diff --git a/src/mol-model-props/rcsb/graphql/symmetry.gql.ts b/src/mol-model-props/rcsb/graphql/symmetry.gql.ts
index d442467aa317be0a3eea756408014b3b413ff145..264166e3ac2ff8bd808f9b8c887b4114068abaf8 100644
--- a/src/mol-model-props/rcsb/graphql/symmetry.gql.ts
+++ b/src/mol-model-props/rcsb/graphql/symmetry.gql.ts
@@ -2,12 +2,16 @@
function gql (strs: TemplateStringsArray) { return strs.raw.join('') }
export default
-gql`query AssemblySymmetry($pdbId: String) {
+gql`query AssemblySymmetry($pdbId: String!) {
assemblies(pdbId: $pdbId) {
assembly_id
rcsb_assembly_symmetry {
source
symmetry_features {
+ symmetry {
+ description
+ value
+ }
clusters {
members
avg_rmsd
@@ -16,9 +20,6 @@ gql`query AssemblySymmetry($pdbId: String) {
description
value
}
- symmetry {
- space_group_name_h_m
- }
symmetry_axes {
start
end
diff --git a/src/mol-model-props/rcsb/graphql/types.ts b/src/mol-model-props/rcsb/graphql/types.ts
index b75b4b0aea64045ce0d4909fd58cc18e34cef3bc..a5c7ebb3ed520bff17eafc1e4d8cd075c49f1202 100644
--- a/src/mol-model-props/rcsb/graphql/types.ts
+++ b/src/mol-model-props/rcsb/graphql/types.ts
@@ -1,5 +1,5 @@
/* tslint:disable */
-/** Generated in 2018-08-17T12:05:55-07:00 */
+/** Generated in 2018-08-20T10:50:59-07:00 */
export enum PdbxLeavingAtomFlag {
N = "N",
@@ -31,7 +31,7 @@ export enum ExperimentalSupport {
SURFACE_PLASMON_RESONANCE = "SURFACE_PLASMON_RESONANCE"
}
-export enum Type {
+export enum SymmetryFeatureType {
GLOBAL = "GLOBAL",
LOCAL = "LOCAL",
PSEUDO = "PSEUDO"
@@ -42,12 +42,6 @@ export enum UnpublishedFlag {
Y = "Y"
}
-export enum PdbxDiffrnProtocol {
- LAUE = "LAUE",
- MAD = "MAD",
- SINGLE_WAVELENGTH = "SINGLE_WAVELENGTH"
-}
-
export enum PdbxMonochromaticOrLaueML {
L = "L",
M = "M"
@@ -59,17 +53,6 @@ export enum PdbxScatteringType {
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"
@@ -115,12 +98,55 @@ export enum VitrificationApplied {
YES = "YES"
}
+export enum Type {
+ NEGATIVE = "NEGATIVE",
+ NONE = "NONE",
+ POSITIVE = "POSITIVE"
+}
+
export enum SrcMethod {
MAN = "MAN",
NAT = "NAT",
SYN = "SYN"
}
+export enum EntityType {
+ MACROLIDE = "MACROLIDE",
+ NON_POLYMER = "NON_POLYMER",
+ POLYMER = "POLYMER",
+ WATER = "WATER"
+}
+
+export enum EntityPolyType {
+ CYCLIC_PSEUDO_PEPTIDE = "CYCLIC_PSEUDO_PEPTIDE",
+ OTHER = "OTHER",
+ PEPTIDE_NUCLEIC_ACID = "PEPTIDE_NUCLEIC_ACID",
+ POLYDEOXYRIBONUCLEOTIDE = "POLYDEOXYRIBONUCLEOTIDE",
+ POLYDEOXYRIBONUCLEOTIDE_POLYRIBONUCLEOTIDE_HYBRID = "POLYDEOXYRIBONUCLEOTIDE_POLYRIBONUCLEOTIDE_HYBRID",
+ POLYPEPTIDE_D = "POLYPEPTIDE_D",
+ POLYPEPTIDE_L = "POLYPEPTIDE_L",
+ POLYRIBONUCLEOTIDE = "POLYRIBONUCLEOTIDE",
+ POLYSACCHARIDE_D = "POLYSACCHARIDE_D",
+ POLYSACCHARIDE_L = "POLYSACCHARIDE_L"
+}
+
+export enum RcsbHostOrganismSource {
+ MMCIF = "MMCIF",
+ NCBI = "NCBI",
+ UNIPROT = "UNIPROT"
+}
+
+export enum RcsbMembraneSource {
+ HOMOLOGY = "HOMOLOGY",
+ MPSTRUCT = "MPSTRUCT"
+}
+
+export enum RcsbOrganismSource {
+ MMCIF = "MMCIF",
+ NCBI = "NCBI",
+ UNIPROT = "UNIPROT"
+}
+
export enum Level {
_100 = "_100",
