molstar 3.0.0 → 3.0.1

package/lib/commonjs/mol-script/language/symbol-table/structure-query.js

@@ -1,281 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2019 Mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.structureQuery = exports.Types = void 0;
-var tslib_1 = require("tslib");
-var type_1 = require("../type");
-var Core = (0, tslib_1.__importStar)(require("./core"));
-var symbol_1 = require("../symbol");
-var helpers_1 = require("../helpers");
-var Types;
-(function (Types) {
-    Types.ElementSymbol = type_1.Type.Value('Structure', 'ElementSymbol');
-    Types.AtomName = type_1.Type.Value('Structure', 'AtomName');
-    Types.BondFlag = type_1.Type.OneOf('Structure', 'BondFlag', type_1.Type.Str, ['covalent', 'metallic', 'ion', 'hydrogen', 'sulfide', 'computed', 'aromatic']);
-    Types.BondFlags = Core.Types.Flags(Types.BondFlag, 'BondFlags');
-    Types.SecondaryStructureFlag = type_1.Type.OneOf('Structure', 'SecondaryStructureFlag', type_1.Type.Str, ['alpha', 'beta', '3-10', 'pi', 'sheet', 'strand', 'helix', 'turn', 'none']);
-    Types.SecondaryStructureFlags = Core.Types.Flags(Types.SecondaryStructureFlag, 'SecondaryStructureFlag');
-    Types.RingFingerprint = type_1.Type.Value('Structure', 'RingFingerprint');
-    Types.EntityType = type_1.Type.OneOf('Structure', 'EntityType', type_1.Type.Str, ['polymer', 'non-polymer', 'water', 'branched']);
-    Types.EntitySubtype = type_1.Type.OneOf('Structure', 'EntitySubtype', type_1.Type.Str, ['other', 'polypeptide(D)', 'polypeptide(L)', 'polydeoxyribonucleotide', 'polyribonucleotide', 'polydeoxyribonucleotide/polyribonucleotide hybrid', 'cyclic-pseudo-peptide', 'peptide nucleic acid', 'oligosaccharide']);
-    Types.ObjectPrimitive = type_1.Type.OneOf('Structure', 'ObjectPrimitive', type_1.Type.Str, ['atomistic', 'sphere', 'gaussian', 'other']);
-    Types.ResidueId = type_1.Type.Value('Structure', 'ResidueId');
-    Types.ElementSet = type_1.Type.Value('Structure', 'ElementSet');
-    Types.ElementSelection = type_1.Type.Value('Structure', 'ElementSelection');
-    Types.ElementReference = type_1.Type.Value('Structure', 'ElementReference');
-    Types.ElementSelectionQuery = Core.Types.Fn(Types.ElementSelection, 'ElementSelectionQuery');
-})(Types = exports.Types || (exports.Types = {}));
-var type = {
-    '@header': 'Types',
-    elementSymbol: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({ 0: (0, symbol_1.Argument)(type_1.Type.Str) }), Types.ElementSymbol, 'Create element symbol representation from a string value.'),
-    atomName: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({ 0: (0, symbol_1.Argument)(type_1.Type.AnyValue) }), Types.AtomName, 'Convert a value to an atom name.'),
-    entityType: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({ 0: (0, symbol_1.Argument)(Types.EntityType) }), Types.EntityType, "Create normalized representation of entity type: ".concat(type_1.Type.oneOfValues(Types.EntityType).join(', '), ".")),
-    bondFlags: (0, helpers_1.symbol)(symbol_1.Arguments.List(Types.BondFlag), Types.BondFlags, "Create bond flags representation from a list of strings. Allowed flags: ".concat(type_1.Type.oneOfValues(Types.BondFlag).join(', '), ".")),
-    ringFingerprint: (0, helpers_1.symbol)(symbol_1.Arguments.List(Types.ElementSymbol, { nonEmpty: true }), Types.RingFingerprint, 'Create ring fingerprint from the supplied atom element list.'),
-    secondaryStructureFlags: (0, helpers_1.symbol)(symbol_1.Arguments.List(Types.SecondaryStructureFlag), Types.SecondaryStructureFlags, "Create secondary structure flags representation from a list of strings. Allowed flags: ".concat(type_1.Type.oneOfValues(Types.SecondaryStructureFlag).join(', '), ".")),
-    authResidueId: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(type_1.Type.Str, { description: 'auth_asym_id' }),
-        1: (0, symbol_1.Argument)(type_1.Type.Num, { description: 'auth_seq_id' }),
-        2: (0, symbol_1.Argument)(type_1.Type.Str, { description: 'pdbx_PDB_ins_code', isOptional: true })
-    }), Types.ResidueId, "Residue identifier based on \"auth_\" annotation."),
-    labelResidueId: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(type_1.Type.Str, { description: 'label_entity_id' }),
-        1: (0, symbol_1.Argument)(type_1.Type.Str, { description: 'label_asym_id' }),
-        2: (0, symbol_1.Argument)(type_1.Type.Num, { description: 'label_seq_id' }),
-        3: (0, symbol_1.Argument)(type_1.Type.Str, { description: 'pdbx_PDB_ins_code', isOptional: true })
-    }), Types.ResidueId, "Residue identifier based on mmCIF's \"label_\" annotation.")
