molstar
Version:
A comprehensive macromolecular library.
86 lines (85 loc) • 4.33 kB
JavaScript
"use strict";
/**
* Copyright (c) 2017-2020 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>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.ModelSymmetry = void 0;
const mmcif_1 = require("../../../mol-io/reader/cif/schema/mmcif");
const geometry_1 = require("../../../mol-math/geometry");
const linear_algebra_1 = require("../../../mol-math/linear-algebra");
const assembly_1 = require("./assembly");
const property_1 = require("../common/property");
var ModelSymmetry;
(function (ModelSymmetry) {
ModelSymmetry.Descriptor = {
name: 'model_symmetry',
};
ModelSymmetry.Provider = property_1.FormatPropertyProvider.create(ModelSymmetry.Descriptor);
function fromData(data) {
const assemblies = (0, assembly_1.createAssemblies)(data.pdbx_struct_assembly, data.pdbx_struct_assembly_gen, data.pdbx_struct_oper_list);
const spacegroup = getSpacegroup(data.symmetry, data.cell);
const isNonStandardCrystalFrame = checkNonStandardCrystalFrame(data.atom_sites, spacegroup);
return { assemblies, spacegroup, isNonStandardCrystalFrame, ncsOperators: getNcsOperators(data.struct_ncs_oper) };
}
ModelSymmetry.fromData = fromData;
function fromCell(size, anglesInRadians) {
const spaceCell = geometry_1.SpacegroupCell.create('P 1', size, anglesInRadians);
const spacegroup = geometry_1.Spacegroup.create(spaceCell);
return { assemblies: [], spacegroup, isNonStandardCrystalFrame: false };
}
ModelSymmetry.fromCell = fromCell;
})(ModelSymmetry || (exports.ModelSymmetry = ModelSymmetry = {}));
function checkNonStandardCrystalFrame(atom_sites, spacegroup) {
if (atom_sites._rowCount === 0)
return false;
// TODO: parse atom_sites transform and check if it corresponds to the toFractional matrix
return false;
}
function getSpacegroupNameOrNumber(symmetry) {
const groupNumber = symmetry['Int_Tables_number'].value(0);
const groupName = symmetry['space_group_name_H-M'].value(0);
if (!symmetry['Int_Tables_number'].isDefined)
return groupName;
if (!symmetry['space_group_name_H-M'].isDefined)
return groupNumber;
return groupName;
}
function getSpacegroup(symmetry, cell) {
if (symmetry._rowCount === 0 || cell._rowCount === 0)
return geometry_1.Spacegroup.ZeroP1;
const a = cell.length_a.value(0);
const b = cell.length_b.value(0);
const c = cell.length_c.value(0);
if (a === 0 || b === 0 || c === 0)
return geometry_1.Spacegroup.ZeroP1;
const alpha = cell.angle_alpha.value(0);
const beta = cell.angle_beta.value(0);
const gamma = cell.angle_gamma.value(0);
if (alpha === 0 || beta === 0 || gamma === 0)
return geometry_1.Spacegroup.ZeroP1;
const nameOrNumber = getSpacegroupNameOrNumber(symmetry);
const spaceCell = geometry_1.SpacegroupCell.create(nameOrNumber, linear_algebra_1.Vec3.create(a, b, c), linear_algebra_1.Vec3.scale((0, linear_algebra_1.Vec3)(), linear_algebra_1.Vec3.create(alpha, beta, gamma), Math.PI / 180));
return geometry_1.Spacegroup.create(spaceCell);
}
function getNcsOperators(struct_ncs_oper) {
if (struct_ncs_oper._rowCount === 0)
return void 0;
const { id, matrix, vector } = struct_ncs_oper;
const matrixSpace = mmcif_1.mmCIF_Schema.struct_ncs_oper.matrix.space, vectorSpace = mmcif_1.mmCIF_Schema.struct_ncs_oper.vector.space;
const opers = [];
for (let i = 0; i < struct_ncs_oper._rowCount; i++) {
const m = linear_algebra_1.Tensor.toMat3((0, linear_algebra_1.Mat3)(), matrixSpace, matrix.value(i));
const v = linear_algebra_1.Tensor.toVec3((0, linear_algebra_1.Vec3)(), vectorSpace, vector.value(i));
if (!geometry_1.SymmetryOperator.checkIfRotationAndTranslation(m, v))
continue;
// ignore non-identity 'given' NCS operators
if (struct_ncs_oper.code.value(i) === 'given' && !linear_algebra_1.Mat3.isIdentity(m) && !linear_algebra_1.Vec3.isZero(v))
continue;
const ncsId = id.value(i);
opers[opers.length] = geometry_1.SymmetryOperator.ofRotationAndOffset(`ncs_${ncsId}`, m, v, ncsId);
}
return opers;
}