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Commit e2c9b601 authored by Alexander Rose's avatar Alexander Rose
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wip, structure tools refactoring

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src/mol-plugin/ui/controls.tsx
+ 3
− 242
View file @ e2c9b601
...@@ -13,21 +13,11 @@ import { LociLabelEntry } from '../../mol-plugin/util/loci-label-manager'; ...@@ -13,21 +13,11 @@ import { LociLabelEntry } from '../../mol-plugin/util/loci-label-manager';
import { IconButton, Icon } from './controls/common'; import { IconButton, Icon } from './controls/common';
import { PluginStateObject } from '../../mol-plugin/state/objects'; import { PluginStateObject } from '../../mol-plugin/state/objects';
import { StateTransforms } from '../../mol-plugin/state/transforms'; import { StateTransforms } from '../../mol-plugin/state/transforms';
import { StateTransformer, StateSelection, StateObjectCell, StateTransform, StateBuilder } from '../../mol-state'; import { StateTransformer } from '../../mol-state';
import { ModelFromTrajectory } from '../../mol-plugin/state/transforms/model'; import { ModelFromTrajectory } from '../../mol-plugin/state/transforms/model';
import { AnimationControls } from './state/animation'; import { AnimationControls } from './state/animation';
import { ParamDefinition as PD} from '../../mol-util/param-definition'; import { OverpaintControls } from './structure/overpaint';
import { ColorNames } from '../../mol-util/color/tables'; import { RepresentationControls } from './structure/representation';
import { ParameterControls } from './controls/parameters';
import { formatMolScript } from '../../mol-script/language/expression-formatter';
import { StructureElement, Structure, QueryContext, StructureSelection } from '../../mol-model/structure';
import { isEmptyLoci, EmptyLoci } from '../../mol-model/loci';
import { MolScriptBuilder } from '../../mol-script/language/builder';
import { PluginContext } from '../context';
import { StructureRepresentation3DHelpers } from '../state/transforms/representation';
import { parseMolScript } from '../../mol-script/language/parser';
import { transpileMolScript } from '../../mol-script/script/mol-script/symbols';
import { compile } from '../../mol-script/runtime/query/compiler';
export class TrajectoryViewportControls extends PluginUIComponent<{}, { show: boolean, label: string }> { export class TrajectoryViewportControls extends PluginUIComponent<{}, { show: boolean, label: string }> {
state = { show: false, label: '' } state = { show: false, label: '' }
...@@ -264,235 +254,6 @@ export class LociLabelControl extends PluginUIComponent<{}, { entries: ReadonlyA ...@@ -264,235 +254,6 @@ export class LociLabelControl extends PluginUIComponent<{}, { entries: ReadonlyA
} }
} }
//
function getExpression(loci: StructureElement.Loci | EmptyLoci) {
const scriptExpression = isEmptyLoci(loci)
? MolScriptBuilder.struct.generator.empty()
: StructureElement.Loci.toScriptExpression(loci)
return formatMolScript(scriptExpression)
}
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 class OverpaintControls extends PluginUIComponent<{}, { params: PD.Values<ReturnType<typeof OverpaintControls.getParams>> }> {
state = { params: PD.getDefaultValues(OverpaintControls.getParams(this.plugin)) }
static getParams = (plugin: PluginContext) => {
const { types } = plugin.structureRepresentation.registry
return {
color: PD.Color(ColorNames.cyan),
type: PD.MultiSelect(types.map(t => t[0]), types)
}
}
componentDidMount() {
}
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 });
}
})
}
add = async () => {
this.set(false)
}
clear = async () => {
this.set(true)
}
clearAll = async () => {
await this.eachRepr((update, repr, rootStructure, overpaint) => {
if (overpaint) update.delete(overpaint.transform.ref)
})
}
render() {
return <div className='msp-transform-wrapper'>
<div className='msp-transform-header'>
<button className='msp-btn msp-btn-block'>Current Selection Overpaint</button>
</div>
<div>
<ParameterControls params={OverpaintControls.getParams(this.plugin)} values={this.state.params} onChange={p => {
const params = { ...this.state.params, [p.name]: p.value };
this.setState({ params });
}}/>
<div className='msp-btn-row-group'>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.add}>Add</button>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.clear}>Clear</button>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.clearAll}>Clear All</button>
</div>
</div>
</div>
}
}
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 RepresentationControls extends PluginUIComponent<{}, { params: PD.Values<ReturnType<typeof RepresentationControls.getParams>> }> {
state = { params: PD.getDefaultValues(RepresentationControls.getParams(this.plugin)) }
static getParams = (plugin: PluginContext) => {
