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@@ -7,57 +7,82 @@
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import { StructureViewerState } from '../types';
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import { getStructureSize, StructureSize } from './util';
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import { PluginContext } from 'molstar/lib/mol-plugin/context';
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-import { Structure } from 'molstar/lib/mol-model/structure';
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-import { Loci, EmptyLoci } from 'molstar/lib/mol-model/loci';
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+import { Structure, StructureSelection, QueryContext, StructureElement } from 'molstar/lib/mol-model/structure';
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+import { Loci } from 'molstar/lib/mol-model/loci';
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import { Axes3D } from 'molstar/lib/mol-math/geometry';
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import { Vec3 } from 'molstar/lib/mol-math/linear-algebra';
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import { ValidationReport } from 'molstar/lib/mol-model-props/rcsb/validation-report';
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import { StructureSelectionQueries as SSQ } from 'molstar/lib/mol-plugin/util/structure-selection-helper';
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import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
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-import { AssemblySymmetry } from 'molstar/lib/mol-model-props/rcsb/assembly-symmetry';
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+import { AssemblySymmetry, AssemblySymmetryProvider } from 'molstar/lib/mol-model-props/rcsb/assembly-symmetry';
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+import Expression from 'molstar/lib/mol-script/language/expression';
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+import { compile } from 'molstar/lib/mol-script/runtime/query/compiler';
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+import { Color } from 'molstar/lib/mol-util/color';
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type Target = {
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readonly auth_seq_id?: number
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readonly label_seq_id?: number
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- readonly label_comp_id?: number
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- readonly label_asym_id?: number
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- readonly pdbx_struct_oper_list_ids?: string[]
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+ readonly label_comp_id?: string
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+ readonly label_asym_id?: string
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}
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-function targetToLoci(target: Target, structure: Structure): Loci {
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- return EmptyLoci
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+function targetToExpression(target: Target): Expression {
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+ const residueTests: Expression[] = []
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+ const tests = Object.create(null)
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+
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+ if (target.auth_seq_id) {
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+ residueTests.push(MS.core.rel.eq([target.auth_seq_id, MS.ammp('auth_seq_id')]))
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+ } else if (target.label_seq_id) {
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+ residueTests.push(MS.core.rel.eq([target.label_seq_id, MS.ammp('label_seq_id')]))
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+ }
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+ if (target.label_comp_id) {
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+ residueTests.push(MS.core.rel.eq([target.label_comp_id, MS.ammp('label_comp_id')]))
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+ }
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+ if (residueTests.length === 1) {
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+ tests['residue-test'] = residueTests[0]
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+ } else if (residueTests.length > 1) {
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+ tests['residue-test'] = MS.core.logic.and(residueTests)
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+ }
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+
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+ if (target.label_asym_id) {
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+ tests['chain-test'] = MS.core.rel.eq([target.label_asym_id, MS.ammp('label_asym_id')])
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+ }
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+
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+ if (Object.keys(tests).length > 0) {
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+ return MS.struct.modifier.union([
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+ MS.struct.generator.atomGroups(tests)
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+ ])
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+ } else {
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+ return MS.struct.generator.all
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+ }
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+}
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+
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+type BaseProps = {
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+ assemblyId?: string
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+ modelIndex?: number
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}
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type ValidationProps = {
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kind: 'validation'
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colorTheme?: string
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showClashes?: boolean
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- modelIndex?: number
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-}
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-
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-type AssemblyProps = {
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- kind: 'assembly'
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- assemblyId: string
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- modelIndex?: number
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-}
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+} & BaseProps
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type StandardProps = {
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kind: 'standard'
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-}
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+} & BaseProps
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type SymmetryProps = {
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kind: 'symmetry'
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- assemblyId?: string
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symmetryIndex?: number
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-}
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+} & BaseProps
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type FeatureProps = {
