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Commit e1b7a5b2 authored by Alexander Rose's avatar Alexander Rose
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wip, structure tools, repr presets

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src/mol-plugin/ui/structure/representation.tsx
+ 20
− 13
View file @ e1b7a5b2
......@@ -13,6 +13,8 @@ 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 '../../util/structure-representation-helper';
import { camelCaseToWords } from '../../../mol-util/string';
abstract class BaseStructureRepresentationControls extends PluginUIComponent {
onChange = (value: string) => {
......@@ -49,25 +51,19 @@ abstract class BaseStructureRepresentationControls extends PluginUIComponent {
<span title={this.label}>{this.label}</span>
<div className='msp-select-row'>
<ButtonSelect label='Show' onChange={this.show}>
<optgroup label='Show'>
{Options(types)}
</optgroup>
<optgroup label='Show'>{Options(types)}</optgroup>
</ButtonSelect>
<ButtonSelect label='Hide' onChange={this.hide}>
<optgroup label='Clear'>
<option key={'__all__'} value={'__all__'}>All</option>
</optgroup>
<optgroup label='Hide'>
{Options(types)}
</optgroup>
<optgroup label='Hide'>{Options(types)}</optgroup>
</ButtonSelect>
<ButtonSelect label='Color' onChange={this.color}>
<optgroup label='Clear'>
<option key={-1} value={-1}>Theme</option>
</optgroup>
<optgroup label='Color'>
{ColorOptions()}
</optgroup>
<optgroup label='Color'>{ColorOptions()}</optgroup>
</ButtonSelect>
</div>
</div>
......@@ -90,8 +86,11 @@ class SelectionStructureRepresentationControls extends BaseStructureRepresentati
}
export class StructureRepresentationControls extends PluginUIComponent {
preset = async () => {
await this.plugin.helpers.structureRepresentation.preset()
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 }) => {
......@@ -123,12 +122,20 @@ export class StructureRepresentationControls extends PluginUIComponent {
}
render() {
const presets = Object.keys(P).map(name => {
return [name, camelCaseToWords(name)] as [string, string]
})
return <div className='msp-transform-wrapper'>
<div className='msp-transform-header'>
<button className='msp-btn msp-btn-block'>Representation</button>
</div>
<div className='msp-btn-row-group'>
<button className='msp-btn msp-btn-block msp-form-control' onClick={() => this.preset()}>Preset</button>
<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 />
......
src/mol-plugin/ui/structure/selection.tsx
+ 0
− 2
View file @ e1b7a5b2
......@@ -15,8 +15,6 @@ import { Interactivity } from '../../util/interactivity';
import { ParameterControls } from '../controls/parameters';
import { camelCaseToWords } from '../../../mol-util/string';
type SelectionModifier = 'add' | 'remove' | 'only'
const StructureSelectionParams = {
granularity: Interactivity.Params.granularity,
}
......
src/mol-plugin/util/structure-representation-helper.ts
+ 69
− 12
View file @ e1b7a5b2
......@@ -49,7 +49,7 @@ export class StructureRepresentationHelper {
return selections.length > 0 ? selections[0] : undefined
}
private async _set(modifier: SelectionModifier, type: string, loci: StructureElement.Loci, structure: StructureTransform) {
private async _set(modifier: SelectionModifier, type: string, loci: StructureElement.Loci, structure: StructureTransform, props = {}) {
const state = this.plugin.state.dataState
const update = state.build()
const s = structure.obj!.data
......@@ -69,6 +69,7 @@ export class StructureRepresentationHelper {
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
......@@ -84,23 +85,23 @@ export class StructureRepresentationHelper {
await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }))
}
async set(modifier: SelectionModifier, type: string, lociGetter: (structure: Structure) => StructureElement.Loci) {
async set(modifier: SelectionModifier, type: string, lociGetter: (structure: Structure) => StructureElement.Loci, props = {}) {
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 loci = lociGetter(s)
await this._set(modifier, type, loci, structure)
await this._set(modifier, type, loci, structure, props)
}
}
async setFromExpression(modifier: SelectionModifier, type: string, expression: Expression) {
async setFromExpression(modifier: SelectionModifier, type: string, expression: Expression, props = {}) {
return this.set(modifier, type, (structure) => {
const compiled = compile<StructureSelection>(expression)
const result = compiled(new QueryContext(structure))
return StructureSelection.toLoci2(result)
})
}, props)
}
async clear() {
......@@ -169,16 +170,72 @@ export class StructureRepresentationHelper {
}
async preset() {
// TODO generalize and make configurable
await this.clear()
await this.setFromExpression('add', 'cartoon', Q.all)
await this.setFromExpression('add', 'carbohydrate', Q.all)
await this.setFromExpression('add', 'ball-and-stick', MS.struct.modifier.union([
MS.struct.combinator.merge([ Q.ligandsPlusConnected, Q.branchedConnectedOnly, Q.water ])
]))
// 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) {
