From b807dca2d811c24b020d6387c9924a15cb59ec59 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Fri, 28 Feb 2020 17:13:00 -0800
Subject: [PATCH] wip, StructureRepresentationHelper tweaks
---
.../structure/representation.tsx | 19 +-
.../util/structure-representation-helper.ts | 184 +++++++++---------
2 files changed, 95 insertions(+), 108 deletions(-)
diff --git a/src/mol-plugin-ui/structure/representation.tsx b/src/mol-plugin-ui/structure/representation.tsx
index 2dcc444e1..bef7495ba 100644
--- a/src/mol-plugin-ui/structure/representation.tsx
+++ b/src/mol-plugin-ui/structure/representation.tsx
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -13,8 +13,6 @@ import { Color } from '../../mol-util/color';
import { ButtonSelect, Options } from '../controls/common'
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { VisualQuality, VisualQualityOptions } from '../../mol-geo/geometry/base';
-import { StructureRepresentationPresets as P } from '../../mol-plugin/util/structure-representation-helper';
-import { camelCaseToWords } from '../../mol-util/string';
import { CollapsableControls } from '../base';
import { StateSelection, StateObject } from '../../mol-state';
import { PluginStateObject } from '../../mol-plugin/state/objects';
@@ -133,13 +131,6 @@ export class StructureRepresentationControls extends CollapsableControls<Collaps
this.subscribe(this.plugin.state.dataState.events.isUpdating, v => this.setState({ isDisabled: v }))
}
- preset = async (value: string) => {
- const presetFn = P[value as keyof typeof P]
- if (presetFn) {
- await presetFn(this.plugin.helpers.structureRepresentation)
- }
- }
-
onChange = async (p: { param: PD.Base<any>, name: string, value: any }) => {
if (p.name === 'options') {
await this.plugin.helpers.structureRepresentation.setIgnoreHydrogens(!p.value.showHydrogens)
@@ -178,15 +169,7 @@ export class StructureRepresentationControls extends CollapsableControls<Collaps
}
renderControls() {
- const presets = PD.objectToOptions(P, camelCaseToWords);
return <div>
- <div className='msp-control-row'>
- <div className='msp-select-row'>
- <ButtonSelect label='Preset' onChange={this.preset}>
- <optgroup label='Preset'>{Options(presets)}</optgroup>
- </ButtonSelect>
- </div>
- </div>
<EverythingStructureRepresentationControls />
<SelectionStructureRepresentationControls />
diff --git a/src/mol-plugin/util/structure-representation-helper.ts b/src/mol-plugin/util/structure-representation-helper.ts
index 6e58d3cae..07fc4f7d1 100644
--- a/src/mol-plugin/util/structure-representation-helper.ts
+++ b/src/mol-plugin/util/structure-representation-helper.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -12,8 +12,6 @@ import { PluginContext } from '../context';
import { StructureRepresentation3DHelpers } from '../state/transforms/representation';
import Expression from '../../mol-script/language/expression';
import { compile } from '../../mol-script/runtime/query/compiler';
-import { StructureSelectionQueries as Q } from '../util/structure-selection-helper';
-import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
import { VisualQuality } from '../../mol-geo/geometry/base';
type StructureTransform = StateObjectCell<PSO.Molecule.Structure, StateTransform<StateTransformer<any, PSO.Molecule.Structure, any>>>
@@ -34,6 +32,12 @@ function getCombinedLoci(mode: SelectionModifier, loci: StructureElement.Loci, c
type SelectionModifier = 'add' | 'remove' | 'only'
+type ReprProps = {
+ repr?: {},
+ color?: string | [string, {}],
+ size?: string | [string, {}],
+}
+
export class StructureRepresentationHelper {
getRepresentationStructure(rootRef: string, type: string) {
const state = this.plugin.state.dataState
@@ -49,12 +53,52 @@ export class StructureRepresentationHelper {
return selections.length > 0 ? selections[0] : undefined
}
- private async _set(modifier: SelectionModifier, type: string, loci: StructureElement.Loci, structure: StructureTransform, props = {}) {
+ private getRepresentationParams(structure: Structure, type: string, repr: RepresentationTransform | undefined, props: ReprProps = {}) {
+ const reprProps = {
+ ...(repr?.params && repr.params.values.type.params),
+ ignoreHydrogens: this._ignoreHydrogens,
+ quality: this._quality,
+ ...props.repr
+ }
+ const { themeCtx } = this.plugin.structureRepresentation
+
+ const p: StructureRepresentation3DHelpers.Props = {
+ repr: [
+ this.plugin.structureRepresentation.registry.get(type),
+ () => reprProps
+ ]
+ }
+ if (props.color) {
+ const colorType = props.color instanceof Array ? props.color[0] : props.color
+ const colorTheme = themeCtx.colorThemeRegistry.get(colorType)
