sdf-parser 5.0.2 → 6.0.1

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Files changed (13) hide show
  1. package/README.md +9 -30
  2. package/lib/index.js +141 -132
  3. package/package.json +11 -12
  4. package/src/__tests__/__snapshots__/getEntriesBoundaries.test.js.snap +2 -2
  5. package/src/__tests__/iterator.test.js +183 -0
  6. package/src/__tests__/test.sdf.gz +0 -0
  7. package/src/index.js +1 -1
  8. package/src/iterator.browser.js +3 -0
  9. package/src/iterator.js +54 -0
  10. package/src/parse.js +37 -86
  11. package/src/util/getMolecule.js +55 -0
  12. package/src/__tests__/stream.test.js +0 -98
  13. package/src/stream.js +0 -45
package/README.md CHANGED
@@ -57,39 +57,18 @@ var result = parse(sdf, {
57
57
  });
58
58
  ```
59
59
 
60
- ## Streams
60
+ ## Iterator
61
61
 
62
62
  This API is only available on Node.js.
63
63
 
64
- ### molecules(options)
65
-
66
- Transform an input text stream to a stream of molecule objects.
67
-
68
- #### options
69
-
70
- - `fullResult`: true to emit the full result of `parse` instead of just the molecules.
71
- - All other options from the `parse` function.
72
-
73
- ```js
74
- const { stream } = require('sdf-parser');
75
- fs.createReadStream('test.sdf')
76
- .pipe(stream.molecules())
77
- .on('data', (molecule) => {
78
- console.log(molecule.molfile);
79
- });
80
- ```
81
-
82
- ### entries()
83
-
84
- Transform an input text stream to a stream of sdf entries.
85
-
86
64
  ```js
87
- const { stream } = require('sdf-parser');
88
- fs.createReadStream('test.sdf')
89
- .pipe(stream.entries())
90
- .on('data', (entry) => {
91
- // sdf entry as a string
92
- });
65
+ const { iterator } = require('sdf-parser');
66
+ const readStream = createReadStream(join(__dirname, 'test.sdf.gz'));
67
+ const stream = readStream.pipe(createGunzip());
68
+ const results = [];
69
+ for await (const entry of iterator(stream)) {
70
+ results.push(entry);
71
+ }
93
72
  ```
94
73
 
95
74
  ## License
@@ -98,7 +77,7 @@ fs.createReadStream('test.sdf')
98
77
 
99
78
  [npm-image]: https://img.shields.io/npm/v/sdf-parser.svg?style=flat-square
100
79
  [npm-url]: https://www.npmjs.com/package/sdf-parser
101
- [travis-image]: https://img.shields.io/travis/cheminfo/sdf-parser/master.svg?style=flat-square
80
+ [travis-image]: https://img.shields.io/travis/cheminfo/sdf-parser/main.svg?style=flat-square
102
81
  [travis-url]: https://travis-ci.org/cheminfo/sdf-parser
103
82
  [download-image]: https://img.shields.io/npm/dm/sdf-parser.svg?style=flat-square
104
83
  [download-url]: https://www.npmjs.com/package/sdf-parser
package/lib/index.js CHANGED
@@ -3,17 +3,8 @@
3
3
  Object.defineProperty(exports, '__esModule', { value: true });
4
4
 
5
5
  var ensureString = require('ensure-string');
6
- var pipeline = require('pumpify');
7
- var split2 = require('split2');
8
- var through2 = require('through2');
9
- var filter = require('through2-filter');
10
-
11
- function _interopDefaultLegacy (e) { return e && typeof e === 'object' && 'default' in e ? e : { 'default': e }; }
12
-
13
- var pipeline__default = /*#__PURE__*/_interopDefaultLegacy(pipeline);
14
- var split2__default = /*#__PURE__*/_interopDefaultLegacy(split2);
15
- var through2__default = /*#__PURE__*/_interopDefaultLegacy(through2);
16
- var filter__default = /*#__PURE__*/_interopDefaultLegacy(filter);
6
+ var readline = require('readline');
7
+ var dynamicTyping = require('dynamic-typing');
17
8
 
18
9
  function getEntriesBoundaries(string, substring, eol) {
19
10
  const res = [];
@@ -37,46 +28,106 @@ function getEntriesBoundaries(string, substring, eol) {
37
28
  return res;
38
29
  }
39
30
 
31
+ function getMolecule$1(sdfPart, labels, currentLabels, options) {
32
+ let parts = sdfPart.split(`${options.eol}>`);
33
+ if (parts.length === 0 || parts[0].length <= 5) return;
34
+ let molecule = {};
35
+ molecule.molfile = parts[0] + options.eol;
36
+ for (let j = 1; j < parts.length; j++) {
37
+ let lines = parts[j].split(options.eol);
38
+ let from = lines[0].indexOf('<');
39
+ let to = lines[0].indexOf('>');
40
+ let label = lines[0].substring(from + 1, to);
41
+ currentLabels.push(label);
42
+ if (!labels[label]) {
43
+ labels[label] = {
44
+ counter: 0,
45
+ isNumeric: options.dynamicTyping,
46
+ keep: false,
47
+ };
48
+ if (
49
+ (!options.exclude || options.exclude.indexOf(label) === -1) &&
50
+ (!options.include || options.include.indexOf(label) > -1)
51
+ ) {
52
+ labels[label].keep = true;
