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updated rcsb assembly symmetry

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This commit is contained in:
Alexander Rose
2018-08-17 12:08:08 -07:00
parent fa1a71fc22
commit 5ae732b226
4 changed files with 51 additions and 50 deletions
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2
data/rcsb-graphql/codegen.js
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@@ -1,7 +1,7 @@
const { generate } = require('graphql-code-generator')
const path = require('path')
const basePath = path.join(__dirname, '..', '..', 'src', 'servers', 'model', 'properties', 'rcsb', 'graphql')
const basePath = path.join(__dirname, '..', '..', 'src', 'mol-model-props', 'rcsb', 'graphql')
generate({
args: [

13
src/mol-model-props/rcsb/graphql/symmetry.gql.ts
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@@ -2,26 +2,29 @@
function gql (strs: TemplateStringsArray) { return strs.raw.join('') }
export default
gql`query RcsbSymmetry($pdbId: String) {
gql`query AssemblySymmetry($pdbId: String) {
assemblies(pdbId: $pdbId) {
assembly_id
rcsb_annotation_symmetry {
rcsb_assembly_symmetry {
source
symmetry_features {
type
clusters {
avg_rmsd
members
avg_rmsd
}
stoichiometry {
description
value
}
symmetry {
space_group_name_h_m
}
symmetry_axes {
order
start
end
order
}
type
}
}
}

30
src/mol-model-props/rcsb/graphql/types.ts
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@@ -1,5 +1,5 @@
/* tslint:disable */
/** Generated in 2018-08-03T15:19:31-07:00 */
/** Generated in 2018-08-17T12:05:55-07:00 */
export enum PdbxLeavingAtomFlag {
N = "N",
@@ -121,14 +121,6 @@ export enum SrcMethod {
SYN = "SYN"
}
export enum RcsbType {
DNA = "DNA",
HYBRID = "HYBRID",
OTHER = "OTHER",
POLYPEPTIDE = "POLYPEPTIDE",
RNA = "RNA"
}
export enum Level {
_100 = "_100",
_30 = "_30",
@@ -146,7 +138,7 @@ export enum PdbFormatCompatible {
Y = "Y"
}
export namespace RcsbSymmetry {
export namespace AssemblySymmetry {
export type Variables = {
readonly pdbId?: string | null;
};
@@ -159,27 +151,28 @@ export namespace RcsbSymmetry {
export type Assemblies = {
readonly __typename?: "CoreAssembly";
readonly assembly_id?: number | null;
readonly rcsb_annotation_symmetry?: RcsbAnnotationSymmetry | null;
readonly rcsb_assembly_symmetry?: RcsbAssemblySymmetry | null;
};
export type RcsbAnnotationSymmetry = {
readonly __typename?: "RcsbAnnotationSymmetry";
export type RcsbAssemblySymmetry = {
readonly __typename?: "RcsbAssemblySymmetry";
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?: Symmetry | null;
readonly symmetry_axes?: ReadonlyArray<SymmetryAxes | null> | null;
readonly type?: Type | null;
};
export type Clusters = {
readonly __typename?: "Cluster";
readonly avg_rmsd?: number | null;
readonly members?: ReadonlyArray<string | null> | null;
readonly avg_rmsd?: number | null;
};
export type Stoichiometry = {
@@ -188,10 +181,15 @@ export namespace RcsbSymmetry {
readonly value?: ReadonlyArray<string | null> | null;
};
export type Symmetry = {
readonly __typename?: "Symmetry";
readonly space_group_name_h_m?: string | null;
};
export type SymmetryAxes = {
readonly __typename?: "SymmetryAxis";
readonly order?: number | null;
readonly start?: ReadonlyArray<number | null> | null;
readonly end?: ReadonlyArray<number | null> | null;
readonly order?: number | null;
};
}

