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fix space in the title line #6

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Merged
asiomchen merged 1 commit into from
Apr 16, 2026
Merged

fix space in the title line #6

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13 changes: 8 additions & 5 deletions src/import-utils.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -34,11 +34,14 @@ export function buildYaml(props: Record<string, string>): string {
const lines: string[] = [];
for (const [key, value] of Object.entries(props)) {
if (value.includes('\n')) {
// When the value starts with a newline (e.g. a MOL-block with a blank title
// line), the YAML parser cannot auto-detect indentation from the first line.
// Use an explicit indentation indicator (2) and strip chomping (-) so the
// leading blank line is preserved faithfully.
const header = value.startsWith('\n') ? '|2-' : '|';
// When the first line of the value is blank or whitespace-only (e.g. a
// MOL-block whose title line is empty or a single space), the YAML parser
// cannot reliably auto-detect indentation — it skips leading blank lines and
// picks up the indent from the first "real" line, which already has leading
// spaces, causing it to strip one extra space from every content line on
// re-read. Use an explicit indentation indicator (2) with strip chomping (-).
const firstLine = value.split('\n')[0];
const header = firstLine.trim() === '' ? '|2-' : '|';
lines.push(`${key}: ${header}`);
for (const line of value.split('\n')) {
lines.push(` ${line}`);
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116 changes: 116 additions & 0 deletions tests/data/no_first_name.sdf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,116 @@

-OEChem-04032607062D

24 25 0 0 0 0 0 0 0999 V2000
3.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.7321 -1.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5.5443 0.8047 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.8660 0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5.5443 -0.8047 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.1279 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.8550 1.7553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7479 -0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
3.1121 -2.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
3.7321 -2.6200 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
4.3521 -2.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
6.4443 1.5626 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
6.0476 2.3446 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
5.2656 1.9479 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.3100 1.5369 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4631 1.3100 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6900 0.4631 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 9 2 0 0 0 0
2 10 2 0 0 0 0
3 8 1 0 0 0 0
3 10 1 0 0 0 0
3 12 1 0 0 0 0
4 7 1 0 0 0 0
4 11 1 0 0 0 0
4 13 1 0 0 0 0
5 9 1 0 0 0 0
5 10 1 0 0 0 0
5 14 1 0 0 0 0
6 8 1 0 0 0 0
6 11 2 0 0 0 0
7 8 2 0 0 0 0
7 9 1 0 0 0 0
11 15 1 0 0 0 0
12 16 1 0 0 0 0
12 17 1 0 0 0 0
12 18 1 0 0 0 0
13 19 1 0 0 0 0
13 20 1 0 0 0 0
13 21 1 0 0 0 0
14 22 1 0 0 0 0
14 23 1 0 0 0 0
14 24 1 0 0 0 0
M END
> <PUBCHEM_COMPOUND_CID>
2519

$$$$
caffeine
-OEChem-04032607062D

24 25 0 0 0 0 0 0 0999 V2000
3.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.7321 -1.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5.5443 0.8047 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.8660 0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5.5443 -0.8047 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.1279 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.8550 1.7553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7479 -0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
3.1121 -2.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
3.7321 -2.6200 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
4.3521 -2.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
6.4443 1.5626 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
6.0476 2.3446 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
5.2656 1.9479 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.3100 1.5369 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4631 1.3100 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6900 0.4631 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 9 2 0 0 0 0
2 10 2 0 0 0 0
3 8 1 0 0 0 0
3 10 1 0 0 0 0
3 12 1 0 0 0 0
4 7 1 0 0 0 0
4 11 1 0 0 0 0
4 13 1 0 0 0 0
5 9 1 0 0 0 0
5 10 1 0 0 0 0
5 14 1 0 0 0 0
6 8 1 0 0 0 0
6 11 2 0 0 0 0
7 8 2 0 0 0 0
7 9 1 0 0 0 0
11 15 1 0 0 0 0
12 16 1 0 0 0 0
12 17 1 0 0 0 0
12 18 1 0 0 0 0
13 19 1 0 0 0 0
13 20 1 0 0 0 0
13 21 1 0 0 0 0
14 22 1 0 0 0 0
14 23 1 0 0 0 0
14 24 1 0 0 0 0
M END
> <PUBCHEM_COMPOUND_CID>
2519

$$$$
36 changes: 36 additions & 0 deletions tests/data/no_name_spaces.sdf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@

-INDIGO-04142622472D

6 6 0 0 0 0 0 0 0 0999 V2000
10.1348 -5.5001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.8652 -5.4996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.0016 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.8652 -6.5005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.1348 -6.5050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.0038 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3 1 2 0 0 0 0
1 5 1 0 0 0 0
5 6 2 0 0 0 0
6 4 1 0 0 0 0
4 2 2 0 0 0 0
2 3 1 0 0 0 0
M END
$$$$