-};
-var slot = {
-    '@header': 'Iteration Slots',
-    element: (0, helpers_1.symbol)(symbol_1.Arguments.None, Types.ElementReference, 'A reference to the current element.'),
-    elementSetReduce: (0, helpers_1.symbol)(symbol_1.Arguments.None, type_1.Type.Variable('a', type_1.Type.AnyValue, true), 'Current value of the element set reducer.')
-};
-var generator = {
-    '@header': 'Generators',
-    all: (0, helpers_1.symbol)(symbol_1.Arguments.None, Types.ElementSelectionQuery, 'The entire structure.'),
-    atomGroups: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        'entity-test': (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true, defaultValue: true, description: 'Test for the 1st atom of every entity' }),
-        'chain-test': (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true, defaultValue: true, description: 'Test for the 1st atom of every chain' }),
-        'residue-test': (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true, defaultValue: true, description: 'Test for the 1st atom every residue' }),
-        'atom-test': (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true, defaultValue: true }),
-        'group-by': (0, symbol_1.Argument)(type_1.Type.Any, { isOptional: true, defaultValue: "atom-key", description: 'Group atoms to sets based on this property. Default: each atom has its own set' }),
-    }), Types.ElementSelectionQuery, 'Return all atoms for which the tests are satisfied, grouped into sets.'),
-    bondedAtomicPairs: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true, defaultValue: 'true for covalent bonds', description: 'Test each bond with this predicate. Each bond is visited twice with swapped atom order.' }),
-        // TODO: shoud we support this or just use queryEach to get similar behavior
-        // 'group-by': Argument(Type.Any, { isOptional: true, defaultValue: ``, description: 'Group the bonds using the privided value' }),
-    }), Types.ElementSelectionQuery, 'Return all pairs of atoms for which the test is satisfied.'),
-    rings: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        'fingerprint': (0, symbol_1.Argument)(Types.RingFingerprint, { isOptional: true }),
-        'only-aromatic': (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true, defaultValue: false }),
-    }), Types.ElementSelectionQuery, 'Return all rings or those with the specified fingerprint and/or only aromatic rings.'),
-    queryInSelection: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        query: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        'in-complement': (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true, defaultValue: false })
-    }), Types.ElementSelectionQuery, 'Executes query only on atoms that are in the source selection.'),
-    empty: (0, helpers_1.symbol)(symbol_1.Arguments.None, Types.ElementSelectionQuery, 'Nada.'),
-};
-var modifier = {
-    '@header': 'Selection Modifications',
-    queryEach: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        query: (0, symbol_1.Argument)(Types.ElementSelectionQuery)
-    }), Types.ElementSelectionQuery, 'Query every atom set in the input selection separately.'),
-    intersectBy: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        by: (0, symbol_1.Argument)(Types.ElementSelectionQuery)
-    }), Types.ElementSelectionQuery, 'Intersect each atom set from the first sequence from atoms in the second one.'),
-    exceptBy: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        by: (0, symbol_1.Argument)(Types.ElementSelectionQuery)
-    }), Types.ElementSelectionQuery, "Remove all atoms from 'selection' that occur in 'by'."),
-    unionBy: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        by: (0, symbol_1.Argument)(Types.ElementSelectionQuery)
-    }), Types.ElementSelectionQuery, 'For each atom set A in the orginal sequence, combine all atoms sets in the target selection that intersect with A.'),
-    union: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery)
-    }), Types.ElementSelectionQuery, 'Collects all atom sets in the sequence into a single atom set.'),
-    cluster: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        'min-distance': (0, symbol_1.Argument)(type_1.Type.Num, { isOptional: true, defaultValue: 0 }),
-        'max-distance': (0, symbol_1.Argument)(type_1.Type.Num),
-        'min-size': (0, symbol_1.Argument)(type_1.Type.Num, { description: 'Minimal number of sets to merge, must be at least 2', isOptional: true, defaultValue: 2 }),
-        'max-size': (0, symbol_1.Argument)(type_1.Type.Num, { description: 'Maximal number of sets to merge, if not set, no limit', isOptional: true }),
-    }), Types.ElementSelectionQuery, 'Combines atom sets that have mutual distance in the interval [min-radius, max-radius]. Minimum/maximum size determines how many atom sets can be combined.'),
-    includeSurroundings: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        radius: (0, symbol_1.Argument)(type_1.Type.Num),
-        'atom-radius': (0, symbol_1.Argument)(type_1.Type.Num, { isOptional: true, defaultValue: 0, description: 'Value added to each atom before the distance check, for example VDW radius. Using this argument is computationally demanding.' }),
-        'as-whole-residues': (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true })