53
+ if (options.modifiers[label]) {
54
+ labels[label].modifier = options.modifiers[label];
55
+ }
56
+ if (options.forEach[label]) {
57
+ labels[label].forEach = options.forEach[label];
58
+ }
59
+ }
60
+ }
61
+ if (labels[label].keep) {
62
+ for (let k = 1; k < lines.length - 1; k++) {
63
+ if (molecule[label]) {
64
+ molecule[label] += options.eol + lines[k];
65
+ } else {
66
+ molecule[label] = lines[k];
67
+ }
68
+ }
69
+ if (labels[label].modifier) {
70
+ let modifiedValue = labels[label].modifier(molecule[label]);
71
+ if (modifiedValue === undefined || modifiedValue === null) {
72
+ delete molecule[label];
73
+ } else {
74
+ molecule[label] = modifiedValue;
75
+ }
76
+ }
77
+ if (labels[label].isNumeric) {
78
+ if (!isFinite(molecule[label]) || molecule[label].match(/^0[0-9]/)) {
79
+ labels[label].isNumeric = false;
80
+ }
81
+ }
82
+ }
83
+ }
84
+ return molecule;
85
+ }
86
+
40
87
  /**
41
88
  * Parse a SDF file
42
89
  * @param {string|ArrayBuffer|Uint8Array} sdf SDF file to parse
43
- * @param {any} [options={}]
44
- * @param {array<string>} [options.include] List of fields to include
45
- * @param {array<string>} [options.exclude] List of fields to exclude
90
+ * @param {object} [options={}]
91
+ * @param {string[]} [options.include] List of fields to include
92
+ * @param {string[]} [options.exclude] List of fields to exclude
93
+ * @param {Function} [options.filter] Callback allowing to filter the molecules
46
94
  * @param {boolean} [options.dynamicTyping] Dynamically type the data
47
95
  * @param {object} [options.modifiers] Object containing callbacks to apply on some specific fields
48
96
  * @param {boolean} [options.mixedEOL=false] Set to true if you know there is a mixture between \r\n and \n
97
+ * @param {string} [options.eol] Specify the end of line character. Default will be the one found in the file
49
98
  */
50
99
  function parse(sdf, options = {}) {
51
- const {
52
- include,
53
- exclude,
54
- filter,
55
- modifiers = {},
56
- forEach = {},
57
- dynamicTyping = true,
58
- } = options;
100
+ options = { ...options };
101
+ if (options.modifiers === undefined) options.modifiers = {};
102
+ if (options.forEach === undefined) options.forEach = {};
103
+ if (options.dynamicTyping === undefined) options.dynamicTyping = true;
59
104
 
60
105
  sdf = ensureString.ensureString(sdf);
61
106
  if (typeof sdf !== 'string') {
62
107
  throw new TypeError('Parameter "sdf" must be a string');
63
108
  }
64
109
 
65
- let eol = '\n';
66
- if (options.mixedEOL) {
67
- sdf = sdf.replace(/\r\n/g, '\n');
68
- sdf = sdf.replace(/\r/g, '\n');
69
- } else {
70
- // we will find the delimiter in order to be much faster and not use regular expression
71
- let header = sdf.substr(0, 1000);
72
- if (header.indexOf('\r\n') > -1) {
73
- eol = '\r\n';
74
- } else if (header.indexOf('\r') > -1) {
75
- eol = '\r';
110
+ if (options.eol === undefined) {
111
+ options.eol = '\n';
112
+ if (options.mixedEOL) {
113
+ sdf = sdf.replace(/\r\n/g, '\n');
114
+ sdf = sdf.replace(/\r/g, '\n');
115
+ } else {
116
+ // we will find the delimiter in order to be much faster and not use regular expression
117
+ let header = sdf.substr(0, 1000);
118
+ if (header.indexOf('\r\n') > -1) {
119
+ options.eol = '\r\n';
120
+ } else if (header.indexOf('\r') > -1) {
121
+ options.eol = '\r';
122
+ }
76
123
  }
77
124
  }
78
125
 
79
- let entriesBoundaries = getEntriesBoundaries(sdf, `${eol}$$$$`, eol);
126
+ let entriesBoundaries = getEntriesBoundaries(
127
+ sdf,
128
+ `${options.eol}$$$$`,
129
+ options.eol,
130
+ );
80
131
  let molecules = [];
81
132
  let labels = {};
82
133
 
@@ -84,72 +135,18 @@ function parse(sdf, options = {}) {
84
135
 
85
136
  for (let i = 0; i < entriesBoundaries.length; i++) {
86
137
  let sdfPart = sdf.substring(...entriesBoundaries[i]);
87
- let parts = sdfPart.split(`${eol}>`);
88
- if (parts.length > 0 && parts[0].length > 5) {
89
- let molecule = {};
90
- let currentLabels = [];
91
- molecule.molfile = parts[0] + eol;
92
- for (let j = 1; j < parts.length; j++) {
93
- let lines = parts[j].split(eol);
94
- let from = lines[0].indexOf('<');
95
- let to = lines[0].indexOf('>');
96
- let label = lines[0].substring(from + 1, to);
97
- currentLabels.push(label);
98
- if (!labels[label]) {
99
- labels[label] = {
100
- counter: 0,
101
- isNumeric: dynamicTyping,
102
- keep: false,
103
- };
104
- if (
105
- (!exclude || exclude.indexOf(label) === -1) &&
106