-INDIGO-04

6 6 0 0 0 0 0 0 0 0999 V2000
10.1348 -5.5001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.8652 -5.4996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.0016 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.8652 -6.5005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.1348 -6.5050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.0038 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3 1 2 0 0 0 0
1 5 1 0 0 0 0
5 6 2 0 0 0 0
6 4 1 0 0 0 0
4 2 2 0 0 0 0
2 3 1 0 0 0 0
M END
$$$$
23 changes: 23 additions & 0 deletions tests/import-utils.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@ import { buildYaml, uniquePath } from '../src/import-utils';
const HEADER_LINE = ' -OEChem-04032607062D';
const NAMED_MOLBLOCK = `with_name\n${HEADER_LINE}\n\nM END`;
const BLANK_TITLE_MOLBLOCK = `\n${HEADER_LINE}\n\nM END`;
const SPACE_TITLE_MOLBLOCK = ` \n${HEADER_LINE}\n\nM END`;
const MULTI_SPACE_TITLE_MOLBLOCK = ` \n${HEADER_LINE}\n\nM END`;

describe('buildYaml – block scalar headers', () => {
it('named molblock uses plain | header', () => {
Expand All @@ -18,6 +20,27 @@ describe('buildYaml – block scalar headers', () => {
expect(yaml).toMatch(/^_m2b_molblock: \|2-$/m);
});

it('space-only title molblock uses |2- header', () => {
// no_first_name.sdf: title line is a single space, not a blank line
const yaml = buildYaml({ _m2b_molblock: SPACE_TITLE_MOLBLOCK });
expect(yaml).toMatch(/^_m2b_molblock: \|2-$/m);
});

it('multi-space title molblock uses |2- header', () => {
const yaml = buildYaml({ _m2b_molblock: MULTI_SPACE_TITLE_MOLBLOCK });
expect(yaml).toMatch(/^_m2b_molblock: \|2-$/m);
});

it('multi-space title molblock preserves title line and header line', () => {
const yaml = buildYaml({ _m2b_molblock: MULTI_SPACE_TITLE_MOLBLOCK });
const lines = yaml.split('\n');
const headerIdx = lines.findIndex((l) => l.startsWith('_m2b_molblock:'));
// Line after header: 2-space YAML indent + 3 spaces of title = 5 spaces
expect(lines[headerIdx + 1]).toBe(' ');
// Line after that: 2-space YAML indent + the OEChem header line
expect(lines[headerIdx + 2]).toBe(` ${HEADER_LINE}`);
});

it('|2- block scalar preserves the leading blank line', () => {
const yaml = buildYaml({ _m2b_molblock: BLANK_TITLE_MOLBLOCK });
// After the header line the very next line must be empty (the blank title)
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58 changes: 58 additions & 0 deletions tests/sdf-parser.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ import { readFileSync } from 'fs';
import { join } from 'path';
import { describe, it, expect } from 'vitest';
import { parseSdf } from '../src/sdf-parser';
import { buildYaml } from '../src/import-utils';

const SDF_PATH = join(__dirname, 'data', 'missing_names.sdf');
const sdfContent = readFileSync(SDF_PATH, 'utf-8');
Expand Down Expand Up @@ -77,6 +78,63 @@ describe('parseSdf – no_name_at_all.sdf', () => {
});
});

const NO_NAME_SPACES_PATH = join(__dirname, 'data', 'no_name_spaces.sdf');
const noNameSpacesContent = readFileSync(NO_NAME_SPACES_PATH, 'utf-8');

describe('parseSdf – no_name_spaces.sdf', () => {
const mols = parseSdf(noNameSpacesContent);

it('parses exactly 2 molecules', () => {
expect(mols).toHaveLength(2);
});

it('mol 1 – title line is 3 spaces (not empty, not named)', () => {
// Title line is " " (3 spaces): distinct from both blank (\n) and named titles.
// parseSdf must preserve it as-is so buildYaml can detect the whitespace-only
// first line and choose |2- over |.
const firstLine = mols[0].molblock.split('\n')[0];
expect(firstLine).toBe(' ');
});

it('mol 1 – molblock does NOT start with \\n (whitespace title, not blank title)', () => {
expect(mols[0].molblock.startsWith('\n')).toBe(false);
expect(mols[0].molblock.startsWith(' ')).toBe(true);
});

it('mol 1 – buildYaml uses |2- to prevent YAML indent auto-detection corruption', () => {
// Without |2-, YAML detects indent=4 from the first non-whitespace line
// (" -INDIGO...") and strips 4 spaces from every line, corrupting the molblock.
const yaml = buildYaml({ _m2b_molblock: mols[0].molblock });
expect(yaml).toMatch(/^_m2b_molblock: \|2-$/m);
});

it('mol 1 – molblock content is preserved correctly through buildYaml', () => {
const yaml = buildYaml({ _m2b_molblock: mols[0].molblock });
const lines = yaml.split('\n');
const headerIdx = lines.findIndex((l) => l.startsWith('_m2b_molblock:'));
// Title line: 2-space YAML indent + 3 spaces = 5 spaces
expect(lines[headerIdx + 1]).toBe(' ');
// Program line: 2-space YAML indent + " -INDIGO-..." (2 leading spaces preserved)
expect(lines[headerIdx + 2]).toBe(' -INDIGO-04142622472D');
});

it('mol 2 – blank title line (starts with \\n after leading-newline strip)', () => {
expect(mols[1].molblock.startsWith('\n')).toBe(true);
});

it('both molecules have M END in their molblock', () => {
for (const mol of mols) {
expect(mol.molblock).toContain('M END');
}
});

it('neither molecule has properties', () => {
for (const mol of mols) {
expect(Object.keys(mol.properties)).toHaveLength(0);
}
});
});

const DUP_PATH = join(__dirname, 'data', 'dup_names.sdf');
const dupContent = readFileSync(DUP_PATH, 'utf-8');

Expand Down
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