From ee776e6e3e011cac738e2bc74053a419ba0c6435 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Fri, 2 Aug 2019 17:18:07 -0700
Subject: [PATCH] wip, structure tools
---
.../behavior/dynamic/representation.ts | 2 +-
src/mol-plugin/context.ts | 8 +-
src/mol-plugin/state/actions/structure.ts | 2 +-
src/mol-plugin/state/transforms/model.ts | 11 +-
src/mol-plugin/ui/structure/overpaint.tsx | 65 ++---------
.../ui/structure/representation.tsx | 102 ++----------------
src/mol-plugin/ui/structure/selection.tsx | 54 ++--------
src/mol-plugin/ui/structure/util.ts | 17 ---
src/mol-plugin/util/interactivity.ts | 2 +-
.../util/structure-overpaint-helper.ts | 85 +++++++++++++++
.../util/structure-representation-helper.ts | 102 ++++++++++++++++++
.../util/structure-selection-helper.ts | 55 ++++++++++
12 files changed, 289 insertions(+), 216 deletions(-)
delete mode 100644 src/mol-plugin/ui/structure/util.ts
create mode 100644 src/mol-plugin/util/structure-overpaint-helper.ts
create mode 100644 src/mol-plugin/util/structure-representation-helper.ts
create mode 100644 src/mol-plugin/util/structure-selection-helper.ts
diff --git a/src/mol-plugin/behavior/dynamic/representation.ts b/src/mol-plugin/behavior/dynamic/representation.ts
index edf502302..09fab1853 100644
--- a/src/mol-plugin/behavior/dynamic/representation.ts
+++ b/src/mol-plugin/behavior/dynamic/representation.ts
@@ -49,7 +49,7 @@ export const SelectLoci = PluginBehavior.create({
this.spine.current = cell
const so = this.spine.getRootOfType(SO.Molecule.Structure)
if (so) {
- const loci = this.ctx.helpers.structureSelection.get(so.data)
+ const loci = this.ctx.helpers.structureSelectionManager.get(so.data)
this.lociMarkProvider({ loci }, MarkerAction.Select)
}
}
diff --git a/src/mol-plugin/context.ts b/src/mol-plugin/context.ts
index 024c4046d..e2b6b11a2 100644
--- a/src/mol-plugin/context.ts
+++ b/src/mol-plugin/context.ts
@@ -37,6 +37,9 @@ import { ModifiersKeys } from '../mol-util/input/input-observer';
import { isProductionMode, isDebugMode } from '../mol-util/debug';
import { Model, Structure } from '../mol-model/structure';
import { Interactivity } from './util/interactivity';
+import { StructureRepresentationHelper } from './util/structure-representation-helper';
+import { StructureSelectionHelper } from './util/structure-selection-helper';
+import { StructureOverpaintHelper } from './util/structure-overpaint-helper';
interface Log {
entries: List<LogEntry>
@@ -121,7 +124,10 @@ export class PluginContext {
readonly customParamEditors = new Map<string, StateTransformParameters.Class>();
readonly helpers = {
- structureSelection: new StructureElementSelectionManager(this),
+ structureSelectionManager: new StructureElementSelectionManager(this),
+ structureSelection: new StructureSelectionHelper(this),
+ structureRepresentation: new StructureRepresentationHelper(this),
+ structureOverpaint: new StructureOverpaintHelper(this),
substructureParent: new SubstructureParentHelper(this)
} as const;
diff --git a/src/mol-plugin/state/actions/structure.ts b/src/mol-plugin/state/actions/structure.ts
index 3ecad410b..76914d041 100644
--- a/src/mol-plugin/state/actions/structure.ts
+++ b/src/mol-plugin/state/actions/structure.ts
@@ -352,7 +352,7 @@ export const StructureFromSelection = StateAction.build({
// return t.transformer !== CustomModelProperties;
// }
})(({ a, ref, params, state }, plugin: PluginContext) => {
- const sel = plugin.helpers.structureSelection.get(a.data);
+ const sel = plugin.helpers.structureSelectionManager.get(a.data);
if (sel.kind === 'empty-loci') return Task.constant('', void 0);
const query = StructureElement.Loci.toScriptExpression(sel);
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index 0813edd0c..ddc20811a 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -9,7 +9,7 @@ import { parsePDB } from '../../../mol-io/reader/pdb/parser';