- (!include || include.indexOf(label) > -1)
107
- ) {
108
- labels[label].keep = true;
109
- if (modifiers[label]) {
110
- labels[label].modifier = modifiers[label];
111
- }
112
- if (forEach[label]) {
113
- labels[label].forEach = forEach[label];
114
- }
115
- }
116
- }
117
- if (labels[label].keep) {
118
- for (let k = 1; k < lines.length - 1; k++) {
119
- if (molecule[label]) {
120
- molecule[label] += eol + lines[k];
121
- } else {
122
- molecule[label] = lines[k];
123
- }
124
- }
125
- if (labels[label].modifier) {
126
- let modifiedValue = labels[label].modifier(molecule[label]);
127
- if (modifiedValue === undefined || modifiedValue === null) {
128
- delete molecule[label];
129
- } else {
130
- molecule[label] = modifiedValue;
131
- }
132
- }
133
- if (labels[label].isNumeric) {
134
- if (
135
- !isFinite(molecule[label]) ||
136
- molecule[label].match(/^0[0-9]/)
137
- ) {
138
- labels[label].isNumeric = false;
139
- }
140
- }
141
- }
142
- }
143
- if (!filter || filter(molecule)) {
144
- molecules.push(molecule);
145
- // only now we can increase the counter
146
- for (let j = 0; j < currentLabels.length; j++) {
147
- labels[currentLabels[j]].counter++;
148
- }
138
+
139
+ let currentLabels = [];
140
+ const molecule = getMolecule$1(sdfPart, labels, currentLabels, options);
141
+ if (!molecule) continue;
142
+ if (!options.filter || options.filter(molecule)) {
143
+ molecules.push(molecule);
144
+ // only now we can increase the counter
145
+ for (let j = 0; j < currentLabels.length; j++) {
146
+ labels[currentLabels[j]].counter++;
149
147
  }
150
148
  }
151
149
  }
152
-
153
150
  // all numeric fields should be converted to numbers
154
151
  for (let label in labels) {
155
152
  let currentLabel = labels[label];
@@ -195,45 +192,57 @@ function parse(sdf, options = {}) {
195
192
  };
196
193
  }
197
194
 
198
- const filterStream = filter__default["default"].bind(null, { objectMode: true });
199
-
200
- function filterCb(chunk) {
201
- return chunk.length > 1 && chunk.trim().length > 1;
202
- }
195
+ /**
196
+ * Parse a SDF file
197
+ * @param {NodeJS.ReadableStream} readStream SDF file to parse
198
+ * @param {object} [options={}]
199
+ * @param {Function} [options.filter] Callback allowing to filter the molecules
200
+ * @param {boolean} [options.dynamicTyping] Dynamically type the data
201
+ */
203
202
 
204
- function entries() {
205
- return pipeline__default["default"].obj(
206
- split2__default["default"](/\r?\n\${4}.*\r?\n/),
207
- filterStream(filterCb),
208
- through2__default["default"]({ objectMode: true }, function process(value, encoding, callback) {
209
- const eol = value.includes('\r\n') ? '\r\n' : '\n';
210
- this.push(`${value + eol}$$$$${eol}`);
211
- callback();
212
- }),
213
- );
203
+ async function* iterator(readStream, options = {}) {
204
+ const lines = readline.createInterface(readStream);
205
+ const currentLines = [];
206
+ options = { ...options };
207
+ if (options.dynamicTyping === undefined) options.dynamicTyping = true;
208
+
209
+ options.eol = '\n';
210
+ for await (let line of lines) {
211
+ if (line.startsWith('$$$$')) {
212
+ const molecule = getMolecule(currentLines.join(options.eol), options);
213
+ if (!options.filter || options.filter(molecule)) {
214
+ yield molecule;
215
+ }
216
+ currentLines.length = 0;
217
+ } else {
218
+ currentLines.push(line);
219
+ }
220
+ }
214
221
  }
215
222
 
216
- function molecules(options) {
217
- return pipeline__default["default"].obj(
218
- entries(),
219
- through2__default["default"]({ objectMode: true }, function process(value, encoding, callback) {
220
- try {
221
- const parsed = parse(value, options);
222
- if (parsed.molecules.length === 1) {
223
- if (options && options.fullResult) {
224
- this.push(parsed);
225
- } else {
226
- this.push(parsed.molecules[0]);
227
- }
228
- }
229
- callback();
230
- } catch (e) {
231
- callback(e);
223
+ function getMolecule(sdfPart, options) {
224
+ let parts = sdfPart.split(`${options.eol}>`);
225
+ if (parts.length === 0 || parts[0].length <= 5) return;
226
+ let molecule = {};
227
+ molecule.molfile = parts[0] + options.eol;
228
+ for (let j = 1; j < parts.length; j++) {
229
+ let lines = parts[j].split(options.eol);
230
+ let from = lines[0].indexOf('<');
231
+ let to = lines[0].indexOf('>');
232
+ let label = lines[0].substring(from + 1, to);
233
+ for (let k = 1; k < lines.length - 1; k++) {
234
+ if (molecule[label]) {
235
+ molecule[label] += options.eol + lines[k];
