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molstar

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A comprehensive macromolecular library.

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/** * 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> */ import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif'; import { Spacegroup, SpacegroupCell, SymmetryOperator } from '../../../mol-math/geometry'; import { Tensor, Vec3, Mat3 } from '../../../mol-math/linear-algebra'; import { createAssemblies } from './assembly'; import { FormatPropertyProvider } from '../common/property'; export { ModelSymmetry }; var ModelSymmetry; (function (ModelSymmetry) { ModelSymmetry.Descriptor = { name: 'model_symmetry', }; ModelSymmetry.Provider = FormatPropertyProvider.create(ModelSymmetry.Descriptor); function fromData(data) { const assemblies = 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 = SpacegroupCell.create('P 1', size, anglesInRadians); const spacegroup = Spacegroup.create(spaceCell); return { assemblies: [], spacegroup, isNonStandardCrystalFrame: false }; } ModelSymmetry.fromCell = fromCell; })(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 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 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 Spacegroup.ZeroP1; const nameOrNumber = getSpacegroupNameOrNumber(symmetry); const spaceCell = SpacegroupCell.create(nameOrNumber, Vec3.create(a, b, c), Vec3.scale(Vec3(), Vec3.create(alpha, beta, gamma), Math.PI / 180)); return 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_Schema.struct_ncs_oper.matrix.space, vectorSpace = mmCIF_Schema.struct_ncs_oper.vector.space; const opers = []; for (let i = 0; i < struct_ncs_oper._rowCount; i++) { const m = Tensor.toMat3(Mat3(), matrixSpace, matrix.value(i)); const v = Tensor.toVec3(Vec3(), vectorSpace, vector.value(i)); if (!SymmetryOperator.checkIfRotationAndTranslation(m, v)) continue; // ignore non-identity 'given' NCS operators if (struct_ncs_oper.code.value(i) === 'given' && !Mat3.isIdentity(m) && !Vec3.isZero(v)) continue; const ncsId = id.value(i); opers[opers.length] = SymmetryOperator.ofRotationAndOffset(`ncs_${ncsId}`, m, v, ncsId); } return opers; }