molstar
Version:
A comprehensive macromolecular library.
507 lines (506 loc) • 27.4 kB
JavaScript
"use strict";
/**
* Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.StructureComponentManager = void 0;
const base_1 = require("../../../mol-geo/geometry/base");
const interactions_1 = require("../../../mol-model-props/computed/interactions");
const structure_1 = require("../../../mol-model/structure");
const structure_set_1 = require("../../../mol-model/structure/query/utils/structure-set");
const state_1 = require("../../../mol-plugin/behavior/static/state");
const mol_task_1 = require("../../../mol-task");
const mol_util_1 = require("../../../mol-util");
const names_1 = require("../../../mol-util/color/names");
const object_1 = require("../../../mol-util/object");
const param_definition_1 = require("../../../mol-util/param-definition");
const component_1 = require("../../component");
const structure_overpaint_1 = require("../../helpers/structure-overpaint");
const structure_representation_params_1 = require("../../helpers/structure-representation-params");
const structure_selection_query_1 = require("../../helpers/structure-selection-query");
const representation_1 = require("../../transforms/representation");
const clipping_1 = require("../../../mol-theme/clipping");
const structure_clipping_1 = require("../../helpers/structure-clipping");
const structure_transparency_1 = require("../../helpers/structure-transparency");
const structure_focus_representation_1 = require("../../../mol-plugin/behavior/dynamic/selection/structure-focus-representation");
const structure_substance_1 = require("../../helpers/structure-substance");
const material_1 = require("../../../mol-util/material");
const clip_1 = require("../../../mol-util/clip");
const structure_emissive_1 = require("../../helpers/structure-emissive");
class StructureComponentManager extends component_1.StatefulPluginComponent {
get currentStructures() {
return this.plugin.managers.structure.hierarchy.selection.structures;
}
get pivotStructure() {
return this.currentStructures[0];
}
// To be used only from PluginState.setSnapshot
_setSnapshotState(options) {
this.updateState({ options });
this.events.optionsUpdated.next(void 0);
}
async setOptions(options) {
const interactionChanged = options.interactions !== this.state.options.interactions;
this.updateState({ options });
this.events.optionsUpdated.next(void 0);
const update = this.dataState.build();
for (const s of this.currentStructures) {
for (const c of s.components) {
this.updateReprParams(update, c);
}
}
return this.plugin.dataTransaction(async () => {
await update.commit();
await this.plugin.state.updateBehavior(structure_focus_representation_1.StructureFocusRepresentation, p => {
p.ignoreHydrogens = options.hydrogens !== 'all';
p.ignoreHydrogensVariant = options.hydrogens === 'only-polar' ? 'non-polar' : 'all';
p.ignoreLight = options.ignoreLight;
p.material = options.materialStyle;
p.clip = options.clipObjects;
});
if (interactionChanged)
await this.updateInterationProps();
});
}
updateReprParams(update, component) {
const { hydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
const ignoreHydrogens = hydrogens !== 'all';
const ignoreHydrogensVariant = hydrogens === 'only-polar' ? 'non-polar' : 'all';
for (const r of component.representations) {
if (r.cell.transform.transformer !== representation_1.StructureRepresentation3D)
continue;
const params = r.cell.transform.params;
if (!!params.type.params.ignoreHydrogens !== ignoreHydrogens || params.type.params.ignoreHydrogensVariant !== ignoreHydrogensVariant || params.type.params.quality !== quality || params.type.params.ignoreLight !== ignoreLight || !(0, mol_util_1.shallowEqual)(params.type.params.material, material) || !param_definition_1.ParamDefinition.areEqual(clip_1.Clip.Params, params.type.params.clip, clip)) {
update.to(r.cell).update(old => {
old.type.params.ignoreHydrogens = ignoreHydrogens;
old.type.params.ignoreHydrogensVariant = ignoreHydrogensVariant;
old.type.params.quality = quality;
old.type.params.ignoreLight = ignoreLight;
old.type.params.material = material;
old.type.params.clip = clip;
});
}
}
}
async updateInterationProps() {
var _a, _b, _c;
for (const s of this.currentStructures) {
const interactionParams = interactions_1.InteractionsProvider.getParams((_a = s.cell.obj) === null || _a === void 0 ? void 0 : _a.data);
if (s.properties) {
const oldParams = (_b = s.properties.cell.transform.params) === null || _b === void 0 ? void 0 : _b.properties[interactions_1.InteractionsProvider.descriptor.name];
