From 8802f518d7a16ad6296e52840678329e4177125a Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Fri, 3 Aug 2018 18:26:57 -0700
Subject: [PATCH] wip, symmetry annotation, graphql schema codegen
---
data/rcsb-graphql/codegen.js | 18 ++
data/rcsb-graphql/codegen.json | 8 +
package-lock.json | Bin 399947 -> 418525 bytes
package.json | 9 +-
src/servers/model/properties.ts | 5 +-
.../properties/rcsb/graphql/symmetry.gql.ts | 28 +++
.../model/properties/rcsb/graphql/types.ts | 197 ++++++++++++++++++
src/servers/model/properties/rcsb/symmetry.ts | 150 +++++++++++++
src/servers/model/test.ts | 17 +-
9 files changed, 427 insertions(+), 5 deletions(-)
create mode 100644 data/rcsb-graphql/codegen.js
create mode 100644 data/rcsb-graphql/codegen.json
create mode 100644 src/servers/model/properties/rcsb/graphql/symmetry.gql.ts
create mode 100644 src/servers/model/properties/rcsb/graphql/types.ts
create mode 100644 src/servers/model/properties/rcsb/symmetry.ts
diff --git a/data/rcsb-graphql/codegen.js b/data/rcsb-graphql/codegen.js
new file mode 100644
index 000000000..e66716d8e
--- /dev/null
+++ b/data/rcsb-graphql/codegen.js
@@ -0,0 +1,18 @@
+const { generate } = require('graphql-code-generator')
+const path = require('path')
+
+const basePath = path.join(__dirname, '..', '..', 'src', 'servers', 'model', 'properties', 'rcsb', 'graphql')
+
+generate({
+ args: [
+ path.join(basePath, 'symmetry.gql.ts')
+ ],
+ schema: 'http://rest-experimental.rcsb.org/graphql',
+ template: 'typescript',
+ out: path.join(basePath),
+ skipSchema: true,
+ overwrite: true,
+ config: path.join(__dirname, 'codegen.json')
+}, true).then(
+ console.log('done')
+).catch(e => console.error(e))
\ No newline at end of file
diff --git a/data/rcsb-graphql/codegen.json b/data/rcsb-graphql/codegen.json
new file mode 100644
index 000000000..a005e9369
--- /dev/null
+++ b/data/rcsb-graphql/codegen.json
@@ -0,0 +1,8 @@
+{
+ "flattenTypes": false,
+ "generatorConfig": {
+ "printTime": true,
+ "immutableTypes": true,
+ "resolvers": false
+ }
+}
\ No newline at end of file
diff --git a/package-lock.json b/package-lock.json
index d150b46ca731750dc9d2ed16995cbadd4e52fed2..7c984dd0b938e852ed5cd265f4bf59b79e191c9b 100644
GIT binary patch
delta 8462
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delta 317
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diff --git a/package.json b/package.json
index dead84e32..0627484b0 100644
--- a/package.json
+++ b/package.json
@@ -12,9 +12,9 @@
},
"scripts": {
"lint": "tslint src/**/*.ts",
- "build": "cpx \"src/**/*.{vert,frag,glsl,scss,woff,woff2,ttf,otf,eot,svg,html}\" build/node_modules/ && tsc",
+ "build": "cpx \"src/**/*.{vert,frag,glsl,scss,woff,woff2,ttf,otf,eot,svg,html,gql}\" build/node_modules/ && tsc",
"watch": "tsc -watch",
- "watch-extra": "cpx \"src/**/*.{vert,frag,glsl,scss,woff,woff2,ttf,otf,eot,svg,html}\" build/node_modules/ --watch",
+ "watch-extra": "cpx \"src/**/*.{vert,frag,glsl,scss,woff,woff2,ttf,otf,eot,svg,html,gql}\" build/node_modules/ --watch",
"watch-all-win": "start cmd /K npm run watch & start cmd /K npm run watch-extra & start cmd /K npm run watch-viewer & start http-server -p 1338",
"test": "jest",
"build-viewer": "webpack build/node_modules/apps/viewer/index.js --mode development -o build/viewer/index.js",
@@ -84,6 +84,9 @@
"file-loader": "^1.1.11",
"glslify-import": "^3.1.0",
"glslify-loader": "^1.0.2",
+ "graphql-code-generator": "^0.10.5",
+ "graphql-codegen-typescript-template": "^0.10.5",
+ "graphql-tag": "^2.9.2",
"jest": "^23.4.2",
"jest-raw-loader": "^1.0.1",
"mini-css-extract-plugin": "^0.4.1",
@@ -104,6 +107,8 @@
"argparse": "^1.0.10",
"compression": "^1.7.3",
"express": "^4.16.3",
+ "graphql": "^0.13.2",
+ "graphql-request": "^1.8.0",
"immutable": "^4.0.0-rc.9",
"node-fetch": "^2.2.0",
"react": "^16.4.2",
diff --git a/src/servers/model/properties.ts b/src/servers/model/properties.ts
index b3486a48d..eafa41955 100644
--- a/src/servers/model/properties.ts
+++ b/src/servers/model/properties.ts
@@ -2,15 +2,18 @@
* Copyright (c) 2018 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>
*/
import { Model } from 'mol-model/structure';
import { StructureQualityReport } from './properties/structure-quality-report';
+import { SymmetryAnnotation } from './properties/rcsb/symmetry';
export function attachModelProperties(model: Model): Promise<any>[] {
// return a list of promises that start attaching the props in parallel
// (if there are downloads etc.)
