drugflow-molstar
Version:
Molstar implementation for DrugFlow
796 lines (795 loc) • 207 kB
JavaScript
"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
var tslib_1 = require("tslib");
var mol_plugin_ui_1 = require("molstar/lib/mol-plugin-ui");
var transforms_1 = require("molstar/lib/mol-plugin-state/transforms");
var structure_representation_params_1 = require("molstar/lib/mol-plugin-state/helpers/structure-representation-params");
var commands_1 = require("molstar/lib/mol-plugin/commands");
var spec_1 = require("molstar/lib/mol-plugin-ui/spec");
var model_index_1 = require("molstar/lib/mol-plugin-state/animation/built-in/model-index");
var loci_1 = require("molstar/lib/mol-model/loci");
var helpers_1 = require("./helpers");
var rx_event_helper_1 = require("molstar/lib/mol-util/rx-event-helper");
var structure_1 = require("molstar/lib/mol-model/structure");
var builder_1 = require("molstar/lib/mol-script/language/builder");
var structure_selection_query_1 = require("molstar/lib/mol-plugin-state/helpers/structure-selection-query");
var mol_task_1 = require("molstar/lib/mol-task");
var color_1 = require("molstar/lib/mol-util/color/color");
var structure_2 = require("molstar/lib/mol-model/structure");
var mol_state_1 = require("molstar/lib/mol-state");
var representation_1 = require("molstar/lib/mol-repr/representation");
var representation_2 = require("molstar/lib/mol-repr/structure/representation");
var units_visual_1 = require("molstar/lib/mol-repr/structure/units-visual");
var param_definition_1 = require("molstar/lib/mol-util/param-definition");
var location_iterator_1 = require("molstar/lib/mol-geo/util/location-iterator");
var location_1 = require("molstar/lib/mol-model/location");
var loci_2 = require("molstar/lib/mol-model/loci");
var box_1 = require("molstar/lib/mol-geo/geometry/mesh/builder/box");
var mesh_builder_1 = require("molstar/lib/mol-geo/geometry/mesh/mesh-builder");
var linear_algebra_1 = require("molstar/lib/mol-math/linear-algebra");
var int_1 = require("molstar/lib/mol-data/int");
var names_1 = require("molstar/lib/mol-util/color/names");
var structure_contact3d_1 = require("./structure_contact3d");
var structure_transparency_1 = require("molstar/lib/mol-plugin-state/helpers/structure-transparency");
var interactions_1 = require("molstar/lib/mol-model-props/computed/interactions");
var common_1 = require("molstar/lib/mol-model-props/computed/interactions/common");
require('molstar/lib/mol-plugin-ui/skin/light.scss');
var DrugflowMolstarPlugin = /** @class */ (function () {
function DrugflowMolstarPlugin() {
var _this = this;
this._ev = rx_event_helper_1.RxEventHelper.create();
this.events = {
loadComplete: this._ev()
};
this.assemblyRef = '';
this.granularity = 'residue';
this.selected_info = {
"all": { "polymer": [], "ligand": [], "other": [] },
"prev": { "polymer": [], "ligand": [], "other": [] },
"now": { "polymer": [], "ligand": [], "other": [] }
};
this.isHighlightColorUpdated = false;
// 隐藏状态追踪器
this.hiddenState = {
chains: new Set(), // 隐藏的链ID
ligands: new Set(), // 隐藏的配体（格式: "chainId:resId" 或 "chainId:resName"）
residues: new Set() // 隐藏的残基（格式: "chainId:resId"）
};
this.canvas = {
toggleControls: function (isVisible) {
if (typeof isVisible === 'undefined')
isVisible = !_this.plugin.layout.state.showControls;
commands_1.PluginCommands.Layout.Update(_this.plugin, { state: { showControls: isVisible } });
},
toggleExpanded: function (isExpanded) {
if (typeof isExpanded === 'undefined')
isExpanded = !_this.plugin.layout.state.isExpanded;
commands_1.PluginCommands.Layout.Update(_this.plugin, { state: { isExpanded: isExpanded } });
},
setBgColor: function (color) {
if (!color)
return;
_this.canvas.applySettings({ color: color });
},
applySettings: function (settings) {
if (!settings)
return;
var rendererParams = {};