236
+ } else {
237
+ molecule[label] = lines[k];
232
238
  }
233
- }),
234
- );
239
+ }
240
+ if (options.dynamicTyping) {
241
+ molecule[label] = dynamicTyping.parseString(molecule[label]);
242
+ }
243
+ }
244
+ return molecule;
235
245
  }
236
246
 
237
- exports.entries = entries;
238
- exports.molecules = molecules;
247
+ exports.iterator = iterator;
239
248
  exports.parse = parse;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "sdf-parser",
3
- "version": "5.0.2",
3
+ "version": "6.0.1",
4
4
  "description": "SDF parser",
5
5
  "main": "lib/index.js",
6
6
  "module": "src/index.js",
@@ -8,9 +8,12 @@
8
8
  "lib",
9
9
  "src"
10
10
  ],
11
+ "browser": {
12
+ "./src/iterator.js": "./src/iterator.browser.js"
13
+ },
11
14
  "sideEffects": false,
12
15
  "scripts": {
13
- "build": "npm run compile && cheminfo-build --root SDFParser",
16
+ "build": "cheminfo-build --entry src/index.js --root SDFParser",
14
17
  "compile": "rollup -c",
15
18
  "eslint": "eslint src",
16
19
  "eslint-fix": "npm run eslint -- --fix",
@@ -21,9 +24,6 @@
21
24
  "test-coverage": "jest --coverage",
22
25
  "test-only": "jest"
23
26
  },
24
- "browser": {
25
- "./src/stream.js": "./src/stream.browser.js"
26
- },
27
27
  "repository": {
28
28
  "type": "git",
29
29
  "url": "https://github.com/cheminfo/sdf-parser.git"
@@ -44,20 +44,19 @@
44
44
  "homepage": "https://github.com/cheminfo/sdf-parser",
45
45
  "devDependencies": {
46
46
  "@babel/plugin-transform-modules-commonjs": "^7.18.6",
47
+ "@types/jest": "^29.1.2",
47
48
  "babel-eslint": "^10.1.0",
48
49
  "callback-stream": "^1.1.0",
49
50
  "cheminfo-build": "^1.1.11",
50
- "eslint": "^8.22.0",
51
+ "eslint": "^8.25.0",
51
52
  "eslint-config-cheminfo": "^8.0.2",
52
- "jest": "^28.1.3",
53
+ "filelist-utils": "^1.0.1",
54
+ "jest": "^29.2.0",
53
55
  "openchemlib": "^8.0.1",
54
56
  "prettier": "^2.7.1"
55
57
  },
56
58
  "dependencies": {
57
- "ensure-string": "^1.2.0",
58
- "pumpify": "^2.0.1",
59
- "split2": "^4.1.0",
60
- "through2": "^4.0.2",
61
- "through2-filter": "^3.0.0"
59
+ "dynamic-typing": "^1.0.0",
60
+ "ensure-string": "^1.2.0"
62
61
  }
63
62
  }
package/src/__tests__/__snapshots__/getEntriesBoundaries.test.js.snap CHANGED
@@ -1,8 +1,8 @@
1
1
  // Jest Snapshot v1, https://goo.gl/fbAQLP
2
2
 
3
3
  exports[`should parse sdf files without EOL in the EOF 1`] = `
4
- Array [
5
- Array [
4
+ [
5
+ [
6
6
  0,
7
7
  1473,
8
8
  ],
package/src/__tests__/iterator.test.js ADDED
@@ -0,0 +1,183 @@
1
+ import { createReadStream, ReadStream } from 'fs';
2
+ import { join } from 'path';
3
+ import { createGunzip } from 'zlib';
4
+
5
+ import { fileCollectionFromPath } from 'filelist-utils';
6
+
7
+ import { iterator } from '../iterator';
8
+
9
+ test('iterator', async () => {
10
+ const files = (
11
+ await fileCollectionFromPath(join(__dirname, '.'))
12
+ ).files.filter((file) => file.name === 'test.sdf');
13
+ const results = [];
14
+
15
+ if (parseInt(process.versions.node) >= 18) {
16
+ for await (const entry of iterator(ReadStream.fromWeb(files[0].stream()))) {
17
+ results.push(entry);
18
+ }
19
+ expect(results).toHaveLength(128);
20
+ expect(results[0]).toMatchInlineSnapshot(`
21
+ {
22
+ "CLogP": 2.7,
23
+ "Code": 100380824,
24
+ "Number of H-Acceptors": 3,
25
+ "Number of H-Donors": 1,
26
+ "Number of Rotatable bonds": 1,
27
+ "molfile": "
28
+ -ISIS- 04231216572D
29
+
30
+ 15 16 0 0 0 0 0 0 0 0999 V2000
31
+ 2.4792 1.7000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
32
+ 2.4292 0.3500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
33
+ 0.4042 1.1208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
34
+ 1.2167 2.1833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
35
+ 1.1542 -0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
36
+ -0.9208 1.1208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
37
+ 3.4792 -0.4500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
38
+ 0.8792 3.4458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
39
+ -1.6000 -0.0292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
40
+ -0.9625 -1.1792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
41
+ -1.6208 -2.3292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
42
+ -0.9125 -3.4375 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
43
+ -3.5958 -1.1792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
44
+ -2.9208 -0.0292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
45
