sdf-parser 5.0.0

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Files changed (18) hide show
  1. package/LICENSE +22 -0
  2. package/README.md +104 -0
  3. package/lib/index.js +221 -0
  4. package/package.json +61 -0
  5. package/src/__tests__/checkOptions.test.js +57 -0
  6. package/src/__tests__/checkUndefined.test.js +24 -0
  7. package/src/__tests__/getEntriesBoundaries.test.js +26 -0
  8. package/src/__tests__/index.test.js +76 -0
  9. package/src/__tests__/notWellFormatted.test.js +14 -0
  10. package/src/__tests__/stream.test.js +98 -0
  11. package/src/__tests__/test.sdf +8707 -0
  12. package/src/__tests__/test1.sdf +38 -0
  13. package/src/__tests__/test2.sdf +498 -0
  14. package/src/getEntriesBoundaries.js +16 -0
  15. package/src/index.js +2 -0
  16. package/src/parse.js +148 -0
  17. package/src/stream.browser.js +3 -0
  18. package/src/stream.js +44 -0
package/src/__tests__/stream.test.js ADDED
@@ -0,0 +1,98 @@
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+ import fs from 'fs';
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+
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+ import callbackStream from 'callback-stream';
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+ import OCL from 'openchemlib/minimal';
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+
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+ import { entries, molecules } from '..';
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+
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+ const cbStream = callbackStream.bind(null, { objectMode: true });
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+
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+ describe('stream', () => {
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+ it('entries', () =>
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+ new Promise((resolve) => {
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+ fs.createReadStream(`${__dirname}/test.sdf`)
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+ .pipe(entries())
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+ .pipe(
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+ cbStream((err, data) => {
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+ expect(err).toBeNull();
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+ expect(data).toHaveLength(128);
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+ expect(data[0]).toContain('-ISIS- 04231216572D');
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+ const mol = OCL.Molecule.fromMolfile(data[5]);
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+ expect(mol.toMolfile()).toContain(
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+ '17 18 0 0 0 0 0 0 0 0999 V2000',
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+ );
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+ resolve();
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+ }),
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+ );
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+ }));
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+
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+ it('molecules', () =>
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+ new Promise((resolve) => {
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+ fs.createReadStream(`${__dirname}/test.sdf`)
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+ .pipe(molecules())
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+ .pipe(
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+ cbStream((err, data) => {
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+ expect(err).toBeNull();
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+ expect(data).toHaveLength(128);
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+ expect(data[0]).toMatchObject({
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+ Code: '0100380824',
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+ CLogP: 2.7,
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+ });
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+ expect(data[0].molfile).toContain('-ISIS- 04231216572D');
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+ resolve();
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+ }),
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+ );
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+ }));
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+
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+ it('molecules - full result', () =>
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+ new Promise((resolve) => {
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+ fs.createReadStream(`${__dirname}/test.sdf`)
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+ .pipe(molecules({ fullResult: true }))
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+ .pipe(
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+ cbStream((err, data) => {
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+ expect(err).toBeNull();
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+ expect(data).toHaveLength(128);
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+ expect(data[0]).toMatchObject({
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+ labels: [
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+ 'Code',
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+ 'Number of H-Donors',
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+ 'Number of H-Acceptors',
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+ 'Number of Rotatable bonds',
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+ 'CLogP',
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+ ],
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+ });
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+ expect(data[0].molecules).toHaveLength(1);
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+ resolve();
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+ }),
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+ );
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+ }));
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+
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+ it('molecules with filter', () =>
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+ new Promise((resolve) => {
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+ fs.createReadStream(`${__dirname}/test.sdf`)
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+ .pipe(
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+ molecules({
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+ filter: (entry) => entry.Code === '0100380869',
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+ }),
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+ )
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+ .pipe(
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+ cbStream((err, data) => {
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+ expect(err).toBeNull();
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+ expect(data).toHaveLength(1);
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+ resolve();
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+ }),
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+ );
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+ }));
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+
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+ it('async iteration', async () => {
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+ const stream = fs
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+ .createReadStream(`${__dirname}/test.sdf`)
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+ .pipe(molecules());
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+ let count = 0;
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+ for await (const molecule of stream) {
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+ count++;
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+ expect(molecule.molfile.toString()).toContain('0999 V2000');
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+ }
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+ expect(count).toBe(128);
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+ });
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+ });