diff --git a/src/mol-model-props/rcsb/assembly-symmetry.ts b/src/mol-model-props/rcsb/assembly-symmetry.ts
index 94ef48049231a5cc13bf370f557ea7f8c55f8ff8..b9ef9a2448c5f169152a72cfb916158e51750c1d 100644
--- a/src/mol-model-props/rcsb/assembly-symmetry.ts
+++ b/src/mol-model-props/rcsb/assembly-symmetry.ts
@@ -8,7 +8,7 @@ import { AssemblySymmetryQuery, AssemblySymmetryQueryVariables } from './graphql
import query from './graphql/symmetry.gql';
import { ParamDefinition as PD } from '../../mol-util/param-definition'
-import { CustomPropertyDescriptor, Structure } from '../../mol-model/structure';
+import { CustomPropertyDescriptor, Structure, Model } from '../../mol-model/structure';
import { Database as _Database, Column } from '../../mol-data/db'
import { GraphQLClient } from '../../mol-util/graphql-client';
import { CustomProperty } from '../common/custom-property';
@@ -26,6 +26,18 @@ const BiologicalAssemblyNames = new Set([
'software_defined_assembly'
])
+export function isBiologicalAssembly(structure: Structure): boolean {
+ if (!MmcifFormat.is(structure.models[0].sourceData)) return false
+ const mmcif = structure.models[0].sourceData.data.db
+ if (!mmcif.pdbx_struct_assembly.details.isDefined) return false
+ const id = structure.units[0].conformation.operator.assembly?.id || ''
+ if (id === '' || id === 'deposited') return true
+ const indices = Column.indicesOf(mmcif.pdbx_struct_assembly.id, e => e === id)
+ if (indices.length !== 1) return false
+ const details = mmcif.pdbx_struct_assembly.details.value(indices[0])
+ return BiologicalAssemblyNames.has(details)
+}
+
export namespace AssemblySymmetry {
export enum Tag {
Cluster = 'rcsb-assembly-symmetry-cluster',
@@ -35,19 +47,11 @@ export namespace AssemblySymmetry {
export const DefaultServerUrl = 'https://data-beta.rcsb.org/graphql'
export function isApplicable(structure?: Structure): boolean {
- // check if structure is from pdb entry
- if (!structure || structure.models.length !== 1 || !MmcifFormat.is(structure.models[0].sourceData) || (!structure.models[0].sourceData.data.db.database_2.database_id.isDefined &&
- structure.models[0].entryId.length !== 4)) return false
-
- // check if assembly is 'biological'
- const mmcif = structure.models[0].sourceData.data.db
- if (!mmcif.pdbx_struct_assembly.details.isDefined) return false
- const id = structure.units[0].conformation.operator.assembly?.id || ''
- if (id === '' || id === 'deposited') return true
- const indices = Column.indicesOf(mmcif.pdbx_struct_assembly.id, e => e === id)
- if (indices.length !== 1) return false
- const details = mmcif.pdbx_struct_assembly.details.value(indices[0])
- return BiologicalAssemblyNames.has(details)
+ return (
+ !!structure && structure.models.length === 1 &&
+ Model.isFromPdbArchive(structure.models[0]) &&
+ isBiologicalAssembly(structure)
+ )
}
export async function fetch(ctx: CustomProperty.Context, structure: Structure, props: AssemblySymmetryDataProps): Promise<AssemblySymmetryDataValue> {
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts
index 50b6292dab50b15e0bc47611434c77ab61e8d4d3..8c04d08a79d6683bdbb3e7e2492ddd521eecf4df 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts
@@ -155,6 +155,9 @@ export const AssemblySymmetryPreset = StructureRepresentationPresetProvider({
name: 'Assembly Symmetry', group: 'Annotation',
description: 'Shows Assembly Symmetry axes and cage; colors structure according to assembly symmetry cluster membership. Data calculated with BioJava, obtained via RCSB PDB.'
