molstar
Version:
A comprehensive macromolecular library.
704 lines (703 loc) • 39 kB
JavaScript
"use strict";
/**
* Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.StructureSelectionQueryRegistry = exports.StructureSelectionQueries = exports.StructureSelectionCategory = void 0;
exports.StructureSelectionQuery = StructureSelectionQuery;
exports.ResidueQuery = ResidueQuery;
exports.ElementSymbolQuery = ElementSymbolQuery;
exports.EntityDescriptionQuery = EntityDescriptionQuery;
exports.getElementQueries = getElementQueries;
exports.getNonStandardResidueQueries = getNonStandardResidueQueries;
exports.getPolymerAndBranchedEntityQueries = getPolymerAndBranchedEntityQueries;
exports.applyBuiltInSelection = applyBuiltInSelection;
const structure_1 = require("../../mol-model/structure");
const types_1 = require("../../mol-model/structure/model/types");
const builder_1 = require("../../mol-script/language/builder");
const compiler_1 = require("../../mol-script/runtime/query/compiler");
const set_1 = require("../../mol-util/set");
const transforms_1 = require("../transforms");
const types_2 = require("../../mol-model/structure/model/properties/atomic/types");
const secondary_structure_1 = require("../../mol-model-props/computed/secondary-structure");
var StructureSelectionCategory;
(function (StructureSelectionCategory) {
StructureSelectionCategory["Type"] = "Type";
StructureSelectionCategory["Structure"] = "Structure Property";
StructureSelectionCategory["Atom"] = "Atom Property";
StructureSelectionCategory["Bond"] = "Bond Property";
StructureSelectionCategory["Residue"] = "Residue Property";
StructureSelectionCategory["AminoAcid"] = "Amino Acid";
StructureSelectionCategory["NucleicBase"] = "Nucleic Base";
StructureSelectionCategory["Manipulate"] = "Manipulate Selection";
StructureSelectionCategory["Validation"] = "Validation";
StructureSelectionCategory["Misc"] = "Miscellaneous";
StructureSelectionCategory["Internal"] = "Internal";
})(StructureSelectionCategory || (exports.StructureSelectionCategory = StructureSelectionCategory = {}));
function StructureSelectionQuery(label, expression, props = {}) {
var _a;
let _query;
return {
label,
expression,
description: props.description || '',
category: (_a = props.category) !== null && _a !== void 0 ? _a : StructureSelectionCategory.Misc,
isHidden: !!props.isHidden,
priority: props.priority || 0,
referencesCurrent: !!props.referencesCurrent,
get query() {
if (!_query)
_query = (0, compiler_1.compile)(expression);
return _query;
},
ensureCustomProperties: props.ensureCustomProperties,
async getSelection(plugin, runtime, structure) {
const current = plugin.managers.structure.selection.getStructure(structure);
const currentSelection = current ? structure_1.StructureSelection.Sequence(structure, [current]) : structure_1.StructureSelection.Empty(structure);
if (props.ensureCustomProperties) {
await props.ensureCustomProperties({ runtime, assetManager: plugin.managers.asset }, structure);
}
if (!_query)
_query = (0, compiler_1.compile)(expression);
return _query(new structure_1.QueryContext(structure, { currentSelection }));
}
};
}
const all = StructureSelectionQuery('All', builder_1.MolScriptBuilder.struct.generator.all(), { category: '', priority: 1000 });
const current = StructureSelectionQuery('Current Selection', builder_1.MolScriptBuilder.internal.generator.current(), { category: '', referencesCurrent: true });
const polymer = StructureSelectionQuery('Polymer', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': builder_1.MolScriptBuilder.core.logic.and([
builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'polymer']),
builder_1.MolScriptBuilder.core.str.match([
builder_1.MolScriptBuilder.re('(polypeptide|cyclic-pseudo-peptide|peptide-like|nucleotide|peptide nucleic acid)', 'i'),
builder_1.MolScriptBuilder.ammp('entitySubtype')
])
])
})
]), { category: StructureSelectionCategory.Type });
const trace = StructureSelectionQuery('Trace', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.combinator.merge([
builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'polymer']),
'chain-test': builder_1.MolScriptBuilder.core.set.has([