import { Vec3, Mat4, Quat } from '../../../mol-math/linear-algebra';
import { trajectoryFromMmCIF } from '../../../mol-model-formats/structure/mmcif';
import { trajectoryFromPDB } from '../../../mol-model-formats/structure/pdb';
-import { Model, ModelSymmetry, Queries, QueryContext, Structure, StructureQuery, StructureSelection as Sel, StructureSymmetry, QueryFn } from '../../../mol-model/structure';
+import { Model, ModelSymmetry, Queries, QueryContext, Structure, StructureQuery, StructureSelection as Sel, StructureSymmetry, QueryFn, StructureElement } from '../../../mol-model/structure';
import { Assembly } from '../../../mol-model/structure/model/properties/symmetry';
import { PluginContext } from '../../../mol-plugin/context';
import { MolScriptBuilder } from '../../../mol-script/language/builder';
@@ -27,6 +27,7 @@ import { transpileMolScript } from '../../../mol-script/script/mol-script/symbol
import { shapeFromPly } from '../../../mol-model-formats/shape/ply';
import { SymmetryOperator } from '../../../mol-math/geometry';
import { ensureSecondaryStructure } from './helpers';
+import { formatMolScript } from '../../../mol-script/language/expression-formatter';
export { TrajectoryFromBlob };
export { TrajectoryFromMmCif };
@@ -385,6 +386,14 @@ const UserStructureSelection = PluginStateTransform.BuiltIn({
(cache as { source: Structure }).source = a.data;
const result = compiled(new QueryContext(a.data));
const s = Sel.unionStructure(result);
+
+ // TODO for debug purposes only, later move to StructureSelection where the expression is not visible to the user
+ let loci = Structure.toStructureElementLoci(Structure.Loci(s))
+ if (s.parent) loci = StructureElement.Loci.remap(loci, s.parent)
+ const expression = formatMolScript(StructureElement.Loci.toScriptExpression(loci))
+ console.log({ before: params.query.expression, after: expression })
+ params.query.expression = expression
+
const props = { label: `${params.label || 'Selection'}`, description: structureDesc(s) };
return new SO.Molecule.Structure(s, props);
},
diff --git a/src/mol-plugin/ui/structure/overpaint.tsx b/src/mol-plugin/ui/structure/overpaint.tsx
index c158f2801..5e1070213 100644
--- a/src/mol-plugin/ui/structure/overpaint.tsx
+++ b/src/mol-plugin/ui/structure/overpaint.tsx
@@ -6,20 +6,11 @@
import * as React from 'react';
import { PluginUIComponent } from '../base';
-import { PluginStateObject } from '../../../mol-plugin/state/objects';
-import { StateTransforms } from '../../../mol-plugin/state/transforms';
-import { StateSelection, StateObjectCell, StateTransform, StateBuilder } from '../../../mol-state';
import { ParamDefinition as PD} from '../../../mol-util/param-definition';
import { ColorNames } from '../../../mol-util/color/tables';
import { ParameterControls } from '../controls/parameters';
-import { Structure } from '../../../mol-model/structure';
-import { isEmptyLoci } from '../../../mol-model/loci';
import { PluginContext } from '../../context';
-import { getExpression } from './util';
-
-
-type OverpaintEachReprCallback = (update: StateBuilder.Root, repr: StateObjectCell<PluginStateObject.Molecule.Structure.Representation3D, StateTransform<typeof StateTransforms.Representation.StructureRepresentation3D>>, rootStructure: Structure, overpaint?: StateObjectCell<any, StateTransform<typeof StateTransforms.Representation.OverpaintStructureRepresentation3D>>) => void
-const OverpaintManagerTag = 'overpaint-controls'
+import { Color } from '../../../mol-util/color';
export class StructureOverpaintControls extends PluginUIComponent<{}, { params: PD.Values<ReturnType<typeof StructureOverpaintControls.getParams>> }> {
state = { params: PD.getDefaultValues(StructureOverpaintControls.getParams(this.plugin)) }
@@ -36,58 +27,20 @@ export class StructureOverpaintControls extends PluginUIComponent<{}, { params:
}
- private async eachRepr(callback: OverpaintEachReprCallback) {