+ -3.0333 -2.3292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
46
+ 2 1 1 0 0 0 0
47
+ 3 4 1 0 0 0 0
48
+ 4 1 1 0 0 0 0
49
+ 5 2 1 0 0 0 0
50
+ 6 3 2 0 0 0 0
51
+ 7 2 2 0 0 0 0
52
+ 8 4 2 0 0 0 0
53
+ 9 6 1 0 0 0 0
54
+ 10 9 2 0 0 0 0
55
+ 11 10 1 0 0 0 0
56
+ 12 11 1 0 0 0 0
57
+ 13 14 2 0 0 0 0
58
+ 14 9 1 0 0 0 0
59
+ 15 13 1 0 0 0 0
60
+ 3 5 1 0 0 0 0
61
+ 15 11 2 0 0 0 0
62
+ M END
63
+ ",
64
+ }
65
+ `);
66
+ }
67
+ });
68
+
69
+ test('iterator on stream', async () => {
70
+ const readStream = createReadStream(join(__dirname, 'test.sdf.gz'));
71
+ const stream = readStream.pipe(createGunzip());
72
+ const results = [];
73
+ for await (const entry of iterator(stream)) {
74
+ results.push(entry);
75
+ }
76
+ expect(results).toHaveLength(128);
77
+ expect(results[0]).toMatchInlineSnapshot(`
78
+ {
79
+ "CLogP": 2.7,
80
+ "Code": 100380824,
81
+ "Number of H-Acceptors": 3,
82
+ "Number of H-Donors": 1,
83
+ "Number of Rotatable bonds": 1,
84
+ "molfile": "
85
+ -ISIS- 04231216572D
86
+
87
+ 15 16 0 0 0 0 0 0 0 0999 V2000
88
+ 2.4792 1.7000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
89
+ 2.4292 0.3500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
90
+ 0.4042 1.1208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
91
+ 1.2167 2.1833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
92
+ 1.1542 -0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
93
+ -0.9208 1.1208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
94
+ 3.4792 -0.4500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
95
+ 0.8792 3.4458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
96
+ -1.6000 -0.0292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
97
+ -0.9625 -1.1792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
98
+ -1.6208 -2.3292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
99
+ -0.9125 -3.4375 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
100
+ -3.5958 -1.1792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
101
+ -2.9208 -0.0292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
102
+ -3.0333 -2.3292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
103
+ 2 1 1 0 0 0 0
104
+ 3 4 1 0 0 0 0
105
+ 4 1 1 0 0 0 0
106
+ 5 2 1 0 0 0 0
107
+ 6 3 2 0 0 0 0
108
+ 7 2 2 0 0 0 0
109
+ 8 4 2 0 0 0 0
110
+ 9 6 1 0 0 0 0
111
+ 10 9 2 0 0 0 0
112
+ 11 10 1 0 0 0 0
113
+ 12 11 1 0 0 0 0
114
+ 13 14 2 0 0 0 0
115
+ 14 9 1 0 0 0 0
116
+ 15 13 1 0 0 0 0
117
+ 3 5 1 0 0 0 0
118
+ 15 11 2 0 0 0 0
119
+ M END
120
+ ",
121
+ }
122
+ `);
123
+ });
124
+
125
+ test('iterator on fileCollection stream', async () => {
126
+ const file = (await fileCollectionFromPath(join(__dirname, '.'))).filter(
127
+ (file) => file.size === 32233,
128
+ ).files[0];
129
+ const results = [];
130
+
131
+ if (parseInt(process.versions.node) >= 18) {
132
+ for await (const entry of iterator(ReadStream.fromWeb(file.stream()))) {
133
+ results.push(entry);
134
+ }
135
+ expect(results).toHaveLength(128);
136
+ expect(results[0]).toMatchInlineSnapshot(`
137
+ {
138
+ "CLogP": 2.7,
139
+ "Code": 100380824,
140
+ "Number of H-Acceptors": 3,
141
+ "Number of H-Donors": 1,
142
+ "Number of Rotatable bonds": 1,
143
+ "molfile": "
144
+ -ISIS- 04231216572D
145
+
146
+ 15 16 0 0 0 0 0 0 0 0999 V2000
147
+ 2.4792 1.7000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
148
+ 2.4292 0.3500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
149
+ 0.4042 1.1208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
150
+ 1.2167 2.1833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
151
+ 1.1542 -0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
152
+ -0.9208 1.1208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
153
+ 3.4792 -0.4500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
154
+ 0.8792 3.4458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
155
+ -1.6000 -0.0292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
156
+ -0.9625 -1.1792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
157
+ -1.6208 -2.3292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
158
+ -0.9125 -3.4375 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
159
+ -3.5958 -1.1792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
160
+ -2.9208 -0.0292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
161
+ -3.0333 -2.3292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
162
+ 2 1 1 0 0 0 0
163
+ 3 4 1 0 0 0 0
164
+ 4 1 1 0 0 0 0
165
+ 5 2 1 0 0 0 0
166
+ 6 3 2 0 0 0 0
167
+ 7 2 2 0 0 0 0
168