if (settings.color)
rendererParams['backgroundColor'] = color_1.Color.fromRgb(settings.color.r, settings.color.g, settings.color.b);
if (settings.lighting)
rendererParams['style'] = { name: settings.lighting };
var renderer = _this.plugin.canvas3d.props.renderer;
commands_1.PluginCommands.Canvas3D.SetSettings(_this.plugin, { settings: { renderer: tslib_1.__assign(tslib_1.__assign({}, renderer), rendererParams) } });
},
toggleSelect: function (isSelect) {
_this.plugin.selectionMode = !isSelect;
},
};
this.measure = {
add_distance: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var loci;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
loci = this.plugin.managers.structure.selection.additionsHistory;
if (loci.length < 2) {
console.log('please select two atoms');
return [2 /*return*/];
}
return [4 /*yield*/, this.plugin.managers.structure.measurement.addDistance(loci[0].loci, loci[1].loci)];
case 1:
_b.sent();
return [2 /*return*/];
}
});
}); },
add_angle: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var loci;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
loci = this.plugin.managers.structure.selection.additionsHistory;
if (loci.length < 3) {
console.log('please select three atoms');
return [2 /*return*/];
}
return [4 /*yield*/, this.plugin.managers.structure.measurement.addAngle(loci[0].loci, loci[1].loci, loci[2].loci)];
case 1:
_b.sent();
return [2 /*return*/];
}
});
}); },
add_dihedral: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var loci;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
loci = this.plugin.managers.structure.selection.additionsHistory;
if (loci.length < 4) {
console.log('please select four atoms');
return [2 /*return*/];
}
return [4 /*yield*/, this.plugin.managers.structure.measurement.addDihedral(loci[0].loci, loci[1].loci, loci[2].loci, loci[3].loci)];
case 1:
_b.sent();
return [2 /*return*/];
}
});
}); },
add_orientation: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var locis;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
locis = [];
this.plugin.managers.structure.selection.entries.forEach(function (v) {
locis.push(v.selection);
});
return [4 /*yield*/, this.plugin.managers.structure.measurement.addOrientation(locis)];
case 1:
_b.sent();
return [2 /*return*/];
}
});
}); },
add_plane: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var locis;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
locis = [];
this.plugin.managers.structure.selection.entries.forEach(function (v) {
locis.push(v.selection);
});
return [4 /*yield*/, this.plugin.managers.structure.measurement.addPlane(locis)];
case 1:
_b.sent();
return [2 /*return*/];
}
});
}); },
clean_all_measure: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var state, groupRef, builder;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
state = this.plugin.state.data;
groupRef = mol_state_1.StateSelection.findTagInSubtree(state.tree, mol_state_1.StateTransform.RootRef, 'measurement-group');
builder = this.plugin.state.data.build();
if (!groupRef) return [3 /*break*/, 2];
builder.to(mol_state_1.StateTransform.RootRef).delete(groupRef);
return [4 /*yield*/, this.applyState(builder)];
case 1:
_b.sent();
return [3 /*break*/, 3];
case 2:
console.log('no measurement group');
_b.label = 3;
case 3: return [2 /*return*/];
}
});
}); }
};
this.visual = {
select_all: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var all_query, data;
var _this = this;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
all_query = structure_selection_query_1.StructureSelectionQueries.all;
data = this.plugin.state.data.select(this.assemblyRef)[0].obj.data;
return [4 /*yield*/, this.plugin.runTask(mol_task_1.Task.create('Structure Selection', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var selection, loci;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0: return [4 /*yield*/, all_query.getSelection(this.plugin, runtime, data)];
