diff --git a/data/rcsb-graphql/codegen.js b/data/rcsb-graphql/codegen.js
index e818f2b193bb5a614c43e17fe356796d558b095f..65adefbd350baff8577435bde9bf24537073e805 100644
--- a/data/rcsb-graphql/codegen.js
+++ b/data/rcsb-graphql/codegen.js
@@ -8,7 +8,7 @@ generate({
path.join(basePath, 'symmetry.gql.ts')
],
schema: 'http://rest-experimental.rcsb.org/graphql',
- template: 'typescript',
+ template: 'graphql-codegen-typescript-template',
out: path.join(basePath),
skipSchema: true,
overwrite: true,
diff --git a/data/rcsb-graphql/codegen.json b/data/rcsb-graphql/codegen.json
index a005e9369d5807dfdd581297c9556aa8a08ccbba..3046d2483f176f5b1b29d686dba6a22d7510d09b 100644
--- a/data/rcsb-graphql/codegen.json
+++ b/data/rcsb-graphql/codegen.json
@@ -1,5 +1,5 @@
{
- "flattenTypes": false,
+ "flattenTypes": true,
"generatorConfig": {
"printTime": true,
"immutableTypes": true,
diff --git a/src/apps/canvas/assembly-symmetry.ts b/src/apps/canvas/assembly-symmetry.ts
index 1cc665a5b96b6d4763341d13ab843f0bdaea2b40..0fe6a734730dd50f51c2a8af3ba15af36d5c0517 100644
--- a/src/apps/canvas/assembly-symmetry.ts
+++ b/src/apps/canvas/assembly-symmetry.ts
@@ -16,12 +16,12 @@ import { ColorTheme } from 'mol-theme/color';
import { Location } from 'mol-model/location';
import { StructureElement, Unit, StructureProperties } from 'mol-model/structure';
-export function getAxesShape(featureId: number, assemblySymmetry: AssemblySymmetry) {
- const f = assemblySymmetry.db.rcsb_assembly_symmetry_feature
- const feature = Table.pickRow(f, i => f.id.value(i) === featureId)
- if (!feature) return
+export function getAxesShape(symmetryId: number, assemblySymmetry: AssemblySymmetry) {
+ const s = assemblySymmetry.db.rcsb_assembly_symmetry
+ const symmetry = Table.pickRow(s, i => s.id.value(i) === symmetryId)
+ if (!symmetry) return
- const axes = assemblySymmetry.getAxes(featureId)
+ const axes = assemblySymmetry.getAxes(symmetryId)
if (!axes._rowCount) return
const vectorSpace = AssemblySymmetry.Schema.rcsb_assembly_symmetry_axis.start.space;
@@ -41,7 +41,7 @@ export function getAxesShape(featureId: number, assemblySymmetry: AssemblySymmet
addSphere(meshBuilder, end, radius, 2)
addCylinder(meshBuilder, start, end, 1, cylinderProps)
colors.push(Color(0xCCEE11))
- labels.push(`Axis ${i + 1} for ${feature.symmetry_value} ${feature.type.toLowerCase()} symmetry`)
+ labels.push(`Axis ${i + 1} for ${symmetry.kind} ${symmetry.type.toLowerCase()} symmetry`)
}
const mesh = meshBuilder.getMesh()
const shape = Shape.create('Axes', mesh, colors, labels)
@@ -51,46 +51,45 @@ export function getAxesShape(featureId: number, assemblySymmetry: AssemblySymmet
function getAsymId(unit: Unit): StructureElement.Property<string> {
switch (unit.kind) {
case Unit.Kind.Atomic:
- return StructureProperties.chain.auth_asym_id // TODO
+ return StructureProperties.chain.label_asym_id
case Unit.Kind.Spheres:
case Unit.Kind.Gaussians:
return StructureProperties.coarse.asym_id
}
}
-function memberKey (asym_id: string, oper_list_id?: number) {
- return `${asym_id}|${oper_list_id}`
+function clusterMemberKey (asym_id: string, oper_list_ids: string[]) {
+ return `${asym_id}-${oper_list_ids.join('x')}`
}
-export function getClusterColorTheme(featureId: number, assemblySymmetry: AssemblySymmetry): ColorTheme {
+export function getClusterColorTheme(symmetryId: number, assemblySymmetry: AssemblySymmetry): ColorTheme {
const DefaultColor = Color(0xCCCCCC)
- const f = assemblySymmetry.db.rcsb_assembly_symmetry_feature
- const feature = Table.pickRow(f, i => f.id.value(i) === featureId)
- if (!feature) return { granularity: 'uniform', color: () => DefaultColor }
+ const s = assemblySymmetry.db.rcsb_assembly_symmetry
+ const symmetry = Table.pickRow(s, i => s.id.value(i) === symmetryId)
+ if (!symmetry) return { granularity: 'uniform', color: () => DefaultColor }
- const clusters = assemblySymmetry.getClusters(featureId)
+ const clusters = assemblySymmetry.getClusters(symmetryId)
if (!clusters._rowCount) return { granularity: 'uniform', color: () => DefaultColor }
const clusterByMember = new Map<string, number>()
for (let i = 0, il = clusters._rowCount; i < il; ++i) {
- clusters.members.value(i).forEach(m => {
- const ms = m.split('_')
- const asym_id = ms[0]
- const oper_list_id = ms.length === 2 ? parseInt(ms[1]) : undefined
- clusterByMember.set(memberKey(asym_id, oper_list_id), i)
- })
+ const clusterMembers = assemblySymmetry.getClusterMembers(clusters.id.value(i))
+ for (let j = 0, jl = clusterMembers._rowCount; j < jl; ++j) {
+ const asym_id = clusterMembers.asym_id.value(j)
+ const oper_list_ids = clusterMembers.pdbx_struct_oper_list_ids.value(j)
+ clusterByMember.set(clusterMemberKey(asym_id, oper_list_ids), i)
+ }
}
-
const scale = ColorScale.create({ domain: [ 0, clusters._rowCount - 1 ] })
return {
granularity: 'instance',
color: (location: Location): Color => {
if (StructureElement.isLocation(location)) {
- const ns = location.unit.conformation.operator.name.split('-')
const asym_id = getAsymId(location.unit)
- const oper_list_id = ns.length === 2 ? parseInt(ns[1]) : undefined
- const cluster = clusterByMember.get(memberKey(asym_id(location), oper_list_id))
+ const ns = location.unit.conformation.operator.name.split('-')
+ const oper_list_ids = ns.length === 2 ? ns[1].split('x') : []
+ const cluster = clusterByMember.get(clusterMemberKey(asym_id(location), oper_list_ids))
return cluster !== undefined ? scale.color(cluster) : DefaultColor
}
return DefaultColor
diff --git a/src/apps/canvas/structure-view.ts b/src/apps/canvas/structure-view.ts
index bde3e67e940eed4b22fb034e1dbeee9626f2b9f2..8be00f5eda814f0e67bb04b4bffac7a38fe025c1 100644
--- a/src/apps/canvas/structure-view.ts
+++ b/src/apps/canvas/structure-view.ts
@@ -65,14 +65,14 @@ interface StructureViewProps {
export async function StructureView(app: App, viewer: Canvas3D, models: ReadonlyArray<Model>, props: StructureViewProps = {}): Promise<StructureView> {
const active: { [k: string]: boolean } = {
- cartoon: false,
+ cartoon: true,
point: false,
- surface: true,
+ surface: false,
ballAndStick: false,
carbohydrate: false,
spacefill: false,
distanceRestraint: false,
- symmetryAxes: false,
+ symmetryAxes: true,
// polymerSphere: false,
}
@@ -142,7 +142,7 @@ export async function StructureView(app: App, viewer: Canvas3D, models: Readonly
} else if (model && model.symmetry.assemblies.length) {
assemblyId = model.symmetry.assemblies[0].id
} else if (model) {
- assemblyId = '0'
+ assemblyId = 'deposited'
} else {
assemblyId = '-1'
}
@@ -152,7 +152,7 @@ export async function StructureView(app: App, viewer: Canvas3D, models: Readonly
function getAssemblyIds() {
const assemblyIds: { id: string, label: string }[] = [
- { id: '0', label: '0: model' }
+ { id: 'deposited', label: 'deposited' }
]
if (model) model.symmetry.assemblies.forEach(a => {
assemblyIds.push({ id: a.id, label: `${a.id}: ${a.details}` })
@@ -165,9 +165,9 @@ export async function StructureView(app: App, viewer: Canvas3D, models: Readonly
if (newSymmetryFeatureId !== undefined) {
symmetryFeatureId = newSymmetryFeatureId
} else if (assemblySymmetry) {
- const f = assemblySymmetry.getFeatures(assemblyId)
- if (f._rowCount) {
- symmetryFeatureId = f.id.value(0)
+ const s = assemblySymmetry.getSymmetries(assemblyId)
+ if (s._rowCount) {
+ symmetryFeatureId = s.id.value(0)
} else {
symmetryFeatureId = -1
}
@@ -180,13 +180,13 @@ export async function StructureView(app: App, viewer: Canvas3D, models: Readonly
function getSymmetryFeatureIds() {
const symmetryFeatureIds: { id: number, label: string }[] = []
if (assemblySymmetry) {
- const symmetryFeatures = assemblySymmetry.getFeatures(assemblyId)
- for (let i = 0, il = symmetryFeatures._rowCount; i < il; ++i) {
- const id = symmetryFeatures.id.value(i)
- const symmetry = symmetryFeatures.symmetry_value.value(i)
- const type = symmetryFeatures.type.value(i)
- const stoichiometry = symmetryFeatures.stoichiometry_value.value(i)
- const label = `${id}: ${symmetry} ${type} ${stoichiometry}`
+ const symmetries = assemblySymmetry.getSymmetries(assemblyId)
+ for (let i = 0, il = symmetries._rowCount; i < il; ++i) {
+ const id = symmetries.id.value(i)
+ const kind = symmetries.kind.value(i)
+ const type = symmetries.type.value(i)
