sdf-parser 7.0.4 → 8.0.0

package/lib/MolfileStream.d.ts

@@ -0,0 +1,20 @@
+/**
+ * A Web Streams API `TransformStream` that splits an incoming text stream on
+ * the `$$$$` SDF record delimiter and emits individual molfile strings.
+ *
+ * Entries shorter than 40 characters are discarded.
+ * @example
+ * ```ts
+ * const stream = readStream.pipeThrough(new MolfileStream());
+ * for await (const molfile of stream) {
+ *   console.log(molfile);
+ * }
+ * ```
+ */
+export declare class MolfileStream extends TransformStream<string, string> {
+    #private;
+    constructor(_options?: {
+        eol?: string;
+    });
+}
+//# sourceMappingURL=MolfileStream.d.ts.map

package/lib/MolfileStream.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"MolfileStream.d.ts","sourceRoot":"","sources":["../src/MolfileStream.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AACH,qBAAa,aAAc,SAAQ,eAAe,CAAC,MAAM,EAAE,MAAM,CAAC;;gBAIpD,QAAQ,CAAC,EAAE;QAAE,GAAG,CAAC,EAAE,MAAM,CAAA;KAAE;CAmCxC"}

package/lib/MolfileStream.js

@@ -0,0 +1,52 @@
+/**
+ * A Web Streams API `TransformStream` that splits an incoming text stream on
+ * the `$$$$` SDF record delimiter and emits individual molfile strings.
+ *
+ * Entries shorter than 40 characters are discarded.
+ * @example
+ * ```ts
+ * const stream = readStream.pipeThrough(new MolfileStream());
+ * for await (const molfile of stream) {
+ *   console.log(molfile);
+ * }
+ * ```
+ */
+export class MolfileStream extends TransformStream {
+    #buffer = [];
+    // eslint-disable-next-line @typescript-eslint/no-unused-vars
+    constructor(_options) {
+        super({
+            transform: (chunk, controller) => {
+                this.#buffer.push(chunk);
+                const combined = this.#buffer.join('');
+                this.#buffer.length = 0;
+                let begin = 0;
+                let index = 0;
+                while ((index = combined.indexOf('$$$$', index)) !== -1) {
+                    const endOfDelimiter = combined.indexOf('\n', index);
+                    if (endOfDelimiter === -1) {
+                        index = begin;
+                        break;
+                    }
+                    const eolLength = combined[endOfDelimiter - 1] === '\r' ? 2 : 1;
+                    // Remove the last eol before enqueuing
+                    if (index - eolLength - begin > 40) {
+                        controller.enqueue(combined.slice(begin, index - eolLength));
+                    }
+                    index = endOfDelimiter + eolLength;
+                    begin = index;
+                }
+                if (begin < combined.length) {
+                    this.#buffer.push(combined.slice(begin));
+                }
+            },
+            flush: (controller) => {
+                const remaining = this.#buffer.join('');
+                if (remaining && remaining.length > 40) {
+                    controller.enqueue(remaining);
+                }
+            },
+        });
+    }
+}
+//# sourceMappingURL=MolfileStream.js.map

