molstar
Version:
A comprehensive macromolecular library.
238 lines • 15.3 kB
JavaScript
/**
* Copyright (c) 2019-2021 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>
*/
import { __assign, __awaiter, __extends, __generator } from "tslib";
import { InteractionsRepresentationProvider } from '../../../../mol-model-props/computed/representations/interactions';
import { InteractionTypeColorThemeProvider } from '../../../../mol-model-props/computed/themes/interaction-type';
import { StructureElement } from '../../../../mol-model/structure';
import { createStructureRepresentationParams } from '../../../../mol-plugin-state/helpers/structure-representation-params';
import { StateTransforms } from '../../../../mol-plugin-state/transforms';
import { PluginBehavior } from '../../../behavior';
import { MolScriptBuilder as MS } from '../../../../mol-script/language/builder';
import { StateSelection, StateTransform } from '../../../../mol-state';
import { SizeTheme } from '../../../../mol-theme/size';
import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
import { PluginCommands } from '../../../commands';
var StructureFocusRepresentationParams = function (plugin) {
var reprParams = StateTransforms.Representation.StructureRepresentation3D.definition.params(void 0, plugin);
return {
expandRadius: PD.Numeric(5, { min: 1, max: 10, step: 1 }),
targetParams: PD.Group(reprParams, {
label: 'Target',
customDefault: createStructureRepresentationParams(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.26, alpha: 0.51 } })
}),
surroundingsParams: PD.Group(reprParams, {
label: 'Surroundings',
customDefault: createStructureRepresentationParams(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.16 } })
}),
nciParams: PD.Group(reprParams, {
label: 'Non-covalent Int.',
customDefault: createStructureRepresentationParams(plugin, void 0, {
type: InteractionsRepresentationProvider,
color: InteractionTypeColorThemeProvider,
size: SizeTheme.BuiltIn.uniform
})
}),
components: PD.MultiSelect(FocusComponents, PD.arrayToOptions(FocusComponents)),
excludeTargetFromSurroundings: PD.Boolean(false, { label: 'Exclude Target', description: 'Exclude the focus "target" from the surroudings component.' }),
ignoreHydrogens: PD.Boolean(false)
};
};
var FocusComponents = ['target', 'surroundings', 'interactions'];
export var StructureFocusRepresentationTags;
(function (StructureFocusRepresentationTags) {
StructureFocusRepresentationTags["TargetSel"] = "structure-focus-target-sel";
StructureFocusRepresentationTags["TargetRepr"] = "structure-focus-target-repr";
StructureFocusRepresentationTags["SurrSel"] = "structure-focus-surr-sel";
StructureFocusRepresentationTags["SurrRepr"] = "structure-focus-surr-repr";
StructureFocusRepresentationTags["SurrNciRepr"] = "structure-focus-surr-nci-repr";
})(StructureFocusRepresentationTags || (StructureFocusRepresentationTags = {}));
var TagSet = new Set([StructureFocusRepresentationTags.TargetSel, StructureFocusRepresentationTags.TargetRepr, StructureFocusRepresentationTags.SurrSel, StructureFocusRepresentationTags.SurrRepr, StructureFocusRepresentationTags.SurrNciRepr]);
var StructureFocusRepresentationBehavior = /** @class */ (function (_super) {
__extends(StructureFocusRepresentationBehavior, _super);
function StructureFocusRepresentationBehavior() {
var _this = _super !== null && _super.apply(this, arguments) || this;
_this.currentSource = void 0;
return _this;
}
Object.defineProperty(StructureFocusRepresentationBehavior.prototype, "surrLabel", {
get: function () { return "[Focus] Surroundings (" + this.params.expandRadius + " \u00C5)"; },
enumerable: false,
configurable: true
});
StructureFocusRepresentationBehavior.prototype.getReprParams = function (reprParams) {
return __assign(__assign({}, this.params.targetParams), { type: {
name: reprParams.type.name,
params: __assign(__assign({}, reprParams.type.params), { ignoreHydrogens: this.params.ignoreHydrogens })