+ const stoichiometry = symmetries.stoichiometry.value(i)
+ const label = `${id}: ${kind} ${type} ${stoichiometry}`
symmetryFeatureIds.push({ id, label })
}
}
@@ -255,20 +255,15 @@ export async function StructureView(app: App, viewer: Canvas3D, models: Readonly
async function createSymmetryRepr() {
if (assemblySymmetry) {
- const features = assemblySymmetry.getFeatures(assemblyId)
- if (features._rowCount) {
+ const symmetries = assemblySymmetry.getSymmetries(assemblyId)
+ if (symmetries._rowCount) {
const axesShape = getAxesShape(symmetryFeatureId, assemblySymmetry)
if (axesShape) {
// const colorTheme = getClusterColorTheme(symmetryFeatureId, assemblySymmetry)
- // await cartoon.createOrUpdate({
- // colorTheme: { name: 'custom', color: colorTheme.color, granularity: colorTheme.granularity },
- // sizeTheme: { name: 'uniform', value: 0.2 },
- // useFog: false // TODO fog not working properly
- // }).run()
- // await ballAndStick.createOrUpdate({
- // colorTheme: { name: 'custom', color: colorTheme.color, granularity: colorTheme.granularity },
- // sizeTheme: { name: 'uniform', value: 0.1 },
- // useFog: false // TODO fog not working properly
+ // await structureRepresentations['cartoon'].createOrUpdate({
+ // colorTheme: 'custom',
+ // colorFunction: colorTheme.color,
+ // colorGranularity: colorTheme.granularity,
// }).run()
await symmetryAxes.createOrUpdate({}, axesShape).run()
viewer.add(symmetryAxes)
diff --git a/src/apps/canvas/util.ts b/src/apps/canvas/util.ts
index 27581f68cbc2fdd956de7d61e04a65da7c21a92c..e9b7dfdf2b61830f00422f6ffd1ae9d3a3404d52 100644
--- a/src/apps/canvas/util.ts
+++ b/src/apps/canvas/util.ts
@@ -43,7 +43,7 @@ export async function getModelsFromMmcif(cif: CifBlock) {
export async function getStructureFromModel(model: Model, assembly: string) {
const assemblies = model.symmetry.assemblies
- if (assembly === '0') {
+ if (assembly === 'deposited') {
return Structure.ofModel(model)
} else if (assemblies.find(a => a.id === assembly)) {
return await StructureSymmetry.buildAssembly(Structure.ofModel(model), assembly).run()
diff --git a/src/mol-geo/geometry/color-data.ts b/src/mol-geo/geometry/color-data.ts
index 5b58eef7d09168f7feeaf0713a1eecc5688d737d..457c6a14db1e9fdcae82fa889966685f43852537 100644
--- a/src/mol-geo/geometry/color-data.ts
+++ b/src/mol-geo/geometry/color-data.ts
@@ -10,7 +10,7 @@ import { Color } from 'mol-util/color';
import { Vec2, Vec3 } from 'mol-math/linear-algebra';
import { LocationIterator } from '../util/location-iterator';
import { NullLocation } from 'mol-model/location';
-import { LocationColor, ColorThemeProps, ColorTheme, ColorThemeName } from 'mol-theme/color';
+import { LocationColor, ColorThemeProps, ColorTheme, ColorThemeName, ScaleLegend, TableLegend } from 'mol-theme/color';
import { RuntimeContext } from 'mol-task';
import { getGranularity } from './geometry';
import { Structure } from 'mol-model/structure';
@@ -27,20 +27,25 @@ export type ColorData = {
export interface ColorProps {
colorTheme: ColorThemeName
+ colorDomain?: [number, number]
colorValue?: Color
+ colorFunction?: LocationColor,
+ colorGranularity?: ColorType,
+ colorDescription?: string,
+ colorLegend?: ScaleLegend | TableLegend
structure?: Structure
}
export function getColorThemeProps(props: ColorProps): ColorThemeProps {
return {
name: props.colorTheme,
- // domain: [number, number],
+ domain: props.colorDomain,
value: props.colorValue,
structure: props.structure,
- // color?: LocationColor,
- // granularity?: ColorType,
- // description?: string,
- // legend?: ScaleLegend | TableLegend
+ color: props.colorFunction,
+ granularity: props.colorGranularity,
+ description: props.colorDescription,
+ legend: props.colorLegend
}
}
diff --git a/src/mol-math/geometry/symmetry-operator.ts b/src/mol-math/geometry/symmetry-operator.ts
index 86884a935653dd7c49a68632d93e885a93cd3829..88d12323f27647b6921f9d827232f1746729c697 100644
--- a/src/mol-math/geometry/symmetry-operator.ts
+++ b/src/mol-math/geometry/symmetry-operator.ts
@@ -52,7 +52,7 @@ namespace SymmetryOperator {
return create(name, t);
}
- // Apply the 1st and then 2nd operator. ( = second.matrix * first.matrix)
+ /** Apply the 1st and then 2nd operator. ( = second.matrix * first.matrix). */
export function compose(first: SymmetryOperator, second: SymmetryOperator) {
const matrix = Mat4.mul(Mat4.zero(), second.matrix, first.matrix);
return create(second.name, matrix, second.hkl);
diff --git a/src/mol-model-props/rcsb/graphql/symmetry.gql.ts b/src/mol-model-props/rcsb/graphql/symmetry.gql.ts
index 264166e3ac2ff8bd808f9b8c887b4114068abaf8..7c9fe867fba16519314ab819357d46675e29225a 100644
--- a/src/mol-model-props/rcsb/graphql/symmetry.gql.ts
+++ b/src/mol-model-props/rcsb/graphql/symmetry.gql.ts
@@ -4,29 +4,28 @@ function gql (strs: TemplateStringsArray) { return strs.raw.join('') }
export default
gql`query AssemblySymmetry($pdbId: String!) {
assemblies(pdbId: $pdbId) {
- assembly_id
- rcsb_assembly_symmetry {
- source
- symmetry_features {
- symmetry {
- description
- value
- }
- clusters {
- members
- avg_rmsd
- }
- stoichiometry {
- description
- value
- }
- symmetry_axes {
- start
- end
- order
+ pdbx_struct_assembly {
+ id
+ }
+ rcsb_struct_symmetry {
+ clusters {
+ avg_rmsd
+ members {
+ asym_id
+ pdbx_struct_oper_list_ids
}
- type
}
+ kind
+ oligomeric_state
+ rotation_axes {
+ start
+ end
+ order
+ }
+ stoichiometry
+ symbol
+ type
}
+ rcsb_struct_symmetry_provenance
}
}`
\ No newline at end of file
diff --git a/src/mol-model-props/rcsb/graphql/types.ts b/src/mol-model-props/rcsb/graphql/types.ts
index b97fd46b849b6f387f4ce5c3bb9c68f6d44a7e21..1c89e3aae72dd79fc4dcabb22fd7c9b23ca8a1f9 100644
--- a/src/mol-model-props/rcsb/graphql/types.ts
+++ b/src/mol-model-props/rcsb/graphql/types.ts
@@ -1,18 +1,190 @@
/* tslint:disable */
-/** Generated in 2018-08-22T17:02:01-07:00 */
+/** Generated in 2018-10-31T12:19:29-07:00 */
-export enum PdbxLeavingAtomFlag {
+// ====================================================
+// START: Typescript template
+// ====================================================
+
+// ====================================================
+// Scalars
+// ====================================================
+
+/** Built-in scalar representing an instant in time */
+export type Date = any;
+
+// ====================================================
+// Enums
+// ====================================================
+
+export enum ChemCompPdbxIdealCoordinatesMissingFlag {
N = "N",
Y = "Y"
}
-export enum PdbxStereoConfig {
+export enum ChemCompPdbxModelCoordinatesMissingFlag {
+ N = "N",
+ Y = "Y"
+}
+
+export enum ChemCompPdbxProcessingSite {
+ EBI = "EBI",
+ PDBE = "PDBE",
+ PDBJ = "PDBJ",
+ RCSB = "RCSB"
+}
+
+export enum ChemCompPdbxReleaseStatus {
+ DEL = "DEL",
+ HOLD = "HOLD",
+ HPUB = "HPUB",
+ OBS = "OBS",
+ REF_ONLY = "REF_ONLY",
+ REL = "REL"
+}
+
+export enum ChemCompType {
+ DNA_LINKING = "DNA_LINKING",
+ DNA_OH_3_PRIME_TERMINUS = "DNA_OH_3_PRIME_TERMINUS",
+ DNA_OH_5_PRIME_TERMINUS = "DNA_OH_5_PRIME_TERMINUS",
+ D_BETA_PEPTIDE_C_GAMMA_LINKING = "D_BETA_PEPTIDE_C_GAMMA_LINKING",
+ D_GAMMA_PEPTIDE_C_DELTA_LINKING = "D_GAMMA_PEPTIDE_C_DELTA_LINKING",
+ D_PEPTIDE_COOH_CARBOXY_TERMINUS = "D_PEPTIDE_COOH_CARBOXY_TERMINUS",
+ D_PEPTIDE_LINKING = "D_PEPTIDE_LINKING",
+ D_PEPTIDE_NH_3_AMINO_TERMINUS = "D_PEPTIDE_NH_3_AMINO_TERMINUS",
+ D_SACCHARIDE = "D_SACCHARIDE",
+ D_SACCHARIDE_1_4_AND_1_4_LINKING = "D_SACCHARIDE_1_4_AND_1_4_LINKING",
+ D_SACCHARIDE_1_4_AND_1_6_LINKING = "D_SACCHARIDE_1_4_AND_1_6_LINKING",
+ L_BETA_PEPTIDE_C_GAMMA_LINKING = "L_BETA_PEPTIDE_C_GAMMA_LINKING",
+ L_DNA_LINKING = "L_DNA_LINKING",
+ L_GAMMA_PEPTIDE_C_DELTA_LINKING = "L_GAMMA_PEPTIDE_C_DELTA_LINKING",
+ L_PEPTIDE_COOH_CARBOXY_TERMINUS = "L_PEPTIDE_COOH_CARBOXY_TERMINUS",
+ L_PEPTIDE_LINKING = "L_PEPTIDE_LINKING",
+ L_PEPTIDE_NH_3_AMINO_TERMINUS = "L_PEPTIDE_NH_3_AMINO_TERMINUS",
+ L_RNA_LINKING = "L_RNA_LINKING",
+ L_SACCHARIDE = "L_SACCHARIDE",
+ L_SACCHARIDE_1_4_AND_1_4_LINKING = "L_SACCHARIDE_1_4_AND_1_4_LINKING",
+ L_SACCHARIDE_1_4_AND_1_6_LINKING = "L_SACCHARIDE_1_4_AND_1_6_LINKING",
+ NON_POLYMER = "NON_POLYMER",
+ OTHER = "OTHER",
+ PEPTIDE_LIKE = "PEPTIDE_LIKE",
+ PEPTIDE_LINKING = "PEPTIDE_LINKING",