+ const colorProps = {
+ ...(repr?.params && repr.params.values.colorTheme.params),
+ ...(props.color instanceof Array ? props.color[1] : {})
+ }
+ p.color = [colorTheme, () => colorProps]
+ }
+ if (props.size) {
+ const sizeType = props.size instanceof Array ? props.size[0] : props.size
+ const sizeTheme = themeCtx.sizeThemeRegistry.get(sizeType)
+ const sizeProps = {
+ ...(repr?.params && repr.params.values.sizeTheme.params),
+ ...(props.size instanceof Array ? props.size[1] : {})
+ }
+ p.size = [sizeTheme, () => sizeProps]
+ }
+ if (props.size) p.size = props.size
+
+ return StructureRepresentation3DHelpers.createParams(this.plugin, structure, p)
+ }
+
+ private async _set(modifier: SelectionModifier, type: string, loci: StructureElement.Loci, structure: StructureTransform, props: ReprProps = {}) {
const state = this.plugin.state.dataState
const update = state.build()
const s = structure.obj!.data
+ const repr = this.getRepresentation(structure.transform.ref, type)
const reprStructure = this.getRepresentationStructure(structure.transform.ref, type)
+ const reprParams = this.getRepresentationParams(s, type, repr, props)
if (reprStructure) {
const currentLoci = StructureElement.Bundle.toLoci(reprStructure.params!.values.bundle, s)
@@ -64,14 +108,9 @@ export class StructureRepresentationHelper {
...reprStructure.params!.values,
bundle: StructureElement.Bundle.fromLoci(combinedLoci)
})
+ if (repr) update.to(repr).update(reprParams)
} else {
const combinedLoci = getCombinedLoci(modifier, loci, StructureElement.Loci.none(s))
- const params = StructureRepresentation3DHelpers.getDefaultParams(this.plugin, type as any, s)
-
- const p = params.type.params
- Object.assign(p, props)
- if (p.ignoreHydrogens !== undefined) p.ignoreHydrogens = this._ignoreHydrogens
- if (p.quality !== undefined) p.quality = this._quality
update.to(structure.transform.ref)
.apply(
@@ -79,13 +118,13 @@ export class StructureRepresentationHelper {
{ bundle: StructureElement.Bundle.fromLoci(combinedLoci), label: type },
{ tags: [ RepresentationManagerTag, getRepresentationManagerTag(type) ] }
)
- .apply( StateTransforms.Representation.StructureRepresentation3D, params)
+ .apply(StateTransforms.Representation.StructureRepresentation3D, reprParams)
}
await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }))
}
- async set(modifier: SelectionModifier, type: string, lociGetter: (structure: Structure) => StructureElement.Loci, props = {}) {
+ async set(modifier: SelectionModifier, type: string, lociGetter: (structure: Structure) => StructureElement.Loci, props: ReprProps = {}) {
const state = this.plugin.state.dataState;
const structures = state.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure))
@@ -96,7 +135,7 @@ export class StructureRepresentationHelper {
}
}
- async setFromExpression(modifier: SelectionModifier, type: string, expression: Expression, props = {}) {
+ async setFromExpression(modifier: SelectionModifier, type: string, expression: Expression, props: ReprProps = {}) {
return this.set(modifier, type, (structure) => {
const compiled = compile<StructureSelection>(expression)
const result = compiled(new QueryContext(structure))
@@ -104,44 +143,76 @@ export class StructureRepresentationHelper {
}, props)
}
- async clear() {
+ async eachStructure(callback: (structure: StructureTransform, type: string, update: StateBuilder.Root) => void) {
const { registry } = this.plugin.structureRepresentation
const state = this.plugin.state.dataState;
const update = state.build()
const structures = state.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure))
- const bundle = StructureElement.Bundle.Empty
for (const structure of structures) {
for (let i = 0, il = registry.types.length; i < il; ++i) {
const type = registry.types[i][0]
const reprStructure = this.getRepresentationStructure(structure.transform.ref, type)
- if (reprStructure) {
- update.to(reprStructure).update({ ...reprStructure.params!.values, bundle })
- }
+ if (reprStructure) callback(reprStructure, type, update)
}
}
await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }))
}
- async eachRepresentation(callback: (repr: RepresentationTransform, update: StateBuilder.Root) => void) {
+ async clear() {
+ const bundle = StructureElement.Bundle.Empty
+ await this.eachStructure((structure, type, update) => {
+ update.to(structure).update({ ...structure.params!.values, bundle })
+ })
+ }
+
+ async clearExcept(exceptTypes: string[]) {
+ const bundle = StructureElement.Bundle.Empty
+ await this.eachStructure((structure, type, update) => {
+ if (!exceptTypes.includes(type)) {