return [
- StructureQualityReport.attachFromPDBeApi(model)
+ StructureQualityReport.attachFromPDBeApi(model),
+ SymmetryAnnotation.attachFromRCSB(model)
];
}
\ No newline at end of file
diff --git a/src/servers/model/properties/rcsb/graphql/symmetry.gql.ts b/src/servers/model/properties/rcsb/graphql/symmetry.gql.ts
new file mode 100644
index 000000000..0a01a456f
--- /dev/null
+++ b/src/servers/model/properties/rcsb/graphql/symmetry.gql.ts
@@ -0,0 +1,28 @@
+ // workaround so the query gets found by the codegen
+function gql (strs: TemplateStringsArray) { return strs.raw.join('') }
+
+export default
+gql`query RcsbSymmetry($pdbId: String) {
+ assemblies(pdbId: $pdbId) {
+ assembly_id
+ rcsb_annotation_symmetry {
+ source
+ symmetry_features {
+ type
+ clusters {
+ avg_rmsd
+ members
+ }
+ stoichiometry {
+ description
+ value
+ }
+ symmetry_axes {
+ order
+ start
+ end
+ }
+ }
+ }
+ }
+}`
\ No newline at end of file
diff --git a/src/servers/model/properties/rcsb/graphql/types.ts b/src/servers/model/properties/rcsb/graphql/types.ts
new file mode 100644
index 000000000..5283fa12d
--- /dev/null
+++ b/src/servers/model/properties/rcsb/graphql/types.ts
@@ -0,0 +1,197 @@
+/* tslint:disable */
+/** Generated in 2018-08-03T15:19:31-07:00 */
+
+export enum PdbxLeavingAtomFlag {
+ N = "N",
+ Y = "Y"
+}
+
+export enum PdbxStereoConfig {
+ N = "N",
+ R = "R",
+ S = "S"
+}
+
+export enum ExperimentalSupport {
+ ASSAY_FOR_OLIGOMERIZATION = "ASSAY_FOR_OLIGOMERIZATION",
+ CROSS_LINKING = "CROSS_LINKING",
+ EQUILIBRIUM_CENTRIFUGATION = "EQUILIBRIUM_CENTRIFUGATION",
+ FLUORESCENCE_RESONANCE_ENERGY_TRANSFER = "FLUORESCENCE_RESONANCE_ENERGY_TRANSFER",
+ GEL_FILTRATION = "GEL_FILTRATION",
+ HOMOLOGY = "HOMOLOGY",
+ IMMUNOPRECIPITATION = "IMMUNOPRECIPITATION",
+ ISOTHERMAL_TITRATION_CALORIMETRY = "ISOTHERMAL_TITRATION_CALORIMETRY",
+ LIGHT_SCATTERING = "LIGHT_SCATTERING",
+ MASS_SPECTROMETRY = "MASS_SPECTROMETRY",
+ MICROSCOPY = "MICROSCOPY",
+ NATIVE_GEL_ELECTROPHORESIS = "NATIVE_GEL_ELECTROPHORESIS",
+ NONE = "NONE",
+ SAXS = "SAXS",
+ SCANNING_TRANSMISSION_ELECTRON_MICROSCOPY = "SCANNING_TRANSMISSION_ELECTRON_MICROSCOPY",
+ SURFACE_PLASMON_RESONANCE = "SURFACE_PLASMON_RESONANCE"
+}
+
+export enum Type {
+ GLOBAL = "GLOBAL",
+ LOCAL = "LOCAL",
+ PSEUDO = "PSEUDO"
+}
+
+export enum UnpublishedFlag {
+ N = "N",
+ Y = "Y"
+}
+
+export enum PdbxDiffrnProtocol {
+ LAUE = "LAUE",
+ MAD = "MAD",
+ SINGLE_WAVELENGTH = "SINGLE_WAVELENGTH"
+}
+
+export enum PdbxMonochromaticOrLaueML {
+ L = "L",
+ M = "M"
+}
+
+export enum PdbxScatteringType {
+ ELECTRON = "ELECTRON",
+ NEUTRON = "NEUTRON",
+ X_RAY = "X_RAY"
+}
+
+export enum Source {
+ ELECTRON_MICROSCOPE = "ELECTRON_MICROSCOPE",
+ FREE_ELECTRON_LASER = "FREE_ELECTRON_LASER",
+ LIQUID_ANODE = "LIQUID_ANODE",
