molstar
Version:
A comprehensive macromolecular library.
87 lines (86 loc) • 3.58 kB
JavaScript
;
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.PDBePreferredAssembly = void 0;
const db_1 = require("../../mol-data/db");
const schema_1 = require("../../mol-io/reader/cif/schema");
const cif_1 = require("../../mol-io/writer/cif");
const symmetry_1 = require("../../mol-model-formats/structure/property/symmetry");
const mmcif_1 = require("../../mol-model-formats/structure/mmcif");
const custom_property_1 = require("../../mol-model/custom-property");
var PDBePreferredAssembly;
(function (PDBePreferredAssembly) {
function getFirstFromModel(model) {
const symmetry = symmetry_1.ModelSymmetry.Provider.get(model);
return (symmetry === null || symmetry === void 0 ? void 0 : symmetry.assemblies.length) ? symmetry.assemblies[0].id : '';
}
PDBePreferredAssembly.getFirstFromModel = getFirstFromModel;
function get(model) {
return model._staticPropertyData.__PDBePreferredAssebly__ || getFirstFromModel(model);
}
PDBePreferredAssembly.get = get;
function set(model, prop) {
model._staticPropertyData.__PDBePreferredAssebly__ = prop;
}
PDBePreferredAssembly.Schema = {
pdbe_preferred_assembly: {
assembly_id: db_1.Column.Schema.str
}
};
PDBePreferredAssembly.Descriptor = (0, custom_property_1.CustomPropertyDescriptor)({
name: 'pdbe_preferred_assembly',
cifExport: {
prefix: 'pdbe',
context(ctx) { return get(ctx.firstModel); },
categories: [{
name: 'pdbe_preferred_assembly',
instance(ctx) {
return cif_1.CifWriter.Category.ofTable(db_1.Table.ofArrays(PDBePreferredAssembly.Schema.pdbe_preferred_assembly, { assembly_id: [ctx] }));
}
}]
}
});
function fromCifData(model) {
if (!mmcif_1.MmcifFormat.is(model.sourceData))
return void 0;
const cat = model.sourceData.data.frame.categories.pdbe_preferred_assembly;
if (!cat)
return void 0;
return (0, schema_1.toTable)(PDBePreferredAssembly.Schema.pdbe_preferred_assembly, cat).assembly_id.value(0) || getFirstFromModel(model);
}
async function attachFromCifOrApi(model, params) {
if (model.customProperties.has(PDBePreferredAssembly.Descriptor))
return true;
let asmName = fromCifData(model);
if (asmName === void 0 && params.PDBe_apiSourceJson) {
const data = await params.PDBe_apiSourceJson(model);
if (!data)
return false;
asmName = asmNameFromJson(model, data);
}
else {
return false;
}
if (!asmName)
return false;
model.customProperties.add(PDBePreferredAssembly.Descriptor);
set(model, asmName);
return true;
}
PDBePreferredAssembly.attachFromCifOrApi = attachFromCifOrApi;
})(PDBePreferredAssembly || (exports.PDBePreferredAssembly = PDBePreferredAssembly = {}));
function asmNameFromJson(modelData, data) {
const assemblies = data[0] && data[0].assemblies;
if (!assemblies || !assemblies.length)
return PDBePreferredAssembly.getFirstFromModel(modelData);
for (const asm of assemblies) {
if (asm.preferred) {
return asm.assembly_id;
}
}
return assemblies[0].assembly_id;
}