molstar/lib/commonjs/mol-model/structure/query/queries/internal.js

A comprehensive macromolecular library.

"use strict";
/**
 * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 */
Object.defineProperty(exports, "__esModule", { value: true });
exports.bundleGenerator = exports.bundleElementImpl = exports.spheres = exports.atomicHet = exports.water = exports.atomicSequence = exports.defaultBondTest = void 0;
var int_1 = require("../../../../mol-data/int");
var element_1 = require("../../../../mol-model/structure/structure/element");
var structure_1 = require("../../structure");
var structure_2 = require("../../structure/structure");
var selection_1 = require("../selection");
var types_1 = require("../../model/types");
var bundle_1 = require("../../structure/element/bundle");
function defaultBondTest(ctx) {
    return types_1.BondType.isCovalent(ctx.atomicBond.type);
}
exports.defaultBondTest = defaultBondTest;
function atomicSequence() {
    return function query_atomicSequence(ctx) {
        var inputStructure = ctx.inputStructure;
        var l = element_1.StructureElement.Location.create(inputStructure);
        var units = [];
        for (var _i = 0, _a = inputStructure.units; _i < _a.length; _i++) {
            var unit = _a[_i];
            if (unit.kind !== 0 /* Atomic */)
                continue;
            l.unit = unit;
            var elements = unit.elements;
            l.element = elements[0];
            if (structure_1.StructureProperties.entity.type(l) !== 'polymer')
                continue;
            var residuesIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
            var residueCount = 0;
            while (residuesIt.hasNext) {
                residueCount++;
                residuesIt.move();
            }
            if (residueCount < 8)
                continue;
            units.push(unit);
        }
        return selection_1.StructureSelection.Singletons(inputStructure, structure_2.Structure.create(units, { parent: inputStructure }));
    };
}
exports.atomicSequence = atomicSequence;
function water() {
    return function query_water(ctx) {
        var inputStructure = ctx.inputStructure;
        var l = element_1.StructureElement.Location.create(inputStructure);
        var units = [];
        for (var _i = 0, _a = inputStructure.units; _i < _a.length; _i++) {
            var unit = _a[_i];
            if (unit.kind !== 0 /* Atomic */)
                continue;
            l.unit = unit;
            var elements = unit.elements;
            l.element = elements[0];
            if (structure_1.StructureProperties.entity.type(l) !== 'water')
                continue;
            units.push(unit);
        }
        return selection_1.StructureSelection.Singletons(inputStructure, structure_2.Structure.create(units, { parent: inputStructure }));
    };
}
exports.water = water;
function atomicHet() {
    return function query_atomicHet(ctx) {
        var inputStructure = ctx.inputStructure;
        var l = element_1.StructureElement.Location.create(inputStructure);
        var units = [];
        for (var _i = 0, _a = inputStructure.units; _i < _a.length; _i++) {
            var unit = _a[_i];
            if (unit.kind !== 0 /* Atomic */)
                continue;
            l.unit = unit;
            var elements = unit.elements;
            l.element = elements[0];
            if (structure_1.StructureProperties.entity.type(l) === 'water')
                continue;
            if (structure_1.StructureProperties.entity.type(l) === 'polymer') {
                var residuesIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
                var residueCount = 0;
                while (residuesIt.hasNext) {
                    residueCount++;
                    residuesIt.move();
                }
                if (residueCount >= 8)
                    continue;
            }
            units.push(unit);
        }
        return selection_1.StructureSelection.Singletons(inputStructure, structure_2.Structure.create(units, { parent: inputStructure }));
    };
}
exports.atomicHet = atomicHet;
function spheres() {
    return function query_spheres(ctx) {
        var inputStructure = ctx.inputStructure;
        var units = [];
        for (var _i = 0, _a = inputStructure.units; _i < _a.length; _i++) {
            var unit = _a[_i];
            if (unit.kind !== 1 /* Spheres */)
                continue;
            units.push(unit);
        }
        return selection_1.StructureSelection.Singletons(inputStructure, structure_2.Structure.create(units, { parent: inputStructure }));
    };
}
exports.spheres = spheres;
function bundleElementImpl(groupedUnits, ranges, set) {
    return {
        groupedUnits: groupedUnits,
        ranges: ranges,
        set: set
    };
}
exports.bundleElementImpl = bundleElementImpl;
function bundleGenerator(elements) {
    return function query_bundleGenerator(ctx) {
        var bundle = {
            hash: ctx.inputStructure.hashCode,
            elements: elements
        };
        return selection_1.StructureSelection.Sequence(ctx.inputStructure, [bundle_1.Bundle.toStructure(bundle, ctx.inputStructure)]);
    };
}
exports.bundleGenerator = bundleGenerator;
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