+ RNA_LINKING = "RNA_LINKING",
+ RNA_OH_3_PRIME_TERMINUS = "RNA_OH_3_PRIME_TERMINUS",
+ RNA_OH_5_PRIME_TERMINUS = "RNA_OH_5_PRIME_TERMINUS",
+ SACCHARIDE = "SACCHARIDE"
+}
+
+export enum ChemCompAtomPdbxAromaticFlag {
+ N = "N",
+ Y = "Y"
+}
+
+export enum ChemCompAtomPdbxLeavingAtomFlag {
+ N = "N",
+ Y = "Y"
+}
+
+export enum ChemCompAtomPdbxPolymerType {
+ NON_POLYMER = "NON_POLYMER",
+ POLYMER = "POLYMER"
+}
+
+export enum ChemCompAtomPdbxStereoConfig {
N = "N",
R = "R",
S = "S"
}
-export enum ExperimentalSupport {
+export enum ChemCompBondPdbxAromaticFlag {
+ N = "N",
+ Y = "Y"
+}
+
+export enum ChemCompBondPdbxStereoConfig {
+ E = "E",
+ N = "N",
+ Z = "Z"
+}
+
+export enum ChemCompBondValueOrder {
+ AROM = "AROM",
+ DELO = "DELO",
+ DOUB = "DOUB",
+ PI = "PI",
+ POLY = "POLY",
+ QUAD = "QUAD",
+ SING = "SING",
+ TRIP = "TRIP"
+}
+
+export enum PdbxChemCompAuditActionType {
+ CREATE_COMPONENT = "CREATE_COMPONENT",
+ INITIAL_RELEASE = "INITIAL_RELEASE",
+ MODIFY_AROMATIC_FLAG = "MODIFY_AROMATIC_FLAG",
+ MODIFY_ATOM_ID = "MODIFY_ATOM_ID",
+ MODIFY_CHARGE = "MODIFY_CHARGE",
+ MODIFY_COMPONENT_ATOM_ID = "MODIFY_COMPONENT_ATOM_ID",
+ MODIFY_COMPONENT_COMP_ID = "MODIFY_COMPONENT_COMP_ID",
+ MODIFY_COORDINATES = "MODIFY_COORDINATES",
+ MODIFY_DESCRIPTOR = "MODIFY_DESCRIPTOR",
+ MODIFY_FORMAL_CHARGE = "MODIFY_FORMAL_CHARGE",
+ MODIFY_FORMULA = "MODIFY_FORMULA",
+ MODIFY_IDENTIFIER = "MODIFY_IDENTIFIER",
+ MODIFY_INTERNAL_TYPE = "MODIFY_INTERNAL_TYPE",
+ MODIFY_LEAVING_ATOM_FLAG = "MODIFY_LEAVING_ATOM_FLAG",
+ MODIFY_LINKING_TYPE = "MODIFY_LINKING_TYPE",
+ MODIFY_MODEL_COORDINATES_CODE = "MODIFY_MODEL_COORDINATES_CODE",
+ MODIFY_NAME = "MODIFY_NAME",
+ MODIFY_ONE_LETTER_CODE = "MODIFY_ONE_LETTER_CODE",
+ MODIFY_PARENT_RESIDUE = "MODIFY_PARENT_RESIDUE",
+ MODIFY_PROCESSING_SITE = "MODIFY_PROCESSING_SITE",
+ MODIFY_SUBCOMPONENT_LIST = "MODIFY_SUBCOMPONENT_LIST",
+ MODIFY_SYNONYMS = "MODIFY_SYNONYMS",
+ MODIFY_VALUE_ORDER = "MODIFY_VALUE_ORDER",
+ OBSOLETE_COMPONENT = "OBSOLETE_COMPONENT",
+ OTHER_MODIFICATION = "OTHER_MODIFICATION"
+}
+
+export enum PdbxChemCompDescriptorType {
+ IN_CH_I = "IN_CH_I",
+ IN_CH_I_CHARGE = "IN_CH_I_CHARGE",
+ IN_CH_I_FIXEDH = "IN_CH_I_FIXEDH",
+ IN_CH_I_ISOTOPE = "IN_CH_I_ISOTOPE",
+ IN_CH_I_KEY = "IN_CH_I_KEY",
+ IN_CH_I_MAIN = "IN_CH_I_MAIN",
+ IN_CH_I_MAIN_CONNECT = "IN_CH_I_MAIN_CONNECT",
+ IN_CH_I_MAIN_FORMULA = "IN_CH_I_MAIN_FORMULA",
+ IN_CH_I_MAIN_HATOM = "IN_CH_I_MAIN_HATOM",
+ IN_CH_I_RECONNECT = "IN_CH_I_RECONNECT",
+ IN_CH_I_STEREO = "IN_CH_I_STEREO",
+ SMILES = "SMILES",
+ SMILES_CANNONICAL = "SMILES_CANNONICAL",
+ SMILES_CANONICAL = "SMILES_CANONICAL"
+}
+
+export enum PdbxChemCompIdentifierType {
+ CAS_REGISTRY_NUMBER = "CAS_REGISTRY_NUMBER",
+ COMMON_NAME = "COMMON_NAME",
+ CONDENSED_IUPAC_CARB_NAME = "CONDENSED_IUPAC_CARB_NAME",
+ IUPAC_CARB_NAME = "IUPAC_CARB_NAME",
+ MDL_IDENTIFIER = "MDL_IDENTIFIER",
+ PUBCHEM_IDENTIFIER = "PUBCHEM_IDENTIFIER",
+ SYNONYM = "SYNONYM",
+ SYSTEMATIC_NAME = "SYSTEMATIC_NAME"
+}
+
+export enum PdbxStructAssemblyRcsbCandidateAssembly {
+ N = "N",
+ Y = "Y"
+}
+
+export enum PdbxStructAssemblyRcsbDetails {
+ AUTHOR_AND_SOFTWARE_DEFINED_ASSEMBLY = "AUTHOR_AND_SOFTWARE_DEFINED_ASSEMBLY",
+ AUTHOR_DEFINED_ASSEMBLY = "AUTHOR_DEFINED_ASSEMBLY",
+ SOFTWARE_DEFINED_ASSEMBLY = "SOFTWARE_DEFINED_ASSEMBLY"
+}
+
+export enum PdbxStructAssemblyAuthEvidenceExperimentalSupport {
ASSAY_FOR_OLIGOMERIZATION = "ASSAY_FOR_OLIGOMERIZATION",
CROSS_LINKING = "CROSS_LINKING",
EQUILIBRIUM_CENTRIFUGATION = "EQUILIBRIUM_CENTRIFUGATION",
@@ -31,41 +203,124 @@ export enum ExperimentalSupport {
SURFACE_PLASMON_RESONANCE = "SURFACE_PLASMON_RESONANCE"
}
-export enum SymmetryFeatureType {
+export enum PdbxStructAssemblyPropType {
+ ABSA_A_2 = "ABSA_A_2",
+ MORE = "MORE",
+ SSA_A_2 = "SSA_A_2"
+}
+
+export enum PdbxStructOperListType {
+ BUILD_2_D_CRYSTAL_ASYMMETRIC_UNIT = "BUILD_2_D_CRYSTAL_ASYMMETRIC_UNIT",
+ BUILD_3_D_CRYSTAL_ASYMMETRIC_UNIT = "BUILD_3_D_CRYSTAL_ASYMMETRIC_UNIT",
+ BUILD_HELICAL_ASYMMETRIC_UNIT = "BUILD_HELICAL_ASYMMETRIC_UNIT",
+ BUILD_POINT_ASYMMETRIC_UNIT = "BUILD_POINT_ASYMMETRIC_UNIT",
+ CRYSTAL_SYMMETRY_OPERATION = "CRYSTAL_SYMMETRY_OPERATION",
+ HELICAL_SYMMETRY_OPERATION = "HELICAL_SYMMETRY_OPERATION",
+ IDENTITY_OPERATION = "IDENTITY_OPERATION",
+ POINT_SYMMETRY_OPERATION = "POINT_SYMMETRY_OPERATION",
+ TRANSFORM_TO_2_D_CRYSTAL_FRAME = "TRANSFORM_TO_2_D_CRYSTAL_FRAME",
+ TRANSFORM_TO_3_D_CRYSTAL_FRAME = "TRANSFORM_TO_3_D_CRYSTAL_FRAME",
+ TRANSFORM_TO_CRYSTAL_FRAME = "TRANSFORM_TO_CRYSTAL_FRAME",
+ TRANSFORM_TO_HELICAL_FRAME = "TRANSFORM_TO_HELICAL_FRAME",
+ TRANSFORM_TO_POINT_FRAME = "TRANSFORM_TO_POINT_FRAME",
+ _2_D_CRYSTAL_SYMMETRY_OPERATION = "_2_D_CRYSTAL_SYMMETRY_OPERATION",
+ _3_D_CRYSTAL_SYMMETRY_OPERATION = "_3_D_CRYSTAL_SYMMETRY_OPERATION"
+}
+
+export enum RcsbStructSymmetryKind {
GLOBAL = "GLOBAL",
LOCAL = "LOCAL",
PSEUDO = "PSEUDO"
}
-export enum UnpublishedFlag {
+export enum RcsbStructSymmetryType {
+ ASYMMETRIC = "ASYMMETRIC",
+ CYCLIC = "CYCLIC",
+ DIHEDRAL = "DIHEDRAL",
+ HELICAL = "HELICAL",
+ ICOSAHEDRAL = "ICOSAHEDRAL",
+ OCTAHEDRAL = "OCTAHEDRAL",
+ TETRAHEDRAL = "TETRAHEDRAL"
+}
+
+export enum CitationCoordinateLinkage {
+ N = "N",
+ NO = "NO",
+ Y = "Y",
+ YES = "YES"
+}
+
+export enum CitationUnpublishedFlag {
N = "N",
Y = "Y"
}
-export enum PdbxMonochromaticOrLaueMl {
+export enum DiffrnRadiationPdbxMonochromaticOrLaueMl {
L = "L",
M = "M"
}
-export enum PdbxScatteringType {
+export enum DiffrnRadiationPdbxScatteringType {
ELECTRON = "ELECTRON",
NEUTRON = "NEUTRON",
X_RAY = "X_RAY"
}
-export enum RefSpace {
+export enum Em2dCrystalEntitySpaceGroupNameHm {
+ C_1_2 = "C_1_2",
+ C_2_2_2 = "C_2_2_2",
+ P_1 = "P_1",
+ P_1_2 = "P_1_2",
+ P_1_21 = "P_1_21",
+ P_2 = "P_2",
+ P_2_21_21 = "P_2_21_21",
+ P_2_2_2 = "P_2_2_2",
+ P_2_2_21 = "P_2_2_21",
+ P_3 = "P_3",
+ P_3_1_2 = "P_3_1_2",
+ P_3_2_1 = "P_3_2_1",
+ P_4 = "P_4",
+ P_4_21_2 = "P_4_21_2",
+ P_4_2_2 = "P_4_2_2",
+ P_6 = "P_6",
+ P_6_2_2 = "P_6_2_2"
+}
+
+export enum Em3dFittingRefProtocol {
+ AB_INITIO_MODEL = "AB_INITIO_MODEL",
+ BACKBONE_TRACE = "BACKBONE_TRACE",
+ FLEXIBLE_FIT = "FLEXIBLE_FIT",
+ OTHER = "OTHER",
+ RIGID_BODY_FIT = "RIGID_BODY_FIT"
+}
+
+export enum Em3dFittingRefSpace {
REAL = "REAL",
RECIPROCAL = "RECIPROCAL"
}
-export enum SymmetryType {
+export enum Em3dReconstructionRefinementType {
+ HALF_MAPS_REFINED_AGAINST_SAME_DATA = "HALF_MAPS_REFINED_AGAINST_SAME_DATA",
+ HALF_MAPS_REFINED_INDEPENDENTLY = "HALF_MAPS_REFINED_INDEPENDENTLY",
+ HALF_MAPS_REFINED_INDEPENDENTLY_WITH_FREQUENCY_RANGE_OMITTED = "HALF_MAPS_REFINED_INDEPENDENTLY_WITH_FREQUENCY_RANGE_OMITTED",
+ HALF_MAPS_REFINED_WITH_FREQUENCY_RANGE_OMITTED = "HALF_MAPS_REFINED_WITH_FREQUENCY_RANGE_OMITTED",
+ OTHER = "OTHER"
+}
+
+export enum Em3dReconstructionSymmetryType {
HELICAL = "HELICAL",
POINT = "POINT",
_2_D_CRYSTAL = "_2_D_CRYSTAL",
_3_D_CRYSTAL = "_3_D_CRYSTAL"
}
-export enum AggregationState {
+export enum EmEntityAssemblySource {
+ MULTIPLE_SOURCES = "MULTIPLE_SOURCES",
+ NATURAL = "NATURAL",
+ RECOMBINANT = "RECOMBINANT"
+}
+
+export enum EmExperimentAggregationState {
CELL = "CELL",
FILAMENT = "FILAMENT",
HELICAL_ARRAY = "HELICAL_ARRAY",
@@ -75,7 +330,7 @@ export enum AggregationState {
_3_D_ARRAY = "_3_D_ARRAY"
}
-export enum ReconstructionMethod {
+export enum EmExperimentReconstructionMethod {
CRYSTALLOGRAPHY = "CRYSTALLOGRAPHY",
HELICAL = "HELICAL",
SINGLE_PARTICLE = "SINGLE_PARTICLE",
@@ -83,40 +338,244 @@ export enum ReconstructionMethod {
TOMOGRAPHY = "TOMOGRAPHY"
}
-export enum EmbeddingApplied {
+export enum EmImageRecordingDetectorMode {
+ COUNTING = "COUNTING",
+ INTEGRATING = "INTEGRATING",
+ OTHER = "OTHER",
+ SUPER_RESOLUTION = "SUPER_RESOLUTION"
+}
+
+export enum EmImagingAlignmentProcedure {
+ BASIC = "BASIC",
+ COMA_FREE = "COMA_FREE",
+ NONE = "NONE",
+ OTHER = "OTHER",
+ ZEMLIN_TABLEAU = "ZEMLIN_TABLEAU"
+}
+
+export enum EmImagingCryogen {
+ HELIUM = "HELIUM",
+ NITROGEN = "NITROGEN"
+}
+
+export enum EmImagingIlluminationMode {
+ FLOOD_BEAM = "FLOOD_BEAM",
+ OTHER = "OTHER",
+ SPOT_SCAN = "SPOT_SCAN"
+}
+
+export enum EmImagingMicroscopeModel {
+ FEI_MORGAGNI = "FEI_MORGAGNI",
+ FEI_PHILIPS_CM_10 = "FEI_PHILIPS_CM_10",
