improved naming of PDBe and RCSB PDB provided properties

src/mol-model-props/pdbe/structure-quality-report.ts

@@ -119,7 +119,7 @@ export type StructureQualityReportParams = typeof StructureQualityReportParams
 export type StructureQualityReportProps = PD.Values<StructureQualityReportParams>
 
 export const StructureQualityReportProvider: CustomModelProperty.Provider<StructureQualityReportParams, StructureQualityReport> = CustomModelProperty.createProvider({
-    label: 'PDBe Structure Quality Report',
+    label: 'Structure Quality Report',
     descriptor: CustomPropertyDescriptor<ReportExportContext, any>({
         name: 'pdbe_structure_quality_report',
         cifExport: {

src/mol-model-props/pdbe/themes/structure-quality-report.ts

@@ -72,13 +72,13 @@ export function StructureQualityReportColorTheme(ctx: ThemeDataContext, props: P
         granularity: 'group',
         color: color,
         props: props,
-        description: 'Assigns residue colors according to the number of issues or a specific issue in the PDBe Validation Report.',
+        description: 'Assigns residue colors according to the number of quality issues or a specific quality issue. Data from wwPDB Validation Report, obtained via PDBe.',
         legend: TableLegend(ValidationColorTable)
     }
 }
 
 export const StructureQualityReportColorThemeProvider: ColorTheme.Provider<Params> =  {
-    label: 'PDBe Structure Quality Report',
+    label: 'Structure Quality Report',
     category: 'PDBe',
     factory: StructureQualityReportColorTheme,
     getParams: ctx => {

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

@@ -329,5 +329,5 @@ function getCageShape(ctx: RuntimeContext, data: Structure, props: AssemblySymme
 
 export type AssemblySymmetryRepresentation = Representation<Structure, AssemblySymmetryParams>
 export function AssemblySymmetryRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, AssemblySymmetryParams>): AssemblySymmetryRepresentation {
-    return Representation.createMulti('Symmetry', ctx, getParams, Representation.StateBuilder, AssemblySymmetryVisuals as unknown as Representation.Def<Structure, AssemblySymmetryParams>)
+    return Representation.createMulti('Assembly Symmetry', ctx, getParams, Representation.StateBuilder, AssemblySymmetryVisuals as unknown as Representation.Def<Structure, AssemblySymmetryParams>)
 }

src/mol-model-props/rcsb/representations/validation-report-clashes.ts

@@ -279,8 +279,8 @@ export function ClashesRepresentation(ctx: RepresentationContext, getParams: Rep
 }
 
 export const ClashesRepresentationProvider: StructureRepresentationProvider<ClashesParams> = {
-    label: 'RCSB Clashes',
-    description: 'Displays clashes between atoms as disks.',
+    label: 'Validation Clashes',
+    description: 'Displays clashes between atoms as disks. Data from wwPDB Validation Report, obtained via RCSB PDB.',
     factory: ClashesRepresentation,
     getParams: getClashesParams,
     defaultValues: PD.getDefaultValues(ClashesParams),

src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts

@@ -86,13 +86,13 @@ export function AssemblySymmetryClusterColorTheme(ctx: ThemeDataContext, props:
         color,
         props,
         contextHash,
-        description: 'Assigns chain colors according to assembly symmetry cluster membership.',
+        description: 'Assigns chain colors according to assembly symmetry cluster membership calculated with BioJava and obtained via RCSB PDB.',
         legend
     }
 }
 
 export const AssemblySymmetryClusterColorThemeProvider: ColorTheme.Provider<AssemblySymmetryClusterColorThemeParams> = {
-    label: 'RCSB Assembly Symmetry Cluster',
+    label: 'Assembly Symmetry Cluster',
     category: 'RCSB',
     factory: AssemblySymmetryClusterColorTheme,
     getParams: getAssemblySymmetryClusterColorThemeParams,