_30 = "_30",
@@ -140,7 +166,7 @@ export enum PdbFormatCompatible {
export namespace AssemblySymmetry {
export type Variables = {
- readonly pdbId?: string | null;
+ readonly pdbId: string;
};
export type Query = {
@@ -150,46 +176,47 @@ export namespace AssemblySymmetry {
export type Assemblies = {
readonly __typename?: "CoreAssembly";
- readonly assembly_id?: number | null;
+ readonly assembly_id: number;
readonly rcsb_assembly_symmetry?: RcsbAssemblySymmetry | null;
};
export type RcsbAssemblySymmetry = {
readonly __typename?: "RcsbAssemblySymmetry";
- readonly source?: string | null;
- readonly symmetry_features?: ReadonlyArray<SymmetryFeatures | null> | null;
+ readonly source: string;
+ readonly symmetry_features: ReadonlyArray<SymmetryFeatures | null>;
};
export type SymmetryFeatures = {
readonly __typename?: "SymmetryFeature";
- readonly clusters?: ReadonlyArray<Clusters | null> | null;
- readonly stoichiometry?: Stoichiometry | null;
- readonly symmetry?: Symmetry | null;
+ readonly symmetry: Symmetry;
+ readonly clusters: ReadonlyArray<Clusters | null>;
+ readonly stoichiometry: Stoichiometry;
readonly symmetry_axes?: ReadonlyArray<SymmetryAxes | null> | null;
- readonly type?: Type | null;
+ readonly type: SymmetryFeatureType;
+ };
+
+ export type Symmetry = {
+ readonly __typename?: "QuaternarySymmetry";
+ readonly description: string;
+ readonly value: string;
};
export type Clusters = {
readonly __typename?: "Cluster";
- readonly members?: ReadonlyArray<string | null> | null;
+ readonly members: ReadonlyArray<string | null>;
readonly avg_rmsd?: number | null;
};
export type Stoichiometry = {
readonly __typename?: "Stoichiometry";
- readonly description?: string | null;
- readonly value?: ReadonlyArray<string | null> | null;
- };
-
- export type Symmetry = {
- readonly __typename?: "Symmetry";
- readonly space_group_name_h_m?: string | null;
+ readonly description: string;
+ readonly value: ReadonlyArray<string | null>;
};
export type SymmetryAxes = {
readonly __typename?: "SymmetryAxis";
- readonly start?: ReadonlyArray<number | null> | null;
- readonly end?: ReadonlyArray<number | null> | null;
+ readonly start: ReadonlyArray<number | null>;
+ readonly end: ReadonlyArray<number | null>;
readonly order?: number | null;
};
}
diff --git a/src/mol-model-props/rcsb/symmetry.ts b/src/mol-model-props/rcsb/symmetry.ts
index 7690babf4ba6616c4089491ebc578a98f105f4b1..b3114645c81af51635607625ccdd9b592f86f210 100644
--- a/src/mol-model-props/rcsb/symmetry.ts
+++ b/src/mol-model-props/rcsb/symmetry.ts
@@ -15,6 +15,8 @@ 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';
+import { toTable } from 'mol-io/reader/cif/schema';
+import { CifCategory } from 'mol-io/reader/cif';
const { str, int, float, Aliased, Vector, List } = Column.Schema;
@@ -38,28 +40,31 @@ function createDatabase(assemblies: ReadonlyArray<AssemblySymmetryGraphQL.Assemb
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_assembly_symmetry!.source!
- const symmetry_features = a.rcsb_assembly_symmetry!.symmetry_features!