if (param_definition_1.ParamDefinition.areEqual(interactionParams, oldParams, this.state.options.interactions))
continue;
await this.dataState.build().to(s.properties.cell)
.update(old => {
old.properties[interactions_1.InteractionsProvider.descriptor.name] = this.state.options.interactions;
})
.commit();
}
else {
const pd = this.plugin.customStructureProperties.getParams((_c = s.cell.obj) === null || _c === void 0 ? void 0 : _c.data);
const params = param_definition_1.ParamDefinition.getDefaultValues(pd);
if (param_definition_1.ParamDefinition.areEqual(interactionParams, params.properties[interactions_1.InteractionsProvider.descriptor.name], this.state.options.interactions))
continue;
params.properties[interactions_1.InteractionsProvider.descriptor.name] = this.state.options.interactions;
await this.plugin.builders.structure.insertStructureProperties(s.cell, params);
}
}
}
applyPreset(structures, provider, params) {
return this.plugin.dataTransaction(async () => {
for (const s of structures) {
const preset = await this.plugin.builders.structure.representation.applyPreset(s.cell, provider, params);
await this.syncPreset(s, preset);
}
}, { canUndo: 'Preset' });
}
syncPreset(root, preset) {
if (!preset || !preset.components)
return this.clearComponents([root]);
const keptRefs = new Set();
(0, object_1.objectForEach)(preset.components, c => {
if (c)
keptRefs.add(c.ref);
});
if (preset.representations) {
(0, object_1.objectForEach)(preset.representations, r => {
if (r)
keptRefs.add(r.ref);
});
}
if (keptRefs.size === 0)
return this.clearComponents([root]);
let changed = false;
const update = this.dataState.build();
const sync = (r) => {
if (!keptRefs.has(r.cell.transform.ref)) {
changed = true;
update.delete(r.cell);
}
};
for (const c of root.components) {
sync(c);
for (const r of c.representations)
sync(r);
if (c.genericRepresentations) {
for (const r of c.genericRepresentations)
sync(r);
}
}
if (root.genericRepresentations) {
for (const r of root.genericRepresentations) {
sync(r);
}
}
if (changed)
return update.commit();
}
clear(structures) {
return this.clearComponents(structures);
}
selectThis(components) {
var _a;
const mng = this.plugin.managers.structure.selection;
mng.clear();
for (const c of components) {
const loci = structure_1.Structure.toSubStructureElementLoci(c.structure.cell.obj.data, (_a = c.cell.obj) === null || _a === void 0 ? void 0 : _a.data);
mng.fromLoci('set', loci);
}
}
canBeModified(ref) {
return this.plugin.builders.structure.isComponentTransform(ref.cell);
}
modifyByCurrentSelection(components, action) {
return this.plugin.runTask(mol_task_1.Task.create('Modify Component', async (taskCtx) => {
const b = this.dataState.build();
for (const c of components) {
if (!this.canBeModified(c))
continue;
const selection = this.plugin.managers.structure.selection.getStructure(c.structure.cell.obj.data);
if (!selection || selection.elementCount === 0)
continue;
this.modifyComponent(b, c, selection, action);
}
await this.dataState.updateTree(b, { canUndo: 'Modify Selection' }).runInContext(taskCtx);
}));
}
toggleVisibility(components, reprPivot) {
if (components.length === 0)
return;
if (!reprPivot) {
const isHidden = !components[0].cell.state.isHidden;
for (const c of components) {
(0, state_1.setSubtreeVisibility)(this.dataState, c.cell.transform.ref, isHidden);
}
}
else {
const index = components[0].representations.indexOf(reprPivot);
const isHidden = !reprPivot.cell.state.isHidden;
for (const c of components) {
// TODO: is it ok to use just the index here? Could possible lead to ugly edge cases, but perhaps not worth the trouble to "fix".
const repr = c.representations[index];
if (!repr)
continue;
(0, state_1.setSubtreeVisibility)(this.dataState, repr.cell.transform.ref, isHidden);
}
}
}
removeRepresentations(components, pivot) {
if (components.length === 0)
return;
const toRemove = [];
if (pivot) {
const index = components[0].representations.indexOf(pivot);
if (index < 0)
return;
for (const c of components) {
if (c.representations[index])
toRemove.push(c.representations[index]);
}
}
else {
for (const c of components) {
for (const r of c.representations) {
toRemove.push(r);
}
}
}
return this.plugin.managers.structure.hierarchy.remove(toRemove, true);
}
updateRepresentations(components, pivot, params) {
if (components.length === 0)
return Promise.resolve();
const index = components[0].representations.indexOf(pivot);
if (index < 0)
return Promise.resolve();
const update = this.dataState.build();
for (const c of components) {
// TODO: is it ok to use just the index here? Could possible lead to ugly edge cases, but perhaps not worth the trouble to "fix".
