sdf-parser 5.0.1 → 5.0.2

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Files changed (7) hide show
  1. package/lib/index.js +9 -4
  2. package/package.json +8 -8
  3. package/src/__tests__/__snapshots__/getEntriesBoundaries.test.js.snap +10 -0
  4. package/src/__tests__/getEntriesBoundaries.test.js +7 -0
  5. package/src/__tests__/test4.sdf +37 -0
  6. package/src/getEntriesBoundaries.js +7 -2
  7. package/src/parse.js +2 -2
package/lib/index.js CHANGED
@@ -23,8 +23,13 @@ function getEntriesBoundaries(string, substring, eol) {
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  next = string.indexOf(substring, previous);
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  if (next !== -1) {
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  res.push([previous, next]);
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- previous = next =
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- string.indexOf(eol, next + substring.length) + eol.length;
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+ const nextMatch = string.indexOf(eol, next + substring.length);
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+ if (nextMatch === -1) {
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+ next = -1;
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+ } else {
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+ previous = nextMatch + eol.length;
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+ next = previous;
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+ }
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  } else {
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  res.push([previous, string.length]);
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  }
@@ -184,9 +189,9 @@ function parse(sdf, options = {}) {
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  return {
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  time: Date.now() - start,
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- molecules: molecules,
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+ molecules,
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  labels: Object.keys(labels),
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- statistics: statistics,
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+ statistics,
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  };
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  }
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package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "sdf-parser",
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- "version": "5.0.1",
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+ "version": "5.0.2",
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  "description": "SDF parser",
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  "main": "lib/index.js",
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  "module": "src/index.js",
@@ -43,18 +43,18 @@
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  },
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  "homepage": "https://github.com/cheminfo/sdf-parser",
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  "devDependencies": {
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- "@babel/plugin-transform-modules-commonjs": "^7.16.8",
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+ "@babel/plugin-transform-modules-commonjs": "^7.18.6",
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  "babel-eslint": "^10.1.0",
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  "callback-stream": "^1.1.0",
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  "cheminfo-build": "^1.1.11",
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- "eslint": "^8.10.0",
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- "eslint-config-cheminfo": "^7.3.0",
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- "jest": "^27.5.1",
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- "openchemlib": "^7.4.3",
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- "prettier": "^2.5.1"
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+ "eslint": "^8.22.0",
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+ "eslint-config-cheminfo": "^8.0.2",
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+ "jest": "^28.1.3",
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+ "openchemlib": "^8.0.1",
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+ "prettier": "^2.7.1"
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  },
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  "dependencies": {
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- "ensure-string": "^1.1.0",
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+ "ensure-string": "^1.2.0",
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  "pumpify": "^2.0.1",
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  "split2": "^4.1.0",
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  "through2": "^4.0.2",
package/src/__tests__/__snapshots__/getEntriesBoundaries.test.js.snap ADDED
@@ -0,0 +1,10 @@
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+ // Jest Snapshot v1, https://goo.gl/fbAQLP
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+
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+ exports[`should parse sdf files without EOL in the EOF 1`] = `
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+ Array [
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+ Array [
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+ 0,
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+ 1473,
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+ ],
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+ ]
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+ `;
package/src/__tests__/getEntriesBoundaries.test.js CHANGED
@@ -24,3 +24,10 @@ let sdf2 = fs.readFileSync(`${__dirname}/test2.sdf`, 'utf-8');
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  );
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  });
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  });
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+
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+ test('should parse sdf files without EOL in the EOF', () => {
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+ const eol = '\n';
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+ const sdf = fs.readFileSync(`${__dirname}/test4.sdf`, 'utf-8');
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+
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+ expect(getEntriesBoundaries(sdf, `${eol}$$$$`, eol)).toMatchSnapshot();
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+ });
package/src/__tests__/test4.sdf ADDED
@@ -0,0 +1,37 @@
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+
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+ -ISIS- 04231216572D
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+
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+ 15 16 0 0 0 0 0 0 0 0999 V2000
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+ 2.4792 1.7000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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+ 2.4292 0.3500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 0.4042 1.1208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 1.2167 2.1833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 1.1542 -0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
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+ -0.9208 1.1208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 3.4792 -0.4500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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+ 0.8792 3.4458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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+ -1.6000 -0.0292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ -0.9625 -1.1792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ -1.6208 -2.3292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ -0.9125 -3.4375 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
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+ -3.5958 -1.1792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ -2.9208 -0.0292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ -3.0333 -2.3292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 2 1 1 0 0 0 0
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+ 3 4 1 0 0 0 0
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+ 4 1 1 0 0 0 0
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+ 5 2 1 0 0 0 0
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+ 6 3 2 0 0 0 0
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+ 7 2 2 0 0 0 0
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+ 8 4 2 0 0 0 0
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+ 9 6 1 0 0 0 0
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+ 10 9 2 0 0 0 0
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+ 11 10 1 0 0 0 0
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+ 12 11 1 0 0 0 0
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+ 13 14 2 0 0 0 0
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+ 14 9 1 0 0 0 0
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+ 15 13 1 0 0 0 0
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+ 3 5 1 0 0 0 0
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+ 15 11 2 0 0 0 0
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+ M END
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+ $$$$
package/src/getEntriesBoundaries.js CHANGED
@@ -6,8 +6,13 @@ export function getEntriesBoundaries(string, substring, eol) {
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  next = string.indexOf(substring, previous);
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  if (next !== -1) {
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  res.push([previous, next]);
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- previous = next =
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- string.indexOf(eol, next + substring.length) + eol.length;
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+ const nextMatch = string.indexOf(eol, next + substring.length);
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+ if (nextMatch === -1) {
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+ next = -1;
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+ } else {
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+ previous = nextMatch + eol.length;
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+ next = previous;
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+ }
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  } else {
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  res.push([previous, string.length]);
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  }
package/src/parse.js CHANGED
@@ -153,8 +153,8 @@ export function parse(sdf, options = {}) {
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  return {
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  time: Date.now() - start,
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- molecules: molecules,
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+ molecules,
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  labels: Object.keys(labels),
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- statistics: statistics,
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+ statistics,
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  };
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  }