- const state = this.plugin.state.dataState;
- const reprs = state.select(StateSelection.Generators.ofType(PluginStateObject.Molecule.Structure.Representation3D));
-
- const update = state.build();
- for (const r of reprs) {
- const overpaint = state.select(StateSelection.Generators.ofTransformer(StateTransforms.Representation.OverpaintStructureRepresentation3D, r.transform.ref).withTag(OverpaintManagerTag));
-
- const structure = r.obj!.data.source.data
- const rootStructure = structure.parent || structure
-
- callback(update, r, rootStructure, overpaint[0])
- }
-
- await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }));
- }
-
- set = async (clear: boolean) => {
- await this.eachRepr((update, repr, rootStructure, overpaint) => {
- if (!this.state.params.type.includes(repr.params!.values.type.name)) return
-
- const loci = this.plugin.helpers.structureSelection.get(rootStructure)
- if (isEmptyLoci(loci) || loci.elements.length === 0) return
- const expression = getExpression(loci)
-
- const layer = {
- script: { language: 'mol-script', expression },
- color: this.state.params.color,
- clear
- }
-
- if (overpaint) {
- update.to(overpaint).update({ layers: [ ...overpaint.params!.values.layers, layer ], alpha: 1 })
- } else {
- update.to(repr.transform.ref)
- .apply(StateTransforms.Representation.OverpaintStructureRepresentation3D, { layers: [ layer ], alpha: 1 }, { tags: OverpaintManagerTag });
- }
- })
+ set = (color: Color | -1) => {
+ this.plugin.helpers.structureOverpaint.set(color, this.state.params.type)
}
- add = async () => {
- this.set(false)
+ add = () => {
+ this.set(this.state.params.color)
}
- clear = async () => {
- this.set(true)
+ clear = () => {
+ this.set(-1)
}
- clearAll = async () => {
- await this.eachRepr((update, repr, rootStructure, overpaint) => {
- if (overpaint) update.delete(overpaint.transform.ref)
- })
+ clearAll = () => {
+ this.plugin.helpers.structureOverpaint.clearAll()
}
render() {
diff --git a/src/mol-plugin/ui/structure/representation.tsx b/src/mol-plugin/ui/structure/representation.tsx
index 54e06dfce..5e05374e2 100644
--- a/src/mol-plugin/ui/structure/representation.tsx
+++ b/src/mol-plugin/ui/structure/representation.tsx
@@ -6,35 +6,9 @@
import * as React from 'react';
import { PluginUIComponent } from '../base';
-import { PluginStateObject } from '../../../mol-plugin/state/objects';
-import { StateTransforms } from '../../../mol-plugin/state/transforms';
-import { StateTransformer, StateSelection, StateObjectCell, StateTransform, StateBuilder } from '../../../mol-state';
import { ParamDefinition as PD} from '../../../mol-util/param-definition';
import { ParameterControls } from '../controls/parameters';
-import { StructureElement, QueryContext, StructureSelection } from '../../../mol-model/structure';
-import { isEmptyLoci } from '../../../mol-model/loci';
import { PluginContext } from '../../context';
-import { getExpression } from './util';
-import { parseMolScript } from '../../../mol-script/language/parser';
-import { transpileMolScript } from '../../../mol-script/script/mol-script/symbols';
-import { compile } from '../../../mol-script/runtime/query/compiler';
-import { StructureRepresentation3DHelpers } from '../../state/transforms/representation';
-
-type RepresentationEachStructureCallback = (update: StateBuilder.Root, structure: StateObjectCell<PluginStateObject.Molecule.Structure, StateTransform<StateTransformer<any, PluginStateObject.Molecule.Structure, any>>>) => void
-const RepresentationManagerTag = 'representation-controls'
-
-function getRepresentationManagerTag(type: string) {
- return `${RepresentationManagerTag}-${type}`
-}
-
-function getCombinedLoci(mode: 'add' | 'remove' | 'only' | 'all', loci: StructureElement.Loci, currentLoci: StructureElement.Loci): StructureElement.Loci {
- switch (mode) {
- case 'add': return StructureElement.Loci.union(loci, currentLoci)