const repr = c.representations[index];
if (!repr)
continue;
if (repr.cell.transform.transformer !== pivot.cell.transform.transformer)
continue;
update.to(repr.cell).update(params);
}
return update.commit({ canUndo: 'Update Representation' });
}
updateRepresentationsTheme(components, paramsOrProvider) {
var _a, _b, _c, _d;
if (components.length === 0)
return;
const update = this.dataState.build();
for (const c of components) {
for (const repr of c.representations) {
const old = repr.cell.transform.params;
const params = typeof paramsOrProvider === 'function' ? paramsOrProvider(c, repr) : paramsOrProvider;
const colorTheme = params.color === 'default'
? (0, structure_representation_params_1.createStructureColorThemeParams)(this.plugin, (_a = c.structure.cell.obj) === null || _a === void 0 ? void 0 : _a.data, old === null || old === void 0 ? void 0 : old.type.name)
: params.color
? (0, structure_representation_params_1.createStructureColorThemeParams)(this.plugin, (_b = c.structure.cell.obj) === null || _b === void 0 ? void 0 : _b.data, old === null || old === void 0 ? void 0 : old.type.name, params.color, params.colorParams)
: void 0;
const sizeTheme = params.size === 'default'
? (0, structure_representation_params_1.createStructureSizeThemeParams)(this.plugin, (_c = c.structure.cell.obj) === null || _c === void 0 ? void 0 : _c.data, old === null || old === void 0 ? void 0 : old.type.name)
: params.color
? (0, structure_representation_params_1.createStructureSizeThemeParams)(this.plugin, (_d = c.structure.cell.obj) === null || _d === void 0 ? void 0 : _d.data, old === null || old === void 0 ? void 0 : old.type.name, params.size, params.sizeParams)
: void 0;
if (colorTheme || sizeTheme) {
update.to(repr.cell).update(prev => {
if (colorTheme)
prev.colorTheme = colorTheme;
if (sizeTheme)
prev.sizeTheme = sizeTheme;
});
}
}
}
return update.commit({ canUndo: 'Update Theme' });
}
addRepresentation(components, type) {
if (components.length === 0)
return;
const { hydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
const ignoreHydrogens = hydrogens !== 'all';
const ignoreHydrogensVariant = hydrogens === 'only-polar' ? 'non-polar' : 'all';
const typeParams = { ignoreHydrogens, ignoreHydrogensVariant, quality, ignoreLight, material, clip };
return this.plugin.dataTransaction(async () => {
for (const component of components) {
await this.plugin.builders.structure.representation.addRepresentation(component.cell, {
type: this.plugin.representation.structure.registry.get(type),
typeParams
});
}
}, { canUndo: 'Add Representation' });
}
tryFindComponent(structure, selection) {
if (structure.components.length === 0)
return;
return this.plugin.runTask(mol_task_1.Task.create('Find Component', async (taskCtx) => {
var _a, _b;
const data = (_a = structure.cell.obj) === null || _a === void 0 ? void 0 : _a.data;
if (!data)
return;
const sel = structure_1.StructureSelection.unionStructure(await selection.getSelection(this.plugin, taskCtx, data));
for (const c of structure.components) {
const comp = (_b = c.cell.obj) === null || _b === void 0 ? void 0 : _b.data;
if (!comp || !c.cell.parent)
continue;
if ((0, structure_set_1.structureAreEqual)(sel, comp))
return c.cell;
}
}));
}
async add(params, structures) {
return this.plugin.dataTransaction(async () => {
const xs = structures || this.currentStructures;
if (xs.length === 0)
return;
const { hydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
const ignoreHydrogens = hydrogens !== 'all';
const ignoreHydrogensVariant = hydrogens === 'only-polar' ? 'non-polar' : 'all';
const typeParams = { ignoreHydrogens, ignoreHydrogensVariant, quality, ignoreLight, material, clip };
const componentKey = mol_util_1.UUID.create22();
for (const s of xs) {
let component = void 0;
if (params.options.checkExisting) {
component = await this.tryFindComponent(s, params.selection);
}
if (!component) {
component = await this.plugin.builders.structure.tryCreateComponentFromSelection(s.cell, params.selection, componentKey, {
label: params.options.label || (params.selection === structure_selection_query_1.StructureSelectionQueries.current ? 'Custom Selection' : ''),