polymerAndLigand(this)
} else if (s.elementCount < 200000) {
proteinAndNucleic(this)
} else {
if (s.unitSymmetryGroups[0].units.length > 10) {
capsid(this)
} else {
coarseCapsid(this)
}
}
}
constructor(private plugin: PluginContext) {
}
}
//
async function polymerAndLigand(r: StructureRepresentationHelper) {
await r.clear()
await r.setFromExpression('add', 'cartoon', Q.all)
await r.setFromExpression('add', 'carbohydrate', Q.all)
await r.setFromExpression('add', 'ball-and-stick', MS.struct.modifier.union([
MS.struct.combinator.merge([ Q.ligandPlusConnected, Q.branchedConnectedOnly, Q.water ])
]))
}
async function proteinAndNucleic(r: StructureRepresentationHelper) {
await r.clear()
await r.setFromExpression('add', 'cartoon', Q.protein)
await r.setFromExpression('add', 'gaussian-surface', Q.nucleic)
await r.setFromExpression('add', 'carbohydrate', Q.all)
await r.setFromExpression('add', 'ball-and-stick', MS.struct.modifier.union([
MS.struct.combinator.merge([ Q.ligandPlusConnected, Q.branchedConnectedOnly, Q.water ])
]))
}
async function capsid(r: StructureRepresentationHelper) {
await r.clear()
await r.setFromExpression('add', 'gaussian-surface', Q.polymer, {
smoothness: 0.5,
})
}
async function coarseCapsid(r: StructureRepresentationHelper) {
await r.clear()
await r.setFromExpression('add', 'gaussian-surface', Q.trace, {
radiusOffset: 1,
smoothness: 0.5,
visuals: ['structure-gaussian-surface-mesh']
})
}
export const StructureRepresentationPresets = {
polymerAndLigand,
proteinAndNucleic,
capsid,
coarseCapsid
}
\ No newline at end of file
src/mol-plugin/util/structure-selection-helper.ts
+ 62
− 25
View file @ e1b7a5b2
......@@ -15,17 +15,52 @@ import Expression from '../../mol-script/language/expression';
const all = MS.struct.generator.all()
const polymers = MS.struct.modifier.union([
const polymer = MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer'])
})
])
const backboneTrace = MS.struct.modifier.union([
const trace = MS.struct.modifier.union([
MS.struct.combinator.merge([
MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
'chain-test': MS.core.set.has([
MS.set('sphere', 'gaussian'), MS.ammp('objectPrimitive')
])
})
]),
MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
'atom-test': MS.core.set.has([MS.set('CA', 'P'), MS.ammp('label_atom_id')])
})
])
])
])
const protein = MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'entity-test': MS.core.logic.and([
MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
MS.core.str.match([
MS.re('(polypeptide|cyclic-pseudo-peptide)', 'i'),
MS.ammp('entitySubtype')
])
])
})
])
const nucleic = MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'atom-test': MS.core.logic.or([
MS.core.rel.eq([MS.ammp('label_atom_id'), 'CA']),
MS.core.rel.eq([MS.ammp('label_atom_id'), 'P'])
'entity-test': MS.core.logic.and([
MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
MS.core.str.match([
MS.re('(nucleotide|peptide nucleic acid)', 'i'),
MS.ammp('entitySubtype')
])
])
})
])
......@@ -37,19 +72,18 @@ const water = MS.struct.modifier.union([
])
const branched = MS.struct.modifier.union([
MS.struct.combinator.merge([
MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'branched'])
})
]),
MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'non-polymer']),
'residue-test': MS.core.str.match([MS.re('saccharide', 'i'), MS.ammp('chemCompType')])
})
MS.struct.generator.atomGroups({
'entity-test': MS.core.logic.or([
MS.core.rel.eq([MS.ammp('entityType'), 'branched']),
MS.core.logic.and([
MS.core.rel.eq([MS.ammp('entityType'), 'non-polymer']),
MS.core.str.match([
MS.re('oligosaccharide', 'i'),
MS.ammp('entitySubtype')
])
])
])
])
})
])
const branchedPlusConnected = MS.struct.modifier.union([
......@@ -65,21 +99,22 @@ const branchedConnectedOnly = MS.struct.modifier.union([
})
])
const ligands = MS.struct.modifier.union([
const ligand = MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'entity-test': MS.core.logic.and([
MS.core.rel.neq([MS.ammp('entityType'), 'branched']),
MS.core.rel.eq([MS.ammp('entityType'), 'non-polymer'])
]),
'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
'residue-test': MS.core.logic.not([
MS.core.str.match([MS.re('saccharide', 'i'), MS.ammp('chemCompType')])
])
})
])
const ligandsPlusConnected = MS.struct.modifier.union([
const ligandPlusConnected = MS.struct.modifier.union([
MS.struct.modifier.includeConnected({
0: ligands, 'layer-count': 1, 'as-whole-residues': true
0: ligand, 'layer-count': 1, 'as-whole-residues': true
})
])
......@@ -93,20 +128,22 @@ const coarse = MS.struct.modifier.union([
export const StructureSelectionQueries = {
all,
polymers,
backboneTrace,
polymer,
trace,
protein,
nucleic,
water,
branched,
branchedPlusConnected,
branchedConnectedOnly,
ligands,
ligandsPlusConnected,
ligand,
ligandPlusConnected,
coarse,
}
//
type SelectionModifier = 'add' | 'remove' | 'only'
export type SelectionModifier = 'add' | 'remove' | 'only'
export class StructureSelectionHelper {
private get structures() {
......
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