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kind: 'feature'
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- assemblyId: string
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target: Target
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-}
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+} & BaseProps
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-export type PresetProps = ValidationProps | AssemblyProps | StandardProps | SymmetryProps | FeatureProps
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+export type PresetProps = ValidationProps | StandardProps | SymmetryProps | FeatureProps
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export class PresetManager {
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get customState() {
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@@ -65,23 +90,22 @@ export class PresetManager {
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}
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async apply(props?: PresetProps) {
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- if (!props) props = { kind: 'assembly', assemblyId: 'deposited' }
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+ if (!props) props = { kind: 'standard', assemblyId: 'deposited' }
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+
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switch (props.kind) {
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- case 'assembly':
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- return this.assembly(props.assemblyId, props.modelIndex)
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case 'feature':
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- return this.feature(props.target, props.assemblyId)
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+ return this.feature(props.target, props.assemblyId, props.modelIndex)
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case 'standard':
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- return this.standard()
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+ return this.standard(props.assemblyId, props.modelIndex)
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case 'symmetry':
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- return this.symmetry(props.symmetryIndex, props.assemblyId)
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+ return this.symmetry(props.symmetryIndex, props.assemblyId, props.modelIndex)
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case 'validation':
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- return this.validation(props.colorTheme, props.showClashes, props.modelIndex)
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+ return this.validation(props.colorTheme, props.showClashes, props.assemblyId, props.modelIndex)
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}
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}
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async default() {
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- const assembly = this.customState.structureView.getAssembly()
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+ const assembly = this.customState.structureView.getAssembly()?.obj
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if (!assembly || assembly.data.isEmpty) return
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const r = this.plugin.helpers.structureRepresentation
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@@ -130,77 +154,87 @@ export class PresetManager {
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}
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}
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- async standard() {
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+ async standard(assemblyId?: string, modelIndex?: number) {
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+ await this.ensureAssembly(assemblyId, modelIndex)
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await this.customState.structureView.setSymmetry(-1)
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await this.default()
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- this.focus()
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- }
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-
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- async assembly(assemblyId: string, modelIndex?: number) {
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- if (modelIndex !== undefined) {
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- await this.customState.structureView.setModel(modelIndex)
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- }
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- await this.customState.structureView.setAssembly(assemblyId)
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- await this.default()
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- this.focus()
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- }
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-
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- async model(modelIndex: number) {
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- await this.customState.structureView.setModel(modelIndex)
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- await this.default()
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- this.focus()
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+ this.focusOnLoci()
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}
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async feature(target: Target, assemblyId?: string, modelIndex?: number) {
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- if (modelIndex !== undefined) {
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- await this.customState.structureView.setModel(modelIndex)
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- }
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- if (assemblyId !== undefined) {
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- await this.customState.structureView.setAssembly(assemblyId)
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- }
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- const assembly = this.customState.structureView.getAssembly()
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- if (!assembly || assembly.data.isEmpty) return
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+ await this.ensureAssembly(assemblyId, modelIndex, true)
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+ const r = this.plugin.helpers.structureRepresentation
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- const loci = targetToLoci(target, assembly.data)
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- // TODO show target and surrounding residues in detail if small
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- this.focus(loci)
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- }
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+ const assembly = this.customState.structureView.getAssembly()?.obj
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+ if (!assembly || assembly.data.isEmpty) return
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- async symmetry(symmetryIndex?: number, assemblyId?: string) {
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- if (assemblyId !== undefined) {
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- await this.customState.structureView.setAssembly(assemblyId)
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+ const expression = targetToExpression(target)
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+ const query = compile<StructureSelection>(expression)