src/mol-model-props/rcsb/themes/density-fit.ts

@@ -55,13 +55,13 @@ export function DensityFitColorTheme(ctx: ThemeDataContext, props: {}): ColorThe
         color,
         props,
         contextHash,
-        description: 'Assigns residue colors according to the density fit using normalized Real Space R (RSRZ) for polymer residues and real space correlation coefficient (RSCC) for ligands. Colors range from poor (RSRZ = 2 or RSCC = 0.678) - to better (RSRZ = 0 or RSCC = 1.0).',
+        description: 'Assigns residue colors according to the density fit using normalized Real Space R (RSRZ) for polymer residues and real space correlation coefficient (RSCC) for ligands. Colors range from poor (RSRZ = 2 or RSCC = 0.678) - to better (RSRZ = 0 or RSCC = 1.0). Data from wwPDB Validation Report, obtained via RCSB PDB.',
         legend: scaleRsrz.legend
     }
 }
 
 export const DensityFitColorThemeProvider: ColorTheme.Provider<{}> = {
-    label: 'RCSB Density Fit',
+    label: 'Density Fit',
     category: 'RCSB',
     factory: DensityFitColorTheme,
     getParams: () => ({}),

src/mol-model-props/rcsb/themes/geometry-quality.ts

@@ -95,13 +95,13 @@ export function GeometryQualityColorTheme(ctx: ThemeDataContext, props: PD.Value
         color,
         props,
         contextHash,
-        description: 'Assigns residue colors according to the number of (filtered) geometry issues.',
+        description: 'Assigns residue colors according to the number of (filtered) geometry issues. Data from wwPDB Validation Report, obtained via RCSB PDB.',
         legend: ColorLegend
     }
 }
 
 export const GeometryQualityColorThemeProvider: ColorTheme.Provider<GeometricQualityColorThemeParams> = {
-    label: 'RCSB Geometry Quality',
+    label: 'Geometry Quality',
     category: 'RCSB',
     factory: GeometryQualityColorTheme,
     getParams: getGeometricQualityColorThemeParams,

src/mol-model-props/rcsb/themes/random-coil-index.ts

@@ -46,13 +46,13 @@ export function RandomCoilIndexColorTheme(ctx: ThemeDataContext, props: {}): Col
         color,
         props,
         contextHash,
-        description: 'Assigns residue colors according to the Random Coil Index value.',
+        description: 'Assigns residue colors according to the Random Coil Index value. Data from wwPDB Validation Report, obtained via RCSB PDB.',
         legend: scale.legend
     }
 }
 
 export const RandomCoilIndexColorThemeProvider: ColorTheme.Provider<{}> = {
-    label: 'RCSB Random Coil Index',
+    label: 'Random Coil Index',
     category: 'RCSB',
     factory: RandomCoilIndexColorTheme,
     getParams: () => ({}),

src/mol-model-props/rcsb/validation-report.ts

@@ -162,7 +162,7 @@ export type ValidationReportParams = typeof ValidationReportParams
 export type ValidationReportProps = PD.Values<ValidationReportParams>
 
 export const ValidationReportProvider: CustomModelProperty.Provider<ValidationReportParams, ValidationReport> = CustomModelProperty.createProvider({
-    label: 'RCSB Validation Report',
+    label: 'Validation Report',
     descriptor: CustomPropertyDescriptor({
         name: 'rcsb_validation_report',
         symbols: ValidationReport.symbols

src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts

@@ -15,7 +15,10 @@ import { PluginBehavior } from '../../../behavior';
 export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
     name: 'pdbe-structure-quality-report-prop',
     category: 'custom-props',
-    display: { name: 'PDBe Structure Quality Report' },
+    display: {
+        name: 'Structure Quality Report',
+        description: 'Data from wwPDB Validation Report, obtained via PDBe.'
+    },
     ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
 
         private provider = StructureQualityReportProvider
@@ -32,8 +35,8 @@ export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: bo
 
                     const se = StructureElement.Location.create(loci.structure, u, u.elements[OrderedSet.getAt(e.indices, 0)]);
                     const issues = StructureQualityReport.getIssues(se);
-                    if (issues.length === 0) return 'PDBe Validation: No Issues';
-                    return `PDBe Validation: ${issues.join(', ')}`;
+                    if (issues.length === 0) return 'Validation: No Issues';
+                    return `Validation: ${issues.join(', ')}`;
 
                 default: return void 0;
             }

src/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry.ts

@@ -19,7 +19,10 @@ const Tag = AssemblySymmetry.Tag
 export const RCSBAssemblySymmetry = PluginBehavior.create<{ autoAttach: boolean }>({
     name: 'rcsb-assembly-symmetry-prop',
     category: 'custom-props',
-    display: { name: 'RCSB Assembly Symmetry' },
+    display: {
+        name: 'Assembly Symmetry',
+        description: 'Assembly Symmetry data calculated with BioJava, obtained via RCSB PDB.'
+    },
     ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean }> {
         private provider = AssemblySymmetryProvider
 
