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Alexander Rose authoredAlexander Rose authored
structure-selection-helper.ts 5.50 KiB
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
import { StateSelection } from '../../mol-state';
import { PluginStateObject } from '../state/objects';
import { QueryContext, StructureSelection } from '../../mol-model/structure';
import { compile } from '../../mol-script/runtime/query/compiler';
import { Loci } from '../../mol-model/loci';
import { PluginContext } from '../context';
import Expression from '../../mol-script/language/expression';
const all = MS.struct.generator.all()
const polymer = MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer'])
})
])
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({
'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')
])
])
})
])
const water = MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'water'])
})
])
const branched = MS.struct.modifier.union([
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([
MS.struct.modifier.includeConnected({
0: branched, 'layer-count': 1, 'as-whole-residues': true
})
])
const branchedConnectedOnly = MS.struct.modifier.union([
MS.struct.modifier.exceptBy({
0: branchedPlusConnected,
by: branched
})
])
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 ligandPlusConnected = MS.struct.modifier.union([
MS.struct.modifier.includeConnected({
0: ligand, 'layer-count': 1, 'as-whole-residues': true
})
])
const coarse = MS.struct.modifier.union([
MS.struct.generator.atomGroups({
'chain-test': MS.core.set.has([
MS.set('sphere', 'gaussian'), MS.ammp('objectPrimitive')
])
})
])
export const StructureSelectionQueries = {
all,
polymer,
trace,
protein,
nucleic,
water,
branched,
branchedPlusConnected,
branchedConnectedOnly,
ligand,
ligandPlusConnected,
coarse,
}
//
export type SelectionModifier = 'add' | 'remove' | 'only'
export class StructureSelectionHelper {
private get structures() {
const state = this.plugin.state.dataState
return state.select(StateSelection.Generators.rootsOfType(PluginStateObject.Molecule.Structure))
}
private _set(modifier: SelectionModifier, loci: Loci) {
switch (modifier) {
case 'add':
this.plugin.interactivity.lociSelects.select({ loci })
break
case 'remove':
this.plugin.interactivity.lociSelects.deselect({ loci })
break
case 'only':
this.plugin.interactivity.lociSelects.selectOnly({ loci })
break
}
}
set(modifier: SelectionModifier, query: Expression) {
const compiled = compile<StructureSelection>(query)
for (const so of this.structures) {
const s = so.obj!.data
const result = compiled(new QueryContext(s))
const loci = StructureSelection.toLoci2(result)
this._set(modifier, loci)
}
}
constructor(private plugin: PluginContext) {
}
}