const { types } = plugin.structureRepresentation.registry
return {
type: PD.Select(types[0][0], types)
}
}
componentDidMount() {
}
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)
)
}
})
}
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));
await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }));
}
render() {
return <div className='msp-transform-wrapper'>
<div className='msp-transform-header'>
<button className='msp-btn msp-btn-block'>Current Selection Representation</button>
</div>
<div>
<ParameterControls params={RepresentationControls.getParams(this.plugin)} values={this.state.params} onChange={p => {
const params = { ...this.state.params, [p.name]: p.value };
this.setState({ params });
}}/>
<div className='msp-btn-row-group'>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.show}>Show</button>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.hide}>Hide</button>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.only}>Only</button>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.showAll}>Show All</button>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.hideAll}>Hide All</button>
</div>
</div>
</div>
}
}
export class StructureToolsWrapper extends PluginUIComponent { export class StructureToolsWrapper extends PluginUIComponent {
render() { render() {
return <div> return <div>
......
src/mol-plugin/ui/structure/overpaint.tsx 0 → 100644
+ 112
− 0
View file @ e2c9b601
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
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'
export class OverpaintControls extends PluginUIComponent<{}, { params: PD.Values<ReturnType<typeof OverpaintControls.getParams>> }> {
state = { params: PD.getDefaultValues(OverpaintControls.getParams(this.plugin)) }
static getParams = (plugin: PluginContext) => {
const { types } = plugin.structureRepresentation.registry
return {
color: PD.Color(ColorNames.cyan),
type: PD.MultiSelect(types.map(t => t[0]), types)
}
}
componentDidMount() {
}
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 });
}
})
}
add = async () => {
this.set(false)
}
clear = async () => {
this.set(true)
}
clearAll = async () => {
await this.eachRepr((update, repr, rootStructure, overpaint) => {
if (overpaint) update.delete(overpaint.transform.ref)
})
}
render() {
return <div className='msp-transform-wrapper'>
<div className='msp-transform-header'>
<button className='msp-btn msp-btn-block'>Current Selection Overpaint</button>
</div>
<div>
<ParameterControls params={OverpaintControls.getParams(this.plugin)} values={this.state.params} onChange={p => {
const params = { ...this.state.params, [p.name]: p.value };
this.setState({ params });
}}/>
<div className='msp-btn-row-group'>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.add}>Add</button>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.clear}>Clear</button>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.clearAll}>Clear All</button>
</div>
</div>
</div>
}
}
\ No newline at end of file
src/mol-plugin/ui/structure/representation.tsx 0 → 100644
+ 147
− 0
View file @ e2c9b601
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
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 RepresentationControls extends PluginUIComponent<{}, { params: PD.Values<ReturnType<typeof RepresentationControls.getParams>> }> {
state = { params: PD.getDefaultValues(RepresentationControls.getParams(this.plugin)) }
static getParams = (plugin: PluginContext) => {
const { types } = plugin.structureRepresentation.registry
return {
type: PD.Select(types[0][0], types)
}
}
componentDidMount() {
}
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)
)
}
})
}
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));
await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }));
}
render() {
return <div className='msp-transform-wrapper'>
<div className='msp-transform-header'>
<button className='msp-btn msp-btn-block'>Current Selection Representation</button>
</div>
<div>
<ParameterControls params={RepresentationControls.getParams(this.plugin)} values={this.state.params} onChange={p => {
const params = { ...this.state.params, [p.name]: p.value };
this.setState({ params });
}}/>
<div className='msp-btn-row-group'>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.show}>Show</button>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.hide}>Hide</button>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.only}>Only</button>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.showAll}>Show All</button>
<button className='msp-btn msp-btn-block msp-form-control' onClick={this.hideAll}>Hide All</button>
</div>
</div>
</div>
}
}
\ No newline at end of file
src/mol-plugin/ui/structure/util.ts 0 → 100644
+ 17
− 0
View file @ e2c9b601
/**
* 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
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