From 8d9604edf298fa55bc11503824fccd050e958f59 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Sun, 5 Nov 2017 16:12:09 +0100
Subject: [PATCH] domain annotation server (prototype)
---
package-lock.json | Bin 156627 -> 170121 bytes
package.json | 14 ++-
src/apps/domain-annotation-server/mapping.ts | 102 +++++++++++++++++++
src/apps/domain-annotation-server/schemas.ts | 89 ++++++++++++++++
src/apps/domain-annotation-server/server.ts | 48 +++++++++
src/apps/domain-annotation-server/test.ts | 14 +++
src/apps/domain-annotation-server/utils.ts | 43 ++++++++
src/mol-io/writer/cif/encoder.ts | 2 +-
8 files changed, 308 insertions(+), 4 deletions(-)
create mode 100644 src/apps/domain-annotation-server/mapping.ts
create mode 100644 src/apps/domain-annotation-server/schemas.ts
create mode 100644 src/apps/domain-annotation-server/server.ts
create mode 100644 src/apps/domain-annotation-server/test.ts
create mode 100644 src/apps/domain-annotation-server/utils.ts
diff --git a/package-lock.json b/package-lock.json
index 1ce79bb2dc8d4d8557caa3e2f73f46de4c4992d2..445a602d57c899a8e98f013ba74f05382363076a 100644
GIT binary patch
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diff --git a/package.json b/package.json
index d6ddc61c4..3185d9554 100644
--- a/package.json
+++ b/package.json
@@ -24,15 +24,20 @@
"transform": {
"\\.ts$": "<rootDir>/node_modules/ts-jest/preprocessor.js"
},
- "moduleDirectories": ["node_modules", "build/node_modules"],
+ "moduleDirectories": [
+ "node_modules",
+ "build/node_modules"
+ ],
"testRegex": "\\.spec\\.ts$"
},
"author": "",
"license": "MIT",
"devDependencies": {
"@types/benchmark": "^1.0.30",
+ "@types/express": "^4.0.39",
"@types/jest": "^21.1.5",
"@types/node": "^8.0.47",
+ "@types/node-fetch": "^1.6.7",
"benchmark": "^2.1.4",
"download-cli": "^1.0.5",
"jest": "^21.2.1",
@@ -45,8 +50,11 @@
"ts-jest": "^21.1.4",
"tslint": "^5.8.0",
"typescript": "^2.6.1",
- "uglify-js": "^3.1.6",
+ "uglify-js": "^3.1.7",
"util.promisify": "^1.0.0"
},
- "dependencies": {}
+ "dependencies": {
+ "express": "^4.16.2",
+ "node-fetch": "^1.7.3"
+ }
}
diff --git a/src/apps/domain-annotation-server/mapping.ts b/src/apps/domain-annotation-server/mapping.ts
new file mode 100644
index 000000000..4489cb959
--- /dev/null
+++ b/src/apps/domain-annotation-server/mapping.ts
@@ -0,0 +1,102 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Table } from 'mol-base/collections/database'
+import { CIFEncoder, create as createEncoder } from 'mol-io/writer/cif'
+import * as S from './schemas'
+import { getCategoryInstanceProvider } from './utils'
+
+export default function create(allData: any) {
+ const mols = Object.keys(allData);
+ if (!mols.length) return '#';
+
+ const data = allData[mols[0]];
+
+ const enc = createEncoder();
+ enc.startDataBlock(mols[0]);
+
+ for (const cat of Object.keys(S.categories)) {
+ writeDomain(enc, getDomain(cat, (S.categories as any)[cat], data));
+ }
+ return enc.getData();
+}
+
+interface DomainAnnotation {
+ name: string,
+ domains: Table<any>,
+ mappings: Table<S.mapping>
+}
+type MappingRow = Table.Row<S.mapping>;
+
+function writeDomain(enc: CIFEncoder<any>, domain: DomainAnnotation | undefined) {
+ if (!domain) return;
+ enc.writeCategory(getCategoryInstanceProvider(`pdbx_${domain.name}_domain_annotation`, domain.domains));
+ enc.writeCategory(getCategoryInstanceProvider(`pdbx_${domain.name}_domain_mapping`, domain.mappings));
+}
+
+function getMappings(startId: number, group_id: number, mappings: any): MappingRow[] {
+ const rows: MappingRow[] = [];
+
+ const n = (v: any) => v === null ? void 0 : v;
+
+ for (const entry of mappings) {
+ if (entry.start && entry.end) {
+ rows.push({
+ id: startId++,
+ group_id,
+ label_entity_id: '' + entry.entity_id,
