molstar/lib/mol-model-props/sequence/best-database-mapping.js

A comprehensive macromolecular library.

/**
 * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 */
import { __awaiter, __generator } from "tslib";
import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
import { CustomModelProperty } from '../common/custom-model-property';
export { BestDatabaseSequenceMapping };
var BestDatabaseSequenceMapping;
(function (BestDatabaseSequenceMapping) {
    var _this = this;
    BestDatabaseSequenceMapping.Provider = CustomModelProperty.createProvider({
        label: 'Best Database Sequence Mapping',
        descriptor: CustomPropertyDescriptor({
            name: 'molstar_best_database_sequence_mapping'
        }),
        type: 'static',
        defaultParams: {},
        getParams: function () { return ({}); },
        isApplicable: function (data) { var _a, _b; return MmcifFormat.is(data.sourceData) && ((_b = (_a = data.sourceData.data.frame.categories) === null || _a === void 0 ? void 0 : _a.atom_site) === null || _b === void 0 ? void 0 : _b.fieldNames.indexOf('db_name')) >= 0; },
        obtain: function (ctx, data) { return __awaiter(_this, void 0, void 0, function () {
            return __generator(this, function (_a) {
                return [2 /*return*/, { value: fromCif(data) }];
            });
        }); }
    });
    function getKey(loc) {
        var model = loc.unit.model;
        var data = BestDatabaseSequenceMapping.Provider.get(model).value;
        if (!data)
            return '';
        var eI = loc.unit.elements[loc.element];
        var rI = model.atomicHierarchy.residueAtomSegments.offsets[eI];
        return data.accession[rI];
    }
    BestDatabaseSequenceMapping.getKey = getKey;
    function getLabel(loc) {
        var model = loc.unit.model;
        var data = BestDatabaseSequenceMapping.Provider.get(model).value;
        if (!data)
            return;
        var eI = loc.unit.elements[loc.element];
        var rI = model.atomicHierarchy.residueAtomSegments.offsets[eI];
        var dbName = data.dbName[rI];
        if (!dbName)
            return;
        return dbName + " " + data.accession[rI] + " " + data.num[rI] + " " + data.residue[rI];
    }
    BestDatabaseSequenceMapping.getLabel = getLabel;
    function fromCif(model) {
        if (!MmcifFormat.is(model.sourceData))
            return;
        var atom_site = model.sourceData.data.frame.categories.atom_site;
        var db_name = atom_site.getField('db_name');
        var db_acc = atom_site.getField('db_acc');
        var db_num = atom_site.getField('db_num');
        var db_res = atom_site.getField('db_res');
        if (!db_name || !db_acc || !db_num || !db_res)
            return;
        var atomSourceIndex = model.atomicHierarchy.atomSourceIndex;
        var _a = model.atomicHierarchy.residueAtomSegments, count = _a.count, residueOffsets = _a.offsets;
        var dbName = new Array(count);
        var accession = new Array(count);
        var num = new Array(count);
        var residue = new Array(count);
        for (var i = 0; i < count; i++) {
            var row = atomSourceIndex.value(residueOffsets[i]);
            if (db_name.valueKind(row) !== 0 /* Present */) {
                dbName[row] = '';
                accession[row] = '';
                num[row] = 0;
                residue[row] = '';
                continue;
            }
            dbName[row] = db_name.str(row);
            accession[row] = db_acc.str(row);
            num[row] = db_num.int(row);
            residue[row] = db_res.str(row);
        }
        return { dbName: dbName, accession: accession, num: num, residue: residue };
    }
})(BestDatabaseSequenceMapping || (BestDatabaseSequenceMapping = {}));
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