- case 'remove': return StructureElement.Loci.subtract(currentLoci, loci)
- case 'only': return loci
- case 'all': return StructureElement.Loci.all(loci.structure)
- }
-}
export class StructureRepresentationControls extends PluginUIComponent<{}, { params: PD.Values<ReturnType<typeof StructureRepresentationControls.getParams>> }> {
state = { params: PD.getDefaultValues(StructureRepresentationControls.getParams(this.plugin)) }
@@ -50,77 +24,17 @@ export class StructureRepresentationControls extends PluginUIComponent<{}, { par
}
- private async eachStructure(callback: RepresentationEachStructureCallback) {
- const state = this.plugin.state.dataState;
- const structures = state.select(StateSelection.Generators.rootsOfType(PluginStateObject.Molecule.Structure));
-
- const update = state.build();
- for (const s of structures) {
- callback(update, s)
- }
-
- await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }));
- }
-
- set = async (mode: 'add' | 'remove' | 'only' | 'all') => {
- const state = this.plugin.state.dataState
- const { type } = this.state.params
-
- await this.eachStructure((update, structure) => {
- const s = structure.obj!.data
- const _loci = this.plugin.helpers.structureSelection.get(s)
- const loci = isEmptyLoci(_loci) ? StructureElement.Loci(s, []) : _loci
-
- const selections = state.select(StateSelection.Generators.ofType(PluginStateObject.Molecule.Structure, structure.transform.ref).withTag(getRepresentationManagerTag(type)));
-
- if (selections.length > 0) {
- const parsed = parseMolScript(selections[0].params!.values.query.expression)
- if (parsed.length === 0) return
-
- const query = transpileMolScript(parsed[0])
- const compiled = compile(query)
- const result = compiled(new QueryContext(structure.obj!.data))
- const currentLoci = StructureSelection.toLoci2(result)
-
- const combinedLoci = getCombinedLoci(mode, loci, currentLoci)
-
- update.to(selections[0]).update({
- ...selections[0].params!.values,
- query: { language: 'mol-script', expression: getExpression(combinedLoci) }
- })
- } else {
- const combinedLoci = getCombinedLoci(mode, loci, StructureElement.Loci(loci.structure, []))
-
- update.to(structure.transform.ref)
- .apply(
- StateTransforms.Model.UserStructureSelection,
- {
- query: { language: 'mol-script', expression: getExpression(combinedLoci) },
- label: type
- },
- { tags: [ RepresentationManagerTag, getRepresentationManagerTag(type) ] }
- )
- .apply(
- StateTransforms.Representation.StructureRepresentation3D,
- StructureRepresentation3DHelpers.getDefaultParams(this.plugin, type as any, s)
- )
- }
- })
+ set = (mode: 'add' | 'remove' | 'only' | 'all') => {
+ this.plugin.helpers.structureRepresentation.setSelected(mode, this.state.params.type)
}
- show = async () => { this.set('add') }
- hide = async () => { this.set('remove') }
- only = async () => { this.set('only') }
- showAll = async () => { this.set('all') }
-
- hideAll = async () => {
- const { type } = this.state.params
- const state = this.plugin.state.dataState;
- const update = state.build();
-
- state.select(StateSelection.Generators.ofType(PluginStateObject.Molecule.Structure).withTag(getRepresentationManagerTag(type))).forEach(structure => update.delete(structure.transform.ref));
+ show = () => { this.set('add') }
+ hide = () => { this.set('remove') }
+ only = () => { this.set('only') }
+ showAll = () => { this.set('all') }
- await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }));
+ hideAll = () => {
+ this.plugin.helpers.structureRepresentation.hideAll(this.state.params.type)
}
render() {
diff --git a/src/mol-plugin/ui/structure/selection.tsx b/src/mol-plugin/ui/structure/selection.tsx
index 62b48e5fb..41c23ec88 100644
--- a/src/mol-plugin/ui/structure/selection.tsx
+++ b/src/mol-plugin/ui/structure/selection.tsx
@@ -6,22 +6,9 @@
import * as React from 'react';
import { PluginUIComponent } from '../base';