package/lib/MolfileStream.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"MolfileStream.js","sourceRoot":"","sources":["../src/MolfileStream.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AACH,MAAM,OAAO,aAAc,SAAQ,eAA+B;IACvD,OAAO,GAAa,EAAE,CAAC;IAEhC,6DAA6D;IAC7D,YAAY,QAA2B;QACrC,KAAK,CAAC;YACJ,SAAS,EAAE,CAAC,KAAK,EAAE,UAAU,EAAE,EAAE;gBAC/B,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;gBACzB,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACvC,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC;gBAExB,IAAI,KAAK,GAAG,CAAC,CAAC;gBACd,IAAI,KAAK,GAAG,CAAC,CAAC;gBACd,OAAO,CAAC,KAAK,GAAG,QAAQ,CAAC,OAAO,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC;oBACxD,MAAM,cAAc,GAAG,QAAQ,CAAC,OAAO,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC;oBACrD,IAAI,cAAc,KAAK,CAAC,CAAC,EAAE,CAAC;wBAC1B,KAAK,GAAG,KAAK,CAAC;wBACd,MAAM;oBACR,CAAC;oBACD,MAAM,SAAS,GAAG,QAAQ,CAAC,cAAc,GAAG,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;oBAChE,uCAAuC;oBACvC,IAAI,KAAK,GAAG,SAAS,GAAG,KAAK,GAAG,EAAE,EAAE,CAAC;wBACnC,UAAU,CAAC,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAC,KAAK,EAAE,KAAK,GAAG,SAAS,CAAC,CAAC,CAAC;oBAC/D,CAAC;oBACD,KAAK,GAAG,cAAc,GAAG,SAAS,CAAC;oBACnC,KAAK,GAAG,KAAK,CAAC;gBAChB,CAAC;gBACD,IAAI,KAAK,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC;oBAC5B,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC;gBAC3C,CAAC;YACH,CAAC;YACD,KAAK,EAAE,CAAC,UAAU,EAAE,EAAE;gBACpB,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACxC,IAAI,SAAS,IAAI,SAAS,CAAC,MAAM,GAAG,EAAE,EAAE,CAAC;oBACvC,UAAU,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;gBAChC,CAAC;YACH,CAAC;SACF,CAAC,CAAC;IACL,CAAC;CACF"}

package/lib/getEntriesBoundaries.d.ts

@@ -0,0 +1,11 @@
+/**
+ * Get the [start, end] boundaries of each SDF entry in a string.
+ *
+ * Uses `indexOf` for fast splitting without regex overhead.
+ * @param string - The full SDF string.
+ * @param substring - The delimiter to search for (e.g. `'\n$$$$'`).
+ * @param eol - The end-of-line character used to skip past the delimiter line.
+ * @returns An array of `[start, end]` index pairs, one per SDF entry.
+ */
+export declare function getEntriesBoundaries(string: string, substring: string, eol: string): Array<[number, number]>;
+//# sourceMappingURL=getEntriesBoundaries.d.ts.map

package/lib/getEntriesBoundaries.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"getEntriesBoundaries.d.ts","sourceRoot":"","sources":["../src/getEntriesBoundaries.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AACH,wBAAgB,oBAAoB,CAClC,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,MAAM,EACjB,GAAG,EAAE,MAAM,GACV,KAAK,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAoBzB"}

package/lib/getEntriesBoundaries.js

@@ -0,0 +1,33 @@
+/**
+ * Get the [start, end] boundaries of each SDF entry in a string.
+ *
+ * Uses `indexOf` for fast splitting without regex overhead.
+ * @param string - The full SDF string.
+ * @param substring - The delimiter to search for (e.g. `'\n$$$$'`).
+ * @param eol - The end-of-line character used to skip past the delimiter line.
+ * @returns An array of `[start, end]` index pairs, one per SDF entry.
+ */
+export function getEntriesBoundaries(string, substring, eol) {
+    const res = [];
+    let previous = 0;
+    let next = 0;
+    while (next !== -1) {
+        next = string.indexOf(substring, previous);
+        if (next !== -1) {
+            res.push([previous, next]);
+            const nextMatch = string.indexOf(eol, next + substring.length);
+            if (nextMatch === -1) {
+                next = -1;
+            }
+            else {
+                previous = nextMatch + eol.length;
+                next = previous;
+            }
+        }
+        else {
+            res.push([previous, string.length]);
+        }
+    }
+    return res;
+}
+//# sourceMappingURL=getEntriesBoundaries.js.map