builder_1.MolScriptBuilder.set('sphere', 'gaussian'), builder_1.MolScriptBuilder.ammp('objectPrimitive')
])
})
]),
builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'polymer']),
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('objectPrimitive'), 'atomistic']),
'atom-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set('CA', 'P'), builder_1.MolScriptBuilder.ammp('label_atom_id')])
})
])
])
]), { category: StructureSelectionCategory.Structure });
const _proteinEntityTest = builder_1.MolScriptBuilder.core.logic.and([
builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'polymer']),
builder_1.MolScriptBuilder.core.str.match([
builder_1.MolScriptBuilder.re('(polypeptide|cyclic-pseudo-peptide|peptide-like)', 'i'),
builder_1.MolScriptBuilder.ammp('entitySubtype')
])
]);
const _nucleiEntityTest = builder_1.MolScriptBuilder.core.logic.and([
builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'polymer']),
builder_1.MolScriptBuilder.core.str.match([
builder_1.MolScriptBuilder.re('(nucleotide|peptide nucleic acid)', 'i'),
builder_1.MolScriptBuilder.ammp('entitySubtype')
])
]);
/**
* this is to get non-polymer and peptide terminus components in polymer entities,
* - non-polymer, e.g. PXZ in 4HIV or generally ACE
* - carboxy terminus, e.g. FC0 in 4BP9, or ETA in 6DDE
* - amino terminus, e.g. ARF in 3K4V, or 4MM in 3EGV
*/
const _nonPolymerResidueTest = builder_1.MolScriptBuilder.core.str.match([
builder_1.MolScriptBuilder.re('non-polymer|(amino|carboxy) terminus|peptide-like', 'i'),
builder_1.MolScriptBuilder.ammp('chemCompType')
]);
// TODO maybe pre-calculate backbone atom properties
const backbone = StructureSelectionQuery('Backbone', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.combinator.merge([
builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': _proteinEntityTest,
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('objectPrimitive'), 'atomistic']),
'residue-test': builder_1.MolScriptBuilder.core.logic.not([_nonPolymerResidueTest]),
'atom-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set(...set_1.SetUtils.toArray(types_1.ProteinBackboneAtoms)), builder_1.MolScriptBuilder.ammp('label_atom_id')])
})
]),
builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': _nucleiEntityTest,
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('objectPrimitive'), 'atomistic']),
'residue-test': builder_1.MolScriptBuilder.core.logic.not([_nonPolymerResidueTest]),
'atom-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set(...set_1.SetUtils.toArray(types_1.NucleicBackboneAtoms)), builder_1.MolScriptBuilder.ammp('label_atom_id')])
})
])
])
]), { category: StructureSelectionCategory.Structure });
// TODO maybe pre-calculate sidechain atom property
const sidechain = StructureSelectionQuery('Sidechain', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.combinator.merge([
builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': _proteinEntityTest,
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('objectPrimitive'), 'atomistic']),
'residue-test': builder_1.MolScriptBuilder.core.logic.not([_nonPolymerResidueTest]),
'atom-test': builder_1.MolScriptBuilder.core.logic.or([
builder_1.MolScriptBuilder.core.logic.not([
builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set(...set_1.SetUtils.toArray(types_1.ProteinBackboneAtoms)), builder_1.MolScriptBuilder.ammp('label_atom_id')])
])
])
})
]),
builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': _nucleiEntityTest,
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('objectPrimitive'), 'atomistic']),
'residue-test': builder_1.MolScriptBuilder.core.logic.not([_nonPolymerResidueTest]),
'atom-test': builder_1.MolScriptBuilder.core.logic.or([
builder_1.MolScriptBuilder.core.logic.not([
builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set(...set_1.SetUtils.toArray(types_1.NucleicBackboneAtoms)), builder_1.MolScriptBuilder.ammp('label_atom_id')])
])
])
})
])
])
]), { category: StructureSelectionCategory.Structure });
// TODO maybe pre-calculate sidechain atom property
const sidechainWithTrace = StructureSelectionQuery('Sidechain with Trace', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.combinator.merge([
builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': _proteinEntityTest,
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('objectPrimitive'), 'atomistic']),
'residue-test': builder_1.MolScriptBuilder.core.logic.not([_nonPolymerResidueTest]),
'atom-test': builder_1.MolScriptBuilder.core.logic.or([
builder_1.MolScriptBuilder.core.logic.not([
builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set(...set_1.SetUtils.toArray(types_1.ProteinBackboneAtoms)), builder_1.MolScriptBuilder.ammp('label_atom_id')])
]),
builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('label_atom_id'), 'CA']),
builder_1.MolScriptBuilder.core.logic.and([
builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('auth_comp_id'), 'PRO']),
builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('label_atom_id'), 'N'])
])
])
})
]),
builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': _nucleiEntityTest,
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('objectPrimitive'), 'atomistic']),
'residue-test': builder_1.MolScriptBuilder.core.logic.not([_nonPolymerResidueTest]),
'atom-test': builder_1.MolScriptBuilder.core.logic.or([
builder_1.MolScriptBuilder.core.logic.not([
builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set(...set_1.SetUtils.toArray(types_1.NucleicBackboneAtoms)), builder_1.MolScriptBuilder.ammp('label_atom_id')])
]),
builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('label_atom_id'), 'P'])
])
})
])
])
]), { category: StructureSelectionCategory.Structure });
const protein = StructureSelectionQuery('Protein', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({ 'entity-test': _proteinEntityTest })
]), { category: StructureSelectionCategory.Type });
const nucleic = StructureSelectionQuery('Nucleic', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({ 'entity-test': _nucleiEntityTest })
]), { category: StructureSelectionCategory.Type });
const helix = StructureSelectionQuery('Helix', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': _proteinEntityTest,
'residue-test': builder_1.MolScriptBuilder.core.flags.hasAny([
builder_1.MolScriptBuilder.ammp('secondaryStructureFlags'),
builder_1.MolScriptBuilder.core.type.bitflags([2 /* SecondaryStructureType.Flag.Helix */])
])
})
]), {
category: StructureSelectionCategory.Structure,
ensureCustomProperties: (ctx, structure) => {
return secondary_structure_1.SecondaryStructureProvider.attach(ctx, structure);
}
});
const beta = StructureSelectionQuery('Beta Strand/Sheet', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': _proteinEntityTest,
'residue-test': builder_1.MolScriptBuilder.core.flags.hasAny([
builder_1.MolScriptBuilder.ammp('secondaryStructureFlags'),
builder_1.MolScriptBuilder.core.type.bitflags([4 /* SecondaryStructureType.Flag.Beta */])
])
})
]), {
category: StructureSelectionCategory.Structure,
ensureCustomProperties: (ctx, structure) => {
return secondary_structure_1.SecondaryStructureProvider.attach(ctx, structure);
}
});
const water = StructureSelectionQuery('Water', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'water'])
})
]), { category: StructureSelectionCategory.Type });
const ion = StructureSelectionQuery('Ion', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entitySubtype'), 'ion'])
})
]), { category: StructureSelectionCategory.Type });
const lipid = StructureSelectionQuery('Lipid', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entitySubtype'), 'lipid'])
})
]), { category: StructureSelectionCategory.Type });
const branched = StructureSelectionQuery('Carbohydrate', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': builder_1.MolScriptBuilder.core.logic.or([
builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'branched']),
builder_1.MolScriptBuilder.core.logic.and([
builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'non-polymer']),
builder_1.MolScriptBuilder.core.str.match([
builder_1.MolScriptBuilder.re('oligosaccharide', 'i'),
builder_1.MolScriptBuilder.ammp('entitySubtype')
])
])
])
})
]), { category: StructureSelectionCategory.Type });
const branchedPlusConnected = StructureSelectionQuery('Carbohydrate with Connected', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.includeConnected({
