diff --git a/src/apps/basic-wrapper/coloring.ts b/src/apps/basic-wrapper/coloring.ts
new file mode 100644
index 0000000000000000000000000000000000000000..54c89117c7f78c5209364fab76dcd1d35f3f7599
--- /dev/null
+++ b/src/apps/basic-wrapper/coloring.ts
@@ -0,0 +1,30 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { CustomElementProperty } from 'mol-model-props/common/custom-element-property';
+import { Model, ElementIndex } from 'mol-model/structure';
+import { Color } from 'mol-util/color';
+
+export const StripedResidues = CustomElementProperty.create<number>({
+ isStatic: true,
+ name: 'basic-wrapper-residue-striping',
+ display: 'Residue Stripes',
+ getData(model: Model) {
+ const map = new Map<ElementIndex, number>();
+ const residueIndex = model.atomicHierarchy.residueAtomSegments.index;
+ for (let i = 0, _i = model.atomicHierarchy.atoms._rowCount; i < _i; i++) {
+ map.set(i as ElementIndex, residueIndex[i] % 2);
+ }
+ return map;
+ },
+ coloring: {
+ getColor(e) { return e === 0 ? Color(0xff0000) : Color(0x0000ff) },
+ defaultColor: Color(0x777777)
+ },
+ format(e) {
+ return e === 0 ? 'Odd stripe' : 'Even stripe'
+ }
+})
\ No newline at end of file
diff --git a/src/apps/basic-wrapper/index.html b/src/apps/basic-wrapper/index.html
index e18b1e38c324e755ea68fdb183646e1f245f4950..efa0b8c9f43fe1a4085acd2509b11096e997234c 100644
--- a/src/apps/basic-wrapper/index.html
+++ b/src/apps/basic-wrapper/index.html
@@ -100,6 +100,10 @@
addControl('Play Loop', () => BasicMolStarWrapper.animate.modelIndex.loop());
addControl('Stop', () => BasicMolStarWrapper.animate.modelIndex.stop());
+ addHeader('Misc');
+
+ addControl('Apply Stripes', () => BasicMolStarWrapper.coloring.applyStripes());
+
////////////////////////////////////////////////////////
function addControl(label, action) {
diff --git a/src/apps/basic-wrapper/index.ts b/src/apps/basic-wrapper/index.ts
index ec4ed52e3ce2bc31bfb56da127e952ca6000f459..f030ff31181b3c406ea3aaf2c77337d0fb23af0c 100644
--- a/src/apps/basic-wrapper/index.ts
+++ b/src/apps/basic-wrapper/index.ts
@@ -11,9 +11,10 @@ import { PluginCommands } from 'mol-plugin/command';
import { StateTransforms } from 'mol-plugin/state/transforms';
import { StructureRepresentation3DHelpers } from 'mol-plugin/state/transforms/representation';
import { Color } from 'mol-util/color';
-import { PluginStateObject as PSO } from 'mol-plugin/state/objects';
+import { PluginStateObject as PSO, PluginStateObject } from 'mol-plugin/state/objects';
import { AnimateModelIndex } from 'mol-plugin/state/animation/built-in';
import { StateBuilder } from 'mol-state';
+import { StripedResidues } from './coloring';
require('mol-plugin/skin/light.scss')
type SupportedFormats = 'cif' | 'pdb'
@@ -30,6 +31,10 @@ class BasicWrapper {
showControls: false
}
});
+
+ this.plugin.structureRepresentation.themeCtx.colorThemeRegistry.add(StripedResidues.Descriptor.name, StripedResidues.colorTheme!);
+ this.plugin.lociLabels.addProvider(StripedResidues.labelProvider);
+ this.plugin.customModelProperties.register(StripedResidues.propertyProvider);
}
private download(b: StateBuilder.To<PSO.Root>, url: string) {
@@ -43,6 +48,7 @@ class BasicWrapper {
return parsed
.apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 })
+ .apply(StateTransforms.Model.CustomModelProperties, { properties: [StripedResidues.Descriptor.name] }, { ref: 'props', props: { isGhost: false } })
.apply(StateTransforms.Model.StructureAssemblyFromModel, { id: assemblyId || 'deposited' }, { ref: 'asm' });
}
@@ -110,6 +116,22 @@ class BasicWrapper {
stop: () => this.plugin.state.animation.stop()
}
}
+
+ coloring = {
+ applyStripes: async () => {
+ const state = this.plugin.state.dataState;
+
+ const visuals = state.selectQ(q => q.ofType(PluginStateObject.Molecule.Representation3D).filter(c => c.transform.transformer === StateTransforms.Representation.StructureRepresentation3D));
+ const tree = state.build();
+ const colorTheme = { name: StripedResidues.Descriptor.name, params: this.plugin.structureRepresentation.themeCtx.colorThemeRegistry.get(StripedResidues.Descriptor.name).defaultValues };
+
+ for (const v of visuals) {
+ tree.to(v.transform.ref).update(StateTransforms.Representation.StructureRepresentation3D, old => ({ ...old, colorTheme }));
+ }
+
+ await PluginCommands.State.Update.dispatch(this.plugin, { state, tree });
+ }
+ }
}
(window as any).BasicMolStarWrapper = new BasicWrapper();
\ No newline at end of file
diff --git a/src/mol-model-props/common/custom-element-property.ts b/src/mol-model-props/common/custom-element-property.ts
index 3b84056bd06ae87e9d11be11c390d263d4011a48..609674ae6f8b420e841e2033f366c1e91fa72969 100644
--- a/src/mol-model-props/common/custom-element-property.ts
