diff --git a/src/mol-plugin/ui/structure/representation.tsx b/src/mol-plugin/ui/structure/representation.tsx
index a7ddbea462fdb632ea14ea92b3e28ea8562a378c..ba82755cbdf17a7e19a3483a4a26b21f95cb0f37 100644
--- a/src/mol-plugin/ui/structure/representation.tsx
+++ b/src/mol-plugin/ui/structure/representation.tsx
@@ -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 />
diff --git a/src/mol-plugin/ui/structure/selection.tsx b/src/mol-plugin/ui/structure/selection.tsx
index 10adf56a4ff2f63a73cc7a9d5947d577b435c052..36ac44600da2ef4f57bb16736c9f8a587c35bfea 100644
--- a/src/mol-plugin/ui/structure/selection.tsx
+++ b/src/mol-plugin/ui/structure/selection.tsx
@@ -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,
}
diff --git a/src/mol-plugin/util/structure-representation-helper.ts b/src/mol-plugin/util/structure-representation-helper.ts
index c2b389e75ae620508390abf7832669a9db3eb8a9..3f73b7d75b3d7b64859c1e439c77cff58f7eaf6b 100644
--- a/src/mol-plugin/util/structure-representation-helper.ts
+++ b/src/mol-plugin/util/structure-representation-helper.ts
@@ -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
diff --git a/src/mol-plugin/util/structure-selection-helper.ts b/src/mol-plugin/util/structure-selection-helper.ts
index c474561bd3a0c508c5461bcb6d3ab0281e0c2df3..49ca344c4e77f4e2f1f6a35b1c789ad3b9be47c8 100644
--- a/src/mol-plugin/util/structure-selection-helper.ts
+++ b/src/mol-plugin/util/structure-selection-helper.ts
@@ -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() {