molstar
Version:
A comprehensive macromolecular library.
698 lines • 40.4 kB
JavaScript
"use strict";
/**
* Copyright (c) 2019-2020 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 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 });
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 });
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.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
})
])
]),
]), { 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])
? "[" + 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.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 = 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.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 = "" + 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.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;
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