0: branched.expression, 'layer-count': 1, 'as-whole-residues': true
})
]), { category: StructureSelectionCategory.Internal, isHidden: true });
const branchedConnectedOnly = StructureSelectionQuery('Connected to Carbohydrate', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.exceptBy({
0: branchedPlusConnected.expression,
by: branched.expression
})
]), { category: StructureSelectionCategory.Internal, isHidden: true });
const ligand = StructureSelectionQuery('Ligand', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.exceptBy({
0: builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.combinator.merge([
builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': builder_1.MolScriptBuilder.core.logic.and([
builder_1.MolScriptBuilder.core.logic.or([
builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'non-polymer']),
builder_1.MolScriptBuilder.core.rel.neq([builder_1.MolScriptBuilder.ammp('entityPrdId'), ''])
]),
builder_1.MolScriptBuilder.core.logic.not([builder_1.MolScriptBuilder.core.str.match([
builder_1.MolScriptBuilder.re('(oligosaccharide|lipid|ion)', 'i'),
builder_1.MolScriptBuilder.ammp('entitySubtype')
])])
]),
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('objectPrimitive'), 'atomistic']),
'residue-test': builder_1.MolScriptBuilder.core.logic.not([
builder_1.MolScriptBuilder.core.str.match([builder_1.MolScriptBuilder.re('saccharide', 'i'), builder_1.MolScriptBuilder.ammp('chemCompType')])
])
})
]),
builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'polymer']),
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('objectPrimitive'), 'atomistic']),
'residue-test': _nonPolymerResidueTest
})
])
]),
]),
by: builder_1.MolScriptBuilder.struct.combinator.merge([
builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'polymer']),
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('objectPrimitive'), 'atomistic']),
'residue-test': builder_1.MolScriptBuilder.core.set.has([
builder_1.MolScriptBuilder.set(...set_1.SetUtils.toArray(types_1.PolymerNames)), builder_1.MolScriptBuilder.ammp('label_comp_id')
])
}),
]),
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('objectPrimitive'), 'atomistic']),
'residue-test': builder_1.MolScriptBuilder.core.set.has([
builder_1.MolScriptBuilder.set(...set_1.SetUtils.toArray(types_1.CommonProteinCaps)),
builder_1.MolScriptBuilder.ammp('label_comp_id'),
]),
}),
])
})
]), { category: StructureSelectionCategory.Type });
// don't include branched entities as they have their own link representation
const ligandPlusConnected = StructureSelectionQuery('Ligand with Connected', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.exceptBy({
0: builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.includeConnected({
0: ligand.expression,
'layer-count': 1,
'as-whole-residues': true,
'bond-test': builder_1.MolScriptBuilder.core.flags.hasAny([
builder_1.MolScriptBuilder.struct.bondProperty.flags(),
builder_1.MolScriptBuilder.core.type.bitflags([
1 /* BondType.Flag.Covalent */ | 2 /* BondType.Flag.MetallicCoordination */
])
])
})
]),
by: branched.expression
})
]), { category: StructureSelectionCategory.Internal, isHidden: true });
const ligandConnectedOnly = StructureSelectionQuery('Connected to Ligand', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.exceptBy({
0: ligandPlusConnected.expression,
by: ligand.expression
})
]), { category: StructureSelectionCategory.Internal, isHidden: true });
// residues connected to ligands or branched entities
const connectedOnly = StructureSelectionQuery('Connected to Ligand or Carbohydrate', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.combinator.merge([
branchedConnectedOnly.expression,
ligandConnectedOnly.expression
]),
]), { category: StructureSelectionCategory.Internal, isHidden: true });
const disulfideBridges = StructureSelectionQuery('Disulfide Bridges', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.combinator.merge([
builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.wholeResidues([
builder_1.MolScriptBuilder.struct.filter.isConnectedTo({
0: builder_1.MolScriptBuilder.struct.generator.atomGroups({
'residue-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set('CYS'), builder_1.MolScriptBuilder.ammp('auth_comp_id')]),
