updated rcsb assembly symmetry

data/rcsb-graphql/codegen.js

@@ -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: [

src/mol-model-props/rcsb/graphql/symmetry.gql.ts

@@ -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
             }
         }
     }

src/mol-model-props/rcsb/graphql/types.ts

@@ -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;
   };
 }

src/mol-model-props/rcsb/symmetry.ts

@@ -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__;
     }
 }