package/lib/getEntriesBoundaries.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"getEntriesBoundaries.js","sourceRoot":"","sources":["../src/getEntriesBoundaries.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AACH,MAAM,UAAU,oBAAoB,CAClC,MAAc,EACd,SAAiB,EACjB,GAAW;IAEX,MAAM,GAAG,GAA4B,EAAE,CAAC;IACxC,IAAI,QAAQ,GAAG,CAAC,CAAC;IACjB,IAAI,IAAI,GAAG,CAAC,CAAC;IACb,OAAO,IAAI,KAAK,CAAC,CAAC,EAAE,CAAC;QACnB,IAAI,GAAG,MAAM,CAAC,OAAO,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAC;QAC3C,IAAI,IAAI,KAAK,CAAC,CAAC,EAAE,CAAC;YAChB,GAAG,CAAC,IAAI,CAAC,CAAC,QAAQ,EAAE,IAAI,CAAC,CAAC,CAAC;YAC3B,MAAM,SAAS,GAAG,MAAM,CAAC,OAAO,CAAC,GAAG,EAAE,IAAI,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC;YAC/D,IAAI,SAAS,KAAK,CAAC,CAAC,EAAE,CAAC;gBACrB,IAAI,GAAG,CAAC,CAAC,CAAC;YACZ,CAAC;iBAAM,CAAC;gBACN,QAAQ,GAAG,SAAS,GAAG,GAAG,CAAC,MAAM,CAAC;gBAClC,IAAI,GAAG,QAAQ,CAAC;YAClB,CAAC;QACH,CAAC;aAAM,CAAC;YACN,GAAG,CAAC,IAAI,CAAC,CAAC,QAAQ,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;QACtC,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC"}

package/lib/index.d.ts

@@ -0,0 +1,4 @@
+export * from './parse.ts';
+export * from './iterator.ts';
+export * from './MolfileStream.ts';
+//# sourceMappingURL=index.d.ts.map

package/lib/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,YAAY,CAAC;AAC3B,cAAc,eAAe,CAAC;AAC9B,cAAc,oBAAoB,CAAC"}

