molstar 3.0.0 → 3.0.1

package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js

@@ -1,723 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019-2021 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.applyBuiltInSelection = exports.getPolymerAndBranchedEntityQueries = exports.getNonStandardResidueQueries = exports.getElementQueries = exports.EntityDescriptionQuery = exports.ElementSymbolQuery = exports.ResidueQuery = exports.StructureSelectionQuery = exports.StructureSelectionCategory = void 0;
-var tslib_1 = require("tslib");
-var structure_1 = require("../../mol-model/structure");
-var types_1 = require("../../mol-model/structure/model/types");
-var builder_1 = require("../../mol-script/language/builder");
-var compiler_1 = require("../../mol-script/runtime/query/compiler");
-var set_1 = require("../../mol-util/set");
-var transforms_1 = require("../transforms");
-var types_2 = require("../../mol-model/structure/model/properties/atomic/types");
-var 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 || (exports.StructureSelectionCategory = {}));
-function StructureSelectionQuery(label, expression, props) {
-    var _a;
-    if (props === void 0) { props = {}; }
-    var _query;
-    return {
-        label: label,
-        expression: 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,
-        getSelection: function (plugin, runtime, structure) {
-            return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-                var current, currentSelection;
-                return (0, tslib_1.__generator)(this, function (_a) {
-                    switch (_a.label) {
-                        case 0:
-                            current = plugin.managers.structure.selection.getStructure(structure);
-                            currentSelection = current ? structure_1.StructureSelection.Sequence(structure, [current]) : structure_1.StructureSelection.Empty(structure);
-                            if (!props.ensureCustomProperties) return [3 /*break*/, 2];
-                            return [4 /*yield*/, props.ensureCustomProperties({ runtime: runtime, assetManager: plugin.managers.asset }, structure)];
-                        case 1:
-                            _a.sent();
-                            _a.label = 2;
-                        case 2:
-                            if (!_query)
-                                _query = (0, compiler_1.compile)(expression);
-                            return [2 /*return*/, _query(new structure_1.QueryContext(structure, { currentSelection: currentSelection }))];
-                    }
-                });
-            });
-        }
-    };
-}
-exports.StructureSelectionQuery = StructureSelectionQuery;
-var all = StructureSelectionQuery('All', builder_1.MolScriptBuilder.struct.generator.all(), { category: '', priority: 1000 });
-var current = StructureSelectionQuery('Current Selection', builder_1.MolScriptBuilder.internal.generator.current(), { category: '', referencesCurrent: true });
-var 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 });
-var 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 });
-var _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')
-    ])
-]);
-var _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
- */
-var _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
-var 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.apply(builder_1.MolScriptBuilder, 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.apply(builder_1.MolScriptBuilder, set_1.SetUtils.toArray(types_1.NucleicBackboneAtoms)), builder_1.MolScriptBuilder.ammp('label_atom_id')])
-            })
-        ])
-    ])
-]), { category: StructureSelectionCategory.Structure });
-// TODO maybe pre-calculate sidechain atom property
-var 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.apply(builder_1.MolScriptBuilder, 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.apply(builder_1.MolScriptBuilder, set_1.SetUtils.toArray(types_1.NucleicBackboneAtoms)), builder_1.MolScriptBuilder.ammp('label_atom_id')])
-                    ])
-                ])
-            })
-        ])
-    ])
-]), { category: StructureSelectionCategory.Structure });
-// TODO maybe pre-calculate sidechain atom property
-var 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.apply(builder_1.MolScriptBuilder, 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.apply(builder_1.MolScriptBuilder, 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 });
-var protein = StructureSelectionQuery('Protein', builder_1.MolScriptBuilder.struct.modifier.union([
-    builder_1.MolScriptBuilder.struct.generator.atomGroups({ 'entity-test': _proteinEntityTest })
-]), { category: StructureSelectionCategory.Type });
-var nucleic = StructureSelectionQuery('Nucleic', builder_1.MolScriptBuilder.struct.modifier.union([
-    builder_1.MolScriptBuilder.struct.generator.atomGroups({ 'entity-test': _nucleiEntityTest })
-]), { category: StructureSelectionCategory.Type });
-var 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 /* Helix */])
-        ])
-    })
-]), {
-    category: StructureSelectionCategory.Structure,
-    ensureCustomProperties: function (ctx, structure) {
-        return secondary_structure_1.SecondaryStructureProvider.attach(ctx, structure);
-    }
-});
-var 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 /* Beta */])
-        ])
-    })
