diff --git a/src/examples/proteopedia-wrapper/helpers.ts b/src/examples/proteopedia-wrapper/helpers.ts
index b111c230900fad13e1f56813c2767d21225e0c59..17082c93c22762304fcf3c7357e623bd6e3524c3 100644
--- a/src/examples/proteopedia-wrapper/helpers.ts
+++ b/src/examples/proteopedia-wrapper/helpers.ts
@@ -111,5 +111,7 @@ export enum StateElements {
HetVisual = 'het-visual',
Het3DSNFG = 'het-3dsnfg',
Water = 'water',
- WaterVisual = 'water-visual'
+ WaterVisual = 'water-visual',
+
+ HetGroupFocus = 'het-group-focus'
}
\ No newline at end of file
diff --git a/src/examples/proteopedia-wrapper/index.html b/src/examples/proteopedia-wrapper/index.html
index 43b6dc6866cedc3beaea03e9ebd705cca38e6137..0bd3bb60714bbb09f32c05ed522103c05f93fef7 100644
--- a/src/examples/proteopedia-wrapper/index.html
+++ b/src/examples/proteopedia-wrapper/index.html
@@ -99,6 +99,7 @@
PluginWrapper.events.modelInfo.subscribe(function (info) {
console.log('Model Info', info);
+ listHetGroups(info);
});
addControl('Load Asym Unit', () => PluginWrapper.load({ url: url, format: format }));
@@ -145,6 +146,12 @@
addControl('Apply Evo Cons', () => PluginWrapper.coloring.evolutionaryConservation());
addControl('Default Visuals', () => PluginWrapper.updateStyle());
+ addSeparator();
+ addHeader('HET Groups');
+
+ addControl('Reset', () => PluginWrapper.hetGroups.reset());
+ addHetGroupsContainer();
+
addSeparator();
addHeader('State');
@@ -163,6 +170,12 @@
////////////////////////////////////////////////////////
+ function addHetGroupsContainer() {
+ var div = document.createElement('div');
+ div.id = 'het-groups';
+ $('controls').appendChild(div);
+ }
+
function addControl(label, action) {
var btn = document.createElement('button');
btn.onclick = action;
@@ -180,6 +193,19 @@
h.innerText = header;
$('controls').appendChild(h);
}
+
+ function listHetGroups(info) {
+ var div = $('het-groups');
+ div.innerHTML = '';
+ info.hetResidues.forEach(function (r) {
+ var l = document.createElement('button');
+ l.innerText = r.name;
+ l.onclick = function () {
+ PluginWrapper.hetGroups.focusFirst(r.name);
+ };
+ div.appendChild(l);
+ });
+ }
</script>
</body>
</html>
\ No newline at end of file
diff --git a/src/examples/proteopedia-wrapper/index.ts b/src/examples/proteopedia-wrapper/index.ts
index 6d49de844f3e6a36f1b36bddafc64cd406103160..fdef0b0f3f375965e5c088521c90826d18fd4455 100644
--- a/src/examples/proteopedia-wrapper/index.ts
+++ b/src/examples/proteopedia-wrapper/index.ts
@@ -21,6 +21,14 @@ import { ControlsWrapper } from './ui/controls';
import { PluginState } from 'mol-plugin/state';
import { Scheduler } from 'mol-task';
import { createProteopediaCustomTheme } from './coloring';
+import { MolScriptBuilder as MS } from 'mol-script/language/builder';
+import { BuiltInStructureRepresentations } from 'mol-repr/structure/registry';
+import { BuiltInColorThemes } from 'mol-theme/color';
+import { BuiltInSizeThemes } from 'mol-theme/size';
+import { ColorNames } from 'mol-util/color/tables';
+// import { Vec3 } from 'mol-math/linear-algebra';
+// import { ParamDefinition } from 'mol-util/param-definition';
+// import { Text } from 'mol-geo/geometry/text/text';
require('mol-plugin/skin/light.scss')
class MolStarProteopediaWrapper {
@@ -257,6 +265,69 @@ class MolStarProteopediaWrapper {
}
}
+ hetGroups = {
+ reset: () => {
+ const update = this.state.build().delete(StateElements.HetGroupFocus);
+ PluginCommands.State.Update.dispatch(this.plugin, { state: this.state, tree: update });
+ PluginCommands.Camera.Reset.dispatch(this.plugin, { });
+ },
+ focusFirst: async (resn: string) => {
+ if (!this.state.transforms.has(StateElements.Assembly)) return;
+
+ // const asm = (this.state.select(StateElements.Assembly)[0].obj as PluginStateObject.Molecule.Structure).data;
+
+ const update = this.state.build();
+
+ update.delete(StateElements.HetGroupFocus);
+