+ NUCLEAR_REACTOR = "NUCLEAR_REACTOR",
+ ROTATING_ANODE = "ROTATING_ANODE",
+ SEALED_TUBE = "SEALED_TUBE",
+ SPALLATION_SOURCE = "SPALLATION_SOURCE",
+ SYNCHROTRON = "SYNCHROTRON"
+}
+
+export enum RefSpace {
+ REAL = "REAL",
+ RECIPROCAL = "RECIPROCAL"
+}
+
+export enum SymmetryType {
+ HELICAL = "HELICAL",
+ POINT = "POINT",
+ _2_D_CRYSTAL = "_2_D_CRYSTAL",
+ _3_D_CRYSTAL = "_3_D_CRYSTAL"
+}
+
+export enum AggregationState {
+ CELL = "CELL",
+ FILAMENT = "FILAMENT",
+ HELICAL_ARRAY = "HELICAL_ARRAY",
+ PARTICLE = "PARTICLE",
+ TISSUE = "TISSUE",
+ _2_D_ARRAY = "_2_D_ARRAY",
+ _3_D_ARRAY = "_3_D_ARRAY"
+}
+
+export enum ReconstructionMethod {
+ CRYSTALLOGRAPHY = "CRYSTALLOGRAPHY",
+ HELICAL = "HELICAL",
+ SINGLE_PARTICLE = "SINGLE_PARTICLE",
+ SUBTOMOGRAM_AVERAGING = "SUBTOMOGRAM_AVERAGING",
+ TOMOGRAPHY = "TOMOGRAPHY"
+}
+
+export enum EmbeddingApplied {
+ NO = "NO",
+ YES = "YES"
+}
+
+export enum StainingApplied {
+ NO = "NO",
+ YES = "YES"
+}
+
+export enum VitrificationApplied {
+ NO = "NO",
+ YES = "YES"
+}
+
+export enum SrcMethod {
+ MAN = "MAN",
+ NAT = "NAT",
+ SYN = "SYN"
+}
+
+export enum RcsbType {
+ DNA = "DNA",
+ HYBRID = "HYBRID",
+ OTHER = "OTHER",
+ POLYPEPTIDE = "POLYPEPTIDE",
+ RNA = "RNA"
+}
+
+export enum Level {
+ _100 = "_100",
+ _30 = "_30",
+ _40 = "_40",
+ _50 = "_50",
+ _60 = "_60",
+ _70 = "_70",
+ _80 = "_80",
+ _90 = "_90",
+ _95 = "_95"
+}
+
+export enum PdbFormatCompatible {
+ N = "N",
+ Y = "Y"
+}
+
+export namespace RcsbSymmetry {
+ export type Variables = {
+ readonly pdbId?: string | null;
+ };
+
+ export type Query = {
+ readonly __typename?: "Query";
+ readonly assemblies?: ReadonlyArray<Assemblies | null> | null;
+ };
+
+ export type Assemblies = {
+ readonly __typename?: "CoreAssembly";
+ readonly assembly_id?: number | null;
+ readonly rcsb_annotation_symmetry?: RcsbAnnotationSymmetry | null;
+ };
+
+ export type RcsbAnnotationSymmetry = {
+ readonly __typename?: "RcsbAnnotationSymmetry";
+ readonly source?: string | null;
+ readonly symmetry_features?: ReadonlyArray<SymmetryFeatures | null> | null;
+ };
+
+ export type SymmetryFeatures = {
+ readonly __typename?: "SymmetryFeature";
+ readonly type?: Type | null;
+ readonly clusters?: ReadonlyArray<Clusters | null> | null;
+ readonly stoichiometry?: Stoichiometry | null;
+ readonly symmetry_axes?: ReadonlyArray<SymmetryAxes | null> | null;
+ };
+
+ export type Clusters = {
+ readonly __typename?: "Cluster";
+ readonly avg_rmsd?: number | null;
+ readonly members?: ReadonlyArray<string | null> | null;
+ };
+
+ export type Stoichiometry = {
+ readonly __typename?: "Stoichiometry";
+ readonly description?: string | null;
+ readonly value?: ReadonlyArray<string | null> | null;
+ };
+
+ export type SymmetryAxes = {
