molstar
Version:
A comprehensive macromolecular library.
102 lines (101 loc) • 4.29 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;
const int_1 = require("../../../../mol-data/int");
const cif_1 = require("../../../../mol-io/writer/cif");
const structure_1 = require("../../structure");
var CifField = cif_1.CifWriter.Field;
const atom_site_1 = require("./atom_site");
const secondary_structure_1 = require("../../../../mol-model-formats/structure/property/secondary-structure");
exports._struct_conf = {
name: 'struct_conf',
instance(ctx) {
const elements = findElements(ctx, 'helix');
return {
fields: struct_conf_fields(),
source: [{ data: elements, rowCount: elements.length }]
};
}
};
exports._struct_sheet_range = {
name: 'struct_sheet_range',
instance(ctx) {
const elements = findElements(ctx, 'sheet').sort(compare_ssr);
return {
fields: struct_sheet_range_fields(),
source: [{ data: elements, rowCount: elements.length }]
};
}
};
function compare_ssr(x, y) {
const 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;
}
;
const struct_conf_fields = () => [
CifField.str('conf_type_id', (i, data) => data[i].element.type_id),
CifField.str('id', (i, data, idx) => `${data[i].element.type_id}${idx + 1}`),
...(0, atom_site_1.residueIdFields)((i, e) => e[i].start, { prefix: 'beg' }),
...(0, atom_site_1.residueIdFields)((i, e) => e[i].end, { prefix: 'end' }),
CifField.str('pdbx_PDB_helix_class', (i, data) => data[i].element.helix_class),
CifField.str('details', (i, data) => data[i].element.details || '', {
valueKind: (i, d) => !!d[i].element.details ? 0 /* Column.ValueKinds.Present */ : 2 /* Column.ValueKinds.Unknown */
}),
CifField.int('pdbx_PDB_helix_length', (i, data) => data[i].length)
];
const struct_sheet_range_fields = () => [
CifField.str('sheet_id', (i, data) => data[i].element.sheet_id),
CifField.index('id'),
...(0, atom_site_1.residueIdFields)((i, e) => e[i].start, { prefix: 'beg' }),
...(0, atom_site_1.residueIdFields)((i, e) => e[i].end, { prefix: 'end' }),
CifField.str('symmetry', (i, data) => '', { valueKind: (i, d) => 2 /* Column.ValueKinds.Unknown */ })
];
function findElements(ctx, kind) {
// TODO: encode secondary structure for different models?
const secondaryStructure = secondary_structure_1.ModelSecondaryStructure.Provider.get(ctx.firstModel);
if (!secondaryStructure)
return [];
const { key, elements } = secondaryStructure;
const ssElements = [];
const structure = ctx.structures[0];
for (const { units } of structure.unitSymmetryGroups) {
const u = units[0];
if (!structure_1.Unit.isAtomic(u))
continue;
const segs = u.model.atomicHierarchy.residueAtomSegments;
const residues = int_1.Segmentation.transientSegments(segs, u.elements);
let current, move = true;
while (residues.hasNext) {
if (move)
current = residues.move();
const start = current.index;
const startIdx = key[start];
const element = elements[startIdx];
if (element.kind !== kind) {
move = true;
continue;
}
let 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, u, segs.offsets[start]),
end: structure_1.StructureElement.Location.create(structure, u, segs.offsets[prev]),
length: prev - start + 1,
element
};
break;
}
}
}
}
return ssElements;
}