case 1:
selection = _b.sent();
loci = structure_1.StructureSelection.toLociWithSourceUnits(selection);
this.plugin.managers.interactivity.lociSelects.select({ loci: loci });
return [2 /*return*/];
}
});
}); }))];
case 1:
_b.sent();
this.add_selection_info();
return [2 /*return*/];
}
});
}); },
select_none: function () {
_this.plugin.managers.interactivity.lociSelects.deselectAll();
_this.add_selection_info();
},
expand_select: function (expand, type) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var whole_residues, surroundings_query, data;
var _this = this;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
whole_residues = true;
if (type) {
if (type === 'atom')
whole_residues = false;
}
surroundings_query = (0, structure_selection_query_1.StructureSelectionQuery)('Surrounding of Selection', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.exceptBy({
0: builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({
0: builder_1.MolScriptBuilder.internal.generator.current(),
radius: expand,
'as-whole-residues': whole_residues
}),
by: builder_1.MolScriptBuilder.internal.generator.current()
})
]), {
description: 'Select surrounding of the current selection.',
category: structure_selection_query_1.StructureSelectionCategory.Manipulate,
referencesCurrent: true
});
data = this.plugin.state.data.select(this.assemblyRef)[0].obj.data;
return [4 /*yield*/, this.plugin.runTask(mol_task_1.Task.create('Structure Selection', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var selection, loci;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0: return [4 /*yield*/, surroundings_query.getSelection(this.plugin, runtime, data)];
case 1:
selection = _b.sent();
loci = structure_1.StructureSelection.toLociWithSourceUnits(selection);
this.plugin.managers.interactivity.lociSelects.select({ loci: loci });
return [2 /*return*/];
}
});
}); }))];
case 1:
_b.sent();
this.add_selection_info();
return [2 /*return*/];
}
});
}); },
deselect_current: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var current_query, data;
var _this = this;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
current_query = structure_selection_query_1.StructureSelectionQueries.current;
data = this.plugin.state.data.select(this.assemblyRef)[0].obj.data;
return [4 /*yield*/, this.plugin.runTask(mol_task_1.Task.create('Structure Selection', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var current_selection, current_loci;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0: return [4 /*yield*/, current_query.getSelection(this.plugin, runtime, data)];
case 1:
current_selection = _b.sent();
current_loci = structure_1.StructureSelection.toLociWithSourceUnits(current_selection);
this.plugin.managers.interactivity.lociSelects.deselect({ loci: current_loci });
return [2 /*return*/];
}
});
}); }))];
case 1:
_b.sent();
return [2 /*return*/];
}
});
}); },
inverse_select: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var current_query, inverse_query, data;
var _this = this;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
current_query = structure_selection_query_1.StructureSelectionQueries.current;
inverse_query = structure_selection_query_1.StructureSelectionQueries.complement;
data = this.plugin.state.data.select(this.assemblyRef)[0].obj.data;
return [4 /*yield*/, this.plugin.runTask(mol_task_1.Task.create('Structure Selection', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var current_selection, inverse_selection, current_loci, inverse_loci;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0: return [4 /*yield*/, current_query.getSelection(this.plugin, runtime, data)];
case 1:
current_selection = _b.sent();
return [4 /*yield*/, inverse_query.getSelection(this.plugin, runtime, data)];