+ FEI_PHILIPS_CM_12 = "FEI_PHILIPS_CM_12",
+ FEI_PHILIPS_CM_120_T = "FEI_PHILIPS_CM_120_T",
+ FEI_PHILIPS_CM_200_FEG = "FEI_PHILIPS_CM_200_FEG",
+ FEI_PHILIPS_CM_200_FEG_SOPHIE = "FEI_PHILIPS_CM_200_FEG_SOPHIE",
+ FEI_PHILIPS_CM_200_FEG_ST = "FEI_PHILIPS_CM_200_FEG_ST",
+ FEI_PHILIPS_CM_200_FEG_UT = "FEI_PHILIPS_CM_200_FEG_UT",
+ FEI_PHILIPS_CM_200_T = "FEI_PHILIPS_CM_200_T",
+ FEI_PHILIPS_CM_300_FEG_HE = "FEI_PHILIPS_CM_300_FEG_HE",
+ FEI_PHILIPS_CM_300_FEG_ST = "FEI_PHILIPS_CM_300_FEG_ST",
+ FEI_PHILIPS_CM_300_FEG_T = "FEI_PHILIPS_CM_300_FEG_T",
+ FEI_PHILIPS_EM_400 = "FEI_PHILIPS_EM_400",
+ FEI_PHILIPS_EM_420 = "FEI_PHILIPS_EM_420",
+ FEI_POLARA_300 = "FEI_POLARA_300",
+ FEI_TALOS_ARCTICA = "FEI_TALOS_ARCTICA",
+ FEI_TECNAI_10 = "FEI_TECNAI_10",
+ FEI_TECNAI_12 = "FEI_TECNAI_12",
+ FEI_TECNAI_20 = "FEI_TECNAI_20",
+ FEI_TECNAI_ARCTICA = "FEI_TECNAI_ARCTICA",
+ FEI_TECNAI_F_20 = "FEI_TECNAI_F_20",
+ FEI_TECNAI_F_30 = "FEI_TECNAI_F_30",
+ FEI_TECNAI_SPHERA = "FEI_TECNAI_SPHERA",
+ FEI_TECNAI_SPIRIT = "FEI_TECNAI_SPIRIT",
+ FEI_TITAN = "FEI_TITAN",
+ FEI_TITAN_KRIOS = "FEI_TITAN_KRIOS",
+ HITACHI_EF_2000 = "HITACHI_EF_2000",
+ HITACHI_EF_3000 = "HITACHI_EF_3000",
+ HITACHI_HF_2000 = "HITACHI_HF_2000",
+ HITACHI_HF_3000 = "HITACHI_HF_3000",
+ HITACHI_H_7600 = "HITACHI_H_7600",
+ HITACHI_H_9500_SD = "HITACHI_H_9500_SD",
+ JEOL_100_B = "JEOL_100_B",
+ JEOL_100_CX = "JEOL_100_CX",
+ JEOL_1010 = "JEOL_1010",
+ JEOL_1200 = "JEOL_1200",
+ JEOL_1200_EX = "JEOL_1200_EX",
+ JEOL_1200_EXII = "JEOL_1200_EXII",
+ JEOL_1230 = "JEOL_1230",
+ JEOL_1400 = "JEOL_1400",
+ JEOL_2000_EX = "JEOL_2000_EX",
+ JEOL_2000_EXII = "JEOL_2000_EXII",
+ JEOL_2010 = "JEOL_2010",
+ JEOL_2010_F = "JEOL_2010_F",
+ JEOL_2010_HC = "JEOL_2010_HC",
+ JEOL_2010_HT = "JEOL_2010_HT",
+ JEOL_2010_UHR = "JEOL_2010_UHR",
+ JEOL_2011 = "JEOL_2011",
+ JEOL_2100 = "JEOL_2100",
+ JEOL_2100_F = "JEOL_2100_F",
+ JEOL_2200_FS = "JEOL_2200_FS",
+ JEOL_2200_FSC = "JEOL_2200_FSC",
+ JEOL_3000_SFF = "JEOL_3000_SFF",
+ JEOL_3100_FEF = "JEOL_3100_FEF",
+ JEOL_3100_FFC = "JEOL_3100_FFC",
+ JEOL_3200_FS = "JEOL_3200_FS",
+ JEOL_3200_FSC = "JEOL_3200_FSC",
+ JEOL_4000 = "JEOL_4000",
+ JEOL_4000_EX = "JEOL_4000_EX",
+ JEOL_CRYO_ARM_200 = "JEOL_CRYO_ARM_200",
+ JEOL_CRYO_ARM_300 = "JEOL_CRYO_ARM_300",
+ JEOL_KYOTO_3000_SFF = "JEOL_KYOTO_3000_SFF",
+ SIEMENS_SULEIKA = "SIEMENS_SULEIKA",
+ ZEISS_LEO_912 = "ZEISS_LEO_912",
+ ZEISS_LIBRA_120_PLUS = "ZEISS_LIBRA_120_PLUS"
+}
+
+export enum EmImagingMode {
+ BRIGHT_FIELD = "BRIGHT_FIELD",
+ DARK_FIELD = "DARK_FIELD",
+ DIFFRACTION = "DIFFRACTION",
+ OTHER = "OTHER"
+}
+
+export enum EmImagingSpecimenHolderModel {
+ FEI_TITAN_KRIOS_AUTOGRID_HOLDER = "FEI_TITAN_KRIOS_AUTOGRID_HOLDER",
+ FISCHIONE_INSTRUMENTS_DUAL_AXIS_TOMOGRAPHY_HOLDER = "FISCHIONE_INSTRUMENTS_DUAL_AXIS_TOMOGRAPHY_HOLDER",
+ GATAN_626_SINGLE_TILT_LIQUID_NITROGEN_CRYO_TRANSFER_HOLDER = "GATAN_626_SINGLE_TILT_LIQUID_NITROGEN_CRYO_TRANSFER_HOLDER",
+ GATAN_910_MULTI_SPECIMEN_SINGLE_TILT_CRYO_TRANSFER_HOLDER = "GATAN_910_MULTI_SPECIMEN_SINGLE_TILT_CRYO_TRANSFER_HOLDER",
+ GATAN_914_HIGH_TILT_LIQUID_NITROGEN_CRYO_TRANSFER_TOMOGRAPHY_HOLDER = "GATAN_914_HIGH_TILT_LIQUID_NITROGEN_CRYO_TRANSFER_TOMOGRAPHY_HOLDER",
+ GATAN_915_DOUBLE_TILT_LIQUID_NITROGEN_CRYO_TRANSFER_HOLDER = "GATAN_915_DOUBLE_TILT_LIQUID_NITROGEN_CRYO_TRANSFER_HOLDER",
+ GATAN_CHDT_3504_DOUBLE_TILT_HIGH_RESOLUTION_NITROGEN_COOLING_HOLDER = "GATAN_CHDT_3504_DOUBLE_TILT_HIGH_RESOLUTION_NITROGEN_COOLING_HOLDER",
+ GATAN_CT_3500_SINGLE_TILT_LIQUID_NITROGEN_CRYO_TRANSFER_HOLDER = "GATAN_CT_3500_SINGLE_TILT_LIQUID_NITROGEN_CRYO_TRANSFER_HOLDER",
+ GATAN_CT_3500_TR_SINGLE_TILT_ROTATION_LIQUID_NITROGEN_CRYO_TRANSFER_HOLDER = "GATAN_CT_3500_TR_SINGLE_TILT_ROTATION_LIQUID_NITROGEN_CRYO_TRANSFER_HOLDER",
+ GATAN_HCHDT_3010_DOUBLE_TILT_HIGH_RESOLUTION_HELIUM_COOLING_HOLDER = "GATAN_HCHDT_3010_DOUBLE_TILT_HIGH_RESOLUTION_HELIUM_COOLING_HOLDER",
+ GATAN_HCHST_3008_SINGLE_TILT_HIGH_RESOLUTION_HELIUM_COOLING_HOLDER = "GATAN_HCHST_3008_SINGLE_TILT_HIGH_RESOLUTION_HELIUM_COOLING_HOLDER",
+ GATAN_HC_3500_SINGLE_TILT_HEATING_NITROGEN_COOLING_HOLDER = "GATAN_HC_3500_SINGLE_TILT_HEATING_NITROGEN_COOLING_HOLDER",
+ GATAN_HELIUM = "GATAN_HELIUM",
+ GATAN_LIQUID_NITROGEN = "GATAN_LIQUID_NITROGEN",
+ GATAN_UHRST_3500_SINGLE_TILT_ULTRA_HIGH_RESOLUTION_NITROGEN_COOLING_HOLDER = "GATAN_UHRST_3500_SINGLE_TILT_ULTRA_HIGH_RESOLUTION_NITROGEN_COOLING_HOLDER",
+ GATAN_ULTDT_ULTRA_LOW_TEMPERATURE_DOUBLE_TILT_HELIUM_COOLING_HOLDER = "GATAN_ULTDT_ULTRA_LOW_TEMPERATURE_DOUBLE_TILT_HELIUM_COOLING_HOLDER",
+ GATAN_ULTST_ULTRA_LOW_TEMPERATURE_SINGLE_TILT_HELIUM_COOLING_HOLDER = "GATAN_ULTST_ULTRA_LOW_TEMPERATURE_SINGLE_TILT_HELIUM_COOLING_HOLDER",
+ HOME_BUILD = "HOME_BUILD",
+ JEOL = "JEOL",
+ JEOL_3200_FSC_CRYOHOLDER = "JEOL_3200_FSC_CRYOHOLDER",
+ JEOL_CRYOSPECPORTER = "JEOL_CRYOSPECPORTER",
+ OTHER = "OTHER",
+ PHILIPS_ROTATION_HOLDER = "PHILIPS_ROTATION_HOLDER",
+ SIDE_ENTRY_EUCENTRIC = "SIDE_ENTRY_EUCENTRIC"
+}
+
+export enum EmSoftwareCategory {
+ CLASSIFICATION = "CLASSIFICATION",
+ CRYSTALLOGRAPHY_MERGING = "CRYSTALLOGRAPHY_MERGING",
+ CTF_CORRECTION = "CTF_CORRECTION",
+ DIFFRACTION_INDEXING = "DIFFRACTION_INDEXING",
+ FINAL_EULER_ASSIGNMENT = "FINAL_EULER_ASSIGNMENT",
+ IMAGE_ACQUISITION = "IMAGE_ACQUISITION",
+ INITIAL_EULER_ASSIGNMENT = "INITIAL_EULER_ASSIGNMENT",
+ LATTICE_DISTORTION_CORRECTION = "LATTICE_DISTORTION_CORRECTION",
+ LAYERLINE_INDEXING = "LAYERLINE_INDEXING",
+ MASKING = "MASKING",
+ MODEL_FITTING = "MODEL_FITTING",
+ MODEL_REFINEMENT = "MODEL_REFINEMENT",
+ MOLECULAR_REPLACEMENT = "MOLECULAR_REPLACEMENT",
+ OTHER = "OTHER",
+ PARTICLE_SELECTION = "PARTICLE_SELECTION",
+ RECONSTRUCTION = "RECONSTRUCTION",
+ SERIES_ALIGNMENT = "SERIES_ALIGNMENT",
+ SYMMETRY_DETERMINATION = "SYMMETRY_DETERMINATION",
+ VOLUME_SELECTION = "VOLUME_SELECTION"
+}
+
+export enum EmSpecimenEmbeddingApplied {
+ NO = "NO",
+ YES = "YES"
+}
+
+export enum EmSpecimenShadowingApplied {
NO = "NO",
YES = "YES"
}
-export enum StainingApplied {
+export enum EmSpecimenStainingApplied {
NO = "NO",
YES = "YES"
}
-export enum VitrificationApplied {
+export enum EmSpecimenVitrificationApplied {
NO = "NO",
YES = "YES"
}
-export enum Type {
+export enum EmStainingType {
NEGATIVE = "NEGATIVE",
NONE = "NONE",
POSITIVE = "POSITIVE"
}
-export enum SrcMethod {
+export enum EmVitrificationCryogenName {
+ ETHANE = "ETHANE",
+ ETHANE_PROPANE = "ETHANE_PROPANE",
+ FREON_12 = "FREON_12",
+ FREON_22 = "FREON_22",
+ HELIUM = "HELIUM",
+ METHANE = "METHANE",
+ NITROGEN = "NITROGEN",
+ OTHER = "OTHER",
+ PROPANE = "PROPANE"
+}
+
+export enum EmVitrificationInstrument {
+ EMS_002_RAPID_IMMERSION_FREEZER = "EMS_002_RAPID_IMMERSION_FREEZER",
+ FEI_VITROBOT_MARK_I = "FEI_VITROBOT_MARK_I",
+ FEI_VITROBOT_MARK_II = "FEI_VITROBOT_MARK_II",
+ FEI_VITROBOT_MARK_III = "FEI_VITROBOT_MARK_III",
+ FEI_VITROBOT_MARK_IV = "FEI_VITROBOT_MARK_IV",
+ GATAN_CRYOPLUNGE_3 = "GATAN_CRYOPLUNGE_3",
+ HOMEMADE_PLUNGER = "HOMEMADE_PLUNGER",
+ LEICA_EM_CPC = "LEICA_EM_CPC",
+ LEICA_EM_GP = "LEICA_EM_GP",
+ LEICA_KF_80 = "LEICA_KF_80",
+ LEICA_PLUNGER = "LEICA_PLUNGER",
+ REICHERT_JUNG_PLUNGER = "REICHERT_JUNG_PLUNGER",
+ SPOTITON = "SPOTITON",
+ ZEISS_PLUNGE_FREEZER_CRYOBOX = "ZEISS_PLUNGE_FREEZER_CRYOBOX"
+}
+
+export enum EntityRcsbMultipleSourceFlag {
+ N = "N",
+ Y = "Y"
+}
+
+export enum EntitySrcMethod {
MAN = "MAN",
NAT = "NAT",
SYN = "SYN"
}
export enum EntityType {
+ BRANCHED = "BRANCHED",
MACROLIDE = "MACROLIDE",
NON_POLYMER = "NON_POLYMER",
POLYMER = "POLYMER",
WATER = "WATER"
}
+export enum EntityPolyNstdLinkage {
+ N = "N",
+ NO = "NO",
+ Y = "Y",
+ YES = "YES"
+}
+
+export enum EntityPolyNstdMonomer {
+ N = "N",
+ NO = "NO",
+ Y = "Y",
+ YES = "YES"
+}
+
export enum EntityPolyType {
CYCLIC_PSEUDO_PEPTIDE = "CYCLIC_PSEUDO_PEPTIDE",
OTHER = "OTHER",
@@ -130,40 +589,614 @@ export enum EntityPolyType {
POLYSACCHARIDE_L = "POLYSACCHARIDE_L"
}
-export enum RcsbHostOrganismSource {
- MMCIF = "MMCIF",
- NCBI = "NCBI",
- UNIPROT = "UNIPROT"
+export enum EntitySrcGenPdbxAltSourceFlag {
+ MODEL = "MODEL",
+ SAMPLE = "SAMPLE"
+}
+
+export enum EntitySrcGenPdbxSeqType {
+ BIOLOGICAL_SEQUENCE = "BIOLOGICAL_SEQUENCE",
+ C_TERMINAL_TAG = "C_TERMINAL_TAG",
+ LINKER = "LINKER",
+ N_TERMINAL_TAG = "N_TERMINAL_TAG"