-import { MolScriptBuilder as MS } from '../../../mol-script/language/builder';
-import { StateSelection } from '../../../mol-state';
-import { PluginStateObject } from '../../state/objects';
-import { QueryContext, StructureSelection, QueryFn, Queries as _Queries } from '../../../mol-model/structure';
-import { compile } from '../../../mol-script/runtime/query/compiler';
-import { ButtonsType } from '../../../mol-util/input/input-observer';
-import { EmptyLoci } from '../../../mol-model/loci';
+import { StructureSelection, QueryFn, Queries as _Queries } from '../../../mol-model/structure';
import { formatStructureSelectionStats } from '../../util/structure-element-selection';
-
-const Queries = {
- all: () => compile<StructureSelection>(MS.struct.generator.all()),
- polymers: () => _Queries.internal.atomicSequence(),
- water: () => _Queries.internal.water(),
- ligands: () => _Queries.internal.atomicHet(),
- coarse: () => _Queries.internal.spheres(),
-}
+import { StructureSelectionQueries } from '../../util/structure-selection-helper';
export class StructureSelectionControls extends PluginUIComponent<{}, {}> {
state = {}
@@ -33,36 +20,15 @@ export class StructureSelectionControls extends PluginUIComponent<{}, {}> {
}
get stats() {
- return formatStructureSelectionStats(this.plugin.helpers.structureSelection.stats)
+ return formatStructureSelectionStats(this.plugin.helpers.structureSelectionManager.stats)
}
select = (query: QueryFn<StructureSelection>) => {
- const state = this.plugin.state.dataState
- const structures = state.select(StateSelection.Generators.rootsOfType(PluginStateObject.Molecule.Structure))
- const { structureSelection } = this.plugin.helpers
-
- structureSelection.clear()
- for (const so of structures) {
- const s = so.obj!.data
- const result = query(new QueryContext(s))
- const loci = StructureSelection.toLoci2(result)
-
- // TODO use better API when available
- this.plugin.interactivity.lociSelections.apply({
- current: { loci },
- buttons: ButtonsType.Flag.Secondary,
- modifiers: { shift: false, alt: false, control: true, meta: false }
- })
- }
+ this.plugin.helpers.structureSelection.select(query)
}
clear = () => {
- // TODO use better API when available
- this.plugin.interactivity.lociSelections.apply({
- current: { loci: EmptyLoci },
- buttons: ButtonsType.Flag.Secondary,
- modifiers: { shift: false, alt: false, control: true, meta: false }
- })
+ this.plugin.helpers.structureSelection.clearSelection()
}
render() {
@@ -75,14 +41,14 @@ export class StructureSelectionControls extends PluginUIComponent<{}, {}> {
<div>{this.stats}</div>
</div>
<div className='msp-btn-row-group'>
- <button className='msp-btn msp-btn-block msp-form-control' onClick={() => this.select(Queries.all())}>All</button>
+ <button className='msp-btn msp-btn-block msp-form-control' onClick={() => this.select(StructureSelectionQueries.all())}>All</button>
<button className='msp-btn msp-btn-block msp-form-control' onClick={() => this.clear()}>None</button>
</div>
<div className='msp-btn-row-group'>
- <button className='msp-btn msp-btn-block msp-form-control' onClick={() => this.select(Queries.polymers())}>Polymers</button>
- <button className='msp-btn msp-btn-block msp-form-control' onClick={() => this.select(Queries.ligands())}>Ligands</button>
- <button className='msp-btn msp-btn-block msp-form-control' onClick={() => this.select(Queries.water())}>Water</button>
- <button className='msp-btn msp-btn-block msp-form-control' onClick={() => this.select(Queries.coarse())}>Coarse</button>
+ <button className='msp-btn msp-btn-block msp-form-control' onClick={() => this.select(StructureSelectionQueries.polymers())}>Polymers</button>
+ <button className='msp-btn msp-btn-block msp-form-control' onClick={() => this.select(StructureSelectionQueries.ligands())}>Ligands</button>