} });
};
StructureFocusRepresentationBehavior.prototype.ensureShape = function (cell) {
var _a;
var state = this.plugin.state.data, tree = state.tree;
var builder = state.build();
var refs = StateSelection.findUniqueTagsInSubtree(tree, cell.transform.ref, TagSet);
// Selections
if (!refs[StructureFocusRepresentationTags.TargetSel]) {
refs[StructureFocusRepresentationTags.TargetSel] = builder
.to(cell)
.apply(StateTransforms.Model.StructureSelectionFromBundle, { bundle: StructureElement.Bundle.Empty, label: '[Focus] Target' }, { tags: StructureFocusRepresentationTags.TargetSel }).ref;
}
if (!refs[StructureFocusRepresentationTags.SurrSel]) {
refs[StructureFocusRepresentationTags.SurrSel] = builder
.to(cell)
.apply(StateTransforms.Model.StructureSelectionFromExpression, { expression: MS.struct.generator.empty(), label: this.surrLabel }, { tags: StructureFocusRepresentationTags.SurrSel }).ref;
}
var components = this.params.components;
// Representations
if (components.indexOf('target') >= 0 && !refs[StructureFocusRepresentationTags.TargetRepr]) {
refs[StructureFocusRepresentationTags.TargetRepr] = builder
.to(refs[StructureFocusRepresentationTags.TargetSel])
.apply(StateTransforms.Representation.StructureRepresentation3D, this.getReprParams(this.params.targetParams), { tags: StructureFocusRepresentationTags.TargetRepr }).ref;
}
if (components.indexOf('surroundings') >= 0 && !refs[StructureFocusRepresentationTags.SurrRepr]) {
refs[StructureFocusRepresentationTags.SurrRepr] = builder
.to(refs[StructureFocusRepresentationTags.SurrSel])
.apply(StateTransforms.Representation.StructureRepresentation3D, this.getReprParams(this.params.surroundingsParams), { tags: StructureFocusRepresentationTags.SurrRepr }).ref;
}
if (components.indexOf('interactions') >= 0 && !refs[StructureFocusRepresentationTags.SurrNciRepr] && cell.obj && InteractionsRepresentationProvider.isApplicable((_a = cell.obj) === null || _a === void 0 ? void 0 : _a.data)) {
refs[StructureFocusRepresentationTags.SurrNciRepr] = builder
.to(refs[StructureFocusRepresentationTags.SurrSel])
.apply(StateTransforms.Representation.StructureRepresentation3D, this.params.nciParams, { tags: StructureFocusRepresentationTags.SurrNciRepr }).ref;
}
return { state: state, builder: builder, refs: refs };
};
StructureFocusRepresentationBehavior.prototype.clear = function (root) {
var state = this.plugin.state.data;
this.currentSource = void 0;
var foci = state.select(StateSelection.Generators.byRef(root).subtree().withTag(StructureFocusRepresentationTags.TargetSel));
var surrs = state.select(StateSelection.Generators.byRef(root).subtree().withTag(StructureFocusRepresentationTags.SurrSel));
if (foci.length === 0 && surrs.length === 0)
return;
var update = state.build();
var bundle = StructureElement.Bundle.Empty;
for (var _i = 0, foci_1 = foci; _i < foci_1.length; _i++) {
var f = foci_1[_i];
update.to(f).update(StateTransforms.Model.StructureSelectionFromBundle, function (old) { return (__assign(__assign({}, old), { bundle: bundle })); });
}
var expression = MS.struct.generator.empty();
for (var _a = 0, surrs_1 = surrs; _a < surrs_1.length; _a++) {
var s = surrs_1[_a];
update.to(s).update(StateTransforms.Model.StructureSelectionFromExpression, function (old) { return (__assign(__assign({}, old), { expression: expression })); });
}
return PluginCommands.State.Update(this.plugin, { state: state, tree: update, options: { doNotLogTiming: true, doNotUpdateCurrent: true } });
};
StructureFocusRepresentationBehavior.prototype.focus = function (sourceLoci) {
return __awaiter(this, void 0, void 0, function () {
var parent, loci, residueLoci, residueBundle, target, surroundings, _a, state, builder, refs;
var _this = this;
return __generator(this, function (_b) {
switch (_b.label) {
case 0:
parent = this.plugin.helpers.substructureParent.get(sourceLoci.structure);
if (!parent || !parent.obj)
return [2 /*return*/];
this.currentSource = sourceLoci;