+ readonly __typename?: "SymmetryAxis";
+ readonly order?: number | null;
+ readonly start?: ReadonlyArray<number | null> | null;
+ readonly end?: ReadonlyArray<number | null> | null;
+ };
+}
diff --git a/src/servers/model/properties/rcsb/symmetry.ts b/src/servers/model/properties/rcsb/symmetry.ts
new file mode 100644
index 000000000..e34934c8d
--- /dev/null
+++ b/src/servers/model/properties/rcsb/symmetry.ts
@@ -0,0 +1,150 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { GraphQLClient } from 'graphql-request'
+
+import { RcsbSymmetry } from './graphql/types';
+import query from './graphql/symmetry.gql';
+
+import { Model, ModelPropertyDescriptor } from 'mol-model/structure';
+import { CifWriter } from 'mol-io/writer/cif';
+import { Database as _Database, Column, Table } from 'mol-data/db'
+import { Category } from 'mol-io/writer/cif/encoder';
+import { Tensor } from 'mol-math/linear-algebra';
+import { CifExportContext } from 'mol-model/structure/export/mmcif';
+
+const { str, int, float, Aliased, Vector, List } = Column.Schema;
+
+function getInstance(name: keyof SymmetryAnnotation.Schema): (ctx: CifExportContext) => CifWriter.Category.Instance<any, any> {
+ return function(ctx: CifExportContext) {
+ const db = SymmetryAnnotation.get(ctx.model);
+ return db ? Category.ofTable(db[name]) : CifWriter.Category.Empty;
+ }
+}
+
+function getCategory(name: keyof SymmetryAnnotation.Schema) {
+ return { name, instance: getInstance(name) }
+}
+
+function createDatabase(assemblies: ReadonlyArray<RcsbSymmetry.Assemblies>): SymmetryAnnotation.Database {
+ const Schema = SymmetryAnnotation.Schema
+
+ const featureRows: Table.Row<typeof Schema.symmetry_annotation_feature>[] = []
+ const clusterRows: Table.Row<typeof Schema.symmetry_annotation_cluster>[] = []
+ const axisRows: Table.Row<typeof Schema.symmetry_annotation_axis>[] = []
+
+ let id = 0
+ for (let i = 0, il = assemblies.length; i < il; ++i) {
+ const a = assemblies[i]
+ const assembly_id = (a.assembly_id!).toString()
+ const source = a.rcsb_annotation_symmetry!.source!
+ const symmetry_features = a.rcsb_annotation_symmetry!.symmetry_features!
+ for (let j = 0, jl = symmetry_features.length; j < jl; ++j) {
+ const f = symmetry_features[j]!
+ featureRows.push({
+ id,
+ assembly_id,
+ source,
+ type: f.type!,
+ stoichiometry_value: (f.stoichiometry!.value!) as string[],
+ stoichiometry_description: f.stoichiometry!.description!
+ })
+
+ const clusters = f.clusters
+ if (clusters) {
+ for (let k = 0, kl = clusters.length; k < kl; ++k) {
+ const c = clusters[k]!
+ clusterRows.push({
+ feature_id: id,
+ avg_rmsd: c.avg_rmsd!,
+ members: c.members as string[]
+ })
+ }
+ }
+
+ const axes = f.symmetry_axes
+ if (axes) {
+ for (let k = 0, kl = axes.length; k < kl; ++k) {
+ const a = axes[k]!