package/lib/index.js

@@ -1,304 +1,4 @@
-'use strict';
-
-var ensureString = require('ensure-string');
-var dynamicTyping = require('dynamic-typing');
-
-/**
- *
- * @param {*} string
- * @param {*} substring
- * @param {*} eol
- * @returns
- */
-function getEntriesBoundaries(string, substring, eol) {
-  const res = [];
-  let previous = 0;
-  let next = 0;
-  while (next !== -1) {
-    next = string.indexOf(substring, previous);
-    if (next !== -1) {
-      res.push([previous, next]);
-      const nextMatch = string.indexOf(eol, next + substring.length);
-      if (nextMatch === -1) {
-        next = -1;
-      } else {
-        previous = nextMatch + eol.length;
-        next = previous;
-      }
-    } else {
-      res.push([previous, string.length]);
-    }
-  }
-  return res;
-}
-
-/**
- * Parse the molfile and the properties with > < labels >
- * @param {string} sdfPart
- * @param {*} labels
- * @param {*} currentLabels
- * @param {object} options
- * @returns
- */
-function getMolecule$1(sdfPart, labels, currentLabels, options) {
-  let parts = sdfPart.split(`${options.eol}>`);
-  if (parts.length === 0 || parts[0].length <= 5) return;
-  let molecule = {};
-  molecule.molfile = parts[0] + options.eol;
-  for (let j = 1; j < parts.length; j++) {
-    let lines = parts[j].split(options.eol);
-    let from = lines[0].indexOf('<');
-    let to = lines[0].indexOf('>');
-    let label = lines[0].slice(from + 1, to);
-    currentLabels.push(label);
-    if (!labels[label]) {
-      labels[label] = {
-        counter: 0,
-        isNumeric: options.dynamicTyping,
-        keep: false,
-      };
-      if (
-        (!options.exclude || !options.exclude.includes(label)) &&
-        (!options.include || options.include.includes(label))
-      ) {
-        labels[label].keep = true;
-        if (options.modifiers[label]) {
-          labels[label].modifier = options.modifiers[label];
-        }
-        if (options.forEach[label]) {
-          labels[label].forEach = options.forEach[label];
-        }
-      }
-    }
-    if (labels[label].keep) {
-      for (let k = 1; k < lines.length - 1; k++) {
-        if (molecule[label]) {
-          molecule[label] += options.eol + lines[k];
-        } else {
-          molecule[label] = lines[k];
-        }
-      }
-      if (labels[label].modifier) {
-        let modifiedValue = labels[label].modifier(molecule[label]);
-        if (modifiedValue === undefined || modifiedValue === null) {
-          delete molecule[label];
-        } else {
-          molecule[label] = modifiedValue;
-        }
-      }
-      if (
-        labels[label].isNumeric &&
-        (!Number.isFinite(+molecule[label]) || molecule[label].match(/^0[0-9]/))
-      ) {
-        labels[label].isNumeric = false;
-      }
-    }
-  }
-  return molecule;
-}
-
-/**
- *  Parse a SDF file
- * @param {string|ArrayBuffer|Uint8Array} sdf - SDF file to parse
- * @param {object} [options={}]
- * @param {string[]} [options.include] - List of fields to include
- * @param {string[]} [options.exclude] - List of fields to exclude
- * @param {Function} [options.filter] - Callback allowing to filter the molecules
- * @param {boolean} [options.dynamicTyping] - Dynamically type the data
- * @param {object} [options.modifiers] - Object containing callbacks to apply on some specific fields
- * @param {boolean} [options.mixedEOL=false] - Set to true if you know there is a mixture between \r\n and \n
- * @param {string} [options.eol] - Specify the end of line character. Default will be the one found in the file
- * @returns {object} - Object containing the molecules, the labels and the statistics
- */
-function parse(sdf, options = {}) {
-  options = { ...options };
-  if (options.modifiers === undefined) options.modifiers = {};
-  if (options.forEach === undefined) options.forEach = {};
-  if (options.dynamicTyping === undefined) options.dynamicTyping = true;
-
-  sdf = ensureString.ensureString(sdf);
-  if (typeof sdf !== 'string') {
-    throw new TypeError('Parameter "sdf" must be a string');
-  }
-
-  if (options.eol === undefined) {
-    options.eol = '\n';
-    if (options.mixedEOL) {
-      sdf = sdf.replaceAll('\r\n', '\n');
-      sdf = sdf.replaceAll('\r', '\n');
-    } else {
-      // we will find the delimiter in order to be much faster and not use regular expression
-      let header = new Set(sdf.slice(0, 1000));
-      if (header.has('\r\n')) {
-        options.eol = '\r\n';
-      } else if (header.has('\r')) {
-        options.eol = '\r';
-      }
-    }
-  }
-
-  let entriesBoundaries = getEntriesBoundaries(
-    sdf,
-    `${options.eol}$$$$`,
-    options.eol,
-  );
-  let molecules = [];
-  let labels = {};
-
-  let start = Date.now();
-
-  for (let i = 0; i < entriesBoundaries.length; i++) {
-    let sdfPart = sdf.slice(...entriesBoundaries[i]);
-    if (sdfPart.length < 40) continue;
-    let currentLabels = [];
