diff --git a/src/mol-model-props/pdbe/struct-ref-domain.ts b/src/mol-model-props/pdbe/struct-ref-domain.ts
new file mode 100644
index 0000000000000000000000000000000000000000..3872d5a4d470fe0056024f961385846925f79bfe
--- /dev/null
+++ b/src/mol-model-props/pdbe/struct-ref-domain.ts
@@ -0,0 +1,120 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Column, Table } from 'mol-data/db';
+import { toTable } from 'mol-io/reader/cif/schema';
+import { CifWriter } from 'mol-io/writer/cif';
+import { Model, ModelPropertyDescriptor } from 'mol-model/structure';
+import { PropertyWrapper } from '../common/wrapper';
+
+export namespace PDBeStructRefDomain {
+ export type Property = PropertyWrapper<Table<Schema['pdbe_struct_ref_domain']> | undefined>
+
+ export function get(model: Model): Property | undefined {
+ return model._staticPropertyData.__PDBeStructRefSeq__;
+ }
+ function set(model: Model, prop: Property) {
+ (model._staticPropertyData.__PDBeStructRefSeq__ as Property) = prop;
+ }
+
+ export const Schema = {
+ pdbe_struct_ref_domain: {
+ id: Column.Schema.int,
+ db_name: Column.Schema.str,
+ db_code: Column.Schema.str,
+
+ identifier: Column.Schema.str,
+ name: Column.Schema.str,
+
+ label_entity_id: Column.Schema.str,
+ label_asym_id: Column.Schema.str,
+ beg_label_seq_id: Column.Schema.int,
+ beg_pdbx_PDB_ins_code: Column.Schema.str,
+ end_label_seq_id: Column.Schema.int,
+ end_pdbx_PDB_ins_code: Column.Schema.str
+ }
+ };
+ export type Schema = typeof Schema
+
+ export const Descriptor = ModelPropertyDescriptor({
+ isStatic: true,
+ name: 'pdbe_struct_ref_domain',
+ cifExport: {
+ prefix: 'pdbe',
+ context(ctx): Property { return get(ctx.firstModel)!; },
+ categories: [
+ PropertyWrapper.defaultInfoCategory<Property>('pdbe_struct_ref_domain_info', ctx => ctx.info),
+ {
+ name: 'pdbe_struct_ref_domain',
+ instance(ctx: Property) {
+ if (!ctx || !ctx.data) return CifWriter.Category.Empty;
+ return CifWriter.Category.ofTable(ctx.data);
+ }
+ }]
+ }
+ });
+
+ function fromCifData(model: Model): Property['data'] {
+ if (model.sourceData.kind !== 'mmCIF') return void 0;
+ const cat = model.sourceData.frame.categories.pdbe_struct_ref_domain;
+ if (!cat) return void 0;
+ return toTable(Schema.pdbe_struct_ref_domain, cat);
+ }
+
+ export async function attachFromCifOrApi(model: Model, params: {
+ // optional JSON source
+ PDBe_apiSourceJson?: (model: Model) => Promise<any>
+ }) {
+ if (model.customProperties.has(Descriptor)) return true;
+
+
+ let table: Property['data'];
+ let info = PropertyWrapper.tryGetInfoFromCif('pdbe_struct_ref_domain_info', model);
+ if (info) {
+ table = fromCifData(model);
+ } else if (params.PDBe_apiSourceJson) {
+ const data = await params.PDBe_apiSourceJson(model);
+ if (!data) return false;
+ info = PropertyWrapper.createInfo();
+ table = fromPDBeJson(model, data);
+ } else {
+ return false;
+ }
+
+ model.customProperties.add(Descriptor);
+ set(model, { info, data: table });
+ return true;
+ }
+}
+
+function fromPDBeJson(modelData: Model, data: any): PDBeStructRefDomain.Property['data'] {
+ const rows: Table.Row<PDBeStructRefDomain.Schema['pdbe_struct_ref_domain']>[] = [];
+
+ let id = 1;
+ for (const db_name of Object.keys(data)) {
+ const db = data[db_name];
+ for (const db_code of Object.keys(db)) {
+ const domain = db[db_code];
+ for (const map of domain.mappings) {