+ const surroundings = MS.struct.modifier.includeSurroundings({
+ 0: MS.struct.filter.first([
+ MS.struct.generator.atomGroups({
+ 'residue-test': MS.core.rel.eq([MS.struct.atomProperty.macromolecular.label_comp_id(), resn]),
+ 'group-by': MS.struct.atomProperty.macromolecular.residueKey()
+ })
+ ]),
+ radius: 5,
+ 'as-whole-residues': true
+ });
+
+ const sel = update.to(StateElements.Assembly)
+ .apply(StateTransforms.Model.StructureSelection, { label: resn, query: surroundings }, { ref: StateElements.HetGroupFocus });
+
+ sel.apply(StateTransforms.Representation.StructureRepresentation3D, this.createSurVisualParams());
+ // sel.apply(StateTransforms.Representation.StructureLabels3D, {
+ // target: { name: 'residues', params: { } },
+ // options: {
+ // ...ParamDefinition.getDefaultValues(Text.Params),
+ // background: true,
+ // backgroundMargin: 0.2,
+ // backgroundColor: ColorNames.snow,
+ // backgroundOpacity: 0.9,
+ // }
+ // });
+
+ await PluginCommands.State.Update.dispatch(this.plugin, { state: this.state, tree: update });
+
+ const focus = (this.state.select(StateElements.HetGroupFocus)[0].obj as PluginStateObject.Molecule.Structure).data;
+ const sphere = focus.boundary.sphere;
+ // const asmCenter = asm.boundary.sphere.center;
+ // const position = Vec3.sub(Vec3.zero(), sphere.center, asmCenter);
+ // Vec3.normalize(position, position);
+ // Vec3.scaleAndAdd(position, sphere.center, position, sphere.radius);
+ const snapshot = this.plugin.canvas3d.camera.getFocus(sphere.center, 0.75 * sphere.radius);
+ PluginCommands.Camera.SetSnapshot.dispatch(this.plugin, { snapshot, durationMs: 250 });
+ }
+ }
+
+ private createSurVisualParams() {
+ const asm = this.state.select(StateElements.Assembly)[0].obj as PluginStateObject.Molecule.Structure;
+ return StructureRepresentation3DHelpers.createParams(this.plugin, asm.data, {
+ repr: BuiltInStructureRepresentations['ball-and-stick'],
+ color: [BuiltInColorThemes.uniform, () => ({ value: ColorNames.gray })],
+ size: [BuiltInSizeThemes.uniform, () => ({ value: 0.33 } )]
+ });
+ }
+
snapshot = {
get: () => {
return this.plugin.state.getSnapshot();
diff --git a/src/mol-canvas3d/camera.ts b/src/mol-canvas3d/camera.ts
index d61da319e3d6452fddfd17ed06c439af45324766..731dc74e67c6ab1674e39d86924465ea154a5f8d 100644
--- a/src/mol-canvas3d/camera.ts
+++ b/src/mol-canvas3d/camera.ts
@@ -84,7 +84,7 @@ class Camera implements Object3D {
return ret;
}
- focus(target: Vec3, radius: number) {
+ getFocus(target: Vec3, radius: number): Partial<Camera.Snapshot> {
const fov = this.state.fov
const { width, height } = this.viewport
const aspect = width / height
@@ -98,7 +98,11 @@ class Camera implements Object3D {
if (currentDistance < targetDistance) Vec3.negate(this.deltaDirection, this.deltaDirection)
Vec3.add(this.newPosition, this.state.position, this.deltaDirection)
- this.setState({ target, position: this.newPosition })
+ return { target, position: Vec3.clone(this.newPosition) };
+ }
+
+ focus(target: Vec3, radius: number) {
+ this.setState(this.getFocus(target, radius));
}
// lookAt(target: Vec3) {
diff --git a/src/mol-model/structure/query.ts b/src/mol-model/structure/query.ts
index df09d47cb60acb44696a3ebe3ea7d7bb26480c79..8538f0bc795a9043518a5109bf5df6f86609586e 100644
--- a/src/mol-model/structure/query.ts
+++ b/src/mol-model/structure/query.ts
@@ -9,12 +9,14 @@ import { StructureQuery } from './query/query'
export * from './query/context'
import * as generators from './query/queries/generators'
import * as modifiers from './query/queries/modifiers'
+import * as filters from './query/queries/filters'
import * as combinators from './query/queries/combinators'
import * as internal from './query/queries/internal'
import pred from './query/predicates'
export const Queries = {
generators,
+ filters,
modifiers,
combinators,
pred,
diff --git a/src/mol-model/structure/query/queries/filters.ts b/src/mol-model/structure/query/queries/filters.ts