case 2:
inverse_selection = _b.sent();
current_loci = structure_1.StructureSelection.toLociWithSourceUnits(current_selection);
inverse_loci = structure_1.StructureSelection.toLociWithSourceUnits(inverse_selection);
this.plugin.managers.interactivity.lociSelects.select({ loci: inverse_loci });
this.plugin.managers.interactivity.lociSelects.deselect({ loci: current_loci });
return [2 /*return*/];
}
});
}); }))];
case 1:
_b.sent();
this.add_selection_info();
return [2 /*return*/];
}
});
}); },
hideSelect: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var sel, components, _i, sel_1, s;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
sel = this.plugin.managers.structure.hierarchy.getStructuresWithSelection();
components = [];
for (_i = 0, sel_1 = sel; _i < sel_1.length; _i++) {
s = sel_1[_i];
components.push.apply(components, s.components);
}
if (components.length === 0)
return [2 /*return*/];
return [4 /*yield*/, this.plugin.managers.structure.component.modifyByCurrentSelection(components, 'subtract')];
case 1:
_b.sent();
this.update_selected_info();
return [2 /*return*/];
}
});
}); },
_showSelect: function () {
var args_1 = [];
for (var _b = 0; _b < arguments.length; _b++) {
args_1[_b] = arguments[_b];
}
return tslib_1.__awaiter(_this, tslib_1.__spreadArray([], tslib_1.__read(args_1), false), void 0, function (type) {
var sel, components, _i, sel_1, s, _j, _a, c;
if (type === void 0) { type = 'Polymer'; }
return tslib_1.__generator(this, function (_c) {
switch (_c.label) {
case 0:
sel = this.plugin.managers.structure.hierarchy.getStructuresWithSelection();
if (sel.length === 0) {
console.log('sel is empty, ok');
return [2 /*return*/, 0];
}
components = [];
for (_i = 0, sel_1 = sel; _i < sel_1.length; _i++) {
s = sel_1[_i];
for (_j = 0, _a = s.components; _j < _a.length; _j++) {
c = _a[_j];
if (c.key !== type)
continue;
components.push(c);
}
// if (s.components.key !== type) continue;
// components.push.apply(components, s.components);
}
if (components.length === 0) {
console.log('components is empty, need recreate');
return [2 /*return*/, -1];
}
console.log('showSelect components', components);
return [4 /*yield*/, this.plugin.managers.structure.component.modifyByCurrentSelection(components, 'union')];
case 1:
_c.sent();
return [4 /*yield*/, this.visual.deselect_current()];
case 2:
_c.sent();
this.add_selection_info();
return [2 /*return*/, 0];
}
});
});
},
changeProps: function (val) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
return tslib_1.__generator(this, function (_b) {
//todo 切换选中粒度
this.plugin.managers.interactivity.setProps({ granularity: val });
this.granularity = val;
return [2 /*return*/];
});
}); },
toggleSpin: function (isSpinning, resetCamera) {
if (!_this.plugin.canvas3d)
return;
var trackball = _this.plugin.canvas3d.props.trackball;
var toggleSpinParam = trackball.animate.name === 'spin' ? { name: 'off', params: {} } : { name: 'spin', params: { speed: 1 } };
if (typeof isSpinning !== 'undefined') {
toggleSpinParam = { name: 'off', params: {} };
if (isSpinning)
toggleSpinParam = { name: 'spin', params: { speed: 1 } };
}
commands_1.PluginCommands.Canvas3D.SetSettings(_this.plugin, { settings: { trackball: tslib_1.__assign(tslib_1.__assign({}, trackball), { animate: toggleSpinParam }) } });
if (resetCamera)
commands_1.PluginCommands.Camera.Reset(_this.plugin, {});
},
focus: function (params, structureNumber, expand_num) {
var loci = _this.getLociForParams(params, structureNumber);
if (expand_num) {
_this.plugin.managers.camera.focusLoci(loci, { extraRadius: expand_num });
}
else {
_this.plugin.managers.camera.focusLoci(loci);
}
},
get_current_loci: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var current_query, data, ret;
var _this = this;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