+ axisRows.push({
+ feature_id: id,
+ order: a.order!,
+ start: a.start as Tensor.Data,
+ end: a.end as Tensor.Data
+ })
+ }
+ }
+
+ id += 1
+ }
+ }
+
+ return _Database.ofTables('symmetry_annotation', Schema, {
+ symmetry_annotation_feature: Table.ofRows(Schema.symmetry_annotation_feature, featureRows),
+ symmetry_annotation_cluster: Table.ofRows(Schema.symmetry_annotation_cluster, clusterRows),
+ symmetry_annotation_axis: Table.ofRows(Schema.symmetry_annotation_axis, axisRows)
+ })
+}
+
+const _Descriptor: ModelPropertyDescriptor = {
+ isStatic: true,
+ name: 'symmetry_annotation',
+ cifExport: {
+ categories: [
+ getCategory('symmetry_annotation_feature'),
+ getCategory('symmetry_annotation_cluster'),
+ getCategory('symmetry_annotation_axis')
+ ]
+ }
+}
+
+const client = new GraphQLClient('http://rest-experimental.rcsb.org/graphql')
+
+export namespace SymmetryAnnotation {
+ export const Schema = {
+ symmetry_annotation_feature: {
+ id: int,
+ assembly_id: str,
+ source: str,
+ type: Aliased<'GLOBAL' | 'LOCAL' | 'PSEUDO'>(str),
+ stoichiometry_value: List(',', x => x),
+ stoichiometry_description: str
+ },
+ symmetry_annotation_cluster: {
+ feature_id: int,
+ avg_rmsd: float,
+ members: List(',', x => x)
+ },
+ symmetry_annotation_axis: {
+ feature_id: int,
+ order: int,
+ start: Vector(3),
+ end: Vector(3)
+ }
+ }
+ export type Schema = typeof Schema
+ export interface Database extends _Database<Schema> {}
+
+ export const Descriptor = _Descriptor;
+
+ export async function attachFromRCSB(model: Model) {
+ if (model.customProperties.has(Descriptor)) return true;
+
+ const variables: RcsbSymmetry.Variables = { pdbId: model.label.toLowerCase() };
+ const result = await client.request<RcsbSymmetry.Query>(query, variables);
+ if (!result || !result.assemblies) return false;
+
+ const db: Database = createDatabase(result.assemblies as ReadonlyArray<RcsbSymmetry.Assemblies>)
+ model.customProperties.add(Descriptor);
+ model._staticPropertyData.__SymmetryAnnotation__ = db;
+
+ return true;
+ }
+
+ export function get(model: Model): Database | undefined {
+ return model._staticPropertyData.__SymmetryAnnotation__;
+ }
+}
\ No newline at end of file
diff --git a/src/servers/model/test.ts b/src/servers/model/test.ts
index 882c18b6a..14bafb1ba 100644
--- a/src/servers/model/test.ts
+++ b/src/servers/model/test.ts
@@ -1,5 +1,6 @@
import { resolveJob } from './server/query';
import * as fs from 'fs'
+import * as path from 'path'
import { StructureCache } from './server/structure-wrapper';
import { createJob } from './server/jobs';
@@ -33,13 +34,25 @@ function wrapFile(fn: string) {
return w;
}
+const basePath = path.join(__dirname, '..', '..', '..', '..')
+const examplesPath = path.join(basePath, 'examples')
+const outPath = path.join(basePath, 'build', 'test')
+if (!fs.existsSync(outPath)) fs.mkdirSync(outPath);
+
async function run() {
try {
- const request = createJob('_local_', 'e:/test/quick/1cbs_updated.cif', 'residueInteraction', { label_comp_id: 'REA' });
+ // const request = createJob('_local_', 'e:/test/quick/1cbs_updated.cif', 'residueInteraction', { label_comp_id: 'REA' });
+ // const encoder = await resolveJob(request);
+ // const writer = wrapFile('e:/test/mol-star/1cbs_full.cif');
+ // const testFile = '1crn.cif'
+ const testFile = '1grm_updated.cif'
+ const request = createJob('_local_', path.join(examplesPath, testFile), 'full', {});
const encoder = await resolveJob(request);
- const writer = wrapFile('e:/test/mol-star/1cbs_full.cif');
+ const writer = wrapFile(path.join(outPath, testFile));
encoder.writeTo(writer);
writer.end();
+ } catch (e) {
+ console.error(e)
} finally {
StructureCache.expireAll();
}
--
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