}
-export enum RcsbMembraneSource {
+export enum EntitySrcNatPdbxAltSourceFlag {
+ MODEL = "MODEL",
+ SAMPLE = "SAMPLE"
+}
+
+export enum PdbxEntitySrcSynPdbxAltSourceFlag {
+ MODEL = "MODEL",
+ SAMPLE = "SAMPLE"
+}
+
+export enum RcsbEntityHostOrganismProvenanceCode {
+ PDB_PRIMARY_DATA = "PDB_PRIMARY_DATA"
+}
+
+export enum RcsbEntitySourceOrganismProvenanceCode {
+ PDB_PRIMARY_DATA = "PDB_PRIMARY_DATA"
+}
+
+export enum RcsbEntitySourceOrganismSourceType {
+ GENETICALLY_ENGINEERED = "GENETICALLY_ENGINEERED",
+ NATURAL = "NATURAL",
+ SYNTHETIC = "SYNTHETIC"
+}
+
+export enum RcsbMembraneProvenanceSource {
HOMOLOGY = "HOMOLOGY",
MPSTRUCT = "MPSTRUCT"
}
-export enum RcsbOrganismSource {
- MMCIF = "MMCIF",
- NCBI = "NCBI",
- UNIPROT = "UNIPROT"
+export enum StructAsymPdbxBlankPdbChainidFlag {
+ N = "N",
+ Y = "Y"
+}
+
+export enum FeatureType {
+ ACTIVE_SITE = "ACTIVE_SITE",
+ BINDING_SITE = "BINDING_SITE",
+ CALCIUM_BINDING_REGION = "CALCIUM_BINDING_REGION",
+ CHAIN = "CHAIN",
+ COILED_COIL_REGION = "COILED_COIL_REGION",
+ COMPOSITIONALLY_BIASED_REGION = "COMPOSITIONALLY_BIASED_REGION",
+ CROSS_LINK = "CROSS_LINK",
+ DISULFIDE_BOND = "DISULFIDE_BOND",
+ DNA_BINDING_REGION = "DNA_BINDING_REGION",
+ DOMAIN = "DOMAIN",
+ GLYCOSYLATION_SITE = "GLYCOSYLATION_SITE",
+ HELIX = "HELIX",
+ INITIATOR_METHIONINE = "INITIATOR_METHIONINE",
+ INTRAMEMBRANE_REGION = "INTRAMEMBRANE_REGION",
+ LIPID_MOIETY_BINDING_REGION = "LIPID_MOIETY_BINDING_REGION",
+ METAL_ION_BINDING_SITE = "METAL_ION_BINDING_SITE",
+ MODIFIED_RESIDUE = "MODIFIED_RESIDUE",
+ MUTAGENESIS_SITE = "MUTAGENESIS_SITE",
+ NON_CONSECUTIVE_RESIDUES = "NON_CONSECUTIVE_RESIDUES",
+ NON_STANDARD_AMINO_ACID = "NON_STANDARD_AMINO_ACID",
+ NON_TERMINAL_RESIDUE = "NON_TERMINAL_RESIDUE",
+ NUCLEOTIDE_PHOSPHATE_BINDING_REGION = "NUCLEOTIDE_PHOSPHATE_BINDING_REGION",
+ PEPTIDE = "PEPTIDE",
+ PROPEPTIDE = "PROPEPTIDE",
+ REGION_OF_INTEREST = "REGION_OF_INTEREST",
+ REPEAT = "REPEAT",
+ SEQUENCE_CONFLICT = "SEQUENCE_CONFLICT",
+ SEQUENCE_VARIANT = "SEQUENCE_VARIANT",
+ SHORT_SEQUENCE_MOTIF = "SHORT_SEQUENCE_MOTIF",
+ SIGNAL_PEPTIDE = "SIGNAL_PEPTIDE",
+ SITE = "SITE",
+ SPLICE_VARIANT = "SPLICE_VARIANT",
+ STRAND = "STRAND",
+ TOPOLOGICAL_DOMAIN = "TOPOLOGICAL_DOMAIN",
+ TRANSIT_PEPTIDE = "TRANSIT_PEPTIDE",
+ TRANSMEMBRANE_REGION = "TRANSMEMBRANE_REGION",
+ TURN = "TURN",
+ UNSURE_RESIDUE = "UNSURE_RESIDUE",
+ ZINC_FINGER_REGION = "ZINC_FINGER_REGION"
+}
+
+export enum GeneNameType {
+ ORDERED_LOCUS = "ORDERED_LOCUS",
+ ORF = "ORF",
+ PRIMARY = "PRIMARY",
+ SYNONYM = "SYNONYM"
+}
+
+export enum OrganismNameType {
+ ABBREVIATION = "ABBREVIATION",
+ COMMON = "COMMON",
+ FULL = "FULL",
+ SCIENTIFIC = "SCIENTIFIC",
+ SYNONYM = "SYNONYM"
+}
+
+export enum OrganismHostNameType {
+ ABBREVIATION = "ABBREVIATION",
+ COMMON = "COMMON",
+ FULL = "FULL",
+ SCIENTIFIC = "SCIENTIFIC",
+ SYNONYM = "SYNONYM"
+}
+
+export enum ExptlMethod {
+ ELECTRON_CRYSTALLOGRAPHY = "ELECTRON_CRYSTALLOGRAPHY",
+ ELECTRON_MICROSCOPY = "ELECTRON_MICROSCOPY",
+ EPR = "EPR",
+ FIBER_DIFFRACTION = "FIBER_DIFFRACTION",
+ FLUORESCENCE_TRANSFER = "FLUORESCENCE_TRANSFER",
+ INFRARED_SPECTROSCOPY = "INFRARED_SPECTROSCOPY",
+ NEUTRON_DIFFRACTION = "NEUTRON_DIFFRACTION",
+ POWDER_DIFFRACTION = "POWDER_DIFFRACTION",
+ SOLID_STATE_NMR = "SOLID_STATE_NMR",
+ SOLUTION_NMR = "SOLUTION_NMR",
+ SOLUTION_SCATTERING = "SOLUTION_SCATTERING",
+ THEORETICAL_MODEL = "THEORETICAL_MODEL",
+ X_RAY_DIFFRACTION = "X_RAY_DIFFRACTION"
+}
+
+export enum PdbxSgProjectFullNameOfCenter {
+ ACCELERATED_TECHNOLOGIES_CENTER_FOR_GENE_TO_3_D_STRUCTURE = "ACCELERATED_TECHNOLOGIES_CENTER_FOR_GENE_TO_3_D_STRUCTURE",
+ ASSEMBLY_DYNAMICS_AND_EVOLUTION_OF_CELL_CELL_AND_CELL_MATRIX_ADHESIONS = "ASSEMBLY_DYNAMICS_AND_EVOLUTION_OF_CELL_CELL_AND_CELL_MATRIX_ADHESIONS",
+ ATOMS_TO_ANIMALS_THE_IMMUNE_FUNCTION_NETWORK = "ATOMS_TO_ANIMALS_THE_IMMUNE_FUNCTION_NETWORK",
+ BACTERIAL_TARGETS_AT_IGS_CNRS_FRANCE = "BACTERIAL_TARGETS_AT_IGS_CNRS_FRANCE",
+ BERKELEY_STRUCTURAL_GENOMICS_CENTER = "BERKELEY_STRUCTURAL_GENOMICS_CENTER",
+ CENTER_FOR_EUKARYOTIC_STRUCTURAL_GENOMICS = "CENTER_FOR_EUKARYOTIC_STRUCTURAL_GENOMICS",
+ CENTER_FOR_HIGH_THROUGHPUT_STRUCTURAL_BIOLOGY = "CENTER_FOR_HIGH_THROUGHPUT_STRUCTURAL_BIOLOGY",
+ CENTER_FOR_MEMBRANE_PROTEINS_OF_INFECTIOUS_DISEASES = "CENTER_FOR_MEMBRANE_PROTEINS_OF_INFECTIOUS_DISEASES",
+ CENTER_FOR_STRUCTURAL_GENOMICS_OF_INFECTIOUS_DISEASES = "CENTER_FOR_STRUCTURAL_GENOMICS_OF_INFECTIOUS_DISEASES",
+ CENTER_FOR_STRUCTURES_OF_MEMBRANE_PROTEINS = "CENTER_FOR_STRUCTURES_OF_MEMBRANE_PROTEINS",
+ CENTER_FOR_THE_X_RAY_STRUCTURE_DETERMINATION_OF_HUMAN_TRANSPORTERS = "CENTER_FOR_THE_X_RAY_STRUCTURE_DETERMINATION_OF_HUMAN_TRANSPORTERS",
+ CHAPERONE_ENABLED_STUDIES_OF_EPIGENETIC_REGULATION_ENZYMES = "CHAPERONE_ENABLED_STUDIES_OF_EPIGENETIC_REGULATION_ENZYMES",
+ ENZYME_DISCOVERY_FOR_NATURAL_PRODUCT_BIOSYNTHESIS = "ENZYME_DISCOVERY_FOR_NATURAL_PRODUCT_BIOSYNTHESIS",
+ GPCR_NETWORK = "GPCR_NETWORK",
+ INTEGRATED_CENTER_FOR_STRUCTURE_AND_FUNCTION_INNOVATION = "INTEGRATED_CENTER_FOR_STRUCTURE_AND_FUNCTION_INNOVATION",
+ ISRAEL_STRUCTURAL_PROTEOMICS_CENTER = "ISRAEL_STRUCTURAL_PROTEOMICS_CENTER",
+ JOINT_CENTER_FOR_STRUCTURAL_GENOMICS = "JOINT_CENTER_FOR_STRUCTURAL_GENOMICS",
+ MARSEILLES_STRUCTURAL_GENOMICS_PROGRAM_AFMB = "MARSEILLES_STRUCTURAL_GENOMICS_PROGRAM_AFMB",
+ MEDICAL_STRUCTURAL_GENOMICS_OF_PATHOGENIC_PROTOZOA = "MEDICAL_STRUCTURAL_GENOMICS_OF_PATHOGENIC_PROTOZOA",
+ MEMBRANE_PROTEIN_STRUCTURAL_BIOLOGY_CONSORTIUM = "MEMBRANE_PROTEIN_STRUCTURAL_BIOLOGY_CONSORTIUM",
+ MEMBRANE_PROTEIN_STRUCTURES_BY_SOLUTION_NMR = "MEMBRANE_PROTEIN_STRUCTURES_BY_SOLUTION_NMR",
+ MIDWEST_CENTER_FOR_MACROMOLECULAR_RESEARCH = "MIDWEST_CENTER_FOR_MACROMOLECULAR_RESEARCH",
+ MIDWEST_CENTER_FOR_STRUCTURAL_GENOMICS = "MIDWEST_CENTER_FOR_STRUCTURAL_GENOMICS",
+ MITOCHONDRIAL_PROTEIN_PARTNERSHIP = "MITOCHONDRIAL_PROTEIN_PARTNERSHIP",
+ MONTREAL_KINGSTON_BACTERIAL_STRUCTURAL_GENOMICS_INITIATIVE = "MONTREAL_KINGSTON_BACTERIAL_STRUCTURAL_GENOMICS_INITIATIVE",
+ MYCOBACTERIUM_TUBERCULOSIS_STRUCTURAL_PROTEOMICS_PROJECT = "MYCOBACTERIUM_TUBERCULOSIS_STRUCTURAL_PROTEOMICS_PROJECT",
+ NEW_YORK_CONSORTIUM_ON_MEMBRANE_PROTEIN_STRUCTURE = "NEW_YORK_CONSORTIUM_ON_MEMBRANE_PROTEIN_STRUCTURE",
+ NEW_YORK_SGX_RESEARCH_CENTER_FOR_STRUCTURAL_GENOMICS = "NEW_YORK_SGX_RESEARCH_CENTER_FOR_STRUCTURAL_GENOMICS",
+ NEW_YORK_STRUCTURAL_GENOMICS_RESEARCH_CONSORTIUM = "NEW_YORK_STRUCTURAL_GENOMICS_RESEARCH_CONSORTIUM",
+ NEW_YORK_STRUCTURAL_GENOMI_X_RESEARCH_CONSORTIUM = "NEW_YORK_STRUCTURAL_GENOMI_X_RESEARCH_CONSORTIUM",
+ NORTHEAST_STRUCTURAL_GENOMICS_CONSORTIUM = "NORTHEAST_STRUCTURAL_GENOMICS_CONSORTIUM",
+ NUCLEOCYTOPLASMIC_TRANSPORT_A_TARGET_FOR_CELLULAR_CONTROL = "NUCLEOCYTOPLASMIC_TRANSPORT_A_TARGET_FOR_CELLULAR_CONTROL",
+ ONTARIO_CENTRE_FOR_STRUCTURAL_PROTEOMICS = "ONTARIO_CENTRE_FOR_STRUCTURAL_PROTEOMICS",
+ OXFORD_PROTEIN_PRODUCTION_FACILITY = "OXFORD_PROTEIN_PRODUCTION_FACILITY",
+ PARIS_SUD_YEAST_STRUCTURAL_GENOMICS = "PARIS_SUD_YEAST_STRUCTURAL_GENOMICS",
+ PARTNERSHIP_FOR_NUCLEAR_RECEPTOR_SIGNALING_CODE_BIOLOGY = "PARTNERSHIP_FOR_NUCLEAR_RECEPTOR_SIGNALING_CODE_BIOLOGY",
+ PARTNERSHIP_FOR_STEM_CELL_BIOLOGY = "PARTNERSHIP_FOR_STEM_CELL_BIOLOGY",
+ PARTNERSHIP_FOR_T_CELL_BIOLOGY = "PARTNERSHIP_FOR_T_CELL_BIOLOGY",
+ PROGRAM_FOR_THE_CHARACTERIZATION_OF_SECRETED_EFFECTOR_PROTEINS = "PROGRAM_FOR_THE_CHARACTERIZATION_OF_SECRETED_EFFECTOR_PROTEINS",
+ PROTEIN_STRUCTURE_FACTORY = "PROTEIN_STRUCTURE_FACTORY",
+ RIKEN_STRUCTURAL_GENOMICS_PROTEOMICS_INITIATIVE = "RIKEN_STRUCTURAL_GENOMICS_PROTEOMICS_INITIATIVE",
+ SCOTTISH_STRUCTURAL_PROTEOMICS_FACILITY = "SCOTTISH_STRUCTURAL_PROTEOMICS_FACILITY",
+ SEATTLE_STRUCTURAL_GENOMICS_CENTER_FOR_INFECTIOUS_DISEASE = "SEATTLE_STRUCTURAL_GENOMICS_CENTER_FOR_INFECTIOUS_DISEASE",
+ SOUTHEAST_COLLABORATORY_FOR_STRUCTURAL_GENOMICS = "SOUTHEAST_COLLABORATORY_FOR_STRUCTURAL_GENOMICS",
+ SOUTH_AFRICA_STRUCTURAL_TARGETS_ANNOTATION_DATABASE = "SOUTH_AFRICA_STRUCTURAL_TARGETS_ANNOTATION_DATABASE",
+ STRUCTURAL_GENOMICS_CONSORTIUM = "STRUCTURAL_GENOMICS_CONSORTIUM",
+ STRUCTURAL_GENOMICS_CONSORTIUM_FOR_RESEARCH_ON_GENE_EXPRESSION = "STRUCTURAL_GENOMICS_CONSORTIUM_FOR_RESEARCH_ON_GENE_EXPRESSION",
