molstar
Version:
A comprehensive macromolecular library.
116 lines (115 loc) • 7.68 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>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.confalPyramidLabel = exports.DnatcoConfalPyramids = exports.DnatcoConfalPyramidsPreset = void 0;
var tslib_1 = require("tslib");
var color_1 = require("./color");
var property_1 = require("./property");
var representation_1 = require("./representation");
var behavior_1 = require("../../../mol-plugin/behavior/behavior");
var representation_preset_1 = require("../../../mol-plugin-state/builder/structure/representation-preset");
var mol_state_1 = require("../../../mol-state");
var mol_task_1 = require("../../../mol-task");
var param_definition_1 = require("../../../mol-util/param-definition");
exports.DnatcoConfalPyramidsPreset = (0, representation_preset_1.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 property_1.ConfalPyramids.isApplicable(m); });
},
params: function () { return representation_preset_1.StructureRepresentationPresetProvider.CommonParams; },
apply: function (ref, params, plugin) {
var _a;
return tslib_1.__awaiter(this, void 0, void 0, function () {
var structureCell, model, _b, components, representations, pyramids, _c, update, builder, typeParams, pyramidsRepr;
var _this = this;
return tslib_1.__generator(this, function (_d) {
switch (_d.label) {
case 0:
structureCell = mol_state_1.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(mol_task_1.Task.create('Confal Pyramids', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, property_1.ConfalPyramidsProvider.attach({ runtime: runtime, assetManager: plugin.managers.asset }, model)];
case 1:
_a.sent();
return [2 /*return*/];
}
});
}); }))];
case 1:
_d.sent();
return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, tslib_1.__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 = representation_preset_1.StructureRepresentationPresetProvider.reprBuilder(plugin, params), update = _c.update, builder = _c.builder, typeParams = _c.typeParams;
if (representations)
pyramidsRepr = builder.buildRepresentation(update, pyramids, { type: representation_1.ConfalPyramidsRepresentationProvider, typeParams: typeParams, color: color_1.ConfalPyramidsColorThemeProvider }, { tag: 'confal-pyramdis' });
return [4 /*yield*/, update.commit({ revertOnError: true })];
case 4:
_d.sent();
return [2 /*return*/, { components: tslib_1.__assign(tslib_1.__assign({}, components), { pyramids: pyramids }), representations: tslib_1.__assign(tslib_1.__assign({}, representations), { pyramidsRepr: pyramidsRepr }) }];
}
});
});
}
});
exports.DnatcoConfalPyramids = behavior_1.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) {
tslib_1.__extends(class_1, _super);
function class_1() {
var _this = _super !== null && _super.apply(this, arguments) || this;
_this.provider = property_1.ConfalPyramidsProvider;
return _this;
}
class_1.prototype.register = function () {
this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
this.ctx.representation.structure.themes.colorThemeRegistry.add(color_1.ConfalPyramidsColorThemeProvider);
this.ctx.representation.structure.registry.add(representation_1.ConfalPyramidsRepresentationProvider);
this.ctx.builders.structure.representation.registerPreset(exports.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(property_1.ConfalPyramidsProvider.descriptor.name);
this.ctx.representation.structure.registry.remove(representation_1.ConfalPyramidsRepresentationProvider);
this.ctx.representation.structure.themes.colorThemeRegistry.remove(color_1.ConfalPyramidsColorThemeProvider);
this.ctx.builders.structure.representation.unregisterPreset(exports.DnatcoConfalPyramidsPreset);
};
return class_1;
}(behavior_1.PluginBehavior.Handler)),
params: function () { return ({
autoAttach: param_definition_1.ParamDefinition.Boolean(true),
showToolTip: param_definition_1.ParamDefinition.Boolean(true)
}); }
});
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 ");
}
exports.confalPyramidLabel = confalPyramidLabel;