+ 8 4 2 0 0 0 0
169
+ 9 6 1 0 0 0 0
170
+ 10 9 2 0 0 0 0
171
+ 11 10 1 0 0 0 0
172
+ 12 11 1 0 0 0 0
173
+ 13 14 2 0 0 0 0
174
+ 14 9 1 0 0 0 0
175
+ 15 13 1 0 0 0 0
176
+ 3 5 1 0 0 0 0
177
+ 15 11 2 0 0 0 0
178
+ M END
179
+ ",
180
+ }
181
+ `);
182
+ }
183
+ });
package/src/__tests__/test.sdf.gz ADDED
Binary file
package/src/index.js CHANGED
@@ -1,2 +1,2 @@
1
1
  export * from './parse';
2
- export * from './stream';
2
+ export * from './iterator';
package/src/iterator.browser.js ADDED
@@ -0,0 +1,3 @@
1
+ export function iterator() {
2
+ throw new Error('Iterator not implemented in the browser');
3
+ }
package/src/iterator.js ADDED
@@ -0,0 +1,54 @@
1
+ import { createInterface } from 'readline';
2
+
3
+ import { parseString } from 'dynamic-typing';
4
+ /**
5
+ * Parse a SDF file
6
+ * @param {NodeJS.ReadableStream} readStream SDF file to parse
7
+ * @param {object} [options={}]
8
+ * @param {Function} [options.filter] Callback allowing to filter the molecules
9
+ * @param {boolean} [options.dynamicTyping] Dynamically type the data
10
+ */
11
+
12
+ export async function* iterator(readStream, options = {}) {
13
+ const lines = createInterface(readStream);
14
+ const currentLines = [];
15
+ options = { ...options };
16
+ if (options.dynamicTyping === undefined) options.dynamicTyping = true;
17
+
18
+ options.eol = '\n';
19
+ for await (let line of lines) {
20
+ if (line.startsWith('$$$$')) {
21
+ const molecule = getMolecule(currentLines.join(options.eol), options);
22
+ if (!options.filter || options.filter(molecule)) {
23
+ yield molecule;
24
+ }
25
+ currentLines.length = 0;
26
+ } else {
27
+ currentLines.push(line);
28
+ }
29
+ }
30
+ }
31
+
32
+ function getMolecule(sdfPart, options) {
33
+ let parts = sdfPart.split(`${options.eol}>`);
34
+ if (parts.length === 0 || parts[0].length <= 5) return;
35
+ let molecule = {};
36
+ molecule.molfile = parts[0] + options.eol;
37
+ for (let j = 1; j < parts.length; j++) {
38
+ let lines = parts[j].split(options.eol);
39
+ let from = lines[0].indexOf('<');
40
+ let to = lines[0].indexOf('>');
41
+ let label = lines[0].substring(from + 1, to);
42
+ for (let k = 1; k < lines.length - 1; k++) {
43
+ if (molecule[label]) {
44
+ molecule[label] += options.eol + lines[k];
45
+ } else {
46
+ molecule[label] = lines[k];
47
+ }
48
+ }
49
+ if (options.dynamicTyping) {
50
+ molecule[label] = parseString(molecule[label]);
51
+ }
52
+ }
53
+ return molecule;
54
+ }
package/src/parse.js CHANGED
@@ -1,46 +1,51 @@
1
1
  import { ensureString } from 'ensure-string';
2
2
 
3
3
  import { getEntriesBoundaries } from './getEntriesBoundaries';
4
+ import { getMolecule } from './util/getMolecule';
4
5
  /**
5
6
  * Parse a SDF file
6
7
  * @param {string|ArrayBuffer|Uint8Array} sdf SDF file to parse
7
- * @param {any} [options={}]
8
- * @param {array<string>} [options.include] List of fields to include
9
- * @param {array<string>} [options.exclude] List of fields to exclude
8
+ * @param {object} [options={}]
9
+ * @param {string[]} [options.include] List of fields to include
10
+ * @param {string[]} [options.exclude] List of fields to exclude
11
+ * @param {Function} [options.filter] Callback allowing to filter the molecules
10
12
  * @param {boolean} [options.dynamicTyping] Dynamically type the data
11
13
  * @param {object} [options.modifiers] Object containing callbacks to apply on some specific fields
12
14
  * @param {boolean} [options.mixedEOL=false] Set to true if you know there is a mixture between \r\n and \n
15
+ * @param {string} [options.eol] Specify the end of line character. Default will be the one found in the file
13
16
  */
14
17
  export function parse(sdf, options = {}) {
15
- const {
16
- include,
17
- exclude,
18
- filter,
19
- modifiers = {},
20
- forEach = {},
21
- dynamicTyping = true,
22
- } = options;
18
+ options = { ...options };
19
+ if (options.modifiers === undefined) options.modifiers = {};
20
+ if (options.forEach === undefined) options.forEach = {};
21
+ if (options.dynamicTyping === undefined) options.dynamicTyping = true;
23
22
 
24
23
  sdf = ensureString(sdf);
25
24
  if (typeof sdf !== 'string') {
26
25
  throw new TypeError('Parameter "sdf" must be a string');
27
26
  }
28
27
 
29
- let eol = '\n';
30
- if (options.mixedEOL) {
31
- sdf = sdf.replace(/\r\n/g, '\n');
32
- sdf = sdf.replace(/\r/g, '\n');
33
- } else {
34
- // we will find the delimiter in order to be much faster and not use regular expression
35
