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@@ -0,0 +1,91 @@
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+import './index.html'
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+import { CIF, CifCategory, CifField, getCifFieldType } from '../../mol-io/reader/cif';
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+import { CifWriter } from '../../mol-io/writer/cif';
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+import { classifyFloatArray, classifyIntArray } from '../../mol-io/common/binary-cif';
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+
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+async function parseCif(data: string|Uint8Array) {
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+ const comp = CIF.parse(data);
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+ const parsed = await comp.run();
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+ if (parsed.isError) throw parsed;
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+ return parsed.result;
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+}
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+
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+async function downloadCif(url: string, isBinary: boolean) {
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+ const data = await fetch(url);
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+ return parseCif(isBinary ? new Uint8Array(await data.arrayBuffer()) : await data.text());
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+}
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+
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+async function downloadFromPdb(pdb: string) {
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+ const parsed = await downloadCif(`https://webchem.ncbr.muni.cz/ModelServer/static/bcif/${pdb}`, true);
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+ return parsed.blocks[0];
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+}
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+
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+async function init(props = {}) {
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+ const cif = await downloadFromPdb('1brr')
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+ const encoder = CifWriter.createEncoder({
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+ binary: true,
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+ encoderName: 'mol*',
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+ binaryEncodingPovider: CifWriter.createEncodingProviderFromJsonConfig([
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+ {
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+ 'categoryName': 'atom_site',
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+ 'columnName': 'Cartn_y',
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+ 'encoding': 'rle',
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+ 'precision': 0
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+ },
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+ {
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+ 'categoryName': 'atom_site',
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+ 'columnName': 'Cartn_z',
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+ 'encoding': 'delta',
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+ 'precision': 1
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+ },
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+ {
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+ 'categoryName': 'atom_site',
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+ 'columnName': 'label_seq_id',
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+ 'encoding': 'delta-rle'
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+ }
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+ ])
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+ });
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+
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+ encoder.startDataBlock(cif.header);
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+ for (const c of cif.categoryNames) {
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+ const cat = cif.categories[c];
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+ const fields: CifWriter.Field[] = [];
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+ for (const f of cat.fieldNames) {
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+ fields.push(classify(f, cat.getField(f)!))
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+ }
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+
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+ encoder.writeCategory(getCategoryInstanceProvider(cif.categories[c], fields));
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+ }
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+ const ret = encoder.getData() as Uint8Array;
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+
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+ const cif2 = (await parseCif(ret)).blocks[0];
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+ // should be untouched
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+ console.log(cif2.categories['atom_site'].getField('Cartn_x'));
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+ // should have integer precision
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+ console.log(cif2.categories['atom_site'].getField('Cartn_y'));
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+ // should have 1 decimal place
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+ console.log(cif2.categories['atom_site'].getField('Cartn_z'));
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+ console.log(cif2.categories['atom_site'].getField('label_seq_id'));
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+}
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+
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+init()
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+
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+function getCategoryInstanceProvider(cat: CifCategory, fields: CifWriter.Field[]): CifWriter.Category {
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+ return {
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+ name: cat.name,
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+ instance: () => CifWriter.categoryInstance(fields, { data: cat, rowCount: cat.rowCount })
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+ };
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+}
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+
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+function classify(name: string, field: CifField): CifWriter.Field {
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+ const type = getCifFieldType(field);
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+ if (type['@type'] === 'str') {
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+ return { name, type: CifWriter.Field.Type.Str, value: field.str, valueKind: field.valueKind };
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+ } else if (type['@type'] === 'float') {
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+ const encoder = classifyFloatArray(field.toFloatArray({ array: Float64Array }));
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+ return CifWriter.Field.float(name, field.float, { valueKind: field.valueKind, encoder, typedArray: Float64Array });
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+ } else {
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+ const encoder = classifyIntArray(field.toIntArray({ array: Int32Array }));
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+ return CifWriter.Field.int(name, field.int, { valueKind: field.valueKind, encoder, typedArray: Int32Array });
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+ }
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+}
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Sebastian Bittrich