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+/**
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+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
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+ *
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+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
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+ */
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+
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+import { StringBuilder } from '../../../mol-util';
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+import Writer from '../writer';
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+import { Encoder, Category, Field } from '../cif/encoder';
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+import { getCategoryInstanceData } from '../cif/encoder/util';
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+
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+// specification: http://c4.cabrillo.edu/404/ctfile.pdf
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+export class SdfEncoder implements Encoder<string> {
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+ private builder: StringBuilder;
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+ private meta: StringBuilder;
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+ private encoded = false;
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+ private dataBlockCreated = false;
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+ private error = false;
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+
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+ writeTo(stream: Writer) {
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+ const chunks = StringBuilder.getChunks(this.builder);
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+ for (let i = 0, _i = chunks.length; i < _i; i++) {
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+ stream.writeString(chunks[i]);
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+ }
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+ }
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+
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+ getSize() {
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+ return StringBuilder.getSize(this.builder);
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+ }
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+
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+ getData() {
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+ return StringBuilder.getString(this.builder);
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+ }
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+
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+ startDataBlock(name: string) {
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+ this.dataBlockCreated = true;
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+ StringBuilder.write(this.builder, `${name}\nCreated by ${this.encoder}\n\n`);
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+ }
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+
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+ writeCategory<Ctx>(category: Category<Ctx>, context?: Ctx) {
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+ if (this.encoded) {
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+ throw new Error('The writer contents have already been encoded, no more writing.');
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+ }
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+
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+ if (!this.dataBlockCreated) {
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+ throw new Error('No data block created.');
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+ }
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+
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+ if (!this.hideMetaInformation && (category.name === 'model_server_result' || category.name === 'model_server_params' || category.name === 'model_server_stats' || category.name === 'model_server_error')) {
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+ this.writeFullCategory(this.meta, category, context);
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+ // if error: force writing of meta information
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+ if (category.name === 'model_server_error') {
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+ this.error = true;
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+ }
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+ return;
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+ }
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+
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+ // ignore meta, error, and misc categories when writing SDF
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+ if (category.name !== 'atom_site') {
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+ return;
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+ }
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+
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+ // use separate builder because we still need to write Counts and Bonds line
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+ const ctab = StringBuilder.create();
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+ const bonds = StringBuilder.create();
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+ const charges = StringBuilder.create();
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+
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+ // write Atom block and gather data for Bonds and Charges
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+ // 'Specifies the atomic symbol and any mass difference, charge, stereochemistry, and associated hydrogens for each atom.'
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+ const { instance, source, rowCount: atomCount } = getCategoryInstanceData(category, context);
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+ const fields = this.getSortedFields(instance);
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+ const fieldCount = fields.length;
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+ let bondCount = 0;
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+
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+ let index = 0;
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+ for (let _c = 0; _c < source.length; _c++) {
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+ const src = source[_c];
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+ const data = src.data;
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+
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+ if (src.rowCount === 0) continue;
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+
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+ const it = src.keys();
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+ while (it.hasNext) {
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+ const key = it.move();
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+
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+ for (let _f = 0; _f < fieldCount; _f++) {
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+ const f: Field<any, any> = fields[_f]!;
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+ const val = f.value(key, data, index);
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+ this.writeValue(ctab, val, f.type);
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+ }
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+
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+ StringBuilder.writeSafe(ctab, ' 0 0 0 0 0\n');
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+
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+ index++;
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+ }
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+ }
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+
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+ // write counts line
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+ // 'Important specifications here relate to the number of atoms, bonds, and atom lists, the chiral flag setting, and the Ctab version.'
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+ StringBuilder.writeIntegerPadLeft(this.builder, atomCount, 3);
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+ StringBuilder.writeIntegerPadLeft(this.builder, bondCount, 3);
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+ StringBuilder.write(this.builder, ' 0 0 0 0 0 0 0 0999 V2000\n');
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+
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+ StringBuilder.writeSafe(this.builder, StringBuilder.getString(ctab));
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+ StringBuilder.writeSafe(this.builder, StringBuilder.getString(bonds));
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+ StringBuilder.writeSafe(this.builder, StringBuilder.getString(charges));
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+
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+ StringBuilder.writeSafe(this.builder, 'M END\n');
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+ }
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+
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+ private writeFullCategory<Ctx>(sb: StringBuilder, category: Category<Ctx>, context?: Ctx) {
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+ const { instance, source } = getCategoryInstanceData(category, context);
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+ const fields = instance.fields;
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+ const src = source[0];
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+ const data = src.data;
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+
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+ const it = src.keys();
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+ const key = it.move();
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+ for (let _f = 0; _f < fields.length; _f++) {
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+ const f = fields[_f]!;
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+
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+ StringBuilder.writeSafe(sb, `> <${category.name}.${f.name}>\n`);
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+ const val = f.value(key, data, 0);
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+ StringBuilder.writeSafe(sb, val as string);
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+ StringBuilder.writeSafe(sb, '\n\n');
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+ }
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+ }
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+
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+ private writeValue(sb: StringBuilder, val: string | number, t: Field.Type, floatPrecision: number = 4) {
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+ if (t === Field.Type.Str) {
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+ // type_symbol is the only string field - width 2, right-padded
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+ StringBuilder.whitespace1(sb);
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+ StringBuilder.writePadRight(sb, val as string, 2);
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+ } else if (t === Field.Type.Int) {
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+ StringBuilder.writeInteger(sb, val as number);
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+ } else {
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+ // coordinates have width 10 and are left-padded
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+ StringBuilder.writePadLeft(sb, (val as number).toFixed(floatPrecision), 10);
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+ }
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+ }
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+
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+ private getSortedFields<Ctx>(instance: Category.Instance<Ctx>) {
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+ return ['Cartn_x', 'Cartn_y', 'Cartn_z', 'type_symbol']
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+ .map(n => instance.fields.find(f => f.name === n));
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+ }
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+
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+ readonly isBinary = false;
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+ binaryEncodingProvider = void 0;
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+
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+ encode() {
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+ // write meta-information, do so after ctab
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+ if (this.error || !this.hideMetaInformation) {
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+ StringBuilder.writeSafe(this.builder, StringBuilder.getString(this.meta));
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+ }
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+
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+ // terminate file
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+ StringBuilder.writeSafe(this.builder, '$$$$\n');
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+
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+ this.encoded = true;
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+ }
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+
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+ setFilter(filter?: Category.Filter) {}
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+
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+ setFormatter(formatter?: Category.Formatter) {}
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+
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+ isCategoryIncluded(name: string) {
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+ return true;
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+ }
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+
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+ constructor(readonly encoder: string, readonly hideMetaInformation: boolean) {
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+ this.builder = StringBuilder.create();
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+ this.meta = StringBuilder.create();
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+ }
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+}
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JonStargaryen