+ label_asym_id: entry.struct_asym_id,
+ auth_asym_id: entry.chain_id,
+ beg_label_seq_id: n(entry.start.residue_number),
+ beg_auth_seq_id: n(entry.start.author_residue_number),
+ pdbx_beg_PDB_ins_code: entry.start.author_insertion_code,
+ end_label_seq_id: n(entry.end.residue_number),
+ end_auth_seq_id: n(entry.end.author_residue_number),
+ pdbx_end_PDB_ins_code: entry.end.author_insertion_code
+ });
+ } else {
+ rows.push({
+ id: startId++,
+ group_id,
+ label_entity_id: '' + entry.entity_id,
+ label_asym_id: entry.struct_asym_id,
+ auth_asym_id: entry.chain_id
+ } as any);
+ }
+ }
+ return rows;
+}
+
+function getDomainInfo(id: string, mapping_group_id: number, data: any, schema: any) {
+ const props = Object.create(null);
+ for (const k of Object.keys(schema)) props[k] = data[k];
+ return { id, mapping_group_id, identifier: data.identifier, ...props };
+}
+
+function getDomain(name: string, schema: any, allData: any) {
+ if (!allData[name]) return void 0;
+
+ const data = allData[name];
+
+ const domains: any[] = [];
+ const mappings: MappingRow[] = [];
+
+ let mappingSerialId = 1, mapping_group_id = 1;
+
+ for (const id of Object.keys(data)) {
+ const domain = data[id];
+ domains.push(getDomainInfo(id, mapping_group_id, domain, schema));
+ mappings.push(...getMappings(mappingSerialId, mapping_group_id, domain.mappings));
+ mappingSerialId = mappings.length + 1;
+ mapping_group_id++;
+ }
+
+ return domains.length > 0 ? {
+ name,
+ domains: Table.ofRows({ ...S.Base, ...schema }, domains),
+ mappings: Table.ofRows(S.mapping, mappings)
+ } : void 0;
+}
\ No newline at end of file
diff --git a/src/apps/domain-annotation-server/schemas.ts b/src/apps/domain-annotation-server/schemas.ts
new file mode 100644
index 000000000..370bf1786
--- /dev/null
+++ b/src/apps/domain-annotation-server/schemas.ts
@@ -0,0 +1,89 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Column } from 'mol-base/collections/database'
+
+import Type = Column.Type
+
+export const Base = {
+ id: Type.str,
+ identifier: Type.str,
+ mapping_group_id: Type.int
+}
+export type Base = typeof Base
+
+export const mapping = {
+ id: Type.int,
+ group_id: Type.int,
+
+ label_entity_id: Type.str,
+ label_asym_id: Type.str,
+ auth_asym_id: Type.str,
+
+ beg_label_seq_id: Type.int,
+ beg_auth_seq_id: Type.int,
+ pdbx_beg_PDB_ins_code: Type.str,
+
+ end_label_seq_id: Type.int,
+ end_auth_seq_id: Type.int,
+ pdbx_end_PDB_ins_code: Type.str
+}
+export type mapping = typeof mapping
+
+export const Pfam = {
+ description: Type.str
+}
+export type Pfam = typeof Pfam
+
+export const InterPro = {
+ name: Type.str
+}
+export type InterPro = typeof InterPro
+
+export const CATH = {
+ name: Type.str,
+ homology: Type.str,
+ architecture: Type.str,
+ identifier: Type.str,
+ class: Type.str,
+ topology: Type.str,
+}
+export type CATH = typeof CATH
+
+export const EC = {
+ accepted_name: Type.str,
+ reaction: Type.str,
+ systematic_name: Type.str
+}
+export type EC = typeof EC
+
+export const UniProt = {
+ name: Type.str
+}
+export type UniProt = typeof UniProt
+
+export const SCOP = {
+ sccs: Type.str,
+ description: Type.str
+}
+export type SCOP = typeof SCOP
+
+export const GO = {
+ category: Type.str,
+ definition: Type.str,
+ name: Type.str
+}
+export type GO = typeof GO
+
+export const categories = {
+ Pfam,
+ InterPro,
+ CATH,
+ EC,
+ UniProt,
+ SCOP,
+ GO
+}
\ No newline at end of file
diff --git a/src/apps/domain-annotation-server/server.ts b/src/apps/domain-annotation-server/server.ts
new file mode 100644
index 000000000..1d4f192ca
--- /dev/null
+++ b/src/apps/domain-annotation-server/server.ts
@@ -0,0 +1,48 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as express from 'express'
+import fetch from 'node-fetch'