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+ const result = query(new QueryContext(assembly.data))
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+ const loci = StructureSelection.toLociWithSourceUnits(result)
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+
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+ if (target.auth_seq_id !== undefined || target.label_comp_id !== undefined || target.label_seq_id !== undefined ) {
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+ const surroundings = MS.struct.modifier.includeSurroundings({
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+ 0: expression,
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+ radius: 5,
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+ 'as-whole-residues': true
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+ });
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+ const surroundingsOnly = MS.struct.modifier.exceptBy({ 0: surroundings, by: expression });
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+ await r.setFromExpression('add', 'ball-and-stick', surroundings)
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+ await r.setFromExpression('add', 'interactions', surroundings)
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+ await r.setFromExpression('add', 'label', surroundings)
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+ await this.plugin.helpers.structureOverpaint.setFromExpression(Color(0xFFFFFF), surroundingsOnly, undefined, 2/3)
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+ const firstResidue = StructureElement.Loci.firstResidue(loci)
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+ this.focusOnLoci(Loci.isEmpty(firstResidue) ? Structure.Loci(assembly.data) : firstResidue)
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+ } else if(target.label_asym_id) {
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+ await this.default()
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+ const firstChain = StructureElement.Loci.firstChain(loci)
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+ this.focusOnLoci(Loci.isEmpty(firstChain) ? Structure.Loci(assembly.data) : firstChain)
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+ } else {
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await this.default()
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+ this.focusOnLoci()
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}
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+ }
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- const assembly = this.customState.structureView.getAssembly()
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+ async symmetry(symmetryIndex?: number, assemblyId?: string, modelIndex?: number) {
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+ await this.ensureAssembly(assemblyId, modelIndex)
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+ const r = this.plugin.helpers.structureRepresentation
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+
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+ const assembly = this.customState.structureView.getAssembly()?.obj
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if (!assembly || assembly.data.isEmpty) return
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- const r = this.plugin.helpers.structureRepresentation
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+ await this.customState.structureView.attachAssemblySymmetry()
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+ const assemblySymmetry = AssemblySymmetryProvider.get(assembly.data).value
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+ if (!assemblySymmetry || !assemblySymmetry.find(s => s.symbol !== 'C1')) {
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+ this.focusOnLoci()
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+ return
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+ }
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- await this.customState.structureView.setSymmetry(symmetryIndex || 0)
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- r.eachRepresentation((repr, type, update) => {
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+ if (symmetryIndex === undefined) {
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+ symmetryIndex = assemblySymmetry.findIndex(s => s.symbol !== 'C1')
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+ }
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+
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+ await this.customState.structureView.setSymmetry(symmetryIndex)
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+ await r.eachRepresentation((repr, type, update) => {
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if (type !== ValidationReport.Tag.Clashes) {
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- r.setRepresentationParams(repr, type, update, { color: AssemblySymmetry.Tag.Cluster })
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+ r.setRepresentationParams(repr, type, update, {
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+ color: [AssemblySymmetry.Tag.Cluster, { symmetryIndex }]
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+ })
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}
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})
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- // TODO focus on symmetry axes
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- this.focus()
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+ this.focusOnSymmetry(symmetryIndex)
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}
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- async validation(colorTheme?: string, showClashes?: boolean, modelIndex?: number) {
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- if (modelIndex !== undefined) {
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- this.customState.structureView.setModel(modelIndex)
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- await this.default()
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- }
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-
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- const assembly = this.customState.structureView.getAssembly()
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- if (!assembly || assembly.data.isEmpty) return
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-
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+ async validation(colorTheme?: string, showClashes?: boolean, assemblyId?: string, modelIndex?: number) {
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+ await this.ensureAssembly(assemblyId, modelIndex)
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const r = this.plugin.helpers.structureRepresentation
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+ const size = this.customState.structureView.getSize()
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+ if (size === undefined) return
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+
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if (showClashes === undefined) {
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- showClashes = getStructureSize(assembly.data) <= StructureSize.Medium
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+ showClashes = size <= StructureSize.Medium
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}
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await this.customState.structureView.attachValidationReport()
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@@ -212,18 +246,39 @@ export class PresetManager {
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}