},
+ isApplicable(a) {
+ return AssemblySymmetry.isApplicable(a.data)
+ },
params: () => AssemblySymmetryPresetParams,
async apply(ref, params, plugin) {
const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report.ts b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report.ts
index af50e65b45871fbc1c86bfd5a298c9898a720193..96f7e410c8e5d2959d7d4a59d1c9aa60e59d0bed 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report.ts
@@ -20,6 +20,7 @@ import { MolScriptBuilder as MS } from '../../../../../mol-script/language/build
import { Task } from '../../../../../mol-task';
import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../../../../mol-plugin-state/builder/structure/representation-preset';
import { StateObjectRef } from '../../../../../mol-state';
+import { Model } from '../../../../../mol-model/structure';
export const RCSBValidationReport = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
name: 'rcsb-validation-report-prop',
@@ -53,7 +54,10 @@ export const RCSBValidationReport = PluginBehavior.create<{ autoAttach: boolean,
this.ctx.representation.structure.registry.add(ClashesRepresentationProvider)
this.ctx.query.structure.registry.add(hasClash)
- this.ctx.builders.structure.representation.registerPreset(ValidationReportPreset)
+
+ this.ctx.builders.structure.representation.registerPreset(ValidationReportGeometryQualityPreset)
+ this.ctx.builders.structure.representation.registerPreset(ValidationReportDensityFitPreset)
+ this.ctx.builders.structure.representation.registerPreset(ValidationReportRandomCoilIndexPreset)
}
update(p: { autoAttach: boolean, showTooltip: boolean }) {
@@ -78,7 +82,10 @@ export const RCSBValidationReport = PluginBehavior.create<{ autoAttach: boolean,
this.ctx.representation.structure.registry.remove(ClashesRepresentationProvider)
this.ctx.query.structure.registry.remove(hasClash)
- this.ctx.builders.structure.representation.unregisterPreset(ValidationReportPreset)
+
+ this.ctx.builders.structure.representation.unregisterPreset(ValidationReportGeometryQualityPreset)
+ this.ctx.builders.structure.representation.unregisterPreset(ValidationReportDensityFitPreset)
+ this.ctx.builders.structure.representation.unregisterPreset(ValidationReportRandomCoilIndexPreset)
}
},
params: () => ({
@@ -99,7 +106,7 @@ function geometryQualityLabel(loci: Loci): string | undefined {
const validationReport = ValidationReportProvider.get(unit.model).value
if (!validationReport) return
- if (unit.model.customProperties.hasReference(ValidationReportProvider.descriptor)) return
+ if (!unit.model.customProperties.hasReference(ValidationReportProvider.descriptor)) return
const { bondOutliers, angleOutliers } = validationReport
const eI = unit.elements[OrderedSet.start(indices)]
@@ -127,6 +134,7 @@ function geometryQualityLabel(loci: Loci): string | undefined {
for (const { indices, unit } of loci.elements) {
const validationReport = ValidationReportProvider.get(unit.model).value
if (!validationReport) continue
+ if (!unit.model.customProperties.hasReference(ValidationReportProvider.descriptor)) continue
hasValidationReport = true
const { geometryIssues } = validationReport
@@ -180,7 +188,7 @@ function densityFitLabel(loci: Loci): string | undefined {
for (const { indices, unit } of loci.elements) {
const validationReport = ValidationReportProvider.get(unit.model).value
if (!validationReport) continue
- if (unit.model.customProperties.hasReference(ValidationReportProvider.descriptor)) continue
+ if (!unit.model.customProperties.hasReference(ValidationReportProvider.descriptor)) continue
const { rsrz, rscc } = validationReport
const residueIndex = unit.model.atomicHierarchy.residueAtomSegments.index
@@ -237,7 +245,7 @@ function randomCoilIndexLabel(loci: Loci): string | undefined {
for (const { indices, unit } of loci.elements) {
const validationReport = ValidationReportProvider.get(unit.model).value
if (!validationReport) continue
- if (unit.model.customProperties.hasReference(ValidationReportProvider.descriptor)) continue
+ if (!unit.model.customProperties.hasReference(ValidationReportProvider.descriptor)) continue
const { rci } = validationReport
const residueIndex = unit.model.atomicHierarchy.residueAtomSegments.index
@@ -288,24 +296,26 @@ const hasClash = StructureSelectionQuery('Residues with Clashes', MS.struct.modi
//
-export const ValidationReportPreset = StructureRepresentationPresetProvider({
- id: 'preset-structure-representation-rcsb-validation-report',
+export const ValidationReportGeometryQualityPreset = StructureRepresentationPresetProvider({
+ id: 'preset-structure-representation-rcsb-validation-report-geometry-uality',
display: {
- name: 'Validation Report', group: 'Annotation',
+ name: 'Validation Report (Geometry Quality)', group: 'Annotation',
description: 'Color structure based on geometry quality; show geometry clashes. Data from wwPDB Validation Report, obtained via RCSB PDB.'