'atom-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set('SG'), builder_1.MolScriptBuilder.ammp('label_atom_id')])
}),
target: builder_1.MolScriptBuilder.struct.generator.atomGroups({
'residue-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set('CYS'), builder_1.MolScriptBuilder.ammp('auth_comp_id')]),
'atom-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set('SG'), builder_1.MolScriptBuilder.ammp('label_atom_id')])
}),
'bond-test': true
})
])
]),
builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.wholeResidues([
builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.bondedAtomicPairs({
0: builder_1.MolScriptBuilder.core.flags.hasAny([
builder_1.MolScriptBuilder.struct.bondProperty.flags(),
builder_1.MolScriptBuilder.core.type.bitflags([8 /* BondType.Flag.Disulfide */])
])
})
])
])
])
])
]), { category: StructureSelectionCategory.Bond });
const nosBridges = StructureSelectionQuery('NOS Bridges', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.wholeResidues([
builder_1.MolScriptBuilder.struct.filter.isConnectedTo({
0: builder_1.MolScriptBuilder.struct.generator.atomGroups({
'residue-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set('CSO', 'LYS'), builder_1.MolScriptBuilder.ammp('auth_comp_id')]),
'atom-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set('OD', 'NZ'), builder_1.MolScriptBuilder.ammp('label_atom_id')])
}),
target: builder_1.MolScriptBuilder.struct.generator.atomGroups({
'residue-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set('CSO', 'LYS'), builder_1.MolScriptBuilder.ammp('auth_comp_id')]),
'atom-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set('OD', 'NZ'), builder_1.MolScriptBuilder.ammp('label_atom_id')])
}),
'bond-test': true
})
])
]), { category: StructureSelectionCategory.Bond });
const nonStandardPolymer = StructureSelectionQuery('Non-standard Residues in Polymers', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('entityType'), 'polymer']),
'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('objectPrimitive'), 'atomistic']),
'residue-test': builder_1.MolScriptBuilder.ammp('isNonStandard')
})
]), { category: StructureSelectionCategory.Residue });
const coarse = StructureSelectionQuery('Coarse Elements', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'chain-test': builder_1.MolScriptBuilder.core.set.has([
builder_1.MolScriptBuilder.set('sphere', 'gaussian'), builder_1.MolScriptBuilder.ammp('objectPrimitive')
])
})
]), { category: StructureSelectionCategory.Type });
const ring = StructureSelectionQuery('Rings in Residues', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.rings()
]), { category: StructureSelectionCategory.Residue });
const aromaticRing = StructureSelectionQuery('Aromatic Rings in Residues', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.rings({ 'only-aromatic': true })
]), { category: StructureSelectionCategory.Residue });
const surroundings = StructureSelectionQuery('Surrounding Residues (5 \u212B) of Selection', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.exceptBy({
0: builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({
0: builder_1.MolScriptBuilder.internal.generator.current(),
radius: 5,
'as-whole-residues': true
}),
by: builder_1.MolScriptBuilder.internal.generator.current()
})
]), {
description: 'Select residues within 5 \u212B of the current selection.',
category: StructureSelectionCategory.Manipulate,
referencesCurrent: true
});
const surroundingLigands = StructureSelectionQuery('Surrounding Ligands (5 \u212B) of Selection', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.surroundingLigands({
0: builder_1.MolScriptBuilder.internal.generator.current(),
radius: 5,
'include-water': true
})
]), {
description: 'Select ligand components within 5 \u212B of the current selection.',
category: StructureSelectionCategory.Manipulate,
referencesCurrent: true
});
const surroundingAtoms = StructureSelectionQuery('Surrounding Atoms (5 \u212B) of Selection', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.exceptBy({
0: builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({
0: builder_1.MolScriptBuilder.internal.generator.current(),