-]), {
-    category: StructureSelectionCategory.Structure,
-    ensureCustomProperties: function (ctx, structure) {
-        return secondary_structure_1.SecondaryStructureProvider.attach(ctx, structure);
-    }
-});
-var 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 });
-var 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 });
-var 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 });
-var 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 });
-var 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 });
-var 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 });
-var 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.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.apply(builder_1.MolScriptBuilder, set_1.SetUtils.toArray(types_1.PolymerNames)),
-                    builder_1.MolScriptBuilder.ammp('label_comp_id')
-                ])
-            })
-        ])
-    })
-]), { category: StructureSelectionCategory.Type });
-// don't include branched entities as they have their own link representation
-var 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 /* Covalent */ | 2 /* MetallicCoordination */
-                    ])
-                ])
-            })
-        ]),
-        by: branched.expression
-    })
-]), { category: StructureSelectionCategory.Internal, isHidden: true });
-var 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
-var 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 });
-var 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 /* Disulfide */])
-                        ])
-                    })
-                ])
-            ])
-        ])
-    ])
-]), { category: StructureSelectionCategory.Bond });
-var 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 });
-var 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 });
-var 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 });
-var ring = StructureSelectionQuery('Rings in Residues', builder_1.MolScriptBuilder.struct.modifier.union([
-    builder_1.MolScriptBuilder.struct.generator.rings()
-]), { category: StructureSelectionCategory.Residue });
-var aromaticRing = StructureSelectionQuery('Aromatic Rings in Residues', builder_1.MolScriptBuilder.struct.modifier.union([
-    builder_1.MolScriptBuilder.struct.generator.rings({ 'only-aromatic': true })
-]), { category: StructureSelectionCategory.Residue });
-var 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
-});
-var 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
-});
-var 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
-});
-var 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
-});
-var 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
-});
-var 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
-});
-var 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 /* Covalent */ | 2 /* MetallicCoordination */
-            ])
-        ])
-    })
-]), {
-    description: 'Select residues with covalent or metallic bond to current selection.',
-    category: StructureSelectionCategory.Manipulate,
-    referencesCurrent: true
-});
-var 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
-});
-var 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(function (a, b) { return a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0; });
-var StandardNucleicBases = [
-    [['A', 'DA'], 'Adenosine'],
-    [['C', 'DC'], 'Cytidine'],
-    [['T', 'DT'], 'Thymidine'],
-    [['G', 'DG'], 'Guanosine'],
-    [['I', 'DI'], 'Inosine'],
-    [['U', 'DU'], 'Uridine'],
-    [['N', 'DN'], 'Unknown'],
-].sort(function (a, b) { return a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0; });
-function ResidueQuery(_a, category, priority) {
-    var names = _a[0], label = _a[1];
-    if (priority === void 0) { priority = 0; }
-    var description = names.length === 1 && !StandardResidues.has(names[0])
-        ? "[".concat(names[0], "] ").concat(label)
-        : "".concat(label, " (").concat(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.apply(builder_1.MolScriptBuilder, names), builder_1.MolScriptBuilder.ammp('auth_comp_id')])
-        })
-    ]), { category: category, priority: priority, description: description });
-}
-exports.ResidueQuery = ResidueQuery;
-function ElementSymbolQuery(_a, category, priority) {
-    var names = _a[0], label = _a[1];
-    var description = "".concat(label, " (").concat(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.apply(builder_1.MolScriptBuilder, names), builder_1.MolScriptBuilder.acp('elementSymbol')])
-        })
-    ]), { category: category, priority: priority, description: description });
-}
-exports.ElementSymbolQuery = ElementSymbolQuery;
-function EntityDescriptionQuery(_a, category, priority) {
-    var names = _a[0], label = _a[1];
-    var description = "".concat(label);
-    return StructureSelectionQuery("".concat(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.apply(builder_1.MolScriptBuilder, names), builder_1.MolScriptBuilder.ammp('entityDescription')])
-        })
-    ]), { category: category, priority: priority, description: description });
-}
-exports.EntityDescriptionQuery = EntityDescriptionQuery;
-var StandardResidues = set_1.SetUtils.unionMany(types_1.AminoAcidNamesL, types_1.RnaBaseNames, types_1.DnaBaseNames, types_1.WaterNames);
-function getElementQueries(structures) {
-    var uniqueElements = new Set();