current_query = structure_selection_query_1.StructureSelectionQueries.current;
data = this.plugin.state.data.select(this.assemblyRef)[0].obj.data;
ret = loci_1.EmptyLoci;
return [4 /*yield*/, this.plugin.runTask(mol_task_1.Task.create('Structure Selection', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var current_selection;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0: return [4 /*yield*/, current_query.getSelection(this.plugin, runtime, data)];
case 1:
current_selection = _b.sent();
ret = structure_1.StructureSelection.toLociWithSourceUnits(current_selection);
return [2 /*return*/];
}
});
}); }))];
case 1:
_b.sent();
return [2 /*return*/, ret];
}
});
}); },
focus_loci: function (loci) {
_this.plugin.managers.camera.focusLoci(loci);
},
focus_now: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var current_query, data;
var _this = this;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
current_query = structure_selection_query_1.StructureSelectionQueries.current;
data = this.plugin.state.data.select(this.assemblyRef)[0].obj.data;
return [4 /*yield*/, this.plugin.runTask(mol_task_1.Task.create('Structure Selection', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var current_selection, current_loci;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0: return [4 /*yield*/, current_query.getSelection(this.plugin, runtime, data)];
case 1:
current_selection = _b.sent();
current_loci = structure_1.StructureSelection.toLociWithSourceUnits(current_selection);
this.plugin.managers.camera.focusLoci(current_loci);
return [2 /*return*/];
}
});
}); }))];
case 1:
_b.sent();
return [2 /*return*/];
}
});
}); },
select: function (params, deselect) {
if (deselect === void 0) { deselect = false; }
var loci = _this.getLociForParams(params);
if (loci_1.Loci.isEmpty(loci))
return;
if (deselect) {
_this.plugin.managers.interactivity.lociSelects.deselect({ loci: loci });
}
else {
_this.plugin.managers.interactivity.lociSelects.select({ loci: loci });
}
_this.add_selection_info();
},
camera_reset: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0: return [4 /*yield*/, commands_1.PluginCommands.Camera.Reset(this.plugin, { durationMs: 250 })];
case 1:
_b.sent();
return [2 /*return*/];
}
});
}); },
/**
* 应用所有隐藏状态（内部方法）
*/
_applyHiddenState: function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var structures, components, structures_1, structures_1_1, s, chainArray, _loop_1, this_1, i, ligandArray, _loop_2, this_2, i, residuesByChain, _b, _c, residueKey, _d, chainId, resIdStr, resId, _loop_3, this_3, residuesByChain_1, residuesByChain_1_1, _e, chainId, residueIds, e_1_1;
var e_2, _f, e_3, _g, e_1, _h;
var _this = this;
return tslib_1.__generator(this, function (_k) {
switch (_k.label) {
case 0:
structures = this.plugin.managers.structure.hierarchy.current.structures;
components = [];
try {
for (structures_1 = tslib_1.__values(structures), structures_1_1 = structures_1.next(); !structures_1_1.done; structures_1_1 = structures_1.next()) {
s = structures_1_1.value;
components.push.apply(components, tslib_1.__spreadArray([], tslib_1.__read(s.components), false));
}
}
catch (e_2_1) { e_2 = { error: e_2_1 }; }
finally {
try {
if (structures_1_1 && !structures_1_1.done && (_f = structures_1.return)) _f.call(structures_1);
}
finally { if (e_2) throw e_2.error; }
}
if (components.length === 0) {
return [2 /*return*/];
}
// 先清除所有透明度
return [4 /*yield*/, (0, structure_transparency_1.clearStructureTransparency)(this.plugin, components)];
case 1:
// 先清除所有透明度
_k.sent();
// 如果没有需要隐藏的，直接返回
if (this.hiddenState.chains.size === 0 && this.hiddenState.ligands.size === 0 && this.hiddenState.residues.size === 0) {
return [2 /*return*/];
}
chainArray = Array.from(this.hiddenState.chains);
_loop_1 = function (i) {
var chainId;
