TmMolStar/src/mol-model-formats/structure/property/atoms/chem_comp.ts

/**
 * Copyright (c) 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>
 * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
 */

import { Model } from '../../../../mol-model/structure/model/model';
import { CustomPropertyDescriptor } from '../../../../mol-model/custom-property';
import { CifWriter } from '../../../../mol-io/writer/cif';
import { Table } from '../../../../mol-data/db';
import { FormatPropertyProvider } from '../../common/property';
import { CCD_Schema } from '../../../../mol-io/reader/cif/schema/ccd';

export interface ComponentAtom {
    readonly data: Table<CCD_Schema['chem_comp_atom']>
    readonly entries: ReadonlyMap<string, ComponentAtom.Entry>
}

export namespace ComponentAtom {
    export const Descriptor: CustomPropertyDescriptor = {
        name: 'chem_comp_atom',
        cifExport: {
            prefix: '',
            categories: [{
                name: 'chem_comp_atom',
                instance(ctx) {
                    const p = Provider.get(ctx.firstModel);
                    if (!p) return CifWriter.Category.Empty;
                    const chem_comp_atom = p.data;
                    if (!chem_comp_atom) return CifWriter.Category.Empty;

                    const comp_names = ctx.structures[0].uniqueResidueNames;
                    const { comp_id, _rowCount } = chem_comp_atom;
                    const indices: number[] = [];
                    for (let i = 0; i < _rowCount; i++) {
                        if (comp_names.has(comp_id.value(i))) indices[indices.length] = i;
                    }

                    return CifWriter.Category.ofTable(chem_comp_atom, indices);
                }
            }]
        }
    };

    export const Provider = FormatPropertyProvider.create<ComponentAtom>(Descriptor);

    export function chemCompAtomFromTable(model: Model, table: Table<CCD_Schema['chem_comp_atom']>): Table<CCD_Schema['chem_comp_atom']> {
        return Table.pick(table, CCD_Schema.chem_comp_atom, (i: number) => {
            return model.properties.chemicalComponentMap.has(table.comp_id.value(i));
        });
    }

    export function getEntriesFromChemCompAtom(data: Table<CCD_Schema['chem_comp_atom']>) {
        const entries: Map<string, Entry> = new Map();

        function addEntry(id: string) {
            let e = new Entry(id);
            entries.set(id, e);
            return e;
        }

        const { comp_id, atom_id, charge, pdbx_stereo_config, _rowCount } = data;

        let entry = addEntry(comp_id.value(0)!);
        for (let i = 0; i < _rowCount; i++) {
            const name = atom_id.value(i)!;
            const id = comp_id.value(i)!;
            const ch = charge.value(i)!;
            const stereo = pdbx_stereo_config.value(i)!;

            if (entry.id !== id) {
                entry = addEntry(id);
            }

            entry.add(name, ch, stereo);
        }

        return entries;
    }

    export class Entry {
        readonly map: Map<string, { charge: number, stereo_config: CCD_Schema['chem_comp_atom']['pdbx_stereo_config']['T'] }> = new Map();

        add(a: string, charge: number, stereo_config: CCD_Schema['chem_comp_atom']['pdbx_stereo_config']['T']) {
            this.map.set(a, { charge, stereo_config });
        }

        constructor(public readonly id: string) { }
    }
}