-    }), Types.ElementSelectionQuery, 'For each atom set in the selection, include all surrouding atoms/residues that are within the specified radius.'),
-    surroundingLigands: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        radius: (0, symbol_1.Argument)(type_1.Type.Num),
-        'include-water': (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true, defaultValue: true })
-    }), Types.ElementSelectionQuery, 'Find all ligands components around the source query.'),
-    includeConnected: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        'bond-test': (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true, defaultValue: 'true for covalent bonds' }),
-        'layer-count': (0, symbol_1.Argument)(type_1.Type.Num, { isOptional: true, defaultValue: 1, description: 'Number of bonded layers to include.' }),
-        'fixed-point': (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true, defaultValue: false, description: 'Continue adding layers as long as new connections exist.' }),
-        'as-whole-residues': (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true })
-    }), Types.ElementSelectionQuery, 'Pick all atom sets that are connected to the target.'),
-    wholeResidues: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-    }), Types.ElementSelectionQuery, 'Expand the selection to whole residues.'),
-    expandProperty: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        property: (0, symbol_1.Argument)(type_1.Type.AnyValue)
-    }), Types.ElementSelectionQuery, 'To each atom set in the selection, add all atoms that have the same property value that was already present in the set.')
-};
-var filter = {
-    '@header': 'Selection Filters',
-    pick: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        test: (0, symbol_1.Argument)(type_1.Type.Bool)
-    }), Types.ElementSelectionQuery, 'Pick all atom sets that satisfy the test.'),
-    first: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery)
-    }), Types.ElementSelectionQuery, 'Take the 1st atom set in the sequence.'),
-    withSameAtomProperties: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        source: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        property: (0, symbol_1.Argument)(type_1.Type.Any)
-    }), Types.ElementSelectionQuery, 'Pick all atom sets for which the set of given atom properties is a subset of the source properties.'),
-    intersectedBy: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        by: (0, symbol_1.Argument)(Types.ElementSelectionQuery)
-    }), Types.ElementSelectionQuery, 'Pick all atom sets that have non-zero intersection with the target.'),
-    within: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        target: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        'min-radius': (0, symbol_1.Argument)(type_1.Type.Num, { isOptional: true, defaultValue: 0 }),
-        'max-radius': (0, symbol_1.Argument)(type_1.Type.Num),
-        'atom-radius': (0, symbol_1.Argument)(type_1.Type.Num, { isOptional: true, defaultValue: 0, description: 'Value added to each atom before the distance check, for example VDW radius. Using this argument is computationally demanding.' }),
-        invert: (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true, defaultValue: false, description: 'If true, pick only atom sets that are further than the specified radius.' }),
-    }), Types.ElementSelectionQuery, 'Pick all atom sets from selection that have any atom within the radius of any atom from target.'),
-    isConnectedTo: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        target: (0, symbol_1.Argument)(Types.ElementSelectionQuery),
-        'bond-test': (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true, defaultValue: 'true for covalent bonds' }),
-        disjunct: (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true, defaultValue: true, description: 'If true, there must exist a bond to an atom that lies outside the given atom set to pass test.' }),
-        invert: (0, symbol_1.Argument)(type_1.Type.Bool, { isOptional: true, defaultValue: false, description: 'If true, return atom sets that are not connected.' })
-    }), Types.ElementSelectionQuery, 'Pick all atom sets that are connected to the target.'),
-};
-var combinator = {
-    '@header': 'Selection Combinators',
-    intersect: (0, helpers_1.symbol)(symbol_1.Arguments.List(Types.ElementSelectionQuery), Types.ElementSelectionQuery, 'Return all unique atom sets that appear in all of the source selections.'),
-    merge: (0, helpers_1.symbol)(symbol_1.Arguments.List(Types.ElementSelectionQuery), Types.ElementSelectionQuery, 'Merges multiple selections into a single one. Only unique atom sets are kept.'),
-    distanceCluster: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        matrix: (0, symbol_1.Argument)(Core.Types.List(Core.Types.List(type_1.Type.Num)), { description: 'Distance matrix, represented as list of rows (num[][])). Lower triangle is min distance, upper triangle is max distance.' }),
-        selections: (0, symbol_1.Argument)(Core.Types.List(Types.ElementSelectionQuery), { description: 'A list of held selections.' })
-    }), Types.ElementSelectionQuery, 'Pick combinations of atom sets from the source sequences that are mutually within distances specified by a matrix.')