-    const molecule = getMolecule$1(sdfPart, labels, currentLabels, options);
-    if (!molecule) continue;
-    if (!options.filter || options.filter(molecule)) {
-      molecules.push(molecule);
-      // only now we can increase the counter
-      for (let j = 0; j < currentLabels.length; j++) {
-        labels[currentLabels[j]].counter++;
-      }
-    }
-  }
-  // all numeric fields should be converted to numbers
-  for (let label in labels) {
-    let currentLabel = labels[label];
-    if (currentLabel.isNumeric) {
-      currentLabel.minValue = Infinity;
-      currentLabel.maxValue = -Infinity;
-      for (let j = 0; j < molecules.length; j++) {
-        if (molecules[j][label]) {
-          let value = Number.parseFloat(molecules[j][label]);
-          molecules[j][label] = value;
-          if (value > currentLabel.maxValue) {
-            currentLabel.maxValue = value;
-          }
-          if (value < currentLabel.minValue) {
-            currentLabel.minValue = value;
-          }
-        }
-      }
-    }
-  }
-
-  // we check that a label is in all the records
-  for (let key in labels) {
-    if (labels[key].counter === molecules.length) {
-      labels[key].always = true;
-    } else {
-      labels[key].always = false;
-    }
-  }
-
-  let statistics = [];
-  for (let key in labels) {
-    let statistic = labels[key];
-    statistic.label = key;
-    statistics.push(statistic);
-  }
-
-  return {
-    time: Date.now() - start,
-    molecules,
-    labels: Object.keys(labels),
-    statistics,
-  };
-}
-
-class MolfileStream extends TransformStream {
-  #buffer = '';
-
-  constructor() {
-    super({
-      transform: (chunk, controller) => {
-        this.#buffer += chunk;
-        let begin = 0;
-        let index = 0;
-        while ((index = this.#buffer.indexOf('$$$$', index)) !== -1) {
-          // we need to check if the delimiter '\n' is in the current buffer
-          // if it is not we need to wait for the next chunk
-          const endOfDelimiter = this.#buffer.indexOf('\n', index);
-          if (endOfDelimiter === -1) {
-            index = begin;
-            break;
-          }
-          const eolLength = this.#buffer[endOfDelimiter - 1] === '\r' ? 2 : 1;
-          // need to remove the last eol because we will split on eol+'>' in getMolecule
-          if (index - eolLength - begin > 40) {
-            controller.enqueue(this.#buffer.slice(begin, index - eolLength));
-          }
-          index = endOfDelimiter + eolLength;
-          begin = index;
-        }
-        this.#buffer = this.#buffer.slice(begin);
-      },
-      flush: (controller) => {
-        if (this.#buffer && this.#buffer.length > 40) {
-          controller.enqueue(this.#buffer);
-        }
-      },
-    });
-  }
-}
-
-/**
- *  Parse a SDF file as an iterator
- * @param {ReadableStream} readStream - SDF file to parse
- * @param {object} [options={}] - iterator options
- * @param {Function} [options.filter] - Callback allowing to filter the molecules
- * @param {string} [options.eol='\n'] - End of line character
- * @param {boolean} [options.dynamicTyping] - Dynamically type the data
- * @yields {object} - Molecule object
- */
-async function* iterator(readStream, options = {}) {
-  const { eol = '\n', dynamicTyping = true } = options;
-
-  const moleculeStream = readStream.pipeThrough(new MolfileStream({ eol }));
-  for await (const entry of moleculeStream) {
-    const molecule = getMolecule(entry, {
-      eol,
-      dynamicTyping,
-    });
-    if (!options.filter || options.filter(molecule)) {
-      yield molecule;
-    }
-  }
-}
-
-/**
- * Convert a SDF part to an object
- * @param {string} sdfPart - text containing the molfile
- * @param {object} options - options
- * @param {string} options.eol - end of line character
- * @param {boolean} options.dynamicTyping - Dynamically type the data (create numbers and booleans)
- * @returns
- */
-function getMolecule(sdfPart, options) {
-  const { eol, dynamicTyping: dynamicTyping$1 } = options;
-  let parts = sdfPart.split(`${eol}>`);
-  if (parts.length === 0 || parts[0].length <= 5) return;
-  let molecule = {};
-  molecule.molfile = parts[0] + eol;
-  for (let j = 1; j < parts.length; j++) {
-    let lines = parts[j].split(eol);
-    let from = lines[0].indexOf('<');
-    let to = lines[0].indexOf('>');
-    let label = lines[0].slice(from + 1, to);
-    for (let k = 1; k < lines.length - 1; k++) {
-      if (molecule[label]) {
-        molecule[label] += eol + lines[k];
-      } else {
-        molecule[label] = lines[k];
-      }
-    }
-    if (dynamicTyping$1) {
-      molecule[label] = dynamicTyping.parseString(molecule[label]);
-    }
-  }
-  return molecule;
-}
-
-exports.MolfileStream = MolfileStream;
-exports.iterator = iterator;
-exports.parse = parse;
+export * from "./parse.js";
+export * from "./iterator.js";
+export * from "./MolfileStream.js";
+//# sourceMappingURL=index.js.map