index a64cffc38bf15eae0a037b80153a2ac03b8d6fd4..17200a1bfd20a9cf615b2e3a2c2dba984f4fc491 100644
--- a/src/mol-model/structure/query/queries/filters.ts
+++ b/src/mol-model/structure/query/queries/filters.ts
@@ -31,6 +31,25 @@ export function pick(query: StructureQuery, pred: QueryPredicate): StructureQuer
};
}
+export function first(query: StructureQuery): StructureQuery {
+ return ctx => {
+ const sel = query(ctx);
+ const ret = StructureSelection.LinearBuilder(ctx.inputStructure);
+ if (sel.kind === 'singletons') {
+ if (sel.structure.elementCount > 0) {
+ const u = sel.structure.units[0];
+ const s = Structure.create([u.getChild(SortedArray.ofSingleton(u.elements[0]))]);
+ ret.add(s);
+ }
+ } else {
+ if (sel.structures.length > 0) {
+ ret.add(sel.structures[0]);
+ }
+ }
+ return ret.getSelection();
+ };
+}
+
export interface UnitTypeProperties { atomic?: QueryFn, coarse?: QueryFn }
export function getCurrentStructureProperties(ctx: QueryContext, props: UnitTypeProperties, set: Set<any>) {
diff --git a/src/mol-plugin/command.ts b/src/mol-plugin/command.ts
index 05a967dccdd398e0e8815993742a515da3a2a221..01e3375f9552d19827ba5c8c1efeb610f5b9e2b6 100644
--- a/src/mol-plugin/command.ts
+++ b/src/mol-plugin/command.ts
@@ -53,7 +53,7 @@ export const PluginCommands = {
},
Camera: {
Reset: PluginCommand<{}>(),
- SetSnapshot: PluginCommand<{ snapshot: Camera.Snapshot, durationMs?: number }>(),
+ SetSnapshot: PluginCommand<{ snapshot: Partial<Camera.Snapshot>, durationMs?: number }>(),
Snapshots: {
Add: PluginCommand<{ name?: string, description?: string }>(),
Remove: PluginCommand<{ id: string }>(),
diff --git a/src/mol-script/language/symbol-table/structure-query.ts b/src/mol-script/language/symbol-table/structure-query.ts
index 4f9f7377efb220f0dbb65717677675540095a9d1..f7d81aa44419493271ac210e149e5b3fb28f2e0e 100644
--- a/src/mol-script/language/symbol-table/structure-query.ts
+++ b/src/mol-script/language/symbol-table/structure-query.ts
@@ -167,6 +167,10 @@ const filter = {
test: Argument(Type.Bool)
}), Types.ElementSelectionQuery, 'Pick all atom sets that satisfy the test.'),
+ first: symbol(Arguments.Dictionary({
+ 0: Argument(Types.ElementSelectionQuery)
+ }), Types.ElementSelectionQuery, 'Take the 1st atom set in the sequence.'),
+
withSameAtomProperties: symbol(Arguments.Dictionary({
0: Argument(Types.ElementSelectionQuery),
source: Argument(Types.ElementSelectionQuery),
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index ba1072a587beb9c0c8ed2bf3b83dac130894b7f8..4ddbdb8b1945619c723c187001858a952a489ad8 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -186,6 +186,9 @@ const symbols = [
C(MolScript.structureQuery.slot.element, (ctx, _) => ctx.element),
// C(MolScript.structureQuery.slot.elementSetReduce, (ctx, _) => ctx.element),
+ // ============= FILTERS ================
+ D(MolScript.structureQuery.filter.first, (ctx, xs) => Queries.filters.first(xs[0] as any)(ctx)),
+
// ============= GENERATORS ================
D(MolScript.structureQuery.generator.atomGroups, (ctx, xs) => Queries.generators.atoms({
entityTest: xs['entity-test'],
diff --git a/src/mol-script/script/mol-script/symbols.ts b/src/mol-script/script/mol-script/symbols.ts
index 0c4826f7ffc685e85a84b9617b83188def6a6e06..9bd1119533c764200a1ab49b9e0f2e13faed0738 100644
--- a/src/mol-script/script/mol-script/symbols.ts
+++ b/src/mol-script/script/mol-script/symbols.ts
@@ -148,6 +148,7 @@ export const SymbolTable = [
[
'Filters',
Alias(MolScript.structureQuery.filter.pick, 'sel.atom.pick'),
+ Alias(MolScript.structureQuery.filter.first, 'sel.atom.first'),
Alias(MolScript.structureQuery.filter.withSameAtomProperties, 'sel.atom.with-same-atom-properties'),
Alias(MolScript.structureQuery.filter.intersectedBy, 'sel.atom.intersected-by'),
Alias(MolScript.structureQuery.filter.within, 'sel.atom.within'),