation);
 }
-exports.structureLayingTransform = structureLayingTransform;
 /** Return transformation which will align the PCA axes of a sequence
  * of points to the Cartesian axes x, y, z
  * (transformed = rotation * (coords - origin)).
@@ -62,7 +64,6 @@ function layingTransform(coords, referenceRotation) {
     linear_algebra_1.Mat3.mul(R, flip, R);
     return { rotation: R, origin: normAxes.origin };
 }
-exports.layingTransform = layingTransform;
 /** Try these selection strategies until having at least `minAtoms` atoms:
  * 1. only trace atoms (e.g. C-alpha and O3')
  * 2. all non-hydrogen atoms with exception of water (HOH)
@@ -213,4 +214,3 @@ function changeCameraRotation(old, rotation) {
     const newPosition = linear_algebra_1.Vec3.add((0, linear_algebra_1.Vec3)(), old.target, relPosition);
     return { ...old, position: newPosition, up: newUp };
 }
-exports.changeCameraRotation = changeCameraRotation;

package/lib/commonjs/mol-plugin-state/manager/structure/hierarchy-state.js

@@ -5,7 +5,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.StructureHierarchy = exports.buildStructureHierarchy = void 0;
+exports.buildStructureHierarchy = buildStructureHierarchy;
+exports.StructureHierarchy = StructureHierarchy;
 const objects_1 = require("../../objects");
 const mol_state_1 = require("../../../mol-state");
 const transforms_1 = require("../../transforms");
@@ -17,11 +18,9 @@ function buildStructureHierarchy(state, previous) {
         previous.refs.forEach(isRemoved, build);
     return { hierarchy: build.hierarchy, added: build.added, changed: build.changed };
 }
-exports.buildStructureHierarchy = buildStructureHierarchy;
 function StructureHierarchy() {
     return { trajectories: [], models: [], structures: [], refs: new Map() };
 }
-exports.StructureHierarchy = StructureHierarchy;
 function TrajectoryRef(cell) {
     return { kind: 'trajectory', cell, version: cell.transform.version, models: [] };
 }

package/lib/commonjs/mol-plugin-state/manager/structure/hierarchy.d.ts

@@ -27,9 +27,9 @@ export declare class StructureHierarchyManager extends PluginComponent {
     get seletionSet(): Set<string>;
     get current(): StructureHierarchy;
     get selection(): {
-        trajectories: readonly TrajectoryRef[];
-        models: readonly ModelRef[];
-        structures: readonly StructureRef[];
+        trajectories: ReadonlyArray<TrajectoryRef>;
+        models: ReadonlyArray<ModelRef>;
+        structures: ReadonlyArray<StructureRef>;
     };
     getStructuresWithSelection(): StructureRef[];
     findStructure(structure: Structure | undefined): StructureRef | undefined;

package/lib/commonjs/mol-plugin-state/manager/structure/measurement.d.ts

@@ -168,6 +168,7 @@ declare class StructureMeasurementManager extends StatefulPluginComponent<Struct
             doubleSided: boolean;
             flipSided: boolean;
             flatShaded: boolean;
+            celShaded: boolean;
             xrayShaded: boolean | "inverted";
             transparentBackfaces: "on" | "off" | "opaque";
             bumpFrequency: number;
@@ -237,6 +238,7 @@ declare class StructureMeasurementManager extends StatefulPluginComponent<Struct
             doubleSided: boolean;
             flipSided: boolean;
             flatShaded: boolean;
+            celShaded: boolean;
             xrayShaded: boolean | "inverted";
             transparentBackfaces: "on" | "off" | "opaque";
             bumpFrequency: number;
@@ -324,6 +326,7 @@ declare class StructureMeasurementManager extends StatefulPluginComponent<Struct
             flipSided: boolean;
             flatShaded: boolean;
             ignoreLight: boolean;
+            celShaded: boolean;
             xrayShaded: boolean | "inverted";
             transparentBackfaces: "on" | "off" | "opaque";
             bumpFrequency: number;
@@ -365,6 +368,7 @@ declare class StructureMeasurementManager extends StatefulPluginComponent<Struct
             flipSided: boolean;
             flatShaded: boolean;
             ignoreLight: boolean;
+            celShaded: boolean;
             xrayShaded: boolean | "inverted";
             transparentBackfaces: "on" | "off" | "opaque";
             bumpFrequency: number;

package/lib/commonjs/mol-plugin-state/manager/volume/hierarchy-state.js

@@ -5,7 +5,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.VolumeHierarchy = exports.buildVolumeHierarchy = void 0;
+exports.buildVolumeHierarchy = buildVolumeHierarchy;
+exports.VolumeHierarchy = VolumeHierarchy;
 const objects_1 = require("../../objects");
 const mol_state_1 = require("../../../mol-state");
 function buildVolumeHierarchy(state, previous) {
@@ -15,11 +16,9 @@ function buildVolumeHierarchy(state, previous) {
         previous.refs.forEach(isRemoved, build);
     return { hierarchy: build.hierarchy, added: build.added, changed: build.changed };
 }
-exports.buildVolumeHierarchy = buildVolumeHierarchy;
 function VolumeHierarchy() {
     return { volumes: [], lazyVolumes: [], refs: new Map() };
 }
-exports.VolumeHierarchy = VolumeHierarchy;
 function VolumeRef(cell) {
     return { kind: 'volume', cell, version: cell.transform.version, representations: [] };
 }