molstar
Version:
A comprehensive macromolecular library.
240 lines • 13.9 kB
JavaScript
"use strict";
/**
* Copyright (c) 2018-2020 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.DockingViewer = exports.setProductionMode = exports.setDebugMode = exports.version = void 0;
var tslib_1 = require("tslib");
var structure_1 = require("../../mol-model/structure");
var objects_1 = require("../../mol-plugin-state/objects");
var mol_plugin_ui_1 = require("../../mol-plugin-ui");
var spec_1 = require("../../mol-plugin-ui/spec");
var behavior_1 = require("../../mol-plugin/behavior");
var commands_1 = require("../../mol-plugin/commands");
var config_1 = require("../../mol-plugin/config");
var spec_2 = require("../../mol-plugin/spec");
var mol_state_1 = require("../../mol-state");
var mol_task_1 = require("../../mol-task");
var color_1 = require("../../mol-util/color");
var names_1 = require("../../mol-util/color/names");
var param_definition_1 = require("../../mol-util/param-definition");
require("../../mol-util/polyfill");
var type_helpers_1 = require("../../mol-util/type-helpers");
require("./index.html");
var viewport_1 = require("./viewport");
require('mol-plugin-ui/skin/light.scss');
var version_1 = require("../../mol-plugin/version");
Object.defineProperty(exports, "version", { enumerable: true, get: function () { return version_1.PLUGIN_VERSION; } });
var debug_1 = require("../../mol-util/debug");
Object.defineProperty(exports, "setDebugMode", { enumerable: true, get: function () { return debug_1.setDebugMode; } });
Object.defineProperty(exports, "setProductionMode", { enumerable: true, get: function () { return debug_1.setProductionMode; } });
var DefaultViewerOptions = {
extensions: (0, type_helpers_1.ObjectKeys)({}),
layoutIsExpanded: true,
layoutShowControls: true,
layoutShowRemoteState: true,
layoutControlsDisplay: 'reactive',
layoutShowSequence: true,
layoutShowLog: true,
layoutShowLeftPanel: true,
viewportShowExpand: config_1.PluginConfig.Viewport.ShowExpand.defaultValue,
viewportShowControls: config_1.PluginConfig.Viewport.ShowControls.defaultValue,
viewportShowSettings: config_1.PluginConfig.Viewport.ShowSettings.defaultValue,
viewportShowSelectionMode: config_1.PluginConfig.Viewport.ShowSelectionMode.defaultValue,
viewportShowAnimation: config_1.PluginConfig.Viewport.ShowAnimation.defaultValue,
pluginStateServer: config_1.PluginConfig.State.DefaultServer.defaultValue,
volumeStreamingServer: config_1.PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
pdbProvider: config_1.PluginConfig.Download.DefaultPdbProvider.defaultValue,
emdbProvider: config_1.PluginConfig.Download.DefaultEmdbProvider.defaultValue,
};
var Viewer = /** @class */ (function () {
function Viewer(elementOrId, colors, showButtons) {
var _this = this;
if (colors === void 0) { colors = [(0, color_1.Color)(0x992211), (0, color_1.Color)(0xDDDDDD)]; }
if (showButtons === void 0) { showButtons = true; }
var _a;
var o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultViewerOptions), {
layoutIsExpanded: false,
layoutShowControls: false,
layoutShowRemoteState: false,
layoutShowSequence: true,
layoutShowLog: false,
layoutShowLeftPanel: true,
viewportShowExpand: true,
viewportShowControls: false,
viewportShowSettings: false,
viewportShowSelectionMode: false,
viewportShowAnimation: false,
});
var defaultSpec = (0, spec_1.DefaultPluginUISpec)();
var spec = {
actions: defaultSpec.actions,
behaviors: [
spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.Representation.HighlightLoci, { mark: false }),
spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.Representation.DefaultLociLabelProvider),
spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.Camera.FocusLoci),
spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.CustomProps.StructureInfo),
spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.CustomProps.Interactions),
spec_2.PluginSpec.Behavior(behavior_1.PluginBehaviors.CustomProps.SecondaryStructure),
],
animations: defaultSpec.animations,
customParamEditors: defaultSpec.customParamEditors,
layout: {
initial: {
isExpanded: o.layoutIsExpanded,
showControls: o.layoutShowControls,
controlsDisplay: o.layoutControlsDisplay,
},
},
components: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, defaultSpec.components), { controls: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, (_a = defaultSpec.components) === null || _a === void 0 ? void 0 : _a.controls), { top: o.layoutShowSequence ? undefined : 'none', bottom: o.layoutShowLog ? undefined : 'none', left: o.layoutShowLeftPanel ? undefined : 'none' }), remoteState: o.layoutShowRemoteState ? 'default' : 'none', viewport: {
view: viewport_1.ViewportComponent
} }),
config: [
[config_1.PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
[config_1.PluginConfig.Viewport.ShowControls, o.viewportShowControls],
[config_1.PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
[config_1.PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
[config_1.PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
[config_1.PluginConfig.State.DefaultServer, o.pluginStateServer],
[config_1.PluginConfig.State.CurrentServer, o.pluginStateServer],
[config_1.PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