-    for (var _i = 0, structures_1 = structures; _i < structures_1.length; _i++) {
-        var structure = structures_1[_i];
-        structure.uniqueElementSymbols.forEach(function (e) { return uniqueElements.add(e); });
-    }
-    var queries = [];
-    uniqueElements.forEach(function (e) {
-        var label = types_2.ElementNames[e] || e;
-        queries.push(ElementSymbolQuery([[e], label], 'Element Symbol', 0));
-    });
-    return queries;
-}
-exports.getElementQueries = getElementQueries;
-function getNonStandardResidueQueries(structures) {
-    var residueLabels = new Map();
-    var uniqueResidues = new Set();
-    for (var _i = 0, structures_2 = structures; _i < structures_2.length; _i++) {
-        var structure = structures_2[_i];
-        structure.uniqueResidueNames.forEach(function (r) { return uniqueResidues.add(r); });
-        var _loop_1 = function (m) {
-            structure.uniqueResidueNames.forEach(function (r) {
-                var comp = m.properties.chemicalComponentMap.get(r);
-                if (comp)
-                    residueLabels.set(r, comp.name);
-            });
-        };
-        for (var _a = 0, _b = structure.models; _a < _b.length; _a++) {
-            var m = _b[_a];
-            _loop_1(m);
-        }
-    }
-    var queries = [];
-    set_1.SetUtils.difference(uniqueResidues, StandardResidues).forEach(function (r) {
-        var label = residueLabels.get(r) || r;
-        queries.push(ResidueQuery([[r], label], 'Ligand/Non-standard Residue', 200));
-    });
-    return queries;
-}
-exports.getNonStandardResidueQueries = getNonStandardResidueQueries;
-function getPolymerAndBranchedEntityQueries(structures) {
-    var uniqueEntities = new Map();
-    var l = structure_1.StructureElement.Location.create();
-    for (var _i = 0, structures_3 = structures; _i < structures_3.length; _i++) {
-        var structure = structures_3[_i];
-        l.structure = structure;
-        for (var _a = 0, _b = structure.unitSymmetryGroups; _a < _b.length; _a++) {
-            var ug = _b[_a];
-            l.unit = ug.units[0];
-            l.element = ug.elements[0];
-            var entityType = structure_1.StructureProperties.entity.type(l);
-            if (entityType === 'polymer' || entityType === 'branched') {
-                var description = structure_1.StructureProperties.entity.pdbx_description(l);
-                uniqueEntities.set(description.join(', '), description);
-            }
-        }
-    }
-    var queries = [];
-    uniqueEntities.forEach(function (v, k) {
-        queries.push(EntityDescriptionQuery([v, k], 'Polymer/Carbohydrate Entities', 300));
-    });
-    return queries;
-}
-exports.getPolymerAndBranchedEntityQueries = getPolymerAndBranchedEntityQueries;
-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.applyBuiltInSelection = applyBuiltInSelection;
-exports.StructureSelectionQueries = {
-    all: all,
-    current: current,
-    polymer: polymer,
-    trace: trace,
-    backbone: backbone,
-    sidechain: sidechain,
-    sidechainWithTrace: sidechainWithTrace,
-    protein: protein,
-    nucleic: nucleic,
-    helix: helix,
-    beta: beta,
-    water: water,
-    ion: ion,
-    lipid: lipid,
-    branched: branched,
-    branchedPlusConnected: branchedPlusConnected,
-    branchedConnectedOnly: branchedConnectedOnly,
-    ligand: ligand,
-    ligandPlusConnected: ligandPlusConnected,
-    ligandConnectedOnly: ligandConnectedOnly,
-    connectedOnly: connectedOnly,
-    disulfideBridges: disulfideBridges,
-    nosBridges: nosBridges,
-    nonStandardPolymer: nonStandardPolymer,
-    coarse: coarse,
-    ring: ring,
-    aromaticRing: aromaticRing,
-    surroundings: surroundings,
-    surroundingLigands: surroundingLigands,
-    surroundingAtoms: surroundingAtoms,
-    complement: complement,
-    covalentlyBonded: covalentlyBonded,
-    covalentlyOrMetallicBonded: covalentlyOrMetallicBonded,
-    covalentlyBondedComponent: covalentlyBondedComponent,
-    wholeResidues: wholeResidues,
-};
-var StructureSelectionQueryRegistry = /** @class */ (function () {
-    function StructureSelectionQueryRegistry() {
-        var _a, _b;
-        this.list = [];
-        this.options = [];
-        this.version = 1;
-        // add built-in
-        (_a = this.list).push.apply(_a, (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], Object.values(exports.StructureSelectionQueries), false), StandardAminoAcids.map(function (v) { return ResidueQuery(v, StructureSelectionCategory.AminoAcid); }), false), StandardNucleicBases.map(function (v) { return ResidueQuery(v, StructureSelectionCategory.NucleicBase); }), false));
-        (_b = this.options).push.apply(_b, this.list.map(function (q) { return [q, q.label, q.category]; }));
-    }
-    StructureSelectionQueryRegistry.prototype.add = function (q) {
-        this.list.push(q);
-        this.options.push([q, q.label, q.category]);
-        this.version += 1;
-    };
-    StructureSelectionQueryRegistry.prototype.remove = function (q) {
-        var idx = this.list.indexOf(q);
-        if (idx !== -1) {
-            this.list.splice(idx, 1);
-            this.options.splice(idx, 1);
-            this.version += 1;
-        }
-    };
-    return StructureSelectionQueryRegistry;
-}());
-exports.StructureSelectionQueryRegistry = StructureSelectionQueryRegistry;
-//# sourceMappingURL=structure-selection-query.js.map