diff --git a/src/mol-model-props/pdbe/structure-quality-report.ts b/src/mol-model-props/pdbe/structure-quality-report.ts
index e153de014ba3749c37f0700edb55b9f0a01698b3..1950f925299c9d2e8f684e5831dbefe1f36e870c 100644
--- a/src/mol-model-props/pdbe/structure-quality-report.ts
+++ b/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: {
diff --git a/src/mol-model-props/pdbe/themes/structure-quality-report.ts b/src/mol-model-props/pdbe/themes/structure-quality-report.ts
index a4b23e9eb54470a393a5df10319088adc69b6b74..237eb3dcddb24d57becf92e322dab2657e11bdaf 100644
--- a/src/mol-model-props/pdbe/themes/structure-quality-report.ts
+++ b/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 => {
diff --git a/src/mol-model-props/rcsb/representations/assembly-symmetry.ts b/src/mol-model-props/rcsb/representations/assembly-symmetry.ts
index b2c2d994f281bc48e7d52175fdc73f0e2e427969..e36c0b99dcdabc4a6631197b3689bee074c04b8e 100644
--- a/src/mol-model-props/rcsb/representations/assembly-symmetry.ts
+++ b/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>)
}
\ No newline at end of file
diff --git a/src/mol-model-props/rcsb/representations/validation-report-clashes.ts b/src/mol-model-props/rcsb/representations/validation-report-clashes.ts
index be69dbcda1645c51fda6b31ec0768f2cc15460c4..7f05f21e29f49b49b3192d30de8fa4003c9d6b82 100644
--- a/src/mol-model-props/rcsb/representations/validation-report-clashes.ts
+++ b/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),
diff --git a/src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts b/src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts
index cbab8e1e4645869dcf81445f074bce354bf00abb..292ef5c9510cee816687bf3a0a03c91afd0ef977 100644
--- a/src/mol-model-props/rcsb/themes/assembly-symmetry-cluster.ts
+++ b/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,
diff --git a/src/mol-model-props/rcsb/themes/density-fit.ts b/src/mol-model-props/rcsb/themes/density-fit.ts
index 319c3c60297e757a40f7c5880c1db54d23e78ec1..f5c7266779b3eada84f59920c175c57edf1b8309 100644
--- a/src/mol-model-props/rcsb/themes/density-fit.ts
+++ b/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: () => ({}),
diff --git a/src/mol-model-props/rcsb/themes/geometry-quality.ts b/src/mol-model-props/rcsb/themes/geometry-quality.ts
index ca6d54e3507eebe3a716fdb56e70f272864985d2..4ae2c0ca045030f2dcea4fe3452ccd6ade28f350 100644
--- a/src/mol-model-props/rcsb/themes/geometry-quality.ts
+++ b/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,
diff --git a/src/mol-model-props/rcsb/themes/random-coil-index.ts b/src/mol-model-props/rcsb/themes/random-coil-index.ts
index c8a7e90f21bbbd3c54f40048a7312dbe0c21c85f..51e62a32eed81d7f1c52ecdcd14c0c984ef486e3 100644
--- a/src/mol-model-props/rcsb/themes/random-coil-index.ts
+++ b/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: () => ({}),
diff --git a/src/mol-model-props/rcsb/validation-report.ts b/src/mol-model-props/rcsb/validation-report.ts
index 67e22faa6483a82917b7144cbb354a1ef6a2b20a..307c05dc428375e0ecfe5da2a6a0e7ee95578170 100644
--- a/src/mol-model-props/rcsb/validation-report.ts
+++ b/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
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts b/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts
index 69742b2992896625fd383526de1a7e8183c90520..ce22b7c29bed4f7e5215c66bec5bbfdbdc47476e 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/pdbe/structure-quality-report.ts
+++ b/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;
}
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 9b917dc439a51a344213de4fec42f9aa5063b8a5..32aeba1bd6b85eec5bbd8d2580a64fc0686b1900 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
@@ -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) {
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 b893a1b067ef8368fc2919dd9b68dcab797d035f..94b90517cc7f6da20f045dcce6f745acb00e1afd 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
@@ -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[] = []