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if (colorTheme === undefined) colorTheme = ValidationReport.Tag.GeometryQuality
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- r.eachRepresentation((repr, type, update) => {
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+ await r.eachRepresentation((repr, type, update) => {
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if (type !== ValidationReport.Tag.Clashes) {
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r.setRepresentationParams(repr, type, update, { color: colorTheme })
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}
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})
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- this.focus()
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+ this.focusOnLoci()
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+ }
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+
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+ async ensureAssembly(assemblyId?: string, modelIndex?: number, neverApplyDefault?: boolean) {
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+ const oldSize = this.customState.structureView.getSize()
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+
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+ const model = this.customState.structureView.getModel()
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+ if (!model && modelIndex === undefined) modelIndex = 0
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+
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+ const assembly = this.customState.structureView.getAssembly()
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+ if (!assembly && assemblyId === undefined) assemblyId = 'deposited'
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+
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+ if (modelIndex !== undefined) {
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+ await this.customState.structureView.setModel(modelIndex)
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+ }
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+
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+ if (assemblyId !== undefined) {
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+ await this.customState.structureView.setAssembly(assemblyId)
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+ }
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+ const newSize = this.customState.structureView.getSize()
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+
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+ if (!neverApplyDefault && oldSize !== newSize) await this.default()
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}
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- focus(loci?: Loci) {
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+ focusOnLoci(loci?: Loci) {
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if (!loci) {
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- const assembly = this.customState.structureView.getAssembly()
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+ const assembly = this.customState.structureView.getAssembly()?.obj
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if (!assembly || assembly.data.isEmpty) return
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loci = Structure.toStructureElementLoci(assembly.data)
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@@ -232,13 +287,51 @@ export class PresetManager {
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const principalAxes = Loci.getPrincipalAxes(loci)
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if (!principalAxes) return
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- const extraRadius = 4, minRadius = 8, durationMs = 250
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+ const extraRadius = 4, minRadius = 8, durationMs = 0
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const { origin, dirA, dirC } = principalAxes.boxAxes
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const axesRadius = Math.max(...Axes3D.size(Vec3(), principalAxes.boxAxes)) / 2
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const radius = Math.max(axesRadius + extraRadius, minRadius)
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this.plugin.canvas3d!.camera.focus(origin, radius, radius, durationMs, dirA, dirC);
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}
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+ focusOnSymmetry(symmetryIndex: number) {
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+ const assembly = this.customState.structureView.getAssembly()?.obj
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+ if (!assembly || assembly.data.isEmpty) return
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+
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+ const assemblySymmetry = AssemblySymmetryProvider.get(assembly.data).value
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+ const axes = assemblySymmetry?.[symmetryIndex].rotation_axes
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+ if (!axes || !AssemblySymmetry.isRotationAxes(axes)) {
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+ this.focusOnLoci()
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+ return
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+ }
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+
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+ const [aA, aB] = axes
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+ if (!aA) return
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+
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+ const extraRadius = 4, minRadius = 8, durationMs = 0
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+
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+ const axisRadius = Vec3.distance(aA.start, aA.end) / 2
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+ const radius = Math.max(axisRadius + extraRadius, minRadius)
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+
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+ const origin = Vec3()
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+ Vec3.scale(origin, Vec3.add(origin, aA.start, aA.end), 0.5)
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+
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+ const dir = Vec3.sub(Vec3(), aA.start, aA.end)
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+ const up = Vec3()
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+
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+ if (aB) {
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+ Vec3.sub(up, aB.end, aB.start)
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+ } else {
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+ if (Vec3.dot(Vec3.unitY, Vec3.sub(Vec3(), aA.end, aA.start)) === 0) {
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+ Vec3.copy(up, Vec3.unitY)
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+ } else {
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+ Vec3.copy(up, Vec3.unitX)
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+ }
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+ }
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+
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+ this.plugin.canvas3d!.camera.focus(origin, radius, radius, durationMs, up, dir);
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+ }
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+
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constructor(private plugin: PluginContext) {
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}
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Alexander Rose