@@ -49,14 +52,17 @@ export const RCSBAssemblySymmetry = PluginBehavior.create<{ autoAttach: boolean
 });
 
 const InitAssemblySymmetry3D = StateAction.build({
-    display: { name: 'RCSB Assembly Symmetry' },
+    display: {
+        name: 'Assembly Symmetry',
+        description: 'Initialize Assembly Symmetry axes and cage. Data calculated with BioJava, obtained via RCSB PDB.'
+    },
     from: PluginStateObject.Molecule.Structure,
     isApplicable: (a) => AssemblySymmetry.isApplicable(a.data)
-})(({ a, ref, state }, plugin: PluginContext) => Task.create('Init RCSB Assembly Symmetry', async ctx => {
+})(({ a, ref, state }, plugin: PluginContext) => Task.create('Init Assembly Symmetry', async ctx => {
     try {
         await AssemblySymmetryProvider.attach({ runtime: ctx, fetch: plugin.fetch }, a.data)
     } catch(e) {
-        plugin.log.error(`RCSB Assembly Symmetry: ${e}`)
+        plugin.log.error(`Assembly Symmetry: ${e}`)
         return
     }
     const tree = state.build().to(ref).apply(AssemblySymmetry3D);
@@ -68,7 +74,10 @@ export { AssemblySymmetry3D }
 type AssemblySymmetry3D = typeof AssemblySymmetry3D
 const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
     name: Tag.Representation,
-    display: 'RCSB Assembly Symmetry',
+    display: {
+        name: 'Assembly Symmetry',
+        description: 'Assembly Symmetry axes and cage. Data calculated with BioJava, obtained via RCSB PDB.'
+    },
     from: PluginStateObject.Molecule.Structure,
     to: PluginStateObject.Shape.Representation3D,
     params: (a) => {
@@ -82,7 +91,7 @@ const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
         return true;
     },
     apply({ a, params }, plugin: PluginContext) {
-        return Task.create('RCSB Assembly Symmetry', async ctx => {
+        return Task.create('Assembly Symmetry', async ctx => {
             await AssemblySymmetryProvider.attach({ runtime: ctx, fetch: plugin.fetch }, a.data)
             const assemblySymmetry = AssemblySymmetryProvider.get(a.data).value
             if (!assemblySymmetry || assemblySymmetry.length === 0) {
@@ -95,7 +104,7 @@ const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
         });
     },
     update({ a, b, newParams }, plugin: PluginContext) {
-        return Task.create('RCSB Assembly Symmetry', async ctx => {
+        return Task.create('Assembly Symmetry', async ctx => {
             await AssemblySymmetryProvider.attach({ runtime: ctx, fetch: plugin.fetch }, a.data)
             const assemblySymmetry = AssemblySymmetryProvider.get(a.data).value
             if (!assemblySymmetry || assemblySymmetry.length === 0) {

src/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report.ts

@@ -21,7 +21,10 @@ const Tag = ValidationReport.Tag
 export const RCSBValidationReport = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
     name: 'rcsb-validation-report-prop',
     category: 'custom-props',
-    display: { name: 'RCSB Validation Report' },
+    display: {
+        name: 'Validation Report',
+        description: 'Data from wwPDB Validation Report, obtained via RCSB PDB.'
+    },
     ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
         private provider = ValidationReportProvider
 
@@ -99,7 +102,7 @@ function geometryQualityLabel(loci: Loci): string | undefined {
             if (angles) angles.forEach(a => issues.add(angleOutliers.data[a].tag))
 
             if (issues.size === 0) {
-                return `RCSB Geometry Quality <small>(1 Atom)</small>: no issues`;
+                return `Geometry Quality <small>(1 Atom)</small>: no issues`;
             }
 
             const summary: string[] = []