molstar
Version:
A comprehensive macromolecular library.
92 lines (91 loc) • 4.14 kB
JavaScript
/**
* Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Task } from '../../mol-task';
import { CIF } from '../../mol-io/reader/cif';
import { createModels } from './basic/parser';
import { ModelSymmetry } from './property/symmetry';
import { ModelSecondaryStructure } from './property/secondary-structure';
import { Table } from '../../mol-data/db';
import { AtomSiteAnisotrop } from './property/anisotropic';
import { ComponentBond } from './property/bonds/chem_comp';
import { StructConn } from './property/bonds/struct_conn';
import { GlobalModelTransformInfo } from '../../mol-model/structure/model/properties/global-transform';
import { createBasic } from './basic/schema';
function modelSymmetryFromMmcif(model) {
if (!MmcifFormat.is(model.sourceData))
return;
return ModelSymmetry.fromData(model.sourceData.data.db);
}
ModelSymmetry.Provider.formatRegistry.add('mmCIF', modelSymmetryFromMmcif);
function secondaryStructureFromMmcif(model) {
if (!MmcifFormat.is(model.sourceData))
return;
var _a = model.sourceData.data.db, struct_conf = _a.struct_conf, struct_sheet_range = _a.struct_sheet_range;
return ModelSecondaryStructure.fromStruct(struct_conf, struct_sheet_range, model.atomicHierarchy);
}
ModelSecondaryStructure.Provider.formatRegistry.add('mmCIF', secondaryStructureFromMmcif);
function atomSiteAnisotropFromMmcif(model) {
if (!MmcifFormat.is(model.sourceData))
return;
var atom_site_anisotrop = model.sourceData.data.db.atom_site_anisotrop;
var data = Table.ofColumns(AtomSiteAnisotrop.Schema, atom_site_anisotrop);
var elementToAnsiotrop = AtomSiteAnisotrop.getElementToAnsiotrop(model.atomicConformation.atomId, atom_site_anisotrop.id);
return { data: data, elementToAnsiotrop: elementToAnsiotrop };
}
function atomSiteAnisotropApplicableMmcif(model) {
if (!MmcifFormat.is(model.sourceData))
return false;
return model.sourceData.data.db.atom_site_anisotrop.U.isDefined;
}
AtomSiteAnisotrop.Provider.formatRegistry.add('mmCIF', atomSiteAnisotropFromMmcif, atomSiteAnisotropApplicableMmcif);
function componentBondFromMmcif(model) {
if (!MmcifFormat.is(model.sourceData))
return;
var chem_comp_bond = model.sourceData.data.db.chem_comp_bond;
if (chem_comp_bond._rowCount === 0)
return;
return {
data: chem_comp_bond,
entries: ComponentBond.getEntriesFromChemCompBond(chem_comp_bond)
};
}
ComponentBond.Provider.formatRegistry.add('mmCIF', componentBondFromMmcif);
function structConnFromMmcif(model) {
if (!MmcifFormat.is(model.sourceData))
return;
var struct_conn = model.sourceData.data.db.struct_conn;
if (struct_conn._rowCount === 0)
return;
var entries = StructConn.getEntriesFromStructConn(struct_conn, model);
return {
data: struct_conn,
byAtomIndex: StructConn.getAtomIndexFromEntries(entries),
entries: entries,
};
}
StructConn.Provider.formatRegistry.add('mmCIF', structConnFromMmcif);
GlobalModelTransformInfo.Provider.formatRegistry.add('mmCIF', GlobalModelTransformInfo.fromMmCif, GlobalModelTransformInfo.hasData);
//
export { MmcifFormat };
var MmcifFormat;
(function (MmcifFormat) {
function is(x) {
return (x === null || x === void 0 ? void 0 : x.kind) === 'mmCIF';
}
MmcifFormat.is = is;
function fromFrame(frame, db, source) {
if (!db)
db = CIF.schema.mmCIF(frame);
return { kind: 'mmCIF', name: db._name, data: { db: db, frame: frame, source: source } };
}
MmcifFormat.fromFrame = fromFrame;
})(MmcifFormat || (MmcifFormat = {}));
export function trajectoryFromMmCIF(frame) {
var format = MmcifFormat.fromFrame(frame);
var basic = createBasic(format.data.db, true);
return Task.create('Create mmCIF Model', function (ctx) { return createModels(basic, format, ctx); });
}