-};
-var atomSet = {
-    '@header': 'Atom Sets',
-    atomCount: (0, helpers_1.symbol)(symbol_1.Arguments.None, type_1.Type.Num),
-    countQuery: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Types.ElementSelectionQuery)
-    }), type_1.Type.Num, 'Counts the number of occurences of a specific query inside the current atom set.'),
-    reduce: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        initial: (0, symbol_1.Argument)(type_1.Type.Variable('a', type_1.Type.AnyValue, true), { description: 'Initial value assigned to slot.atom-set-reduce. Current atom is set to the 1st atom of the current set for this.' }),
-        value: (0, symbol_1.Argument)(type_1.Type.Variable('a', type_1.Type.AnyValue, true), { description: 'Expression executed for each atom in the set' })
-    }), type_1.Type.Variable('a', type_1.Type.AnyValue, true), 'Execute the value expression for each atom in the current atom set and return the result. Works the same way as Array.reduce in JavaScript (``result = value(value(...value(initial)))``)'),
-    propertySet: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-        0: (0, symbol_1.Argument)(Core.Types.ConstrainedVar),
-    }), Core.Types.Set(Core.Types.ConstrainedVar), 'Returns a set with all values of the given property in the current atom set.'),
-};
-var atomProperty = {
-    '@header': 'Atom Properties',
-    core: {
-        '@header': 'Core Properties',
-        elementSymbol: atomProp(Types.ElementSymbol),
-        vdw: atomProp(type_1.Type.Num, 'Van der Waals radius'),
-        mass: atomProp(type_1.Type.Num, 'Atomic weight'),
-        atomicNumber: atomProp(type_1.Type.Num, 'Atomic number'),
-        x: atomProp(type_1.Type.Num, 'Cartesian X coordinate'),
-        y: atomProp(type_1.Type.Num, 'Cartesian Y coordinate'),
-        z: atomProp(type_1.Type.Num, 'Cartesian Z coordinate'),
-        atomKey: atomProp(type_1.Type.AnyValue, 'Unique value for each atom. Main use case is grouping of atoms.'),
-        bondCount: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
-            0: (0, symbol_1.Argument)(Types.ElementReference, { isOptional: true, defaultValue: 'slot.current-atom' }),
-            flags: (0, symbol_1.Argument)(Types.BondFlags, { isOptional: true, defaultValue: 'covalent' }),
-        }), type_1.Type.Num, 'Number of bonds (by default only covalent bonds are counted).'),
-        sourceIndex: atomProp(type_1.Type.Num, 'Index of the atom/element in the input file.'),
-        operatorName: atomProp(type_1.Type.Str, 'Name of the symmetry operator applied to this element.'),
-        modelIndex: atomProp(type_1.Type.Num, 'Index of the model in the input file.'),
-        modelLabel: atomProp(type_1.Type.Str, 'Label/header of the model in the input file.')
-    },
-    topology: {
-        connectedComponentKey: atomProp(type_1.Type.AnyValue, 'Unique value for each connected component.')