});
}
if (params.representation === 'none' || !component)
continue;
await this.plugin.builders.structure.representation.addRepresentation(component, {
type: this.plugin.representation.structure.registry.get(params.representation),
typeParams
});
}
}, { canUndo: 'Add Selection' });
}
async applyTheme(params, structures) {
return this.plugin.dataTransaction(async (ctx) => {
const xs = structures || this.currentStructures;
if (xs.length === 0)
return;
const getLoci = async (s) => structure_1.StructureSelection.toLociWithSourceUnits(await params.selection.getSelection(this.plugin, ctx, s));
for (const s of xs) {
if (params.action.name === 'color') {
const p = params.action.params;
await (0, structure_overpaint_1.setStructureOverpaint)(this.plugin, s.components, p.color, getLoci, params.representations);
}
else if (params.action.name === 'resetColor') {
await (0, structure_overpaint_1.setStructureOverpaint)(this.plugin, s.components, -1, getLoci, params.representations);
}
else if (params.action.name === 'transparency') {
const p = params.action.params;
await (0, structure_transparency_1.setStructureTransparency)(this.plugin, s.components, p.value, getLoci, params.representations);
}
else if (params.action.name === 'emissive') {
const p = params.action.params;
await (0, structure_emissive_1.setStructureEmissive)(this.plugin, s.components, p.value, getLoci, params.representations);
}
else if (params.action.name === 'material') {
const p = params.action.params;
await (0, structure_substance_1.setStructureSubstance)(this.plugin, s.components, p.material, getLoci, params.representations);
}
else if (params.action.name === 'resetMaterial') {
await (0, structure_substance_1.setStructureSubstance)(this.plugin, s.components, void 0, getLoci, params.representations);
}
else if (params.action.name === 'clipping') {
const p = params.action.params;
await (0, structure_clipping_1.setStructureClipping)(this.plugin, s.components, clipping_1.Clipping.Groups.fromNames(p.excludeGroups), getLoci, params.representations);
}
}
}, { canUndo: 'Apply Theme' });
}
modifyComponent(builder, component, by, action) {
var _a, _b, _c;
const structure = (_a = component.cell.obj) === null || _a === void 0 ? void 0 : _a.data;
if (!structure)
return;
if ((action === 'subtract' || action === 'intersect') && !(0, structure_set_1.structureAreIntersecting)(structure, by))
return;
const parent = (_b = component.structure.cell.obj) === null || _b === void 0 ? void 0 : _b.data;
const modified = action === 'union'
? (0, structure_set_1.structureUnion)(parent, [structure, by])
: action === 'intersect'
? (0, structure_set_1.structureIntersect)(structure, by)
: (0, structure_set_1.structureSubtract)(structure, by);
if (modified.elementCount === 0) {
builder.delete(component.cell.transform.ref);
}
else {
const bundle = structure_1.StructureElement.Bundle.fromSubStructure(parent, modified);
const params = {
type: { name: 'bundle', params: bundle },
nullIfEmpty: true,
label: (_c = component.cell.obj) === null || _c === void 0 ? void 0 : _c.label
};
builder.to(component.cell).update(params);
}
}
updateLabel(component, label) {
var _a, _b;
const params = {
type: (_a = component.cell.params) === null || _a === void 0 ? void 0 : _a.values.type,
nullIfEmpty: (_b = component.cell.params) === null || _b === void 0 ? void 0 : _b.values.nullIfEmpty,
label
};
this.dataState.build().to(component.cell).update(params).commit();
}
get dataState() {
return this.plugin.state.data;
}
clearComponents(structures) {
const deletes = this.dataState.build();
for (const s of structures) {
for (const c of s.components) {
deletes.delete(c.cell.transform.ref);
}
}
return deletes.commit({ canUndo: 'Clear Selections' });
}
constructor(plugin) {
super({ options: param_definition_1.ParamDefinition.getDefaultValues(StructureComponentManager.OptionsParams) });
this.plugin = plugin;
this.events = {
optionsUpdated: this.ev()
};
}
}
exports.StructureComponentManager = StructureComponentManager;
(function (StructureComponentManager) {
StructureComponentManager.OptionsParams = {
