molstar
Version:
A comprehensive macromolecular library.
97 lines (96 loc) • 4.45 kB
JavaScript
;
/**
* Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Dušan Veľký <dvelky@mail.muni.cz>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.TunnelsPreset = exports.SbNcbrTunnels = void 0;
exports.isApplicable = isApplicable;
const behavior_1 = require("../../../mol-plugin/behavior");
const actions_1 = require("./actions");
const param_definition_1 = require("../../../mol-util/param-definition");
const representation_preset_1 = require("../../../mol-plugin-state/builder/structure/representation-preset");
const structure_1 = require("../../../mol-model/structure");
const mol_state_1 = require("../../../mol-state");
const props_1 = require("./props");
const transforms_1 = require("../../../mol-plugin-state/transforms");
const representation_1 = require("./representation");
const mesh_utils_1 = require("../../meshes/mesh-utils");
exports.SbNcbrTunnels = behavior_1.PluginBehavior.create({
name: 'sb-ncbr-tunnels',
category: 'misc',
display: {
name: 'SB NCBR Tunnels',
},
ctor: class extends behavior_1.PluginBehavior.Handler {
register() {
this.ctx.state.data.actions.add(actions_1.DownloadTunnels);
this.ctx.builders.structure.representation.registerPreset(exports.TunnelsPreset);
}
unregister() {
this.ctx.state.data.actions.remove(actions_1.DownloadTunnels);
this.ctx.builders.structure.representation.unregisterPreset(exports.TunnelsPreset);
}
},
params: () => ({
autoAttach: param_definition_1.ParamDefinition.Boolean(true),
})
});
function isApplicable(structure) {
return (!!structure && structure.models.length === 1 &&
structure_1.Model.hasPdbId(structure.models[0]));
}
exports.TunnelsPreset = (0, representation_preset_1.StructureRepresentationPresetProvider)({
id: 'sb-ncbr-preset-structure-tunnels',
display: {
name: 'Tunnels', group: 'Annotation',
description: 'Shows Tunnels from ChannelsDB contained in the structure.'
},
isApplicable(a) {
return isApplicable(a.data);
},
params: (a, plugin) => {
return {
...representation_preset_1.StructureRepresentationPresetProvider.CommonParams,
...getConfiguredDefaultParams(plugin)
};
},
async apply(ref, params, plugin) {
var _a, _b;
const structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
const structure = (_a = structureCell === null || structureCell === void 0 ? void 0 : structureCell.obj) === null || _a === void 0 ? void 0 : _a.data;
if (!structureCell || !structure)
return {};
const update = plugin.build();
const webgl = (_b = plugin.canvas3dContext) === null || _b === void 0 ? void 0 : _b.webgl;
const response = await (await fetch(`${params.serverUrl}/channels/${params.serverType}/${structure.model.entryId.toLowerCase()}`)).json();
const tunnels = [];
Object.entries(response.Channels).forEach(([key, values]) => {
if (values.length > 0) {
values.forEach((item) => {
tunnels.push({ data: item.Profile, props: { id: item.Id, type: item.Type } });
});
}
});
await tunnels.forEach(async (tunnel) => {
await update
.toRoot()
.apply(representation_1.TunnelFromRawData, { data: tunnel })
.apply(representation_1.TunnelShapeProvider, {
webgl,
colorTheme: mesh_utils_1.ColorGenerator.next().value,
})
.apply(transforms_1.StateTransforms.Representation.ShapeRepresentation3D);
await update.commit();
});
const preset = await representation_preset_1.PresetStructureRepresentations.auto.apply(ref, { ...params }, plugin);
return { components: preset.components, representations: { ...preset.representations, } };
}
});
function getConfiguredDefaultParams(plugin) {
const config = (0, props_1.getTunnelsConfig)(plugin);
const params = param_definition_1.ParamDefinition.clone(props_1.TunnelsDataParams);
param_definition_1.ParamDefinition.setDefaultValues(params, { serverType: config.DefaultServerType, serverUrl: config.DefaultServerUrl });
return params;
}