+ STRUCTURAL_GENOMICS_OF_PATHOGENIC_PROTOZOA_CONSORTIUM = "STRUCTURAL_GENOMICS_OF_PATHOGENIC_PROTOZOA_CONSORTIUM",
+ STRUCTURAL_PROTEOMICS_IN_EUROPE = "STRUCTURAL_PROTEOMICS_IN_EUROPE",
+ STRUCTURAL_PROTEOMICS_IN_EUROPE_2 = "STRUCTURAL_PROTEOMICS_IN_EUROPE_2",
+ STRUCTURES_OF_MTB_PROTEINS_CONFERRING_SUSCEPTIBILITY_TO_KNOWN_MTB_INHIBITORS = "STRUCTURES_OF_MTB_PROTEINS_CONFERRING_SUSCEPTIBILITY_TO_KNOWN_MTB_INHIBITORS",
+ STRUCTURE_2_FUNCTION_PROJECT = "STRUCTURE_2_FUNCTION_PROJECT",
+ STRUCTURE_DYNAMICS_AND_ACTIVATION_MECHANISMS_OF_CHEMOKINE_RECEPTORS = "STRUCTURE_DYNAMICS_AND_ACTIVATION_MECHANISMS_OF_CHEMOKINE_RECEPTORS",
+ STRUCTURE_FUNCTION_ANALYSIS_OF_POLYMORPHIC_CDI_TOXIN_IMMUNITY_PROTEIN_COMPLEXES = "STRUCTURE_FUNCTION_ANALYSIS_OF_POLYMORPHIC_CDI_TOXIN_IMMUNITY_PROTEIN_COMPLEXES",
+ STRUCTURE_FUNCTION_STUDIES_OF_TIGHT_JUNCTION_MEMBRANE_PROTEINS = "STRUCTURE_FUNCTION_STUDIES_OF_TIGHT_JUNCTION_MEMBRANE_PROTEINS",
+ TB_STRUCTURAL_GENOMICS_CONSORTIUM = "TB_STRUCTURAL_GENOMICS_CONSORTIUM",
+ TRANSCONTINENTAL_EM_INITIATIVE_FOR_MEMBRANE_PROTEIN_STRUCTURE = "TRANSCONTINENTAL_EM_INITIATIVE_FOR_MEMBRANE_PROTEIN_STRUCTURE",
+ TRANSMEMBRANE_PROTEIN_CENTER = "TRANSMEMBRANE_PROTEIN_CENTER"
+}
+
+export enum PdbxSgProjectId {
+ _1 = "_1",
+ _10 = "_10",
+ _2 = "_2",
+ _3 = "_3",
+ _4 = "_4",
+ _5 = "_5",
+ _6 = "_6",
+ _7 = "_7",
+ _8 = "_8",
+ _9 = "_9"
+}
+
+export enum PdbxSgProjectInitialOfCenter {
+ ATCG_3_D = "ATCG_3_D",
+ BIGS = "BIGS",
+ BSGC = "BSGC",
+ BSGI = "BSGI",
+ CEBS = "CEBS",
+ CELLMAT = "CELLMAT",
+ CESG = "CESG",
+ CHSAM = "CHSAM",
+ CHTSB = "CHTSB",
+ CSGID = "CSGID",
+ CSMP = "CSMP",
+ GPCR = "GPCR",
+ IFN = "IFN",
+ ISFI = "ISFI",
+ ISPC = "ISPC",
+ JCSG = "JCSG",
+ MCMR = "MCMR",
+ MCSG = "MCSG",
+ MPID = "MPID",
+ MPP = "MPP",
+ MPSBC = "MPSBC",
+ MP_SBY_NMR = "MP_SBY_NMR",
+ MSGP = "MSGP",
+ MSGPP = "MSGPP",
+ MTBI = "MTBI",
+ NAT_PRO = "NAT_PRO",
+ NESG = "NESG",
+ NH_RS = "NH_RS",
+ NPC_XSTALS = "NPC_XSTALS",
+ NYCOMPS = "NYCOMPS",
+ NYSGRC = "NYSGRC",
+ NYSGXRC = "NYSGXRC",
+ OCSP = "OCSP",
+ OPPF = "OPPF",
+ PCSEP = "PCSEP",
+ PSF = "PSF",
+ RSGI = "RSGI",
+ SASTAD = "SASTAD",
+ SECSG = "SECSG",
+ SGC = "SGC",
+ SGCGES = "SGCGES",
+ SGPP = "SGPP",
+ SPINE = "SPINE",
+ SPINE_2 = "SPINE_2",
+ SSGCID = "SSGCID",
+ SSPF = "SSPF",
+ STEMCELL = "STEMCELL",
+ S_2_F = "S_2_F",
+ TBSGC = "TBSGC",
+ TCELL = "TCELL",
+ TEMIMPS = "TEMIMPS",
+ TJMP = "TJMP",
+ TMPC = "TMPC",
+ TRANSPORT_PDB = "TRANSPORT_PDB",
+ UC_4_CDI = "UC_4_CDI",
+ XMTB = "XMTB",
+ YSG = "YSG"
+}
+
+export enum PdbxSgProjectProjectName {
+ ENZYME_FUNCTION_INITIATIVE = "ENZYME_FUNCTION_INITIATIVE",
+ NIAID_NATIONAL_INSTITUTE_OF_ALLERGY_AND_INFECTIOUS_DISEASES = "NIAID_NATIONAL_INSTITUTE_OF_ALLERGY_AND_INFECTIOUS_DISEASES",
+ NPPSFA_NATIONAL_PROJECT_ON_PROTEIN_STRUCTURAL_AND_FUNCTIONAL_ANALYSES = "NPPSFA_NATIONAL_PROJECT_ON_PROTEIN_STRUCTURAL_AND_FUNCTIONAL_ANALYSES",
+ PSI_BIOLOGY = "PSI_BIOLOGY",
+ PSI_PROTEIN_STRUCTURE_INITIATIVE = "PSI_PROTEIN_STRUCTURE_INITIATIVE"
+}
+
+export enum PdbxAuditRevisionDetailsDataContentType {
+ NMR_RESTRAINTS = "NMR_RESTRAINTS",
+ NMR_SHIFTS = "NMR_SHIFTS",
+ STRUCTURE_FACTORS = "STRUCTURE_FACTORS",
+ STRUCTURE_MODEL = "STRUCTURE_MODEL"
+}
+
+export enum PdbxAuditRevisionDetailsProvider {
+ AUTHOR = "AUTHOR",
+ REPOSITORY = "REPOSITORY"
+}
+
+export enum PdbxAuditRevisionDetailsType {
+ COORDINATE_REPLACEMENT = "COORDINATE_REPLACEMENT",
+ INITIAL_RELEASE = "INITIAL_RELEASE",
+ OBSOLETE = "OBSOLETE"
}
-export enum Level {
- _100 = "_100",
- _30 = "_30",
- _40 = "_40",
- _50 = "_50",
- _60 = "_60",
- _70 = "_70",
- _80 = "_80",
- _90 = "_90",
- _95 = "_95"
+export enum PdbxAuditRevisionHistoryDataContentType {
+ NMR_RESTRAINTS = "NMR_RESTRAINTS",
+ NMR_SHIFTS = "NMR_SHIFTS",
+ STRUCTURE_FACTORS = "STRUCTURE_FACTORS",
+ STRUCTURE_MODEL = "STRUCTURE_MODEL"
}
-export enum PdbFormatCompatible {
+export enum PdbxDatabasePdbObsSprId {
+ OBSLTE = "OBSLTE",
+ SPRSDE = "SPRSDE"
+}
+
+export enum PdbxDatabaseStatusSgEntry {
N = "N",
Y = "Y"
}
+export enum PdbxDatabaseStatusDepositSite {
+ BMRB = "BMRB",
+ BNL = "BNL",
+ NDB = "NDB",
+ PDBE = "PDBE",
+ PDBJ = "PDBJ",
+ RCSB = "RCSB"
+}
+
+export enum PdbxDatabaseStatusMethodsDevelopmentCategory {
+ CAPRI = "CAPRI",
+ CASD_NMR = "CASD_NMR",
+ CASP = "CASP",
+ D_3_R = "D_3_R",
+ FOLD_IT = "FOLD_IT",
+ GPCR_DOCK = "GPCR_DOCK",
+ RNA_PUZZLES = "RNA_PUZZLES"
+}
+
+export enum PdbxDatabaseStatusPdbFormatCompatible {
+ N = "N",
+ Y = "Y"
+}
+
+export enum PdbxDatabaseStatusProcessSite {
+ BNL = "BNL",
+ NDB = "NDB",
+ PDBE = "PDBE",
+ PDBJ = "PDBJ",
+ RCSB = "RCSB"
+}
+
+export enum PdbxDatabaseStatusStatusCode {
+ AUCO = "AUCO",
+ AUTH = "AUTH",
+ BIB = "BIB",
+ DEL = "DEL",
+ HOLD = "HOLD",
+ HPUB = "HPUB",
+ OBS = "OBS",
+ POLC = "POLC",
+ PROC = "PROC",
+ REFI = "REFI",
+ REL = "REL",
+ REPL = "REPL",
+ REV = "REV",
+ RMVD = "RMVD",
+ TRSF = "TRSF",
+ UPD = "UPD",
+ WAIT = "WAIT",
+ WDRN = "WDRN"
+}
+
+export enum PdbxDatabaseStatusStatusCodeCs {
+ AUTH = "AUTH",
+ HOLD = "HOLD",
+ HPUB = "HPUB",
+ OBS = "OBS",
+ POLC = "POLC",
+ PROC = "PROC",
+ REL = "REL",
+ REPL = "REPL",
+ RMVD = "RMVD",
+ WAIT = "WAIT",
+ WDRN = "WDRN"
+}
+
+export enum PdbxDatabaseStatusStatusCodeMr {
+ AUTH = "AUTH",
+ HOLD = "HOLD",
+ HPUB = "HPUB",
+ OBS = "OBS",
+ POLC = "POLC",
+ PROC = "PROC",
+ REL = "REL",
+ REPL = "REPL",
+ RMVD = "RMVD",
+ WAIT = "WAIT",
+ WDRN = "WDRN"
+}
+
+export enum PdbxDatabaseStatusStatusCodeSf {
+ AUTH = "AUTH",
+ HOLD = "HOLD",
+ HPUB = "HPUB",
+ OBS = "OBS",
+ POLC = "POLC",
+ PROC = "PROC",
+ REL = "REL",
+ REPL = "REPL",
+ RMVD = "RMVD",
+ WAIT = "WAIT",
+ WDRN = "WDRN"
+}
+
+export enum PdbxDepositGroupGroupType {
+ CHANGED_STATE = "CHANGED_STATE",
+ GROUND_STATE = "GROUND_STATE",
+ UNDEFINED = "UNDEFINED"
+}
+
+export enum PdbxMoleculeFeaturesClass {
+ ANTAGONIST = "ANTAGONIST",
+ ANTHELMINTIC = "ANTHELMINTIC",
+ ANTIBIOTIC = "ANTIBIOTIC",
+ ANTIBIOTIC_ANTHELMINTIC = "ANTIBIOTIC_ANTHELMINTIC",
+ ANTIBIOTIC_ANTIMICROBIAL = "ANTIBIOTIC_ANTIMICROBIAL",
+ ANTIBIOTIC_ANTINEOPLASTIC = "ANTIBIOTIC_ANTINEOPLASTIC",
+ ANTICANCER = "ANTICANCER",
+ ANTICOAGULANT = "ANTICOAGULANT",
+ ANTICOAGULANT_ANTITHROMBOTIC = "ANTICOAGULANT_ANTITHROMBOTIC",
+ ANTIFUNGAL = "ANTIFUNGAL",
+ ANTIINFLAMMATORY = "ANTIINFLAMMATORY",
+ ANTIMICROBIAL = "ANTIMICROBIAL",
+ ANTIMICROBIAL_ANTIPARASITIC_ANTIBIOTIC = "ANTIMICROBIAL_ANTIPARASITIC_ANTIBIOTIC",
+ ANTIMICROBIAL_ANTIRETROVIRAL = "ANTIMICROBIAL_ANTIRETROVIRAL",
+ ANTIMICROBIAL_ANTITUMOR = "ANTIMICROBIAL_ANTITUMOR",
+ ANTINEOPLASTIC = "ANTINEOPLASTIC",
+ ANTIPARASITIC = "ANTIPARASITIC",
+ ANTIRETROVIRAL = "ANTIRETROVIRAL",
+ ANTITHROMBOTIC = "ANTITHROMBOTIC",
+ ANTITUMOR = "ANTITUMOR",
+ ANTIVIRAL = "ANTIVIRAL",
+ CASPASE_INHIBITOR = "CASPASE_INHIBITOR",
+ CHAPERONE_BINDING = "CHAPERONE_BINDING",
+ ENZYME_INHIBITOR = "ENZYME_INHIBITOR",
+ GROWTH_FACTOR = "GROWTH_FACTOR",
+ IMMUNOSUPPRESSANT = "IMMUNOSUPPRESSANT",
+ INHIBITOR = "INHIBITOR",
+ LANTIBIOTIC = "LANTIBIOTIC",
+ METABOLISM = "METABOLISM",
+ METAL_TRANSPORT = "METAL_TRANSPORT",
+ OXIDATION_REDUCTION = "OXIDATION_REDUCTION",
+ RECEPTOR = "RECEPTOR",
+ THROMBIN_INHIBITOR = "THROMBIN_INHIBITOR",
+ THROMBIN_INHIBITOR_TRYPSIN_INHIBITOR = "THROMBIN_INHIBITOR_TRYPSIN_INHIBITOR",
+ TOXIN = "TOXIN",
+ TRANSPORT_ACTIVATOR = "TRANSPORT_ACTIVATOR",
+ TRYPSIN_INHIBITOR = "TRYPSIN_INHIBITOR",
+ UNKNOWN = "UNKNOWN"
+}
+
+export enum PdbxMoleculeFeaturesType {
+ AMINOGLYCOSIDE = "AMINOGLYCOSIDE",
+ AMINO_ACID = "AMINO_ACID",
+ ANSAMYCIN = "ANSAMYCIN",
+ ANTHRACYCLINE = "ANTHRACYCLINE",
+ ANTHRAQUINONE = "ANTHRAQUINONE",
+ CHALKOPHORE = "CHALKOPHORE",
+ CHALKOPHORE_POLYPEPTIDE = "CHALKOPHORE_POLYPEPTIDE",
+ CHROMOPHORE = "CHROMOPHORE",
+ CYCLIC_DEPSIPEPTIDE = "CYCLIC_DEPSIPEPTIDE",
+ CYCLIC_LIPOPEPTIDE = "CYCLIC_LIPOPEPTIDE",
+ CYCLIC_PEPTIDE = "CYCLIC_PEPTIDE",
+ GLYCOPEPTIDE = "GLYCOPEPTIDE",
+ HETEROCYCLIC = "HETEROCYCLIC",
+ IMINO_SUGAR = "IMINO_SUGAR",
+ KETO_ACID = "KETO_ACID",
+ LIPOGLYCOPEPTIDE = "LIPOGLYCOPEPTIDE",
+ LIPOPEPTIDE = "LIPOPEPTIDE",
+ MACROLIDE = "MACROLIDE",
+ NON_POLYMER = "NON_POLYMER",
+ NUCLEOSIDE = "NUCLEOSIDE",
+ OLIGOPEPTIDE = "OLIGOPEPTIDE",
+ OLIGOSACCHARIDE = "OLIGOSACCHARIDE",
+ PEPTAIBOL = "PEPTAIBOL",
+ PEPTIDE_LIKE = "PEPTIDE_LIKE",
