cif-core.ts

/**
 * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

import { Column, Table } from '../../mol-data/db';
import { Model, Symmetry } from '../../mol-model/structure/model';
import { MoleculeType } from '../../mol-model/structure/model/types';
import { RuntimeContext, Task } from '../../mol-task';
import { createModels } from './basic/parser';
import { BasicSchema, createBasic } from './basic/schema';
import { ComponentBuilder } from './common/component';
import { EntityBuilder } from './common/entity';
import { ModelFormat } from './format';
import { CifCore_Database } from '../../mol-io/reader/cif/schema/cif-core';
import { CifFrame, CIF } from '../../mol-io/reader/cif';
import { Spacegroup, SpacegroupCell } from '../../mol-math/geometry';
import { Vec3 } from '../../mol-math/linear-algebra';
import { ModelSymmetry } from './property/symmetry';
import { IndexPairBonds } from './property/bonds/index-pair';
import { AtomSiteAnisotrop } from './property/anisotropic';

function getSpacegroupNameOrNumber(space_group: CifCore_Database['space_group']) {
    const groupNumber = space_group.IT_number.value(0)
    const groupName = space_group['name_H-M_full'].value(0)
    if (!space_group.IT_number.isDefined) return groupName
    if (!space_group['name_H-M_full'].isDefined) return groupNumber
    return groupNumber
}

function getSymmetry(db: CifCore_Database): Symmetry {
    const { cell, space_group } = db
    const nameOrNumber = getSpacegroupNameOrNumber(space_group)
    const spaceCell = SpacegroupCell.create(nameOrNumber,
        Vec3.create(cell.length_a.value(0), cell.length_b.value(0), cell.length_c.value(0)),
        Vec3.scale(Vec3.zero(), Vec3.create(cell.angle_alpha.value(0), cell.angle_beta.value(0), cell.angle_gamma.value(0)), Math.PI / 180));

    return {
        spacegroup: Spacegroup.create(spaceCell),
        assemblies : [],
        isNonStandardCrytalFrame: false,
        ncsOperators: []
    }
}

async function getModels(db: CifCore_Database, format: CifCoreFormat, ctx: RuntimeContext): Promise<Model[]> {

    const atomCount = db.atom_site._rowCount
    const MOL = Column.ofConst('MOL', atomCount, Column.Schema.str);
    const A = Column.ofConst('A', atomCount, Column.Schema.str);
    const seq_id = Column.ofConst(1, atomCount, Column.Schema.int);

    const symmetry = getSymmetry(db)
    const m = symmetry.spacegroup.cell.fromFractional

    const { fract_x, fract_y, fract_z } = db.atom_site
    const x = new Float32Array(atomCount)
    const y = new Float32Array(atomCount)
    const z = new Float32Array(atomCount)
    const v = Vec3()
    for (let i = 0; i < atomCount; ++i) {
        Vec3.set(v, fract_x.value(i), fract_y.value(i), fract_z.value(i))
        Vec3.transformMat4(v, v, m)
        x[i] = v[0], y[i] = v[1], z[i] = v[2]
    }

    const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
        auth_asym_id: A,
        auth_atom_id: db.atom_site.label,