56
src/mol-model-props/rcsb/symmetry.ts
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@@ -6,7 +6,7 @@
import { GraphQLClient } from 'graphql-request'
import { RcsbSymmetry } from './graphql/types';
import { AssemblySymmetry as AssemblySymmetryGraphQL } from './graphql/types';
import query from './graphql/symmetry.gql';
import { Model, ModelPropertyDescriptor } from 'mol-model/structure';
@@ -18,30 +18,30 @@ 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> {
function getInstance(name: keyof AssemblySymmetry.Schema): (ctx: CifExportContext) => CifWriter.Category.Instance<any, any> {
return function(ctx: CifExportContext) {
const db = SymmetryAnnotation.get(ctx.model);
const db = AssemblySymmetry.get(ctx.model);
return db ? Category.ofTable(db[name]) : CifWriter.Category.Empty;
}
}
function getCategory(name: keyof SymmetryAnnotation.Schema) {
function getCategory(name: keyof AssemblySymmetry.Schema) {
return { name, instance: getInstance(name) }
}
function createDatabase(assemblies: ReadonlyArray<RcsbSymmetry.Assemblies>): SymmetryAnnotation.Database {
const Schema = SymmetryAnnotation.Schema
function createDatabase(assemblies: ReadonlyArray<AssemblySymmetryGraphQL.Assemblies>): AssemblySymmetry.Database {
const Schema = AssemblySymmetry.Schema
const featureRows: Table.Row<typeof Schema.rcsb_symmetry_annotation_feature>[] = []
const clusterRows: Table.Row<typeof Schema.rcsb_symmetry_annotation_cluster>[] = []
const axisRows: Table.Row<typeof Schema.rcsb_symmetry_annotation_axis>[] = []
const featureRows: Table.Row<typeof Schema.rcsb_assembly_symmetry_feature>[] = []
const clusterRows: Table.Row<typeof Schema.rcsb_assembly_symmetry_cluster>[] = []
const axisRows: Table.Row<typeof Schema.rcsb_assembly_symmetry_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!
const source = a.rcsb_assembly_symmetry!.source!
const symmetry_features = a.rcsb_assembly_symmetry!.symmetry_features!
for (let j = 0, jl = symmetry_features.length; j < jl; ++j) {
const f = symmetry_features[j]!
featureRows.push({
@@ -82,31 +82,31 @@ function createDatabase(assemblies: ReadonlyArray<RcsbSymmetry.Assemblies>): Sym
}
}
return _Database.ofTables('symmetry_annotation', Schema, {
symmetry_annotation_feature: Table.ofRows(Schema.rcsb_symmetry_annotation_feature, featureRows),
symmetry_annotation_cluster: Table.ofRows(Schema.rcsb_symmetry_annotation_cluster, clusterRows),
symmetry_annotation_axis: Table.ofRows(Schema.rcsb_symmetry_annotation_axis, axisRows)
return _Database.ofTables('assembly_symmetry', Schema, {
assembly_symmetry_feature: Table.ofRows(Schema.rcsb_assembly_symmetry_feature, featureRows),
assembly_symmetry_cluster: Table.ofRows(Schema.rcsb_assembly_symmetry_cluster, clusterRows),
assembly_symmetry_axis: Table.ofRows(Schema.rcsb_assembly_symmetry_axis, axisRows)
})
}
const _Descriptor: ModelPropertyDescriptor = {
isStatic: true,
name: 'symmetry_annotation',
name: 'assembly_symmetry',
cifExport: {
prefix: 'rcsb',
categories: [
getCategory('rcsb_symmetry_annotation_feature'),
getCategory('rcsb_symmetry_annotation_cluster'),
getCategory('rcsb_symmetry_annotation_axis')
getCategory('rcsb_assembly_symmetry_feature'),
getCategory('rcsb_assembly_symmetry_cluster'),
getCategory('rcsb_assembly_symmetry_axis')
]
}
}
const client = new GraphQLClient('http://rest-experimental.rcsb.org/graphql')
export namespace SymmetryAnnotation {
export namespace AssemblySymmetry {
export const Schema = {
rcsb_symmetry_annotation_feature: {
rcsb_assembly_symmetry_feature: {
id: int,
assembly_id: str,
source: str,
@@ -114,12 +114,12 @@ export namespace SymmetryAnnotation {
stoichiometry_value: List(',', x => x),
stoichiometry_description: str
},
rcsb_symmetry_annotation_cluster: {
rcsb_assembly_symmetry_cluster: {
feature_id: int,
avg_rmsd: float,
members: List(',', x => x)
},
rcsb_symmetry_annotation_axis: {
rcsb_assembly_symmetry_axis: {
feature_id: int,
order: int,
start: Vector(3),
@@ -134,18 +134,18 @@ export namespace SymmetryAnnotation {
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);
const variables: AssemblySymmetryGraphQL.Variables = { pdbId: model.label.toLowerCase() };
const result = await client.request<AssemblySymmetryGraphQL.Query>(query, variables);
if (!result || !result.assemblies) return false;
const db: Database = createDatabase(result.assemblies as ReadonlyArray<RcsbSymmetry.Assemblies>)
const db: Database = createDatabase(result.assemblies as ReadonlyArray<AssemblySymmetryGraphQL.Assemblies>)
model.customProperties.add(Descriptor);
model._staticPropertyData.__SymmetryAnnotation__ = db;
model._staticPropertyData.__AssemblySymmetry__ = db;
return true;
}
export function get(model: Model): Database | undefined {
return model._staticPropertyData.__SymmetryAnnotation__;
return model._staticPropertyData.__AssemblySymmetry__;
}
}