+import createMapping from './mapping'
+
+async function getMappings(id: string) {
+ const data = await fetch(`https://www.ebi.ac.uk/pdbe/api/mappings/${id}`);
+ const json = await data.json();
+ return createMapping(json);
+};
+
+
+let PORT = process.env.port || 1338;
+
+const app = express();
+
+const PREFIX = '/'
+
+app.get(`${PREFIX}/:id`, async (req, res) => {
+ try {
+ console.log('Requesting ' + req.params.id);
+ const mapping = await getMappings(req.params.id);
+ res.writeHead(200, {
+ 'Content-Type': 'text/plain; charset=utf-8',
+ 'Access-Control-Allow-Origin': '*',
+ 'Access-Control-Allow-Headers': 'X-Requested-With'
+ });
+ res.end(mapping);
+ } catch {
+ console.log('Failed ' + req.params.id);
+ res.writeHead(404, { 'Access-Control-Allow-Origin': '*', 'Access-Control-Allow-Headers': 'X-Requested-With' });
+ res.end();
+ }
+});
+
+app.get(`${PREFIX}`, (req, res) => {
+ res.writeHead(200, { 'Content-Type': 'text/plain; charset=utf-8' });
+ res.end('Usage: /pdb_id, e.g. /1tqn');
+})
+
+app.listen(PORT);
+
+console.log('Running on port ' + PORT);
\ No newline at end of file
diff --git a/src/apps/domain-annotation-server/test.ts b/src/apps/domain-annotation-server/test.ts
new file mode 100644
index 000000000..66911dec6
--- /dev/null
+++ b/src/apps/domain-annotation-server/test.ts
@@ -0,0 +1,14 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import fetch from 'node-fetch'
+import createMapping from './mapping'
+
+(async function () {
+ const data = await fetch('https://www.ebi.ac.uk/pdbe/api/mappings/1tqn?pretty=true');
+ const json = await data.json();
+ console.log(createMapping(json));
+}());
\ No newline at end of file
diff --git a/src/apps/domain-annotation-server/utils.ts b/src/apps/domain-annotation-server/utils.ts
new file mode 100644
index 000000000..cb5c6badd
--- /dev/null
+++ b/src/apps/domain-annotation-server/utils.ts
@@ -0,0 +1,43 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Table } from 'mol-base/collections/database'
+import Iterator from 'mol-base/collections/iterator'
+import * as Encoder from 'mol-io/writer/cif'
+
+function columnValue(k: string) {
+ return (i: number, d: any) => d[k].value(i);
+}
+
+function columnValueKind(k: string) {
+ return (i: number, d: any) => d[k].valueKind(i);
+}
+
+function ofSchema(schema: Table.Schema) {
+ const fields: Encoder.FieldDefinition[] = [];
+ for (const k of Object.keys(schema)) {
+ const t = schema[k];
+ // TODO: matrix/vector/support
+ const type = t.kind === 'str' ? Encoder.FieldType.Str : t.kind === 'int' ? Encoder.FieldType.Int : Encoder.FieldType.Float;
+ fields.push({ name: k, type, value: columnValue(k), valueKind: columnValueKind(k) })
+ }
+ return fields;
+}
+
+function ofTable<S extends Table.Schema>(name: string, table: Table<S>): Encoder.CategoryDefinition<number> {
+ return { name, fields: ofSchema(table._schema) }
+}
+
+export function getCategoryInstanceProvider(name: string, table: Table<any>): Encoder.CategoryProvider {
+ return () => {
+ return {
+ data: table,
+ definition: ofTable(name, table),
+ keys: () => Iterator.Range(0, table._rowCount - 1),
+ rowCount: table._rowCount
+ };
+ }
+}
diff --git a/src/mol-io/writer/cif/encoder.ts b/src/mol-io/writer/cif/encoder.ts
index 64a18622f..f32bec34b 100644
--- a/src/mol-io/writer/cif/encoder.ts
+++ b/src/mol-io/writer/cif/encoder.ts
@@ -57,7 +57,7 @@ export interface CategoryProvider {
(ctx: any): CategoryInstance
}
-export interface CIFEncoder<T, Context> extends Encoder<T> {
+export interface CIFEncoder<T = string | Uint8Array, Context = any> extends Encoder<T> {
startDataBlock(header: string): void,
writeCategory(category: CategoryProvider, contexts?: Context[]): void,
getData(): T
--
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