+ update.to(structure).update({ ...structure.params!.values, bundle })
+ }
+ })
+ }
+
+ async eachRepresentation(callback: (repr: RepresentationTransform, type: string, update: StateBuilder.Root) => void) {
const { registry } = this.plugin.structureRepresentation
const state = this.plugin.state.dataState;
const update = state.build()
const structures = state.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure))
for (const structure of structures) {
for (let i = 0, il = registry.types.length; i < il; ++i) {
- const repr = this.getRepresentation(structure.transform.ref, registry.types[i][0])
- if (repr) callback(repr, update)
+ const type = registry.types[i][0]
+ const repr = this.getRepresentation(structure.transform.ref, type)
+ if (repr) callback(repr, type, update)
}
}
await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }))
}
+ setRepresentationParams(repr: RepresentationTransform, type: string, update: StateBuilder.Root, props: ReprProps) {
+ const state = this.plugin.state.dataState;
+ const structures = state.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure))
+
+ for (const structure of structures) {
+ const s = structure.obj!.data
+ const reprParams = this.getRepresentationParams(s, type, repr, props)
+ update.to(repr).update(reprParams)
+ }
+ }
+
+ async updateRepresentation(repr: RepresentationTransform, type: string, props: ReprProps) {
+ const state = this.plugin.state.dataState;
+ const update = state.build()
+ this.setRepresentationParams(repr, type, update, props)
+ await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }))
+ }
+
private _ignoreHydrogens = false
get ignoreHydrogens () { return this._ignoreHydrogens }
async setIgnoreHydrogens(ignoreHydrogens: boolean) {
if (ignoreHydrogens === this._ignoreHydrogens) return
- await this.eachRepresentation((repr, update) => {
+ await this.eachRepresentation((repr, type, update) => {
if (repr.params && repr.params.values.type.params.ignoreHydrogens !== undefined) {
const { name, params } = repr.params.values.type
update.to(repr.transform.ref).update(
@@ -157,7 +228,7 @@ export class StructureRepresentationHelper {
get quality () { return this._quality }
async setQuality(quality: VisualQuality) {
if (quality === this._quality) return
- await this.eachRepresentation((repr, update) => {
+ await this.eachRepresentation((repr, type, update) => {
if (repr.params && repr.params.values.type.params.quality !== undefined) {
const { name, params } = repr.params.values.type
update.to(repr.transform.ref).update(
@@ -169,74 +240,7 @@ export class StructureRepresentationHelper {
this._quality = quality
}
- async preset() {
- // TODO option to limit to specific structure
- const state = this.plugin.state.dataState;
- const structures = state.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure))
-
- if (structures.length === 0) return
- const s = structures[0].obj!.data
-
- if (s.elementCount < 50000) {
- await polymerAndLigand(this)
- } else if (s.elementCount < 200000) {
- await proteinAndNucleic(this)
- } else {
- if (s.unitSymmetryGroups[0].units.length > 10) {
- await capsid(this)
- } else {
- await coarseCapsid(this)
- }
- }
- }
-
constructor(private plugin: PluginContext) {
}
-}
-
-//
-
-async function polymerAndLigand(r: StructureRepresentationHelper) {
- await r.clear()
- await r.setFromExpression('add', 'cartoon', Q.polymer.expression)
- await r.setFromExpression('add', 'carbohydrate', Q.branchedPlusConnected.expression)
- await r.setFromExpression('add', 'ball-and-stick', MS.struct.modifier.union([
- MS.struct.combinator.merge([
- Q.ligandPlusConnected.expression,
- Q.branchedConnectedOnly.expression,
- Q.disulfideBridges.expression,
- Q.nonStandardPolymer.expression,
- Q.water.expression
- ])
- ]))
-}
-
-async function proteinAndNucleic(r: StructureRepresentationHelper) {
- await r.clear()
- await r.setFromExpression('add', 'cartoon', Q.protein.expression)
- await r.setFromExpression('add', 'gaussian-surface', Q.nucleic.expression)
-}
-
-async function capsid(r: StructureRepresentationHelper) {
- await r.clear()
- await r.setFromExpression('add', 'gaussian-surface', Q.polymer.expression, {
- smoothness: 0.5,
- })
-}
-
-async function coarseCapsid(r: StructureRepresentationHelper) {
- await r.clear()
- await r.setFromExpression('add', 'gaussian-surface', Q.trace.expression, {
- radiusOffset: 1,
- smoothness: 0.5,
- visuals: ['structure-gaussian-surface-mesh']
- })
-}
-
-export const StructureRepresentationPresets = {
- polymerAndLigand,
- proteinAndNucleic,
- capsid,
- coarseCapsid
}
\ No newline at end of file
--
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