+ <button className='msp-btn msp-btn-block msp-form-control' onClick={() => this.select(StructureSelectionQueries.water())}>Water</button>
+ <button className='msp-btn msp-btn-block msp-form-control' onClick={() => this.select(StructureSelectionQueries.coarse())}>Coarse</button>
</div>
</div>
</div>
diff --git a/src/mol-plugin/ui/structure/util.ts b/src/mol-plugin/ui/structure/util.ts
deleted file mode 100644
index ca17b74fe..000000000
--- a/src/mol-plugin/ui/structure/util.ts
+++ /dev/null
@@ -1,17 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { StructureElement } from '../../../mol-model/structure';
-import { EmptyLoci, isEmptyLoci } from '../../../mol-model/loci';
-import { MolScriptBuilder } from '../../../mol-script/language/builder';
-import { formatMolScript } from '../../../mol-script/language/expression-formatter';
-
-export function getExpression(loci: StructureElement.Loci | EmptyLoci) {
- const scriptExpression = isEmptyLoci(loci)
- ? MolScriptBuilder.struct.generator.empty()
- : StructureElement.Loci.toScriptExpression(loci)
- return formatMolScript(scriptExpression)
-}
\ No newline at end of file
diff --git a/src/mol-plugin/util/interactivity.ts b/src/mol-plugin/util/interactivity.ts
index bce545a96..80a5cc7f0 100644
--- a/src/mol-plugin/util/interactivity.ts
+++ b/src/mol-plugin/util/interactivity.ts
@@ -115,7 +115,7 @@ namespace Interactivity {
abstract apply(e: MarkEvent): void
constructor(public readonly ctx: PluginContext, props: Partial<Props> = {}) {
- this.sel = ctx.helpers.structureSelection
+ this.sel = ctx.helpers.structureSelectionManager
this.setProps(props)
}
}
diff --git a/src/mol-plugin/util/structure-overpaint-helper.ts b/src/mol-plugin/util/structure-overpaint-helper.ts
new file mode 100644
index 000000000..9bdbce04a
--- /dev/null
+++ b/src/mol-plugin/util/structure-overpaint-helper.ts
@@ -0,0 +1,85 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { PluginStateObject } from '../../mol-plugin/state/objects';
+import { StateTransforms } from '../../mol-plugin/state/transforms';
+import { StateSelection, StateObjectCell, StateTransform, StateBuilder } from '../../mol-state';
+import { Structure, StructureElement } from '../../mol-model/structure';
+import { isEmptyLoci, EmptyLoci } from '../../mol-model/loci';
+import { PluginContext } from '../context';
+import { Color } from '../../mol-util/color';
+import { MolScriptBuilder } from '../../mol-script/language/builder';
+import { formatMolScript } from '../../mol-script/language/expression-formatter';
+
+type OverpaintEachReprCallback = (update: StateBuilder.Root, repr: StateObjectCell<PluginStateObject.Molecule.Structure.Representation3D, StateTransform<typeof StateTransforms.Representation.StructureRepresentation3D>>, rootStructure: Structure, overpaint?: StateObjectCell<any, StateTransform<typeof StateTransforms.Representation.OverpaintStructureRepresentation3D>>) => void
+const OverpaintManagerTag = 'overpaint-controls'
+
+export function getExpression(loci: StructureElement.Loci | EmptyLoci) {
+ const scriptExpression = isEmptyLoci(loci)
+ ? MolScriptBuilder.struct.generator.empty()
+ : StructureElement.Loci.toScriptExpression(loci)
+ return formatMolScript(scriptExpression)
+}
+
+export class StructureOverpaintHelper {
+ private async eachRepr(callback: OverpaintEachReprCallback) {
+ const state = this.plugin.state.dataState;
+ const reprs = state.select(StateSelection.Generators.ofType(PluginStateObject.Molecule.Structure.Representation3D));
+
+ const update = state.build();
+ for (const r of reprs) {
+ const overpaint = state.select(StateSelection.Generators.ofTransformer(StateTransforms.Representation.OverpaintStructureRepresentation3D, r.transform.ref).withTag(OverpaintManagerTag));
+
+ const structure = r.obj!.data.source.data
+ const rootStructure = structure.parent || structure
+
+ callback(update, r, rootStructure, overpaint[0])
+ }
+
