diff --git a/src/mol-model-props/pdbe/themes/structure-quality-report.ts b/src/mol-model-props/pdbe/themes/structure-quality-report.ts
new file mode 100644
index 0000000000000000000000000000000000000000..a527e58f7797addf3ad4b2a3de9109c5179f330b
--- /dev/null
+++ b/src/mol-model-props/pdbe/themes/structure-quality-report.ts
@@ -0,0 +1,54 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { StructureQualityReport } from 'mol-model-props/pdbe/structure-quality-report';
+import { Location } from 'mol-model/location';
+import { StructureElement } from 'mol-model/structure';
+import { ColorTheme, LocationColor } from 'mol-theme/color';
+import { ThemeDataContext } from 'mol-theme/theme';
+import { Color } from 'mol-util/color';
+import { TableLegend } from 'mol-util/color/tables';
+
+const ValidationColors = [
+ Color.fromRgb(170, 170, 170), // not applicable
+ Color.fromRgb(0, 255, 0), // 0 issues
+ Color.fromRgb(255, 255, 0), // 1
+ Color.fromRgb(255, 128, 0), // 2
+ Color.fromRgb(255, 0, 0), // 3 or more
+]
+
+const ValidationColorTable: [string, Color][] = [
+ ['No Issues', ValidationColors[1]],
+ ['One Issue', ValidationColors[2]],
+ ['Two Issues', ValidationColors[3]],
+ ['Three Or More Issues', ValidationColors[4]],
+ ['Not Applicable', ValidationColors[9]]
+]
+
+export function StructureQualityReportColorTheme(ctx: ThemeDataContext, props: {}): ColorTheme<{}> {
+ let color: LocationColor
+
+ if (ctx.structure && ctx.structure.models[0].customProperties.has(StructureQualityReport.Descriptor)) {
+ const getIssues = StructureQualityReport.getIssues;
+ color = (location: Location) => {
+ if (StructureElement.isLocation(location)) {
+ return ValidationColors[Math.min(3, getIssues(location).length) + 1];
+ }
+ return ValidationColors[0];
+ }
+ } else {
+ color = () => ValidationColors[0];
+ }
+
+ return {
+ factory: StructureQualityReportColorTheme,
+ granularity: 'group',
+ color: color,
+ props: props,
+ description: 'Assigns residue colors according to the number of issues in the PDBe Validation Report.',
+ legend: TableLegend(ValidationColorTable)
+ }
+}
\ No newline at end of file
diff --git a/src/mol-plugin/behavior/dynamic/custom-props.ts b/src/mol-plugin/behavior/dynamic/custom-props.ts
index 2c31fddcf2538e8d0b1dbd62ced3738aa7d7ac24..a6e0ad81e316f9469ae8dc452937f708e48b55fa 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props.ts
@@ -4,15 +4,14 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { ParamDefinition } from 'mol-util/param-definition';
-import { PluginBehavior } from '../behavior';
+import { OrderedSet } from 'mol-data/int';
import { StructureQualityReport } from 'mol-model-props/pdbe/structure-quality-report';
-import { CustomPropertyRegistry } from 'mol-plugin/util/custom-prop-registry';
+import { StructureQualityReportColorTheme } from 'mol-model-props/pdbe/themes/structure-quality-report';
import { Loci } from 'mol-model/loci';
import { StructureElement } from 'mol-model/structure';
-import { OrderedSet } from 'mol-data/int';
-
-// TODO: make auto attach working better for "initial state" by supporting default props in state updates
+import { CustomPropertyRegistry } from 'mol-plugin/util/custom-prop-registry';
+import { ParamDefinition as PD } from 'mol-util/param-definition';
+import { PluginBehavior } from '../behavior';
export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: boolean }>({
name: 'pdbe-structure-quality-report-prop',
@@ -33,6 +32,15 @@ export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: bo
register(): void {
this.ctx.customModelProperties.register(this.provider);
this.ctx.lociLabels.addProvider(labelPDBeValidation);
+
+ // TODO: support filtering of themes based on the input structure
+ // in this case, it would check structure.models[0].customProperties.has(StructureQualityReport.Descriptor)
+ // TODO: add remove functionality
+ this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.add('pdbe-structure-quality-report', {
+ label: 'PDBe Structure Quality Report',
+ factory: StructureQualityReportColorTheme,
+ getParams: () => ({})
+ })
}
update(p: { autoAttach: boolean }) {
@@ -45,10 +53,13 @@ export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: bo
unregister() {
this.ctx.customModelProperties.unregister(StructureQualityReport.Descriptor.name);
this.ctx.lociLabels.removeProvider(labelPDBeValidation);
+
+ // TODO: add remove functionality to registry
+ // this.ctx.structureRepresentation.themeCtx.colorThemeRegistry.remove('pdbe-structure-quality-report')
}
},
params: () => ({
- autoAttach: ParamDefinition.Boolean(false)
+ autoAttach: PD.Boolean(false)
}),
display: { name: 'Focus Loci on Select', group: 'Camera' }
});
diff --git a/src/mol-plugin/state/actions/basic.ts b/src/mol-plugin/state/actions/basic.ts
index ad60f56f20e545aa22f904f1a9d802699f790ab0..e9607ca09b3e91d8f62a8a853092c000d1e8d635 100644
--- a/src/mol-plugin/state/actions/basic.ts
