molstar
Version:
A comprehensive macromolecular library.
112 lines (111 loc) • 7.21 kB
JavaScript
/**
* Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Michal Malý <michal.maly@ibt.cas.cz>
* @author Jiří Černý <jiri.cerny@ibt.cas.cz>
*/
import { __assign, __awaiter, __extends, __generator } from "tslib";
import { ConfalPyramidsColorThemeProvider } from './color';
import { ConfalPyramids, ConfalPyramidsProvider } from './property';
import { ConfalPyramidsRepresentationProvider } from './representation';
import { PluginBehavior } from '../../../mol-plugin/behavior/behavior';
import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../../mol-plugin-state/builder/structure/representation-preset';
import { StateObjectRef } from '../../../mol-state';
import { Task } from '../../../mol-task';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
export var DnatcoConfalPyramidsPreset = StructureRepresentationPresetProvider({
id: 'preset-structure-representation-confal-pyramids',
display: {
name: 'Confal Pyramids', group: 'Annotation',
description: 'Schematic depiction of conformer class and confal value.',
},
isApplicable: function (a) {
return a.data.models.length >= 1 && a.data.models.some(function (m) { return ConfalPyramids.isApplicable(m); });
},
params: function () { return StructureRepresentationPresetProvider.CommonParams; },
apply: function (ref, params, plugin) {
var _a;
return __awaiter(this, void 0, void 0, function () {
var structureCell, model, _b, components, representations, pyramids, _c, update, builder, typeParams, pyramidsRepr;
var _this = this;
return __generator(this, function (_d) {
switch (_d.label) {
case 0:
structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
model = (_a = structureCell === null || structureCell === void 0 ? void 0 : structureCell.obj) === null || _a === void 0 ? void 0 : _a.data.model;
if (!structureCell || !model)
return [2 /*return*/, {}];
return [4 /*yield*/, plugin.runTask(Task.create('Confal Pyramids', function (runtime) { return __awaiter(_this, void 0, void 0, function () {
return __generator(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, ConfalPyramidsProvider.attach({ runtime: runtime, assetManager: plugin.managers.asset }, model)];
case 1:
_a.sent();
return [2 /*return*/];
}
});
}); }))];
case 1:
_d.sent();
return [4 /*yield*/, PresetStructureRepresentations.auto.apply(ref, __assign({}, params), plugin)];
case 2:
_b = _d.sent(), components = _b.components, representations = _b.representations;
return [4 /*yield*/, plugin.builders.structure.tryCreateComponentStatic(structureCell, 'nucleic', { label: 'Confal Pyramids' })];
case 3:
pyramids = _d.sent();
_c = StructureRepresentationPresetProvider.reprBuilder(plugin, params), update = _c.update, builder = _c.builder, typeParams = _c.typeParams;
if (representations)
pyramidsRepr = builder.buildRepresentation(update, pyramids, { type: ConfalPyramidsRepresentationProvider, typeParams: typeParams, color: ConfalPyramidsColorThemeProvider }, { tag: 'confal-pyramdis' });
return [4 /*yield*/, update.commit({ revertOnError: true })];
case 4:
_d.sent();
return [2 /*return*/, { components: __assign(__assign({}, components), { pyramids: pyramids }), representations: __assign(__assign({}, representations), { pyramidsRepr: pyramidsRepr }) }];
}
});
});
}
});
export var DnatcoConfalPyramids = PluginBehavior.create({
name: 'dnatco-confal-pyramids-prop',
category: 'custom-props',
display: {
name: 'Confal Pyramids',
description: 'Schematic depiction of conformer class and confal value.',
},
ctor: /** @class */ (function (_super) {
__extends(class_1, _super);
function class_1() {
var _this = _super !== null && _super.apply(this, arguments) || this;
_this.provider = ConfalPyramidsProvider;
return _this;
}
class_1.prototype.register = function () {
this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
this.ctx.representation.structure.themes.colorThemeRegistry.add(ConfalPyramidsColorThemeProvider);
this.ctx.representation.structure.registry.add(ConfalPyramidsRepresentationProvider);
this.ctx.builders.structure.representation.registerPreset(DnatcoConfalPyramidsPreset);
};
class_1.prototype.update = function (p) {
var updated = this.params.autoAttach !== p.autoAttach;
this.params.autoAttach = p.autoAttach;
this.params.showToolTip = p.showToolTip;
this.ctx.customModelProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
return updated;
};
class_1.prototype.unregister = function () {
this.ctx.customModelProperties.unregister(ConfalPyramidsProvider.descriptor.name);
this.ctx.representation.structure.registry.remove(ConfalPyramidsRepresentationProvider);
this.ctx.representation.structure.themes.colorThemeRegistry.remove(ConfalPyramidsColorThemeProvider);
this.ctx.builders.structure.representation.unregisterPreset(DnatcoConfalPyramidsPreset);
};
return class_1;
}(PluginBehavior.Handler)),
params: function () { return ({
autoAttach: PD.Boolean(true),
showToolTip: PD.Boolean(true)
}); }
});
export function confalPyramidLabel(halfPyramid) {
var step = halfPyramid.step;
return "\n <b>".concat(step.auth_asym_id_1, "</b> |\n <b>").concat(step.label_comp_id_1, " ").concat(step.auth_seq_id_1).concat(step.PDB_ins_code_1).concat(step.label_alt_id_1.length > 0 ? " (alt ".concat(step.label_alt_id_1, ")") : '', "\n ").concat(step.label_comp_id_2, " ").concat(step.auth_seq_id_2).concat(step.PDB_ins_code_2).concat(step.label_alt_id_2.length > 0 ? " (alt ".concat(step.label_alt_id_2, ")") : '', " </b><br />\n <i>NtC:</i> ").concat(step.NtC, " | <i>Confal score:</i> ").concat(step.confal_score, " | <i>RMSD:</i> ").concat(step.rmsd.toFixed(2), "\n ");
}