+ const { assembly_id: _assembly_id, rcsb_assembly_symmetry } = assemblies[i]
+ if (!rcsb_assembly_symmetry) continue
+ const assembly_id = _assembly_id.toString() // TODO type will be fixed to string upstream
+ const source = rcsb_assembly_symmetry.source
+ const symmetry_features = rcsb_assembly_symmetry.symmetry_features
for (let j = 0, jl = symmetry_features.length; j < jl; ++j) {
- const f = symmetry_features[j]!
+ const f = symmetry_features[j]! // TODO upstream, array members should not be nullable
featureRows.push({
id,
assembly_id,
source,
- type: f.type!,
- stoichiometry_value: (f.stoichiometry!.value!) as string[],
- stoichiometry_description: f.stoichiometry!.description!
+ type: f.type,
+ stoichiometry_value: f.stoichiometry.value as string[], // TODO upstream, array members should not be nullable
+ stoichiometry_description: f.stoichiometry.description,
+ symmetry_value: f.symmetry.value,
+ symmetry_description: f.symmetry.description
})
const clusters = f.clusters
if (clusters) {
for (let k = 0, kl = clusters.length; k < kl; ++k) {
- const c = clusters[k]!
+ const c = clusters[k]! // TODO upstream, array members should not be nullable
clusterRows.push({
feature_id: id,
- avg_rmsd: c.avg_rmsd!,
+ avg_rmsd: c.avg_rmsd || 0, // TODO upstream, should not be nullable, or???
members: c.members as string[]
})
}
@@ -71,9 +76,9 @@ function createDatabase(assemblies: ReadonlyArray<AssemblySymmetryGraphQL.Assemb
const a = axes[k]!
axisRows.push({
feature_id: id,
- order: a.order!,
- start: a.start as Tensor.Data,
- end: a.end as Tensor.Data
+ order: a.order!, // TODO upstream, should not be nullable, or???
+ start: a.start as Tensor.Data, // TODO upstream, array members should not be nullable
+ end: a.end as Tensor.Data // TODO upstream, array members should not be nullable
})
}
}
@@ -83,9 +88,9 @@ function createDatabase(assemblies: ReadonlyArray<AssemblySymmetryGraphQL.Assemb
}
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)
+ rcsb_assembly_symmetry_feature: Table.ofRows(Schema.rcsb_assembly_symmetry_feature, featureRows),
+ rcsb_assembly_symmetry_cluster: Table.ofRows(Schema.rcsb_assembly_symmetry_cluster, clusterRows),
+ rcsb_assembly_symmetry_axis: Table.ofRows(Schema.rcsb_assembly_symmetry_axis, axisRows)
})
}
@@ -107,22 +112,39 @@ const client = new GraphQLClient('http://rest-experimental.rcsb.org/graphql')
export namespace AssemblySymmetry {
export const Schema = {
rcsb_assembly_symmetry_feature: {
+ /** Uniquely identifies a record in `rcsb_assembly_symmetry_feature` */
id: int,
+ /** A pointer to `pdbx_struct_assembly.id` */
assembly_id: str,
+ /** Name and version of software used to calculate protein symmetry */
source: str,
+ /** Type of protein symmetry */
type: Aliased<'GLOBAL' | 'LOCAL' | 'PSEUDO'>(str),
+ /** Quantitative description of every individual subunit in a given protein */
stoichiometry_value: List(',', x => x),
- stoichiometry_description: str
+ /** Oligomeric state for a given composition of subunits */
+ stoichiometry_description: str,
+ /** Point group symmetry value */
+ symmetry_value: str,
+ /** Point group symmetry description */
+ symmetry_description: str
},
rcsb_assembly_symmetry_cluster: {
+ /** A pointer to `rcsb_assembly_symmetry_feature.id` */
feature_id: int,
+ /** Average RMSD between members of a given cluster */
avg_rmsd: float,
+ /** List of `auth_label_id` values */
members: List(',', x => x)
},
rcsb_assembly_symmetry_axis: {
+ /** A pointer to `rcsb_assembly_symmetry_feature.id` */
feature_id: int,
+ /** The order of the symmetry axis */
order: int,
+ /** The x,y,z coordinate of the start point of a symmetry axis */
start: Vector(3),
