TmMolStar/src/mol-model-formats/structure/mmcif/atomic.ts

/**
 * Copyright (c) 2017-2019 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 { Column, Table } from '../../../mol-data/db';
import { Interval, Segmentation } from '../../../mol-data/int';
import { mmCIF_Database } from '../../../mol-io/reader/cif/schema/mmcif';
import UUID from '../../../mol-util/uuid';
import { ElementIndex } from '../../../mol-model/structure';
import { Model } from '../../../mol-model/structure/model/model';
import { AtomicConformation, AtomicData, AtomicHierarchy, AtomicSegments, AtomsSchema, ChainsSchema, ResiduesSchema } from '../../../mol-model/structure/model/properties/atomic';
import { getAtomicIndex } from '../../../mol-model/structure/model/properties/utils/atomic-index';
import { ElementSymbol } from '../../../mol-model/structure/model/types';
import { Entities } from '../../../mol-model/structure/model/properties/common';
import { getAtomicDerivedData } from '../../../mol-model/structure/model/properties/utils/atomic-derived';
import { FormatData } from './parser';

type AtomSite = mmCIF_Database['atom_site']

function findHierarchyOffsets(atom_site: AtomSite) {
    if (atom_site._rowCount === 0) return { residues: [], chains: [] };

    const start = 0, end = atom_site._rowCount;
    const residues = [start as ElementIndex], chains = [start as ElementIndex];

    const { label_entity_id, label_asym_id, label_seq_id, auth_seq_id, pdbx_PDB_ins_code } = atom_site;

    for (let i = start + 1 as ElementIndex; i < end; i++) {
        const newChain = !label_entity_id.areValuesEqual(i - 1, i) || !label_asym_id.areValuesEqual(i - 1, i);
        const newResidue = newChain
            || !label_seq_id.areValuesEqual(i - 1, i)
            || !auth_seq_id.areValuesEqual(i - 1, i)
            || !pdbx_PDB_ins_code.areValuesEqual(i - 1, i);
        // not checking label_comp_id to allow for MICROHETEROGENEITY

        if (newResidue) residues[residues.length] = i as ElementIndex;
        if (newChain) chains[chains.length] = i as ElementIndex;
    }
    return { residues, chains };
}

function substUndefinedColumn<T extends Table<any>>(table: T, a: keyof T, b: keyof T) {
    if (!(table as any)[a].isDefined) {
        (table as any)[a] = (table as any)[b];
    }
    if (!(table as any)[b].isDefined) {
        (table as any)[b] = (table as any)[a];
    }
}

function createHierarchyData(atom_site: AtomSite, sourceIndex: Column<number>, offsets: { residues: ArrayLike<number>, chains: ArrayLike<number> }): AtomicData {
    const atoms = Table.ofColumns(AtomsSchema, {
        type_symbol: Column.ofArray({ array: Column.mapToArray(atom_site.type_symbol, ElementSymbol), schema: Column.Schema.Aliased<ElementSymbol>(Column.Schema.str) }),
        label_atom_id: atom_site.label_atom_id,
        auth_atom_id: atom_site.auth_atom_id,
        label_alt_id: atom_site.label_alt_id,
        pdbx_formal_charge: atom_site.pdbx_formal_charge,
        sourceIndex
    });

    const residues = Table.view(atom_site, ResiduesSchema, offsets.residues);

    // Optimize the numeric columns
    Table.columnToArray(residues, 'label_seq_id', Int32Array);
    Table.columnToArray(residues, 'auth_seq_id', Int32Array);

    const chains = Table.view(atom_site, ChainsSchema, offsets.chains);

    // Fix possibly missing auth_/label_ columns
    substUndefinedColumn(atoms, 'label_atom_id', 'auth_atom_id');
    substUndefinedColumn(residues, 'label_seq_id', 'auth_seq_id');
    substUndefinedColumn(residues, 'label_comp_id', 'auth_comp_id');
    substUndefinedColumn(chains, 'label_asym_id', 'auth_asym_id');

    return { atoms, residues, chains };
}

function getConformation(atom_site: AtomSite): AtomicConformation {
    return {
        id: UUID.create22(),
        atomId: atom_site.id,
        occupancy: atom_site.occupancy,
        B_iso_or_equiv: atom_site.B_iso_or_equiv,
        xyzDefined: atom_site.Cartn_x.isDefined && atom_site.Cartn_y.isDefined && atom_site.Cartn_z.isDefined,
        x: atom_site.Cartn_x.toArray({ array: Float32Array }),
        y: atom_site.Cartn_y.toArray({ array: Float32Array }),
        z: atom_site.Cartn_z.toArray({ array: Float32Array }),
    }
}

function isHierarchyDataEqual(a: AtomicData, b: AtomicData) {
    // TODO need to cast because of how TS handles type resolution for interfaces https://github.com/Microsoft/TypeScript/issues/15300
    return Table.areEqual(a.chains as Table<ChainsSchema>, b.chains as Table<ChainsSchema>)
        && Table.areEqual(a.residues as Table<ResiduesSchema>, b.residues as Table<ResiduesSchema>)
        && Table.areEqual(a.atoms as Table<AtomsSchema>, b.atoms as Table<AtomsSchema>)
}

function getAtomicHierarchy(atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, formatData: FormatData, previous?: Model) {
    const hierarchyOffsets = findHierarchyOffsets(atom_site);
    const hierarchyData = createHierarchyData(atom_site, sourceIndex, hierarchyOffsets);

    if (previous && isHierarchyDataEqual(previous.atomicHierarchy, hierarchyData)) {
        return {
            sameAsPrevious: true,
            hierarchy: previous.atomicHierarchy,
        };
    }

    const hierarchySegments: AtomicSegments = {
        residueAtomSegments: Segmentation.ofOffsets(hierarchyOffsets.residues, Interval.ofBounds(0, atom_site._rowCount)),
        chainAtomSegments: Segmentation.ofOffsets(hierarchyOffsets.chains, Interval.ofBounds(0, atom_site._rowCount)),
    }

    const index = getAtomicIndex(hierarchyData, entities, hierarchySegments);
    const derived = getAtomicDerivedData(hierarchyData, index, formatData.chemicalComponentMap);
    const hierarchy: AtomicHierarchy = { ...hierarchyData, ...hierarchySegments, index, derived };
    return { sameAsPrevious: false, hierarchy };
}

export function getAtomicHierarchyAndConformation(atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, formatData: FormatData, previous?: Model) {
    const { sameAsPrevious, hierarchy } = getAtomicHierarchy(atom_site, sourceIndex, entities, formatData, previous)
    const conformation = getConformation(atom_site)
    return { sameAsPrevious, hierarchy, conformation };
}