- let header = sdf.substr(0, 1000);
36
- if (header.indexOf('\r\n') > -1) {
37
- eol = '\r\n';
38
- } else if (header.indexOf('\r') > -1) {
39
- eol = '\r';
28
+ if (options.eol === undefined) {
29
+ options.eol = '\n';
30
+ if (options.mixedEOL) {
31
+ sdf = sdf.replace(/\r\n/g, '\n');
32
+ sdf = sdf.replace(/\r/g, '\n');
33
+ } else {
34
+ // we will find the delimiter in order to be much faster and not use regular expression
35
+ let header = sdf.substr(0, 1000);
36
+ if (header.indexOf('\r\n') > -1) {
37
+ options.eol = '\r\n';
38
+ } else if (header.indexOf('\r') > -1) {
39
+ options.eol = '\r';
40
+ }
40
41
  }
41
42
  }
42
43
 
43
- let entriesBoundaries = getEntriesBoundaries(sdf, `${eol}$$$$`, eol);
44
+ let entriesBoundaries = getEntriesBoundaries(
45
+ sdf,
46
+ `${options.eol}$$$$`,
47
+ options.eol,
48
+ );
44
49
  let molecules = [];
45
50
  let labels = {};
46
51
 
@@ -48,72 +53,18 @@ export function parse(sdf, options = {}) {
48
53
 
49
54
  for (let i = 0; i < entriesBoundaries.length; i++) {
50
55
  let sdfPart = sdf.substring(...entriesBoundaries[i]);
51
- let parts = sdfPart.split(`${eol}>`);
52
- if (parts.length > 0 && parts[0].length > 5) {
53
- let molecule = {};
54
- let currentLabels = [];
55
- molecule.molfile = parts[0] + eol;
56
- for (let j = 1; j < parts.length; j++) {
57
- let lines = parts[j].split(eol);
58
- let from = lines[0].indexOf('<');
59
- let to = lines[0].indexOf('>');
60
- let label = lines[0].substring(from + 1, to);
61
- currentLabels.push(label);
62
- if (!labels[label]) {
63
- labels[label] = {
64
- counter: 0,
65
- isNumeric: dynamicTyping,
66
- keep: false,
67
- };
68
- if (
69
- (!exclude || exclude.indexOf(label) === -1) &&
70
- (!include || include.indexOf(label) > -1)
71
- ) {
72
- labels[label].keep = true;
73
- if (modifiers[label]) {
74
- labels[label].modifier = modifiers[label];
75
- }
76
- if (forEach[label]) {
77
- labels[label].forEach = forEach[label];
78
- }
79
- }
80
- }
81
- if (labels[label].keep) {
82
- for (let k = 1; k < lines.length - 1; k++) {
83
- if (molecule[label]) {
84
- molecule[label] += eol + lines[k];
85
- } else {
86
- molecule[label] = lines[k];
87
- }
88
- }
89
- if (labels[label].modifier) {
90
- let modifiedValue = labels[label].modifier(molecule[label]);
91
- if (modifiedValue === undefined || modifiedValue === null) {
92
- delete molecule[label];
93
- } else {
94
- molecule[label] = modifiedValue;
95
- }
96
- }
97
- if (labels[label].isNumeric) {
98
- if (
99
- !isFinite(molecule[label]) ||
100
- molecule[label].match(/^0[0-9]/)
101
- ) {
102
- labels[label].isNumeric = false;
103
- }
104
- }
105
- }
106
- }
107
- if (!filter || filter(molecule)) {
108
- molecules.push(molecule);
109
- // only now we can increase the counter
110
- for (let j = 0; j < currentLabels.length; j++) {
111
- labels[currentLabels[j]].counter++;
112
- }
56
+
57
+ let currentLabels = [];
58
+ const molecule = getMolecule(sdfPart, labels, currentLabels, options);
59
+ if (!molecule) continue;
60
+ if (!options.filter || options.filter(molecule)) {
61
+ molecules.push(molecule);
62
+ // only now we can increase the counter
63
+ for (let j = 0; j < currentLabels.length; j++) {
64
+ labels[currentLabels[j]].counter++;
113
65
  }
114
66
  }
115
67
  }
116
-
117
68
  // all numeric fields should be converted to numbers
118
69
  for (let label in labels) {
119
70
  let currentLabel = labels[label];
package/src/util/getMolecule.js ADDED
@@ -0,0 +1,55 @@
1
+ export function getMolecule(sdfPart, labels, currentLabels, options) {
2
+ let parts = sdfPart.split(`${options.eol}>`);
3
+ if (parts.length === 0 || parts[0].length <= 5) return;
4
+ let molecule = {};
5
+ molecule.molfile = parts[0] + options.eol;
6
+ for (let j = 1; j < parts.length; j++) {
7
+ let lines = parts[j].split(options.eol);
8
+ let from = lines[0].indexOf('<');
9
+ let to = lines[0].indexOf('>');
10
+ let label = lines[0].substring(from + 1, to);
11
+ currentLabels.push(label);
12
+ if (!labels[label]) {
13
+ labels[label] = {
14
+ counter: 0,
15
+ isNumeric: options.dynamicTyping,
16
+ keep: false,
17
+ };
18
+ if (
19
+ (!options.exclude || options.exclude.indexOf(label) === -1) &&
20
+ (!options.include || options.include.indexOf(label) > -1)
21
+ ) {
22
+ labels[label].keep = true;
23
+ if (options.modifiers[label]) {
24
+ labels[label].modifier = options.modifiers[label];
25
+ }
26
+ if (options.forEach[label]) {
27
+ labels[label].forEach = options.forEach[label];
28
+ }
29