return tslib_1.__generator(this, function (_l) {
switch (_l.label) {
case 0:
chainId = chainArray[i];
return [4 /*yield*/, (0, structure_transparency_1.setStructureTransparency)(this_1.plugin, components, 1, function (structure) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var chainQuery;
var _this = this;
return tslib_1.__generator(this, function (_b) {
chainQuery = (0, structure_selection_query_1.StructureSelectionQuery)("Chain_".concat(chainId), builder_1.MolScriptBuilder.struct.generator.atomGroups({
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('auth_asym_id'), chainId])
}), {
description: "Chain ".concat(chainId),
category: structure_selection_query_1.StructureSelectionCategory.Manipulate
});
return [2 /*return*/, this.plugin.runTask(mol_task_1.Task.create('Select Chain', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var selection;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0: return [4 /*yield*/, chainQuery.getSelection(this.plugin, runtime, structure)];
case 1:
selection = _b.sent();
return [2 /*return*/, structure_1.StructureSelection.toLociWithSourceUnits(selection)];
}
});
}); }))];
});
}); })];
case 1:
_l.sent();
return [2 /*return*/];
}
});
};
this_1 = this;
i = 0;
_k.label = 2;
case 2:
if (!(i < chainArray.length)) return [3 /*break*/, 5];
return [5 /*yield**/, _loop_1(i)];
case 3:
_k.sent();
_k.label = 4;
case 4:
i++;
return [3 /*break*/, 2];
case 5:
ligandArray = Array.from(this.hiddenState.ligands);
_loop_2 = function (i) {
var ligandKey, parts, chainId, identifier, resId, resName, queryConditions;
return tslib_1.__generator(this, function (_m) {
switch (_m.label) {
case 0:
ligandKey = ligandArray[i];
parts = ligandKey.split(':');
chainId = parts[0];
identifier = parts[1];
resId = isNaN(Number(identifier)) ? undefined : Number(identifier);
resName = isNaN(Number(identifier)) ? identifier : undefined;
queryConditions = {
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('auth_asym_id'), chainId])
};
if (resName) {
queryConditions['residue-test'] = builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('auth_comp_id'), resName.toUpperCase()]);
}
else if (resId !== undefined) {
queryConditions['residue-test'] = builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('auth_seq_id'), resId]);
}
return [4 /*yield*/, (0, structure_transparency_1.setStructureTransparency)(this_2.plugin, components, 1, function (structure) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var ligandQuery;
var _this = this;
return tslib_1.__generator(this, function (_b) {
ligandQuery = (0, structure_selection_query_1.StructureSelectionQuery)("Ligand_".concat(ligandKey), builder_1.MolScriptBuilder.struct.generator.atomGroups(queryConditions), {
description: "Ligand at ".concat(ligandKey),
category: structure_selection_query_1.StructureSelectionCategory.Manipulate
});
return [2 /*return*/, this.plugin.runTask(mol_task_1.Task.create('Select Ligand', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var selection;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0: return [4 /*yield*/, ligandQuery.getSelection(this.plugin, runtime, structure)];
case 1:
selection = _b.sent();
return [2 /*return*/, structure_1.StructureSelection.toLociWithSourceUnits(selection)];
}
});
}); }))];
});
}); })];
case 1:
_m.sent();
return [2 /*return*/];
}
});
};
this_2 = this;
i = 0;
_k.label = 6;
case 6:
if (!(i < ligandArray.length)) return [3 /*break*/, 9];
return [5 /*yield**/, _loop_2(i)];
case 7:
_k.sent();
_k.label = 8;
case 8:
i++;
return [3 /*break*/, 6];
case 9:
residuesByChain = new Map();
try {
for (_b = tslib_1.__values(this.hiddenState.residues), _c = _b.next(); !_c.done; _c = _b.next()) {
residueKey = _c.value;
_d = tslib_1.__read(residueKey.split(':'), 2), chainId = _d[0], resIdStr = _d[1];
resId = Number(resIdStr);