+++ b/src/mol-plugin/state/actions/basic.ts
@@ -27,10 +27,23 @@ const DownloadStructure = StateAction.build({
display: { name: 'Download Structure', description: 'Load a structure from the provided source and create its default Assembly and visual.' },
params: {
source: PD.MappedStatic('bcif-static', {
- 'pdbe-updated': PD.Text('1cbs', { label: 'Id' }),
- 'rcsb': PD.Text('1tqn', { label: 'Id' }),
- 'bcif-static': PD.Text('1tqn', { label: 'Id' }),
- 'url': PD.Group({ url: PD.Text(''), isBinary: PD.Boolean(false) }, { isExpanded: true })
+ 'pdbe-updated': PD.Group({
+ id: PD.Text('1cbs', { label: 'Id' }),
+ supportProps: PD.Boolean(false)
+ }, { isExpanded: true }),
+ 'rcsb': PD.Group({
+ id: PD.Text('1tqn', { label: 'Id' }),
+ supportProps: PD.Boolean(false)
+ }, { isExpanded: true }),
+ 'bcif-static': PD.Group({
+ id: PD.Text('1tqn', { label: 'Id' }),
+ supportProps: PD.Boolean(false)
+ }, { isExpanded: true }),
+ 'url': PD.Group({
+ url: PD.Text(''),
+ isBinary: PD.Boolean(false),
+ supportProps: PD.Boolean(false)
+ }, { isExpanded: true })
}, {
options: [
['pdbe-updated', 'PDBe Updated'],
@@ -50,19 +63,19 @@ const DownloadStructure = StateAction.build({
url = src.params;
break;
case 'pdbe-updated':
- url = { url: `https://www.ebi.ac.uk/pdbe/static/entry/${src.params.toLowerCase()}_updated.cif`, isBinary: false, label: `PDBe: ${src.params}` };
+ url = { url: `https://www.ebi.ac.uk/pdbe/static/entry/${src.params.id.toLowerCase()}_updated.cif`, isBinary: false, label: `PDBe: ${src.params}` };
break;
case 'rcsb':
- url = { url: `https://files.rcsb.org/download/${src.params.toUpperCase()}.cif`, isBinary: false, label: `RCSB: ${src.params}` };
+ url = { url: `https://files.rcsb.org/download/${src.params.id.toUpperCase()}.cif`, isBinary: false, label: `RCSB: ${src.params}` };
break;
case 'bcif-static':
- url = { url: `https://webchem.ncbr.muni.cz/ModelServer/static/bcif/${src.params.toLowerCase()}`, isBinary: true, label: `BinaryCIF: ${src.params}` };
+ url = { url: `https://webchem.ncbr.muni.cz/ModelServer/static/bcif/${src.params.id.toLowerCase()}`, isBinary: true, label: `BinaryCIF: ${src.params}` };
break;
default: throw new Error(`${(src as any).name} not supported.`);
}
const data = b.toRoot().apply(StateTransforms.Data.Download, url);
- return state.update(createStructureTree(data));
+ return state.update(createStructureTree(data, params.source.params.supportProps));
});
export const OpenStructure = StateAction.build({
@@ -72,16 +85,20 @@ export const OpenStructure = StateAction.build({
})(({ params, state }) => {
const b = state.build();
const data = b.toRoot().apply(StateTransforms.Data.ReadFile, { file: params.file, isBinary: /\.bcif$/i.test(params.file.name) });
- return state.update(createStructureTree(data));
+ return state.update(createStructureTree(data, false));
});
-function createStructureTree(b: StateTreeBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>): StateTree {
- const root = b
+function createStructureTree(b: StateTreeBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>, supportProps: boolean): StateTree {
+ let root = b
.apply(StateTransforms.Data.ParseCif)
.apply(StateTransforms.Model.TrajectoryFromMmCif, {})
- .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
- .apply(StateTransforms.Model.CustomModelProperties, { properties: [] })
- .apply(StateTransforms.Model.StructureAssemblyFromModel);
+ .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 });
+
+ if (supportProps) {
+ // TODO: implement automatic default property assigment in State.update
+ root = root.apply(StateTransforms.Model.CustomModelProperties, { properties: [] });
+ }
+ root = root.apply(StateTransforms.Model.StructureAssemblyFromModel);
complexRepresentation(root);
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index d7ca14ec8bfe1d0670e1879bf63fe952d51213f6..440d3eb78d6501808bf4a355a0c75a24cd4133b1 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -180,7 +180,7 @@ const CustomModelProperties = PluginStateTransform.BuiltIn({
apply({ a, params }, ctx: PluginContext) {
return Task.create('Custom Props', async taskCtx => {
await attachProps(a.data, ctx, taskCtx, params.properties);
- return new SO.Molecule.Model(a.data, { label: a.label, description: 'Custom Props' });
+ return new SO.Molecule.Model(a.data, { label: 'Props', description: `${params.properties.length} Selected` });
});
}
});
diff --git a/src/mol-plugin/ui/controls.tsx b/src/mol-plugin/ui/controls.tsx
index ac3330b70dfe374eb44afa13e6455cc75639265c..9d5a802b96009435dadc2175cb8a9236034c8b9a 100644
--- a/src/mol-plugin/ui/controls.tsx
+++ b/src/mol-plugin/ui/controls.tsx
@@ -45,7 +45,7 @@ export class LociLabelControl extends PluginComponent<{}, { entries: ReadonlyArr
}
render() {
- return <div>
+ return <div style={{ textAlign: 'right' }}>
{this.state.entries.map((e, i) => <div key={'' + i}>{e}</div>)}
</div>
}