radius: 5,
'as-whole-residues': false
}),
by: builder_1.MolScriptBuilder.internal.generator.current()
})
]), {
description: 'Select atoms within 5 \u212B of the current selection.',
category: StructureSelectionCategory.Manipulate,
referencesCurrent: true
});
const complement = StructureSelectionQuery('Inverse / Complement of Selection', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.exceptBy({
0: builder_1.MolScriptBuilder.struct.generator.all(),
by: builder_1.MolScriptBuilder.internal.generator.current()
})
]), {
description: 'Select everything not in the current selection.',
category: StructureSelectionCategory.Manipulate,
referencesCurrent: true
});
const covalentlyBonded = StructureSelectionQuery('Residues Covalently Bonded to Selection', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.includeConnected({
0: builder_1.MolScriptBuilder.internal.generator.current(), 'layer-count': 1, 'as-whole-residues': true
})
]), {
description: 'Select residues covalently bonded to current selection.',
category: StructureSelectionCategory.Manipulate,
referencesCurrent: true
});
const covalentlyBondedComponent = StructureSelectionQuery('Covalently Bonded Component', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.includeConnected({
0: builder_1.MolScriptBuilder.internal.generator.current(), 'fixed-point': true
})
]), {
description: 'Select covalently bonded component based on current selection.',
category: StructureSelectionCategory.Manipulate,
referencesCurrent: true
});
const covalentlyOrMetallicBonded = StructureSelectionQuery('Residues with Cov. or Metallic Bond to Selection', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.includeConnected({
0: builder_1.MolScriptBuilder.internal.generator.current(),
'layer-count': 1,
'as-whole-residues': true,
'bond-test': builder_1.MolScriptBuilder.core.flags.hasAny([
builder_1.MolScriptBuilder.struct.bondProperty.flags(),
builder_1.MolScriptBuilder.core.type.bitflags([
1 /* BondType.Flag.Covalent */ | 2 /* BondType.Flag.MetallicCoordination */
])
])
})
]), {
description: 'Select residues with covalent or metallic bond to current selection.',
category: StructureSelectionCategory.Manipulate,
referencesCurrent: true
});
const wholeResidues = StructureSelectionQuery('Whole Residues of Selection', builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.modifier.wholeResidues({
0: builder_1.MolScriptBuilder.internal.generator.current()
})
]), {
description: 'Expand current selection to whole residues.',
category: StructureSelectionCategory.Manipulate,
referencesCurrent: true
});
const StandardAminoAcids = [
[['HIS'], 'Histidine'],
[['ARG'], 'Arginine'],
[['LYS'], 'Lysine'],
[['ILE'], 'Isoleucine'],
[['PHE'], 'Phenylalanine'],
[['LEU'], 'Leucine'],
[['TRP'], 'Tryptophan'],
[['ALA'], 'Alanine'],
[['MET'], 'Methionine'],
[['PRO'], 'Proline'],
[['CYS'], 'Cysteine'],
[['ASN'], 'Asparagine'],
[['VAL'], 'Valine'],
[['GLY'], 'Glycine'],
[['SER'], 'Serine'],
[['GLN'], 'Glutamine'],
[['TYR'], 'Tyrosine'],
[['ASP'], 'Aspartic Acid'],
[['GLU'], 'Glutamic Acid'],
[['THR'], 'Threonine'],
[['SEC'], 'Selenocysteine'],
[['PYL'], 'Pyrrolysine'],
[['UNK'], 'Unknown'],
].sort((a, b) => a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0);
const StandardNucleicBases = [
[['A', 'DA'], 'Adenosine'],
[['C', 'DC'], 'Cytidine'],
[['T', 'DT'], 'Thymidine'],
[['G', 'DG'], 'Guanosine'],
[['I', 'DI'], 'Inosine'],
[['U', 'DU'], 'Uridine'],
[['N', 'DN'], 'Unknown'],
].sort((a, b) => a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0);
function ResidueQuery([names, label], category, priority = 0) {
const description = names.length === 1 && !StandardResidues.has(names[0])
? `[${names[0]}] ${label}`
: `${label} (${names.join(', ')})`;
return StructureSelectionQuery(description, builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'residue-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set(...names), builder_1.MolScriptBuilder.ammp('auth_comp_id')])
})
]), { category, priority, description });
}
function ElementSymbolQuery([names, label], category, priority) {
const description = `${label} (${names.join(', ')})`;