loci = StructureElement.Loci.remap(sourceLoci, parent.obj.data);
residueLoci = StructureElement.Loci.extendToWholeResidues(loci);
residueBundle = StructureElement.Bundle.fromLoci(residueLoci);
target = StructureElement.Bundle.toExpression(residueBundle);
surroundings = MS.struct.modifier.includeSurroundings({
0: target,
radius: this.params.expandRadius,
'as-whole-residues': true
});
if (this.params.excludeTargetFromSurroundings) {
surroundings = MS.struct.modifier.exceptBy({
0: surroundings,
by: target
});
}
_a = this.ensureShape(parent), state = _a.state, builder = _a.builder, refs = _a.refs;
builder.to(refs[StructureFocusRepresentationTags.TargetSel]).update(StateTransforms.Model.StructureSelectionFromBundle, function (old) { return (__assign(__assign({}, old), { bundle: residueBundle })); });
builder.to(refs[StructureFocusRepresentationTags.SurrSel]).update(StateTransforms.Model.StructureSelectionFromExpression, function (old) { return (__assign(__assign({}, old), { expression: surroundings, label: _this.surrLabel })); });
return [4 /*yield*/, PluginCommands.State.Update(this.plugin, { state: state, tree: builder, options: { doNotLogTiming: true, doNotUpdateCurrent: true } })];
case 1:
_b.sent();
return [2 /*return*/];
}
});
});
};
StructureFocusRepresentationBehavior.prototype.register = function (ref) {
var _this = this;
this.subscribeObservable(this.plugin.managers.structure.focus.behaviors.current, function (entry) {
if (entry)
_this.focus(entry.loci);
else
_this.clear(StateTransform.RootRef);
});
};
StructureFocusRepresentationBehavior.prototype.update = function (params) {
return __awaiter(this, void 0, void 0, function () {
var old, state, builder, all, components, hasComponent, _i, _a, repr, _b, _c, repr, _d, _e, repr;
return __generator(this, function (_f) {
switch (_f.label) {
case 0:
old = this.params;
this.params = params;
if (old.excludeTargetFromSurroundings !== params.excludeTargetFromSurroundings) {
if (this.currentSource) {
this.focus(this.currentSource);
}
return [2 /*return*/, true];
}
state = this.plugin.state.data;
builder = state.build();
all = StateSelection.Generators.root.subtree();
components = this.params.components;
hasComponent = components.indexOf('target') >= 0;
for (_i = 0, _a = state.select(all.withTag(StructureFocusRepresentationTags.TargetRepr)); _i < _a.length; _i++) {
repr = _a[_i];
if (!hasComponent)
builder.delete(repr.transform.ref);
else
builder.to(repr).update(this.getReprParams(this.params.targetParams));
}
hasComponent = components.indexOf('surroundings') >= 0;
for (_b = 0, _c = state.select(all.withTag(StructureFocusRepresentationTags.SurrRepr)); _b < _c.length; _b++) {
repr = _c[_b];
if (!hasComponent)
builder.delete(repr.transform.ref);
else
builder.to(repr).update(this.getReprParams(this.params.surroundingsParams));
}
hasComponent = components.indexOf('interactions') >= 0;
for (_d = 0, _e = state.select(all.withTag(StructureFocusRepresentationTags.SurrNciRepr)); _d < _e.length; _d++) {
repr = _e[_d];
if (!hasComponent)
builder.delete(repr.transform.ref);
else
builder.to(repr).update(this.params.nciParams);
}
return [4 /*yield*/, PluginCommands.State.Update(this.plugin, { state: state, tree: builder, options: { doNotLogTiming: true, doNotUpdateCurrent: true } })];
case 1:
_f.sent();
if (params.expandRadius !== old.expandRadius) {
if (this.currentSource) {
this.focus(this.currentSource);
}
return [2 /*return*/, true];
}
return [2 /*return*/, true];
}
});
});
};
return StructureFocusRepresentationBehavior;
}(PluginBehavior.WithSubscribers));
export var StructureFocusRepresentation = PluginBehavior.create({
name: 'create-structure-focus-representation',
display: { name: 'Structure Focus Representation' },
category: 'interaction',
ctor: StructureFocusRepresentationBehavior,
params: function (_, plugin) { return StructureFocusRepresentationParams(plugin); }
});
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