hydrogens: param_definition_1.ParamDefinition.Select('all', [['all', 'Show All'], ['hide-all', 'Hide All'], ['only-polar', 'Only Polar']], { description: 'Determine display of hydrogen atoms in representations' }),
visualQuality: param_definition_1.ParamDefinition.Select('auto', base_1.VisualQualityOptions, { description: 'Control the visual/rendering quality of representations' }),
ignoreLight: param_definition_1.ParamDefinition.Boolean(false, { description: 'Ignore light for stylized rendering of representations' }),
materialStyle: material_1.Material.getParam(),
clipObjects: param_definition_1.ParamDefinition.Group(clip_1.Clip.Params),
interactions: param_definition_1.ParamDefinition.Group(interactions_1.InteractionsProvider.defaultParams, { label: 'Non-covalent Interactions' }),
};
function getAddParams(plugin, params) {
const { options } = plugin.query.structure.registry;
params = {
pivot: plugin.managers.structure.component.pivotStructure,
allowNone: true,
hideSelection: false,
checkExisting: false,
...params
};
return {
selection: param_definition_1.ParamDefinition.Select(options[1][0], options, { isHidden: params === null || params === void 0 ? void 0 : params.hideSelection }),
representation: getRepresentationTypesSelect(plugin, params === null || params === void 0 ? void 0 : params.pivot, (params === null || params === void 0 ? void 0 : params.allowNone) ? [['none', '< Create Later >']] : []),
options: param_definition_1.ParamDefinition.Group({
label: param_definition_1.ParamDefinition.Text(''),
checkExisting: param_definition_1.ParamDefinition.Boolean(!!(params === null || params === void 0 ? void 0 : params.checkExisting), { help: () => ({ description: 'Checks if a selection with the specifield elements already exists to avoid creating duplicate components.' }) }),
})
};
}
StructureComponentManager.getAddParams = getAddParams;
function getThemeParams(plugin, pivot) {
const { options } = plugin.query.structure.registry;
return {
selection: param_definition_1.ParamDefinition.Select(options[1][0], options, { isHidden: false }),
action: param_definition_1.ParamDefinition.MappedStatic('color', {
color: param_definition_1.ParamDefinition.Group({
color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.blue, { isExpanded: true }),
}, { isFlat: true }),
resetColor: param_definition_1.ParamDefinition.EmptyGroup({ label: 'Reset Color' }),
transparency: param_definition_1.ParamDefinition.Group({
value: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0, max: 1, step: 0.01 }),
}, { isFlat: true }),
emissive: param_definition_1.ParamDefinition.Group({
value: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0, max: 1, step: 0.01 }),
}, { isFlat: true }),
material: param_definition_1.ParamDefinition.Group({
material: material_1.Material.getParam({ isFlat: true }),
}, { isFlat: true }),
resetMaterial: param_definition_1.ParamDefinition.EmptyGroup({ label: 'Reset Material' }),
clipping: param_definition_1.ParamDefinition.Group({
excludeGroups: param_definition_1.ParamDefinition.MultiSelect([], param_definition_1.ParamDefinition.objectToOptions(clipping_1.Clipping.Groups.Names)),
}, { isFlat: true }),
}),
representations: param_definition_1.ParamDefinition.MultiSelect([], getRepresentationTypes(plugin, pivot), { emptyValue: 'All' })
};
}
StructureComponentManager.getThemeParams = getThemeParams;
function getRepresentationTypes(plugin, pivot) {
var _a, _b;
return ((_a = pivot === null || pivot === void 0 ? void 0 : pivot.cell.obj) === null || _a === void 0 ? void 0 : _a.data)
? plugin.representation.structure.registry.getApplicableTypes((_b = pivot.cell.obj) === null || _b === void 0 ? void 0 : _b.data)
: plugin.representation.structure.registry.types;
}
StructureComponentManager.getRepresentationTypes = getRepresentationTypes;
function getRepresentationTypesSelect(plugin, pivot, custom, label) {
const types = [
...custom,
...getRepresentationTypes(plugin, pivot)
];
return param_definition_1.ParamDefinition.Select(types[0][0], types, { label });
}
})(StructureComponentManager || (exports.StructureComponentManager = StructureComponentManager = {}));