if (!residuesByChain.has(chainId)) {
residuesByChain.set(chainId, []);
}
residuesByChain.get(chainId).push(resId);
}
}
catch (e_3_1) { e_3 = { error: e_3_1 }; }
finally {
try {
if (_c && !_c.done && (_g = _b.return)) _g.call(_b);
}
finally { if (e_3) throw e_3.error; }
}
_loop_3 = function (chainId, residueIds) {
return tslib_1.__generator(this, function (_o) {
switch (_o.label) {
case 0: return [4 /*yield*/, (0, structure_transparency_1.setStructureTransparency)(this_3.plugin, components, 1, function (structure) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var residueQuery;
var _this = this;
return tslib_1.__generator(this, function (_b) {
residueQuery = (0, structure_selection_query_1.StructureSelectionQuery)("Residues_".concat(chainId), builder_1.MolScriptBuilder.struct.generator.atomGroups({
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('auth_asym_id'), chainId]),
'residue-test': builder_1.MolScriptBuilder.core.set.has([
builder_1.MolScriptBuilder.set.apply(builder_1.MolScriptBuilder, tslib_1.__spreadArray([], tslib_1.__read(residueIds), false)),
builder_1.MolScriptBuilder.ammp('auth_seq_id')
])
}), {
description: "Residues in chain ".concat(chainId),
category: structure_selection_query_1.StructureSelectionCategory.Manipulate
});
return [2 /*return*/, this.plugin.runTask(mol_task_1.Task.create('Select Residues', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var selection;
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0: return [4 /*yield*/, residueQuery.getSelection(this.plugin, runtime, structure)];
case 1:
selection = _b.sent();
return [2 /*return*/, structure_1.StructureSelection.toLociWithSourceUnits(selection)];
}
});
}); }))];
});
}); })];
case 1:
_o.sent();
return [2 /*return*/];
}
});
};
this_3 = this;
_k.label = 10;
case 10:
_k.trys.push([10, 15, 16, 17]);
residuesByChain_1 = tslib_1.__values(residuesByChain), residuesByChain_1_1 = residuesByChain_1.next();
_k.label = 11;
case 11:
if (!!residuesByChain_1_1.done) return [3 /*break*/, 14];
_e = tslib_1.__read(residuesByChain_1_1.value, 2), chainId = _e[0], residueIds = _e[1];
return [5 /*yield**/, _loop_3(chainId, residueIds)];
case 12:
_k.sent();
_k.label = 13;
case 13:
residuesByChain_1_1 = residuesByChain_1.next();
return [3 /*break*/, 11];
case 14: return [3 /*break*/, 17];
case 15:
e_1_1 = _k.sent();
e_1 = { error: e_1_1 };
return [3 /*break*/, 17];
case 16:
try {
if (residuesByChain_1_1 && !residuesByChain_1_1.done && (_h = residuesByChain_1.return)) _h.call(residuesByChain_1);
}
finally { if (e_1) throw e_1.error; }
return [7 /*endfinally*/];
case 17: return [2 /*return*/];
}
});
}); },
/**
* 使用透明度隐藏指定的链
* @param chainId 链ID，例如 'A', 'B'
*/
hideChain: function (chainId) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
// 添加到隐藏状态
this.hiddenState.chains.add(chainId);
// 重新应用所有隐藏状态
return [4 /*yield*/, this.visual._applyHiddenState()];
case 1:
// 重新应用所有隐藏状态
_b.sent();
console.log("\u2705 Chain ".concat(chainId, " hidden"));
return [2 /*return*/];
}
});
}); },
/**
* 清除指定链的透明度来显示
* @param chainId 链ID，例如 'A', 'B'
*/
showChain: function (chainId) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
return tslib_1.__generator(this, function (_b) {
switch (_b.label) {
case 0:
// 从隐藏状态中移除
this.hiddenState.chains.delete(chainId);
// 重新应用所有隐藏状态
return [4 /*yield*/, this.visual._applyHiddenState()];
case 1:
// 重新应用所有隐藏状态
_b.sent();
console.log("\u2705 Chain ".concat(chainId, " shown"));
return [2 /*return*/];
}
});
}); },
/**
* 使用透明度隐藏指定链中的残基
* @param chainId 链ID，例如 'A', 'B'
* @param residueIds 残基序号数组，例如 [10, 15, 20] 或范围 { start: 10, end: 20 }
*/
hideResidues: function (chainId, residueIds) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var ids, ids_1, ids_1_1, resId;
var e_4, _b;
return tslib_1.__generator(this, function (_c) {
switch (_c.label) {
case 0: