molstar
Version:
A comprehensive macromolecular library.
102 lines • 5.03 kB
JavaScript
;
/**
* Copyright (c) 2018 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._struct_sheet_range = exports._struct_conf = void 0;
var tslib_1 = require("tslib");
var int_1 = require("../../../../mol-data/int");
var cif_1 = require("../../../../mol-io/writer/cif");
var structure_1 = require("../../structure");
var CifField = cif_1.CifWriter.Field;
var atom_site_1 = require("./atom_site");
var secondary_structure_1 = require("../../../../mol-model-formats/structure/property/secondary-structure");
exports._struct_conf = {
name: 'struct_conf',
instance: function (ctx) {
var elements = findElements(ctx, 'helix');
return {
fields: struct_conf_fields(),
source: [{ data: elements, rowCount: elements.length }]
};
}
};
exports._struct_sheet_range = {
name: 'struct_sheet_range',
instance: function (ctx) {
var elements = findElements(ctx, 'sheet').sort(compare_ssr);
return {
fields: struct_sheet_range_fields(),
source: [{ data: elements, rowCount: elements.length }]
};
}
};
function compare_ssr(x, y) {
var a = x.element, b = y.element;
return a.sheet_id < b.sheet_id ? -1 : a.sheet_id === b.sheet_id ? x.start.element - y.start.element : 1;
}
;
var struct_conf_fields = function () { return (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([
CifField.str('conf_type_id', function (i, data) { return data[i].element.type_id; }),
CifField.str('id', function (i, data, idx) { return "" + data[i].element.type_id + (idx + 1); })
], (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].start; }, { prefix: 'beg' }), true), (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].end; }, { prefix: 'end' }), true), [
CifField.str('pdbx_PDB_helix_class', function (i, data) { return data[i].element.helix_class; }),
CifField.str('details', function (i, data) { return data[i].element.details || ''; }, {
valueKind: function (i, d) { return !!d[i].element.details ? 0 /* Present */ : 2 /* Unknown */; }
}),
CifField.int('pdbx_PDB_helix_length', function (i, data) { return data[i].length; })
], false); };
var struct_sheet_range_fields = function () { return (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([
CifField.str('sheet_id', function (i, data) { return data[i].element.sheet_id; }),
CifField.index('id')
], (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].start; }, { prefix: 'beg' }), true), (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].end; }, { prefix: 'end' }), true), [
CifField.str('symmetry', function (i, data) { return ''; }, { valueKind: function (i, d) { return 2 /* Unknown */; } })
], false); };
function findElements(ctx, kind) {
// TODO: encode secondary structure for different models?
var secondaryStructure = secondary_structure_1.ModelSecondaryStructure.Provider.get(ctx.firstModel);
if (!secondaryStructure)
return [];
var key = secondaryStructure.key, elements = secondaryStructure.elements;
var ssElements = [];
var structure = ctx.structures[0];
for (var _i = 0, _a = structure.units; _i < _a.length; _i++) {
var unit = _a[_i];
// currently can only support this for "identity" operators.
if (!structure_1.Unit.isAtomic(unit) || !unit.conformation.operator.isIdentity)
continue;
var segs = unit.model.atomicHierarchy.residueAtomSegments;
var residues = int_1.Segmentation.transientSegments(segs, unit.elements);
var current = void 0, move = true;
while (residues.hasNext) {
if (move)
current = residues.move();
var start = current.index;
var startIdx = key[start];
var element = elements[startIdx];
if (element.kind !== kind) {
move = true;
continue;
}
var prev = start;
while (residues.hasNext) {
prev = current.index;
current = residues.move();
if (startIdx !== key[current.index]) {
move = false;
ssElements[ssElements.length] = {
start: structure_1.StructureElement.Location.create(structure, unit, segs.offsets[start]),
end: structure_1.StructureElement.Location.create(structure, unit, segs.offsets[prev]),
length: prev - start + 1,
element: element
};
break;
}
}
}
}
return ssElements;
}
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