+ }
30
+ }
31
+ if (labels[label].keep) {
32
+ for (let k = 1; k < lines.length - 1; k++) {
33
+ if (molecule[label]) {
34
+ molecule[label] += options.eol + lines[k];
35
+ } else {
36
+ molecule[label] = lines[k];
37
+ }
38
+ }
39
+ if (labels[label].modifier) {
40
+ let modifiedValue = labels[label].modifier(molecule[label]);
41
+ if (modifiedValue === undefined || modifiedValue === null) {
42
+ delete molecule[label];
43
+ } else {
44
+ molecule[label] = modifiedValue;
45
+ }
46
+ }
47
+ if (labels[label].isNumeric) {
48
+ if (!isFinite(molecule[label]) || molecule[label].match(/^0[0-9]/)) {
49
+ labels[label].isNumeric = false;
50
+ }
51
+ }
52
+ }
53
+ }
54
+ return molecule;
55
+ }
package/src/__tests__/stream.test.js DELETED
@@ -1,98 +0,0 @@
1
- import fs from 'fs';
2
-
3
- import callbackStream from 'callback-stream';
4
- import OCL from 'openchemlib/minimal';
5
-
6
- import { entries, molecules } from '..';
7
-
8
- const cbStream = callbackStream.bind(null, { objectMode: true });
9
-
10
- describe('stream', () => {
11
- it('entries', () =>
12
- new Promise((resolve) => {
13
- fs.createReadStream(`${__dirname}/test.sdf`)
14
- .pipe(entries())
15
- .pipe(
16
- cbStream((err, data) => {
17
- expect(err).toBeNull();
18
- expect(data).toHaveLength(128);
19
- expect(data[0]).toContain('-ISIS- 04231216572D');
20
- const mol = OCL.Molecule.fromMolfile(data[5]);
21
- expect(mol.toMolfile()).toContain(
22
- '17 18 0 0 0 0 0 0 0 0999 V2000',
23
- );
24
- resolve();
25
- }),
26
- );
27
- }));
28
-
29
- it('molecules', () =>
30
- new Promise((resolve) => {
31
- fs.createReadStream(`${__dirname}/test.sdf`)
32
- .pipe(molecules())
33
- .pipe(
34
- cbStream((err, data) => {
35
- expect(err).toBeNull();
36
- expect(data).toHaveLength(128);
37
- expect(data[0]).toMatchObject({
38
- Code: '0100380824',
39
- CLogP: 2.7,
40
- });
41
- expect(data[0].molfile).toContain('-ISIS- 04231216572D');
42
- resolve();
43
- }),
44
- );
45
- }));
46
-
47
- it('molecules - full result', () =>
48
- new Promise((resolve) => {
49
- fs.createReadStream(`${__dirname}/test.sdf`)
50
- .pipe(molecules({ fullResult: true }))
51
- .pipe(
52
- cbStream((err, data) => {
53
- expect(err).toBeNull();
54
- expect(data).toHaveLength(128);
55
- expect(data[0]).toMatchObject({
56
- labels: [
57
- 'Code',
58
- 'Number of H-Donors',
59
- 'Number of H-Acceptors',
60
- 'Number of Rotatable bonds',
61
- 'CLogP',
62
- ],
63
- });
64
- expect(data[0].molecules).toHaveLength(1);
65
- resolve();
66
- }),
67
- );
68
- }));
69
-
70
- it('molecules with filter', () =>
71
- new Promise((resolve) => {
72
- fs.createReadStream(`${__dirname}/test.sdf`)
73
- .pipe(
74
- molecules({
75
- filter: (entry) => entry.Code === '0100380869',
76
- }),
77
- )
78
- .pipe(
79
- cbStream((err, data) => {
80
- expect(err).toBeNull();
81
- expect(data).toHaveLength(1);
82
- resolve();
83
- }),
84
- );
85
- }));
86
-
87
- it('async iteration', async () => {
88
- const stream = fs
89
- .createReadStream(`${__dirname}/test.sdf`)
90
- .pipe(molecules());
91
- let count = 0;
92
- for await (const molecule of stream) {
93
- count++;
94
- expect(molecule.molfile.toString()).toContain('0999 V2000');
95
- }
96
- expect(count).toBe(128);
97
- });
98
- });
package/src/stream.js DELETED
@@ -1,45 +0,0 @@
1
- import pipeline from 'pumpify';
2
- import split2 from 'split2';
3
- import through2 from 'through2';
4
- import filter from 'through2-filter';
5
-
6
- import { parse } from './parse';
7
-
8
- const filterStream = filter.bind(null, { objectMode: true });
9
-
10
- function filterCb(chunk) {
11
- return chunk.length > 1 && chunk.trim().length > 1;
12
- }
13
-
14
- export function entries() {
15
- return pipeline.obj(
16
- split2(/\r?\n\${4}.*\r?\n/),
17
- filterStream(filterCb),
18
- through2({ objectMode: true }, function process(value, encoding, callback) {
19
- const eol = value.includes('\r\n') ? '\r\n' : '\n';
20
- this.push(`${value + eol}$$$$${eol}`);
21
- callback();
22
- }),
23
- );
24
- }
25
-
26
- export function molecules(options) {
27
- return pipeline.obj(
28
- entries(),
29
- through2({ objectMode: true }, function process(value, encoding, callback) {
30
- try {
31
- const parsed = parse(value, options);
32
- if (parsed.molecules.length === 1) {
33
- if (options && options.fullResult) {
34
- this.push(parsed);
35
- } else {
36
- this.push(parsed.molecules[0]);
37
- }
38
- }
39
- callback();
40
- } catch (e) {
41
- callback(e);
42
- }
43
- }),
44
- );
45
- }