return StructureSelectionQuery(description, builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'atom-test': builder_1.MolScriptBuilder.core.set.has([builder_1.MolScriptBuilder.set(...names), builder_1.MolScriptBuilder.acp('elementSymbol')])
})
]), { category, priority, description });
}
function EntityDescriptionQuery([names, label], category, priority) {
const description = `${label}`;
return StructureSelectionQuery(`${label}`, builder_1.MolScriptBuilder.struct.modifier.union([
builder_1.MolScriptBuilder.struct.generator.atomGroups({
'entity-test': builder_1.MolScriptBuilder.core.list.equal([builder_1.MolScriptBuilder.list(...names), builder_1.MolScriptBuilder.ammp('entityDescription')])
})
]), { category, priority, description });
}
const StandardResidues = set_1.SetUtils.unionMany(types_1.AminoAcidNamesL, types_1.RnaBaseNames, types_1.DnaBaseNames, types_1.WaterNames);
function getElementQueries(structures) {
const uniqueElements = new Set();
for (const structure of structures) {
structure.uniqueElementSymbols.forEach(e => uniqueElements.add(e));
}
const queries = [];
uniqueElements.forEach(e => {
const label = types_2.ElementNames[e] || e;
queries.push(ElementSymbolQuery([[e], label], 'Element Symbol', 0));
});
return queries;
}
function getNonStandardResidueQueries(structures) {
const residueLabels = new Map();
const uniqueResidues = new Set();
for (const structure of structures) {
structure.uniqueResidueNames.forEach(r => uniqueResidues.add(r));
for (const m of structure.models) {
structure.uniqueResidueNames.forEach(r => {
const comp = m.properties.chemicalComponentMap.get(r);
if (comp)
residueLabels.set(r, comp.name);
});
}
}
const queries = [];
set_1.SetUtils.difference(uniqueResidues, StandardResidues).forEach(r => {
const label = residueLabels.get(r) || r;
queries.push(ResidueQuery([[r], label], 'Ligand/Non-standard Residue', 200));
});
return queries;
}
function getPolymerAndBranchedEntityQueries(structures) {
const uniqueEntities = new Map();
const l = structure_1.StructureElement.Location.create();
for (const structure of structures) {
l.structure = structure;
for (const ug of structure.unitSymmetryGroups) {
l.unit = ug.units[0];
l.element = ug.elements[0];
const entityType = structure_1.StructureProperties.entity.type(l);
if (entityType === 'polymer' || entityType === 'branched') {
const description = structure_1.StructureProperties.entity.pdbx_description(l);
uniqueEntities.set(description.join(', '), description);
}
}
}
const queries = [];
uniqueEntities.forEach((v, k) => {
queries.push(EntityDescriptionQuery([v, k], 'Polymer/Carbohydrate Entities', 300));
});
return queries;
}
function applyBuiltInSelection(to, query, customTag) {
return to.apply(transforms_1.StateTransforms.Model.StructureSelectionFromExpression, { expression: exports.StructureSelectionQueries[query].expression, label: exports.StructureSelectionQueries[query].label }, { tags: customTag ? [query, customTag] : [query] });
}
exports.StructureSelectionQueries = {
all,
current,
polymer,
trace,
backbone,
sidechain,
sidechainWithTrace,
protein,
nucleic,
helix,
beta,
water,
ion,
lipid,
branched,
branchedPlusConnected,
branchedConnectedOnly,
ligand,
ligandPlusConnected,
ligandConnectedOnly,
connectedOnly,
disulfideBridges,
nosBridges,
nonStandardPolymer,
coarse,
ring,
aromaticRing,
surroundings,
surroundingLigands,
surroundingAtoms,
complement,
covalentlyBonded,
covalentlyOrMetallicBonded,
covalentlyBondedComponent,
wholeResidues,
};
class StructureSelectionQueryRegistry {
add(q) {
this.list.push(q);
this.options.push([q, q.label, q.category]);
this.version += 1;
}
remove(q) {
const idx = this.list.indexOf(q);
if (idx !== -1) {
this.list.splice(idx, 1);
this.options.splice(idx, 1);
this.version += 1;
}
}
constructor() {
this.list = [];
this.options = [];
this.version = 1;
// add built-in
this.list.push(...Object.values(exports.StructureSelectionQueries), ...StandardAminoAcids.map(v => ResidueQuery(v, StructureSelectionCategory.AminoAcid)), ...StandardNucleicBases.map(v => ResidueQuery(v, StructureSelectionCategory.NucleicBase)));
this.options.push(...this.list.map(q => [q, q.label, q.category]));
}
}
exports.StructureSelectionQueryRegistry = StructureSelectionQueryRegistry;