+++ b/src/mol-model-props/common/custom-element-property.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
@@ -9,7 +9,7 @@ import { StructureElement } from 'mol-model/structure/structure';
import { Location } from 'mol-model/location';
import { CustomPropertyRegistry } from './custom-property-registry';
import { Task } from 'mol-task';
-import { ThemeDataContext } from 'mol-theme/theme';
+import { ThemeDataContext, ThemeProvider } from 'mol-theme/theme';
import { ColorTheme, LocationColor } from 'mol-theme/color';
import { Color } from 'mol-util/color';
import { TableLegend } from 'mol-util/color/tables';
@@ -19,12 +19,12 @@ import { OrderedSet } from 'mol-data/int';
export { CustomElementProperty };
namespace CustomElementProperty {
- export interface CreateParams<S, T> {
+ export interface CreateParams<T> {
isStatic: boolean,
name: string,
autoAttach?: boolean,
display: string,
- attachableTo: (model: Model) => boolean,
+ attachableTo?: (model: Model) => boolean,
getData(model: Model): Map<ElementIndex, T> | Promise<Map<ElementIndex, T>>,
format?(e: T): string,
coloring?: {
@@ -33,7 +33,7 @@ namespace CustomElementProperty {
}
}
- export function create<S, T>(params: CreateParams<S, T>) {
+ export function create<T>(params: CreateParams<T>) {
const name = params.name;
const Descriptor = ModelPropertyDescriptor({
@@ -51,6 +51,8 @@ namespace CustomElementProperty {
model._dynamicPropertyData[name] = data;
}
+ model.customProperties.add(Descriptor);
+
return true;
})
}
@@ -58,7 +60,7 @@ namespace CustomElementProperty {
function getStatic(e: StructureElement) { return e.unit.model._staticPropertyData[name].get(e.element); }
function getDynamic(e: StructureElement) { return e.unit.model._staticPropertyData[name].get(e.element); }
- const provider: CustomPropertyRegistry.Provider = {
+ const propertyProvider: CustomPropertyRegistry.Provider = {
option: [name, params.display],
descriptor: Descriptor,
defaultSelected: !!params.autoAttach,
@@ -68,12 +70,14 @@ namespace CustomElementProperty {
const get = params.isStatic ? getStatic : getDynamic;
+ function has(model: Model) { return model.customProperties.has(Descriptor); }
+
function Coloring(ctx: ThemeDataContext, props: {}): ColorTheme<{}> {
let color: LocationColor;
const getColor = params.coloring!.getColor;
const defaultColor = params.coloring!.defaultColor;
- if (ctx.structure && !ctx.structure.isEmpty && ctx.structure.models[0].customProperties.has(Descriptor)) {
+ if (ctx.structure && !ctx.structure.isEmpty && has(ctx.structure.models[0])) {
color = (location: Location) => {
if (StructureElement.isLocation(location)) {
const e = get(location);
@@ -95,9 +99,18 @@ namespace CustomElementProperty {
};
}
+ const colorTheme: ThemeProvider<ColorTheme<{}>, {}> = {
+ label: params.display,
+ factory: Coloring,
+ getParams: () => ({}),
+ defaultValues: {},
+ isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && !ctx.structure.isEmpty && has(ctx.structure.models[0])
+ }
+
function LabelProvider(loci: Loci): string | undefined {
if (loci.kind === 'element-loci') {
const e = loci.elements[0];
+ if (!has(e.unit.model)) return void 0;
return params.format!(get(StructureElement.create(e.unit, e.unit.elements[OrderedSet.getAt(e.indices, 0)])));
}
return void 0;
@@ -107,8 +120,8 @@ namespace CustomElementProperty {
Descriptor,
attach,
get,
- provider,
- colorTheme: params.coloring ? Coloring : void 0,
+ propertyProvider,
+ colorTheme: params.coloring ? colorTheme : void 0,
labelProvider: params.format ? LabelProvider : ((loci: Loci) => void 0)
};
}
diff --git a/src/mol-state/state/selection.ts b/src/mol-state/state/selection.ts
index b70b4c8d19f817601030faa5d23ec96bd5c0fd10..986dc4467fc670796d1928b4ee4a1731cd0b02e8 100644
--- a/src/mol-state/state/selection.ts
+++ b/src/mol-state/state/selection.ts
@@ -97,6 +97,14 @@ namespace StateSelection {
});
}
+ export function ofType(type: StateObject.Ctor) {
+ return build(() => state => {
+ const ctx = { ret: [] as StateObjectCell[], cells: state.cells, type: type.type };
+ StateTree.doPreOrder(state.tree, state.tree.root, ctx, _findOfType);
+ return ctx.ret;
+ });
+ }
+
function _findRootsOfType(n: StateTransform, _: any, s: { type: StateObject.Type, roots: StateObjectCell[], cells: State.Cells }) {
const cell = s.cells.get(n.ref);
if (cell && cell.obj && cell.obj.type === s.type) {
@@ -105,6 +113,14 @@ namespace StateSelection {
}
return true;
}
+
+ function _findOfType(n: StateTransform, _: any, s: { type: StateObject.Type, ret: StateObjectCell[], cells: State.Cells }) {
+ const cell = s.cells.get(n.ref);
+ if (cell && cell.obj && cell.obj.type === s.type) {
+ s.ret.push(cell);
+ }
+ return true;
+ }
}
registerModifier('flatMap', flatMap);