[config_1.PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
[config_1.PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
[viewport_1.ShowButtons, showButtons]
]
};
var element = typeof elementOrId === 'string'
? document.getElementById(elementOrId)
: elementOrId;
if (!element)
throw new Error("Could not get element with id '" + elementOrId + "'");
this.plugin = (0, mol_plugin_ui_1.createPlugin)(element, spec);
this.plugin.customState = {
colorPalette: {
name: 'colors',
params: { list: { colors: colors } }
}
};
this.plugin.behaviors.canvas3d.initialized.subscribe(function (v) {
if (v) {
commands_1.PluginCommands.Canvas3D.SetSettings(_this.plugin, { settings: {
renderer: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, _this.plugin.canvas3d.props.renderer), { backgroundColor: names_1.ColorNames.white }),
camera: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, _this.plugin.canvas3d.props.camera), { helper: { axes: { name: 'off', params: {} } } })
} });
}
});
}
Viewer.prototype.loadStructuresFromUrlsAndMerge = function (sources) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var structures, _i, sources_1, _a, url, format, isBinary, data_1, trajectory, model, modelProperties, structure_2, structureProperties_1, dependsOn, data, structure, structureProperties;
var _this = this;
return (0, tslib_1.__generator)(this, function (_b) {
switch (_b.label) {
case 0:
structures = [];
_i = 0, sources_1 = sources;
_b.label = 1;
case 1:
if (!(_i < sources_1.length)) return [3 /*break*/, 9];
_a = sources_1[_i], url = _a.url, format = _a.format, isBinary = _a.isBinary;
return [4 /*yield*/, this.plugin.builders.data.download({ url: url, isBinary: isBinary })];
case 2:
data_1 = _b.sent();
return [4 /*yield*/, this.plugin.builders.structure.parseTrajectory(data_1, format)];
case 3:
trajectory = _b.sent();
return [4 /*yield*/, this.plugin.builders.structure.createModel(trajectory)];
case 4:
model = _b.sent();
return [4 /*yield*/, this.plugin.builders.structure.insertModelProperties(model)];
case 5:
modelProperties = _b.sent();
return [4 /*yield*/, this.plugin.builders.structure.createStructure(modelProperties || model)];
case 6:
structure_2 = _b.sent();
return [4 /*yield*/, this.plugin.builders.structure.insertStructureProperties(structure_2)];
case 7:
structureProperties_1 = _b.sent();
structures.push({ ref: (structureProperties_1 === null || structureProperties_1 === void 0 ? void 0 : structureProperties_1.ref) || structure_2.ref });
_b.label = 8;
case 8:
_i++;
return [3 /*break*/, 1];
case 9:
// remove current structuresfrom hierarchy as they will be merged
// TODO only works with using loadStructuresFromUrlsAndMerge once
// need some more API metho to work with the hierarchy
this.plugin.managers.structure.hierarchy.updateCurrent(this.plugin.managers.structure.hierarchy.current.structures, 'remove');
dependsOn = structures.map(function (_a) {
var ref = _a.ref;
return ref;
});
data = this.plugin.state.data.build().toRoot().apply(MergeStructures, { structures: structures }, { dependsOn: dependsOn });
return [4 /*yield*/, data.commit()];
case 10:
structure = _b.sent();
return [4 /*yield*/, this.plugin.builders.structure.insertStructureProperties(structure)];
case 11:
structureProperties = _b.sent();
this.plugin.behaviors.canvas3d.initialized.subscribe(function (v) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, this.plugin.builders.structure.representation.applyPreset(structureProperties || structure, viewport_1.StructurePreset)];
case 1:
_a.sent();
return [2 /*return*/];
}
});
}); });
return [2 /*return*/];
}
});
});
};
return Viewer;
}());
exports.DockingViewer = Viewer;
var MergeStructures = objects_1.PluginStateTransform.BuiltIn({
name: 'merge-structures',
display: { name: 'Merge Structures', description: 'Merge Structure' },
from: objects_1.PluginStateObject.Root,
to: objects_1.PluginStateObject.Molecule.Structure,
params: {
structures: param_definition_1.ParamDefinition.ObjectList({
ref: param_definition_1.ParamDefinition.Text('')
}, function (_a) {
var ref = _a.ref;
return ref;
}, { isHidden: true })
}
})({
apply: function (_a) {
var _this = this;
var params = _a.params, dependencies = _a.dependencies;
return mol_task_1.Task.create('Merge Structures', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
var first, builder, _i, _a, ref, s, _b, _c, unit, structure;
return (0, tslib_1.__generator)(this, function (_d) {
if (params.structures.length === 0)
return [2 /*return*/, mol_state_1.StateObject.Null];
first = dependencies[params.structures[0].ref].data;
builder = structure_1.Structure.Builder({ masterModel: first.models[0] });
for (_i = 0, _a = params.structures; _i < _a.length; _i++) {
ref = _a[_i].ref;
s = dependencies[ref].data;
for (_b = 0, _c = s.units; _b < _c.length; _b++) {
unit = _c[_b];
// TODO invariantId
builder.addUnit(unit.kind, unit.model, unit.conformation.operator, unit.elements, unit.traits);
}
}
structure = builder.getStructure();
return [2 /*return*/, new objects_1.PluginStateObject.Molecule.Structure(structure, { label: 'Merged Structure' })];
});
}); });
}
});
window.DockingViewer = Viewer;
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