+ /** The x,y,z coordinate of the end point of a symmetry axis */
end: Vector(3)
}
}
@@ -131,17 +153,49 @@ export namespace AssemblySymmetry {
export const Descriptor = _Descriptor;
- export async function attachFromRCSB(model: Model) {
+ export async function attachFromCifOrAPI(model: Model) {
if (model.customProperties.has(Descriptor)) return true;
- const variables: AssemblySymmetryGraphQL.Variables = { pdbId: model.label.toLowerCase() };
- const result = await client.request<AssemblySymmetryGraphQL.Query>(query, variables);
- if (!result || !result.assemblies) return false;
+ let db: Database
+
+ if (model.sourceData.kind === 'mmCIF' && model.sourceData.frame.categoryNames.includes('rcsb_assembly_symmetry_feature')) {
+ const rcsb_assembly_symmetry_feature = toTable(Schema.rcsb_assembly_symmetry_feature, model.sourceData.frame.categories.rcsb_assembly_symmetry_feature)
+
+ let rcsb_assembly_symmetry_cluster
+ if (model.sourceData.frame.categoryNames.includes('rcsb_assembly_symmetry_cluster')) {
+ rcsb_assembly_symmetry_cluster = toTable(Schema.rcsb_assembly_symmetry_cluster, model.sourceData.frame.categories.rcsb_assembly_symmetry_cluster)
+ } else {
+ rcsb_assembly_symmetry_cluster = CifCategory.empty
+ }
+
+ let rcsb_assembly_symmetry_axis
+ if (model.sourceData.frame.categoryNames.includes('rcsb_assembly_symmetry_axis')) {
+ rcsb_assembly_symmetry_axis = toTable(Schema.rcsb_assembly_symmetry_axis, model.sourceData.frame.categories.rcsb_assembly_symmetry_axis)
+ } else {
+ rcsb_assembly_symmetry_axis = CifCategory.empty
+ }
+
+ db = _Database.ofTables('assembly_symmetry', Schema, {
+ rcsb_assembly_symmetry_feature,
+ rcsb_assembly_symmetry_cluster,
+ rcsb_assembly_symmetry_axis
+ })
+ } else {
+ let result: AssemblySymmetryGraphQL.Query
+ const variables: AssemblySymmetryGraphQL.Variables = { pdbId: model.label.toLowerCase() };
+ try {
+ result = await client.request<AssemblySymmetryGraphQL.Query>(query, variables);
+ } catch (e) {
+ console.error(e)
+ return false;
+ }
+ if (!result || !result.assemblies) return false;
+
+ db = createDatabase(result.assemblies as ReadonlyArray<AssemblySymmetryGraphQL.Assemblies>)
+ }
- const db: Database = createDatabase(result.assemblies as ReadonlyArray<AssemblySymmetryGraphQL.Assemblies>)
model.customProperties.add(Descriptor);
model._staticPropertyData.__AssemblySymmetry__ = db;
-
return true;
}
diff --git a/src/servers/model/properties.ts b/src/servers/model/properties.ts
index 95d1ade02545101bc935dd7644540de94f0ddf8f..fddf09e61fceea5f1f97ee5bc320eebac31ff351 100644
--- a/src/servers/model/properties.ts
+++ b/src/servers/model/properties.ts
@@ -7,13 +7,13 @@
import { Model } from 'mol-model/structure';
import { PDBe_structureQualityReport } from './properties/pdbe';
+import { RCSB_assemblySymmetry } from './properties/rcsb';
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 [
- PDBe_structureQualityReport(model)
- // removed for now because of schema validation error
- // SymmetryAnnotation.attachFromRCSB(model)
+ PDBe_structureQualityReport(model),
+ RCSB_assemblySymmetry(model)
];
}
\ No newline at end of file
diff --git a/src/servers/model/properties/rcsb.ts b/src/servers/model/properties/rcsb.ts
new file mode 100644
index 0000000000000000000000000000000000000000..fbc3347d3f2812891f9fc36e4a1f0387bda80a31
--- /dev/null
+++ b/src/servers/model/properties/rcsb.ts
@@ -0,0 +1,12 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Model } from 'mol-model/structure';
+import { AssemblySymmetry } from 'mol-model-props/rcsb/symmetry';
+
+export function RCSB_assemblySymmetry(model: Model) {
+ return AssemblySymmetry.attachFromCifOrAPI(model)
+}
\ No newline at end of file