},
+ isApplicable(a) {
+ return a.data.models.length === 1 && ValidationReport.isApplicable(a.data.models[0])
+ },
params: () => StructureRepresentationPresetProvider.CommonParams,
async apply(ref, params, plugin) {
const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
const model = structureCell?.obj?.data.model
if (!structureCell || !model) return {};
- const colorTheme = GeometryQualityColorThemeProvider.name as any
-
await plugin.runTask(Task.create('Validation Report', async runtime => {
await ValidationReportProvider.attach({ fetch: plugin.fetch, runtime }, model)
}))
+ const colorTheme = GeometryQualityColorThemeProvider.name as any
const { components, representations } = await PresetStructureRepresentations.auto.apply(ref, { ...params, globalThemeName: colorTheme }, plugin)
const clashes = await plugin.builders.structure.tryCreateComponentFromExpression(structureCell, hasClash.expression, 'clashes', { label: 'Clashes' })
@@ -320,4 +330,52 @@ export const ValidationReportPreset = StructureRepresentationPresetProvider({
await plugin.updateDataState(update, { revertOnError: false });
return { components: { ...components, clashes }, representations: { ...representations, clashesBallAndStick, clashesSnfg3d } };
}
+});
+
+export const ValidationReportDensityFitPreset = StructureRepresentationPresetProvider({
+ id: 'preset-structure-representation-rcsb-validation-report-density-fit',
+ display: {
+ name: 'Validation Report (Density Fit)', group: 'Annotation',
+ description: 'Color structure based on density fit. Data from wwPDB Validation Report, obtained via RCSB PDB.'
+ },
+ isApplicable(a) {
+ return a.data.models.length === 1 && ValidationReport.isApplicable(a.data.models[0]) && Model.hasXrayMap(a.data.models[0])
+ },
+ params: () => StructureRepresentationPresetProvider.CommonParams,
+ async apply(ref, params, plugin) {
+ const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+ const model = structureCell?.obj?.data.model
+ if (!structureCell || !model) return {};
+
+ await plugin.runTask(Task.create('Validation Report', async runtime => {
+ await ValidationReportProvider.attach({ fetch: plugin.fetch, runtime }, model)
+ }))
+
+ const colorTheme = DensityFitColorThemeProvider.name as any
+ return await PresetStructureRepresentations.auto.apply(ref, { ...params, globalThemeName: colorTheme }, plugin)
+ }
+});
+
+export const ValidationReportRandomCoilIndexPreset = StructureRepresentationPresetProvider({
+ id: 'preset-structure-representation-rcsb-validation-report-random-coil-index',
+ display: {
+ name: 'Validation Report (Random Coil Index)', group: 'Annotation',
+ description: 'Color structure based on Random Coil Index. Data from wwPDB Validation Report, obtained via RCSB PDB.'
+ },
+ isApplicable(a) {
+ return a.data.models.length === 1 && ValidationReport.isApplicable(a.data.models[0]) && Model.isFromNmr(a.data.models[0])
+ },
+ params: () => StructureRepresentationPresetProvider.CommonParams,
+ async apply(ref, params, plugin) {
+ const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+ const model = structureCell?.obj?.data.model
+ if (!structureCell || !model) return {};
+
+ await plugin.runTask(Task.create('Validation Report', async runtime => {
+ await ValidationReportProvider.attach({ fetch: plugin.fetch, runtime }, model)
+ }))
+
+ const colorTheme = RandomCoilIndexColorThemeProvider.name as any
+ return await PresetStructureRepresentations.auto.apply(ref, { ...params, globalThemeName: colorTheme }, plugin)
+ }
});
\ No newline at end of file