-    },
-    macromolecular: {
-        '@header': 'Macromolecular Properties (derived from the mmCIF format)',
-        authResidueId: atomProp(Types.ResidueId, "type.auth-residue-id symbol executed on current atom's residue"),
-        labelResidueId: atomProp(Types.ResidueId, "type.label-residue-id symbol executed on current atom's residue"),
-        residueKey: atomProp(type_1.Type.AnyValue, 'Unique value for each tuple ``(label_entity_id,auth_asym_id, auth_seq_id, pdbx_PDB_ins_code)``, main use case is grouping of atoms'),
-        chainKey: atomProp(type_1.Type.AnyValue, 'Unique value for each tuple ``(label_entity_id, auth_asym_id)``, main use case is grouping of atoms'),
-        entityKey: atomProp(type_1.Type.AnyValue, 'Unique value for each tuple ``label_entity_id``, main use case is grouping of atoms'),
-        isHet: atomProp(type_1.Type.Bool, 'Equivalent to atom_site.group_PDB !== ATOM'),
-        id: atomProp(type_1.Type.Num, '_atom_site.id'),
-        label_atom_id: atomProp(Types.AtomName),
-        label_alt_id: atomProp(type_1.Type.Str),
-        label_comp_id: atomProp(type_1.Type.Str),
-        label_asym_id: atomProp(type_1.Type.Str),
-        label_entity_id: atomProp(type_1.Type.Str),
-        label_seq_id: atomProp(type_1.Type.Num),
-        auth_atom_id: atomProp(Types.AtomName),
-        auth_comp_id: atomProp(type_1.Type.Str),
-        auth_asym_id: atomProp(type_1.Type.Str),
-        auth_seq_id: atomProp(type_1.Type.Num),
-        pdbx_PDB_ins_code: atomProp(type_1.Type.Str),
-        pdbx_formal_charge: atomProp(type_1.Type.Num),
-        occupancy: atomProp(type_1.Type.Num),
-        B_iso_or_equiv: atomProp(type_1.Type.Num),
-        entityType: atomProp(Types.EntityType, 'Type of the entity as defined in mmCIF (polymer, non-polymer, branched, water)'),
-        entitySubtype: atomProp(Types.EntitySubtype, 'Subtype of the entity as defined in mmCIF _entity_poly.type and _pdbx_entity_branch.type (other, polypeptide(D), polypeptide(L), polydeoxyribonucleotide, polyribonucleotide, polydeoxyribonucleotide/polyribonucleotide hybrid, cyclic-pseudo-peptide, peptide nucleic acid, oligosaccharide)'),
-        entityPrdId: atomProp(type_1.Type.Str, "The PRD ID of the entity."),
-        entityDescription: atomProp(Core.Types.List(type_1.Type.Str)),
-        objectPrimitive: atomProp(Types.ObjectPrimitive, 'Type of the primitive object used to model this segment as defined in mmCIF/IHM (atomistic, sphere, gaussian, other)'),
-        secondaryStructureKey: atomProp(type_1.Type.AnyValue, 'Unique value for each secondary structure element.'),
-        secondaryStructureFlags: atomProp(Types.SecondaryStructureFlags),
-        isModified: atomProp(type_1.Type.Bool, 'True if the atom belongs to modification of a standard residue.'),
-        modifiedParentName: atomProp(type_1.Type.Str, "'3-letter' code of the modifed parent residue."),
-        isNonStandard: atomProp(type_1.Type.Bool, 'True if this is a non-standard residue.'),
-        chemCompType: atomProp(type_1.Type.Str, "Type of the chemical component as defined in mmCIF."),
-    }
-};
-var bondProperty = {
-    '@header': 'Bond Properties',
-    flags: bondProp(Types.BondFlags),
-    order: bondProp(type_1.Type.Num),
-    length: bondProp(type_1.Type.Num),
-    atomA: bondProp(Types.ElementReference),
-    atomB: bondProp(Types.ElementReference)
-};
-function atomProp(type, description) {
-    return (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({ 0: (0, symbol_1.Argument)(Types.ElementReference, { isOptional: true, defaultValue: 'slot.current-atom' }) }), type, description);
-}
-function bondProp(type, description) {
-    return (0, helpers_1.symbol)(symbol_1.Arguments.None, type, description);
-}
-exports.structureQuery = {
-    '@header': 'Structure Queries',
-    type: type,
-    slot: slot,
-    generator: generator,
-    modifier: modifier,
-    filter: filter,
-    combinator: combinator,
-    atomSet: atomSet,
-    atomProperty: atomProperty,
-    bondProperty: bondProperty
-};
-//# sourceMappingURL=structure-query.js.map