+ await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }));
+ }
+
+ async set(color: Color | -1, types?: string[]) {
+ await this.eachRepr((update, repr, rootStructure, overpaint) => {
+ if (types && !types.includes(repr.params!.values.type.name)) return
+
+ const loci = this.plugin.helpers.structureSelectionManager.get(rootStructure)
+ if (isEmptyLoci(loci) || loci.elements.length === 0) return
+ const expression = getExpression(loci)
+
+ const layer = {
+ script: { language: 'mol-script', expression },
+ color: color === -1 ? Color(0) : color,
+ clear: color === -1
+ }
+
+ if (overpaint) {
+ update.to(overpaint).update({ layers: [ ...overpaint.params!.values.layers, layer ], alpha: 1 })
+ } else {
+ update.to(repr.transform.ref)
+ .apply(StateTransforms.Representation.OverpaintStructureRepresentation3D, { layers: [ layer ], alpha: 1 }, { tags: OverpaintManagerTag });
+ }
+ })
+ }
+
+ add(color: Color, types?: string[]) {
+ this.set(color, types)
+ }
+
+ clear(types?: string[]) {
+ this.set(-1, types)
+ }
+
+ clearAll() {
+ this.eachRepr((update, repr, rootStructure, overpaint) => {
+ if (overpaint) update.delete(overpaint.transform.ref)
+ })
+ }
+
+ constructor(private plugin: PluginContext) {
+
+ }
+}
\ No newline at end of file
diff --git a/src/mol-plugin/util/structure-representation-helper.ts b/src/mol-plugin/util/structure-representation-helper.ts
new file mode 100644
index 000000000..4ada5f0db
--- /dev/null
+++ b/src/mol-plugin/util/structure-representation-helper.ts
@@ -0,0 +1,102 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { PluginStateObject } from '../../mol-plugin/state/objects';
+import { StateTransforms } from '../../mol-plugin/state/transforms';
+import { StateTransformer, StateSelection, StateObjectCell, StateTransform } from '../../mol-state';
+import { StructureElement } from '../../mol-model/structure';
+import { isEmptyLoci } from '../../mol-model/loci';
+import { PluginContext } from '../context';
+import { parseMolScript } from '../../mol-script/language/parser';
+import { StructureRepresentation3DHelpers } from '../state/transforms/representation';
+import Expression from '../../mol-script/language/expression';
+import { formatMolScript } from '../../mol-script/language/expression-formatter';
+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
+
+type StructureTransform = StateObjectCell<PluginStateObject.Molecule.Structure, StateTransform<StateTransformer<any, PluginStateObject.Molecule.Structure, any>>>
+const RepresentationManagerTag = 'representation-controls'
+
+function getRepresentationManagerTag(type: string) {
+ return `${RepresentationManagerTag}-${type}`
+}
+
+function getCombinedExpression(modifier: SelectionModifier, expression: Expression, currentExpression: Expression): Expression {
+ switch (modifier) {
+ case 'add': return MS.struct.combinator.merge([ currentExpression, expression ])
+ case 'remove': return MS.struct.modifier.exceptBy({ 0: currentExpression, by: expression })
+ case 'only': return expression
+ case 'all': return MS.struct.generator.all()
+ }
+}
+
+type SelectionModifier = 'add' | 'remove' | 'only' | 'all'
+
+export class StructureRepresentationHelper {
+ async set(modifier: SelectionModifier, type: string, expression: Expression, structure: StructureTransform) {
+ const state = this.plugin.state.dataState
+ const update = state.build();
+ const s = structure.obj!.data
+
+ const selections = state.select(StateSelection.Generators.ofType(PluginStateObject.Molecule.Structure, structure.transform.ref).withTag(getRepresentationManagerTag(type)));
+
+ if (selections.length > 0) {
+ const parsedExpressions = parseMolScript(selections[0].params!.values.query.expression)
+ if (parsedExpressions.length === 0) return
+ const currentExpression = parsedExpressions[0]
+ const combinedExpression = getCombinedExpression(modifier, expression, currentExpression)
+
+ update.to(selections[0]).update({