+ POLYCYCLIC = "POLYCYCLIC",
+ POLYPEPTIDE = "POLYPEPTIDE",
+ POLYSACCHARIDE = "POLYSACCHARIDE",
+ QUINOLONE = "QUINOLONE",
+ SIDEROPHORE = "SIDEROPHORE",
+ THIOLACTONE = "THIOLACTONE",
+ THIOPEPTIDE = "THIOPEPTIDE",
+ UNKNOWN = "UNKNOWN"
+}
+
+export enum PdbxNmrExptlSampleState {
+ ANISOTROPIC = "ANISOTROPIC",
+ ISOTROPIC = "ISOTROPIC"
+}
+
+export enum PdbxNmrExptlSampleConditionsIonicStrengthUnits {
+ M = "M",
+ M_M = "M_M",
+ NOT_DEFINED = "NOT_DEFINED"
+}
+
+export enum PdbxNmrExptlSampleConditionsPhUnits {
+ NOT_DEFINED = "NOT_DEFINED",
+ P_D = "P_D",
+ P_H = "P_H",
+ P_H_ = "P_H_"
+}
+
+export enum PdbxNmrExptlSampleConditionsTemperatureUnits {
+ C = "C",
+ K = "K",
+ NOT_DEFINED = "NOT_DEFINED"
+}
+
+export enum PdbxNmrSampleDetailsType {
+ BICELLE = "BICELLE",
+ EMULSION = "EMULSION",
+ FIBER = "FIBER",
+ FIBROUS_PROTEIN = "FIBROUS_PROTEIN",
+ FILAMENTOUS_VIRUS = "FILAMENTOUS_VIRUS",
+ GEL_SOLID = "GEL_SOLID",
+ GEL_SOLUTION = "GEL_SOLUTION",
+ LIPOSOME = "LIPOSOME",
+ LYOPHILIZED_POWDER = "LYOPHILIZED_POWDER",
+ MEMBRANE = "MEMBRANE",
+ MICELLE = "MICELLE",
+ ORIENTED_MEMBRANE_FILM = "ORIENTED_MEMBRANE_FILM",
+ POLYCRYSTALLINE_POWDER = "POLYCRYSTALLINE_POWDER",
+ REVERSE_MICELLE = "REVERSE_MICELLE",
+ SINGLE_CRYSTAL = "SINGLE_CRYSTAL",
+ SOLID = "SOLID",
+ SOLUTION = "SOLUTION"
+}
+
+export enum PdbxSerialCrystallographySampleDeliveryMethod {
+ FIXED_TARGET = "FIXED_TARGET",
+ INJECTION = "INJECTION"
+}
+
+export enum RcsbBindingSource {
+ BINDINGDB = "BINDINGDB",
+ BINDINGMOAD = "BINDINGMOAD",
+ PDBBIND = "PDBBIND"
+}
+
+export enum RefineLsMatrixType {
+ ATOMBLOCK = "ATOMBLOCK",
+ DIAGONAL = "DIAGONAL",
+ FULL = "FULL",
+ FULLCYCLE = "FULLCYCLE",
+ SPARSE = "SPARSE",
+ USERBLOCK = "USERBLOCK"
+}
+
+export enum RefinePdbxTlsResidualAdpFlag {
+ LIKELY_RESIDUAL = "LIKELY_RESIDUAL",
+ UNVERIFIED = "UNVERIFIED"
+}
+
+export enum SoftwareLanguage {
+ ADA = "ADA",
+ ASSEMBLER = "ASSEMBLER",
+ AWK = "AWK",
+ BASIC = "BASIC",
+ C = "C",
+ CSH = "CSH",
+ C_ = "C_",
+ C_C = "C_C",
+ FORTRAN = "FORTRAN",
+ FORTRAN_77 = "FORTRAN_77",
+ FORTRAN_77_ = "FORTRAN_77_",
+ FORTRAN_90 = "FORTRAN_90",
+ JAVA = "JAVA",
+ JAVA_FORTRAN = "JAVA_FORTRAN",
+ KSH = "KSH",
+ OTHER = "OTHER",
+ PASCAL = "PASCAL",
+ PERL = "PERL",
+ PYTHON = "PYTHON",
+ PYTHON_C = "PYTHON_C",
+ SH = "SH",
+ TCL = "TCL"
+}
+
+export enum SoftwareType {
+ FILTER = "FILTER",
+ JIFFY = "JIFFY",
+ LIBRARY = "LIBRARY",
+ OTHER = "OTHER",
+ PACKAGE = "PACKAGE",
+ PROGRAM = "PROGRAM"
+}
+
+export enum StructPdbxCaspFlag {
+ N = "N",
+ Y = "Y"
+}
+
+export enum SymmetryCellSetting {
+ CUBIC = "CUBIC",
+ HEXAGONAL = "HEXAGONAL",
+ MONOCLINIC = "MONOCLINIC",
+ ORTHORHOMBIC = "ORTHORHOMBIC",
+ RHOMBOHEDRAL = "RHOMBOHEDRAL",
+ TETRAGONAL = "TETRAGONAL",
+ TRICLINIC = "TRICLINIC",
+ TRIGONAL = "TRIGONAL"
+}
+
+// ====================================================
+// END: Typescript template
+// ====================================================
+
+// ====================================================
+// Documents
+// ====================================================
+
export namespace AssemblySymmetry {
export type Variables = {
readonly pdbId: string;
@@ -171,52 +1204,67 @@ export namespace AssemblySymmetry {
export type Query = {
readonly __typename?: "Query";
+
readonly assemblies?: ReadonlyArray<Assemblies | null> | null;
};
export type Assemblies = {
readonly __typename?: "CoreAssembly";
- readonly assembly_id: number;
- readonly rcsb_assembly_symmetry?: RcsbAssemblySymmetry | null;
+
+ readonly pdbx_struct_assembly?: PdbxStructAssembly | null;
+
+ readonly rcsb_struct_symmetry?: ReadonlyArray<RcsbStructSymmetry | null> | null;
+
+ readonly rcsb_struct_symmetry_provenance?: string | null;
};
- export type RcsbAssemblySymmetry = {
- readonly __typename?: "RcsbAssemblySymmetry";
- readonly source: string;
- readonly symmetry_features: ReadonlyArray<SymmetryFeatures | null>;
+ export type PdbxStructAssembly = {
+ readonly __typename?: "PdbxStructAssembly";
+
+ readonly id: string;
};
- export type SymmetryFeatures = {
- readonly __typename?: "SymmetryFeature";
- readonly symmetry: Symmetry;
+ export type RcsbStructSymmetry = {
+ readonly __typename?: "RcsbStructSymmetry";
+
readonly clusters: ReadonlyArray<Clusters | null>;
- readonly stoichiometry: Stoichiometry;
- readonly symmetry_axes?: ReadonlyArray<SymmetryAxes | null> | null;
- readonly type: SymmetryFeatureType;
- };
- export type Symmetry = {
- readonly __typename?: "QuaternarySymmetry";
- readonly description: string;
- readonly value: string;
+ readonly kind: RcsbStructSymmetryKind;
+
+ readonly oligomeric_state: string;
+
+ readonly rotation_axes?: ReadonlyArray<RotationAxes | null> | null;
+
+ readonly stoichiometry: ReadonlyArray<string | null>;
+
+ readonly symbol: string;
+
+ readonly type: RcsbStructSymmetryType;
};
export type Clusters = {
- readonly __typename?: "Cluster";
- readonly members: ReadonlyArray<string | null>;
+ readonly __typename?: "RcsbStructSymmetryClusters";
+
readonly avg_rmsd?: number | null;
+
+ readonly members: ReadonlyArray<Members | null>;
};
- export type Stoichiometry = {
- readonly __typename?: "Stoichiometry";
- readonly description: string;
- readonly value: ReadonlyArray<string | null>;
+ export type Members = {
+ readonly __typename?: "ClustersMembers";
+
+ readonly asym_id: string;
+
+ readonly pdbx_struct_oper_list_ids?: ReadonlyArray<string | null> | null;
};
- export type SymmetryAxes = {
- readonly __typename?: "SymmetryAxis";
+ export type RotationAxes = {
+ readonly __typename?: "RcsbStructSymmetryRotationAxes";
+
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 379310bde9f7d2552af0a31168a83907b443e7d5..11795b06b3f6de0f4e5e3e6d48940fa855cc9179 100644
--- a/src/mol-model-props/rcsb/symmetry.ts
+++ b/src/mol-model-props/rcsb/symmetry.ts
@@ -17,6 +17,7 @@ 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';
+import { PropertyWrapper } from 'mol-model-props/common/wrapper';
const { str, int, float, Aliased, Vector, List } = Column.Schema;
@@ -31,51 +32,58 @@ function getCategory(name: keyof AssemblySymmetry.Schema) {
return { name, instance: getInstance(name) }
}
-function createDatabase(assemblies: ReadonlyArray<AssemblySymmetryGraphQL.Assemblies>): AssemblySymmetry.Database {
+function createDatabaseFromJson(assemblies: ReadonlyArray<AssemblySymmetryGraphQL.Assemblies>): AssemblySymmetry.Database {
const Schema = AssemblySymmetry.Schema
- const featureRows: Table.Row<typeof Schema.rcsb_assembly_symmetry_feature>[] = []
+ const featureRows: Table.Row<typeof Schema.rcsb_assembly_symmetry>[] = []
const clusterRows: Table.Row<typeof Schema.rcsb_assembly_symmetry_cluster>[] = []
+ const clusterMemberRows: Table.Row<typeof Schema.rcsb_assembly_symmetry_cluster_member>[] = []
const axisRows: Table.Row<typeof Schema.rcsb_assembly_symmetry_axis>[] = []
let id = 1 // start feature ids at 1
for (let i = 0, il = assemblies.length; i < il; ++i) {
- 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]! // TODO upstream, array members should not be nullable
+ const { pdbx_struct_assembly, rcsb_struct_symmetry, rcsb_struct_symmetry_provenance } = assemblies[i]
+ if (!pdbx_struct_assembly || !rcsb_struct_symmetry ||!rcsb_struct_symmetry_provenance) continue
+ const assembly_id = pdbx_struct_assembly.id
+ for (let j = 0, jl = rcsb_struct_symmetry.length; j < jl; ++j) {
+ const rss = rcsb_struct_symmetry[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[], // TODO upstream, array members should not be nullable
- stoichiometry_description: f.stoichiometry.description,
- symmetry_value: f.symmetry.value,
- symmetry_description: f.symmetry.description
+ provenance: rcsb_struct_symmetry_provenance,
+ type: rss.type,
+ stoichiometry: rss.stoichiometry as string[], // TODO upstream, array members should not be nullable
+ kind: rss.kind,
+ symbol: rss.symbol,
+ oligomeric_state: rss.oligomeric_state
})
- const clusters = f.clusters
+ const clusters = rss.clusters
if (clusters) {
for (let k = 0, kl = clusters.length; k < kl; ++k) {
const c = clusters[k]! // TODO upstream, array members should not be nullable
clusterRows.push({
- feature_id: id,
+ id: k,
+ symmetry_id: id,
avg_rmsd: c.avg_rmsd || 0, // TODO upstream, should not be nullable, or???