+ rows.push({
+ id: id++,
+ db_name,
+ db_code,
+ identifier: domain.identifier,
+ name: domain.name,
+ label_entity_id: '' + map.entity_id,
+ label_asym_id: map.struct_asym_id,
+ beg_label_seq_id: map.start.residue_number,
+ beg_pdbx_PDB_ins_code: map.start.author_insertion_code,
+ end_label_seq_id: map.end.residue_number,
+ end_pdbx_PDB_ins_code: map.end.author_insertion_code,
+ })
+ }
+ }
+ }
+
+ return Table.ofRows(PDBeStructRefDomain.Schema.pdbe_struct_ref_domain, rows) as PDBeStructRefDomain.Property['data'];
+}
\ No newline at end of file
diff --git a/src/servers/model/properties/pdbe.ts b/src/servers/model/properties/pdbe.ts
index ca26bad669735f7fc2e9fea5ec5045093b56342c..7f678a19b7656c56395bf110236beb4f6b2a5973 100644
--- a/src/servers/model/properties/pdbe.ts
+++ b/src/servers/model/properties/pdbe.ts
@@ -6,13 +6,14 @@
*/
import { Model } from 'mol-model/structure';
-import { PDBe_structureQualityReport, PDBe_preferredAssembly } from './providers/pdbe';
+import { PDBe_structureQualityReport, PDBe_preferredAssembly, PDBe_structRefDomain } from './providers/pdbe';
export function attachModelProperties(model: Model, cache: object): Promise<any>[] {
// return a list of promises that start attaching the props in parallel
// (if there are downloads etc.)
return [
PDBe_structureQualityReport(model, cache),
- PDBe_preferredAssembly(model, cache)
+ PDBe_preferredAssembly(model, cache),
+ PDBe_structRefDomain(model, cache)
];
}
\ No newline at end of file
diff --git a/src/servers/model/properties/providers/pdbe.ts b/src/servers/model/properties/providers/pdbe.ts
index d0d60dc0bc3963ad9e90995e38fd11569a6388fc..31a04a731644b81f11e23de5ca463e0f5c78529a 100644
--- a/src/servers/model/properties/providers/pdbe.ts
+++ b/src/servers/model/properties/providers/pdbe.ts
@@ -10,6 +10,7 @@ import { StructureQualityReport } from 'mol-model-props/pdbe/structure-quality-r
import { fetchRetry } from '../../utils/fetch-retry';
import { UUID } from 'mol-util';
import { PDBePreferredAssembly } from 'mol-model-props/pdbe/preferred-assembly';
+import { PDBeStructRefDomain } from 'mol-model-props/pdbe/struct-ref-domain';
const USE_FILE_SOURCE = false;
@@ -29,10 +30,22 @@ export function PDBe_preferredAssembly(model: Model, cache: any) {
});
}
+export function PDBe_structRefDomain(model: Model, cache: any) {
+ return PDBeStructRefDomain.attachFromCifOrApi(model, {
+ PDBe_apiSourceJson: USE_FILE_SOURCE
+ ? void 0
+ : struct_ref_domain.getDataFromApiProvider(cache)
+ });
+}
+
namespace preferred_assembly {
export const getDataFromApiProvider = apiQueryProvider('https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary');
}
+namespace struct_ref_domain {
+ export const getDataFromApiProvider = apiQueryProvider('https://www.ebi.ac.uk/pdbe/api/mappings/sequence_domains');
+}
+
namespace residuewise_outlier_summary {
const json = new Map<string, any>();
diff --git a/src/servers/model/test.ts b/src/servers/model/test.ts
index 58dc7414865a62af1f384d04bbdaa276a16f00ae..8d7f85b1e4dcbd354389f57bb6227c346e728608 100644
--- a/src/servers/model/test.ts
+++ b/src/servers/model/test.ts
@@ -49,7 +49,7 @@ async function run() {
// queryName: 'full',
// queryParams: { },
// });
- const testFile = '1grm_updated.cif'
+ const testFile = '1cbs_updated.cif'
const request = createJob({
entryId: path.join(examplesPath, testFile),
queryName: 'full',