+ ...selections[0].params!.values,
+ query: { language: 'mol-script', expression: formatMolScript(combinedExpression) }
+ })
+ } else {
+ const combinedExpression = getCombinedExpression(modifier, expression, MS.struct.generator.empty())
+
+ update.to(structure.transform.ref)
+ .apply(
+ StateTransforms.Model.UserStructureSelection,
+ {
+ query: { language: 'mol-script', expression: formatMolScript(combinedExpression) },
+ label: type
+ },
+ { tags: [ RepresentationManagerTag, getRepresentationManagerTag(type) ] }
+ )
+ .apply(
+ StateTransforms.Representation.StructureRepresentation3D,
+ StructureRepresentation3DHelpers.getDefaultParams(this.plugin, type as any, s)
+ )
+ }
+
+ await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }));
+ }
+
+ async setSelected(modifier: SelectionModifier, type: string) {
+ const state = this.plugin.state.dataState;
+ const structures = state.select(StateSelection.Generators.rootsOfType(PluginStateObject.Molecule.Structure));
+
+ for (const structure of structures) {
+ const s = structure.obj!.data
+ const _loci = this.plugin.helpers.structureSelectionManager.get(s)
+ const loci = isEmptyLoci(_loci) ? StructureElement.Loci(s, []) : _loci
+ const expression = StructureElement.Loci.toScriptExpression(loci)
+
+ await this.set(modifier, type, expression, structure)
+ }
+ }
+
+ async hideAll(type: string) {
+ const state = this.plugin.state.dataState;
+ const update = state.build();
+
+ state.select(StateSelection.Generators.ofType(PluginStateObject.Molecule.Structure).withTag(getRepresentationManagerTag(type))).forEach(structure => update.delete(structure.transform.ref));
+
+ await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }));
+ }
+
+ constructor(private plugin: PluginContext) {
+
+ }
+}
\ No newline at end of file
diff --git a/src/mol-plugin/util/structure-selection-helper.ts b/src/mol-plugin/util/structure-selection-helper.ts
new file mode 100644
index 000000000..f159f000a
--- /dev/null
+++ b/src/mol-plugin/util/structure-selection-helper.ts
@@ -0,0 +1,55 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
+import { StateSelection } from '../../mol-state';
+import { PluginStateObject } from '../state/objects';
+import { QueryContext, StructureSelection, QueryFn, Queries as _Queries } from '../../mol-model/structure';
+import { compile } from '../../mol-script/runtime/query/compiler';
+import { ButtonsType } from '../../mol-util/input/input-observer';
+import { EmptyLoci } from '../../mol-model/loci';
+import { PluginContext } from '../context';
+
+export const StructureSelectionQueries = {
+ all: () => compile<StructureSelection>(MS.struct.generator.all()),
+ polymers: () => _Queries.internal.atomicSequence(),
+ water: () => _Queries.internal.water(),
+ ligands: () => _Queries.internal.atomicHet(),
+ coarse: () => _Queries.internal.spheres(),
+}
+
+export class StructureSelectionHelper {
+ select(query: QueryFn<StructureSelection>) {
+ const state = this.plugin.state.dataState
+ const structures = state.select(StateSelection.Generators.rootsOfType(PluginStateObject.Molecule.Structure))
+
+ for (const so of structures) {
+ const s = so.obj!.data
+ const result = query(new QueryContext(s))
+ const loci = StructureSelection.toLoci2(result)
+
+ // TODO use better API when available
+ this.plugin.interactivity.lociSelections.apply({
+ current: { loci },
+ buttons: ButtonsType.Flag.Secondary,
+ modifiers: { shift: false, alt: false, control: true, meta: false }
+ })
+ }
+ }
+
+ clearSelection() {
+ // TODO use better API when available
+ this.plugin.interactivity.lociSelections.apply({
+ current: { loci: EmptyLoci },
+ buttons: ButtonsType.Flag.Secondary,
+ modifiers: { shift: false, alt: false, control: true, meta: false }
+ })
+ }
+
+ constructor(private plugin: PluginContext) {
+
+ }
+}
\ No newline at end of file
--
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