- members: c.members as string[] // TODO upstream, array members should not be nullable
})
+ for (let l = 0, ll = c.members.length; l < ll; ++l) {
+ const m = c.members[l]! // TODO upstream, array members should not be nullable
+ clusterMemberRows.push({
+ cluster_id: k,
+ asym_id: m.asym_id,
+ pdbx_struct_oper_list_ids: (m.pdbx_struct_oper_list_ids || []) as string[]
+ })
+ }
}
}
- const axes = f.symmetry_axes
+ const axes = rss.rotation_axes
if (axes) {
for (let k = 0, kl = axes.length; k < kl; ++k) {
const a = axes[k]!
axisRows.push({
- feature_id: id,
+ symmetry_id: id,
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
@@ -88,20 +96,57 @@ function createDatabase(assemblies: ReadonlyArray<AssemblySymmetryGraphQL.Assemb
}
return _Database.ofTables('assembly_symmetry', Schema, {
- rcsb_assembly_symmetry_feature: Table.ofRows(Schema.rcsb_assembly_symmetry_feature, featureRows),
+ rcsb_assembly_symmetry: Table.ofRows(Schema.rcsb_assembly_symmetry, featureRows),
rcsb_assembly_symmetry_cluster: Table.ofRows(Schema.rcsb_assembly_symmetry_cluster, clusterRows),
+ rcsb_assembly_symmetry_cluster_member: Table.ofRows(Schema.rcsb_assembly_symmetry_cluster_member, clusterMemberRows),
rcsb_assembly_symmetry_axis: Table.ofRows(Schema.rcsb_assembly_symmetry_axis, axisRows)
})
}
+function createDatabaseFromCif(model: Model): AssemblySymmetry.Database {
+ const Schema = AssemblySymmetry.Schema
+
+ const rcsb_assembly_symmetry = toTable(Schema.rcsb_assembly_symmetry, 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_cluster_member
+ if (model.sourceData.frame.categoryNames.includes('rcsb_assembly_symmetry_cluster_member')) {
+ rcsb_assembly_symmetry_cluster_member = toTable(Schema.rcsb_assembly_symmetry_cluster_member, model.sourceData.frame.categories.rcsb_assembly_symmetry_cluster_member)
+ } else {
+ rcsb_assembly_symmetry_cluster_member = 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
+ }
+
+ return _Database.ofTables('rcsb_assembly_symmetry', Schema, {
+ rcsb_assembly_symmetry,
+ rcsb_assembly_symmetry_cluster,
+ rcsb_assembly_symmetry_cluster_member,
+ rcsb_assembly_symmetry_axis
+ })
+}
+
const _Descriptor: ModelPropertyDescriptor = {
isStatic: true,
- name: 'assembly_symmetry',
+ name: 'rcsb_assembly_symmetry',
cifExport: {
prefix: 'rcsb',
categories: [
- getCategory('rcsb_assembly_symmetry_feature'),
+ PropertyWrapper.defaultInfoCategory<CifExportContext>('rcsb_assembly_symmetry_info', ctx => PropertyWrapper.createInfo()),
+ getCategory('rcsb_assembly_symmetry'),
getCategory('rcsb_assembly_symmetry_cluster'),
+ getCategory('rcsb_assembly_symmetry_cluster_member'),
getCategory('rcsb_assembly_symmetry_axis')
]
}
@@ -111,56 +156,85 @@ const client = new GraphQLClient('http://rest-experimental.rcsb.org/graphql')
export interface AssemblySymmetry {
db: AssemblySymmetry.Database
- getFeatures(assemblyId: string): Table<AssemblySymmetry.Schema['rcsb_assembly_symmetry_feature']>
- getClusters(featureId: number): Table<AssemblySymmetry.Schema['rcsb_assembly_symmetry_cluster']>
- getAxes(featureId: number): Table<AssemblySymmetry.Schema['rcsb_assembly_symmetry_axis']>
+ getSymmetries(assemblyId: string): Table<AssemblySymmetry.Schema['rcsb_assembly_symmetry']>
+ getClusters(symmetryId: number): Table<AssemblySymmetry.Schema['rcsb_assembly_symmetry_cluster']>
+ getClusterMembers(clusterId: number): Table<AssemblySymmetry.Schema['rcsb_assembly_symmetry_cluster_member']>
+ getAxes(symmetryId: number): Table<AssemblySymmetry.Schema['rcsb_assembly_symmetry_axis']>
}
export function AssemblySymmetry(db: AssemblySymmetry.Database): AssemblySymmetry {
- const f = db.rcsb_assembly_symmetry_feature
+ const f = db.rcsb_assembly_symmetry
const c = db.rcsb_assembly_symmetry_cluster
+ const cm = db.rcsb_assembly_symmetry_cluster_member
const a = db.rcsb_assembly_symmetry_axis
return {
db,
- getFeatures: (assemblyId: string) => Table.pick(f, f._schema, i => f.assembly_id.value(i) === assemblyId),
- getClusters: (featureId: number) => Table.pick(c, c._schema, i => c.feature_id.value(i) === featureId),
- getAxes: (featureId: number) => Table.pick(a, a._schema, i => a.feature_id.value(i) === featureId)
+ getSymmetries: (assemblyId: string) => Table.pick(f, f._schema, i => f.assembly_id.value(i) === assemblyId),
+ getClusters: (symmetryId: number) => Table.pick(c, c._schema, i => c.symmetry_id.value(i) === symmetryId),
+ getClusterMembers: (clusterId: number) => Table.pick(cm, cm._schema, i => cm.cluster_id.value(i) === clusterId),
+ getAxes: (symmetryId: number) => Table.pick(a, a._schema, i => a.symmetry_id.value(i) === symmetryId)
}
}
export namespace AssemblySymmetry {
export const Schema = {
- rcsb_assembly_symmetry_feature: {
- /** Uniquely identifies a record in `rcsb_assembly_symmetry_feature` */
+ rcsb_assembly_symmetry_info: {
+ updated_datetime_utc: Column.Schema.str
+ },
+ rcsb_assembly_symmetry: {
+ /** Uniquely identifies a record in `rcsb_assembly_symmetry` */
id: int,
- /** A pointer to `pdbx_struct_assembly.id` */
+ /**
+ * A pointer to `pdbx_struct_assembly.id`.
+ * The value 'deposited' refers to the coordinates as given in the file.
+ * */
assembly_id: str,
- /** Name and version of software used to calculate protein symmetry */
- source: str,
+ /** Name and version of software used to calculate assembly symmetry */
+ provenance: str,
/** Type of protein symmetry */
- type: Aliased<'GLOBAL' | 'LOCAL' | 'PSEUDO'>(str),
+ kind: Aliased<'GLOBAL' | 'LOCAL' | 'PSEUDO'>(str),
/** Quantitative description of every individual subunit in a given protein */
- stoichiometry_value: List(',', x => x),
- /** 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
+ stoichiometry: List(',', x => x),
+ /**
+ * Symmetry symbol refers to point group or helical symmetry of identical subunits.
+ * Contains point group symbol (e.g., C2, C5, D2, T, O, I) or H for helical symmetry.
+ */
+ symbol: str,
+ /** Point group or helical symmetry */
+ type: Aliased<'ASYMMETRIC' | 'CYCLIC' | 'DIHEDRAL' | 'HELICAL' | 'ICOSAHEDRAL' | 'OCTAHEDRAL' | 'TETRAHEDRAL'>(str),
+ /**
+ * Oligomeric state refers to a composition of subunits in quaternary structure.
+ * Quaternary structure may be composed either exclusively of several copies of identical
+ * subunits, in which case they are termed homo-oligomers, or alternatively by at least
+ * one copy of different subunits (hetero-oligomers). Quaternary structure composed of
+ * a single subunit is demoted as 'Monomer'.
+ */
+ oligomeric_state: str,
},
rcsb_assembly_symmetry_cluster: {
- /** A pointer to `rcsb_assembly_symmetry_feature.id` */
- feature_id: int,
+ /** Uniquely identifies a record in `rcsb_assembly_symmetry_cluster` */
+ id: int,
+ /** A pointer to `rcsb_assembly_symmetry.id` */
+ symmetry_id: int,
/** Average RMSD between members of a given cluster */
- avg_rmsd: float,
- /** List of `auth_label_id` values */
- members: List(',', x => x)
+ avg_rmsd: float
+ },
+ rcsb_assembly_symmetry_cluster_member: {
+ /** A pointer to `rcsb_assembly_symmetry_cluster.id` */
+ cluster_id: int,
+ /** The `label_asym_id` value of the member */
+ asym_id: str,
+ /** List of `pdbx_struct_oper_list_id` values of the member */
+ pdbx_struct_oper_list_ids: List(',', x => x)
},
rcsb_assembly_symmetry_axis: {
- /** A pointer to `rcsb_assembly_symmetry_feature.id` */
- feature_id: int,
- /** The order of the symmetry axis */
+ /** A pointer to `rcsb_assembly_symmetry.id` */
+ symmetry_id: int,
+ /**
+ * The number of times (order of rotation) that a subunit can be repeated by a rotation
+ * operation, being transformed into a new state indistinguishable from its starting state.
+ */
order: int,
/** The x,y,z coordinate of the start point of a symmetry axis */
start: Vector(3),
@@ -177,32 +251,9 @@ export namespace AssemblySymmetry {
if (model.customProperties.has(Descriptor)) return true;
let db: Database
-
- // TODO: there should be a "meta field" that indicates the property was added (see for example PDBe structure report)
- // the reason for this is that the feature might not be present and therefore the "default" categories would
- // not be created. This would result in an unnecessarily failed web request.
- 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
- })
+ let info = PropertyWrapper.tryGetInfoFromCif('rcsb_assembly_symmetry_info', model);
+ if (info) {
+ db = createDatabaseFromCif(model)
} else {
let result: AssemblySymmetryGraphQL.Query
const variables: AssemblySymmetryGraphQL.Variables = { pdbId: model.label.toLowerCase() };
@@ -214,15 +265,15 @@ export namespace AssemblySymmetry {
}
if (!result || !result.assemblies) return false;
- db = createDatabase(result.assemblies as ReadonlyArray<AssemblySymmetryGraphQL.Assemblies>)
+ db = createDatabaseFromJson(result.assemblies as ReadonlyArray<AssemblySymmetryGraphQL.Assemblies>)
}
model.customProperties.add(Descriptor);
- model._staticPropertyData.__AssemblySymmetry__ = AssemblySymmetry(db);
+ model._staticPropertyData.__RCSBAssemblySymmetry__ = AssemblySymmetry(db);
return true;
}
export function get(model: Model): AssemblySymmetry | undefined {
- return model._staticPropertyData.__AssemblySymmetry__;
+ return model._staticPropertyData.__RCSBAssemblySymmetry__;
}
}
\ No newline at end of file