package/lib/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,YAAY,CAAC;AAC3B,cAAc,eAAe,CAAC;AAC9B,cAAc,oBAAoB,CAAC"}

package/lib/iterator.d.ts

@@ -0,0 +1,49 @@
+/**
+ * A molecule entry returned by the {@link iterator} async generator.
+ * The `molfile` field contains the raw V2000/V3000 molfile block.
+ * Additional fields are populated from the SDF `> <field>` sections.
+ */
+export interface IteratorMolecule {
+    /** The raw V2000/V3000 molfile block. */
+    molfile: string;
+    [label: string]: any;
+}
+/**
+ * Options for the {@link iterator} async generator.
+ */
+export interface IteratorOptions {
+    /**
+     * End-of-line character used to split field entries.
+     * @default '\n'
+     */
+    eol?: string;
+    /**
+     * When `true`, numeric string values are automatically converted to numbers.
+     * @default true
+     */
+    dynamicTyping?: boolean;
+    /**
+     * A predicate function to filter molecules. Only molecules for which this
+     * function returns `true` are yielded.
+     */
+    filter?: (molecule: IteratorMolecule) => boolean;
+}
+/**
+ * Asynchronously iterate over molecules from a text-decoded SDF stream.
+ * @param readStream - A `ReadableStream<string>` supplying SDF text content.
+ * @param options - Iterator options.
+ * @yields {IteratorMolecule} Individual molecule objects.
+ * @example
+ * ```ts
+ * import { openAsBlob } from 'node:fs';
+ * import { iterator } from 'sdf-parser';
+ *
+ * const blob = await openAsBlob('compounds.sdf');
+ * const textDecoder = new TextDecoderStream();
+ * for await (const molecule of iterator(blob.stream().pipeThrough(textDecoder))) {
+ *   console.log(molecule.molfile);
+ * }
+ * ```
+ */
+export declare function iterator(readStream: ReadableStream<string>, options?: IteratorOptions): AsyncGenerator<IteratorMolecule>;
+//# sourceMappingURL=iterator.d.ts.map

package/lib/iterator.d.ts.map

@@ -0,0 +1 @@
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package/lib/iterator.js

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+import { parseString } from 'dynamic-typing';
+import { MolfileStream } from "./MolfileStream.js";
+/**
+ * Asynchronously iterate over molecules from a text-decoded SDF stream.
+ * @param readStream - A `ReadableStream<string>` supplying SDF text content.
+ * @param options - Iterator options.
+ * @yields {IteratorMolecule} Individual molecule objects.
+ * @example
+ * ```ts
+ * import { openAsBlob } from 'node:fs';
+ * import { iterator } from 'sdf-parser';
+ *
+ * const blob = await openAsBlob('compounds.sdf');
+ * const textDecoder = new TextDecoderStream();
+ * for await (const molecule of iterator(blob.stream().pipeThrough(textDecoder))) {
+ *   console.log(molecule.molfile);
+ * }
+ * ```
+ */
+export async function* iterator(readStream, options = {}) {
+    const { eol = '\n', dynamicTyping = true } = options;
+    const moleculeStream = readStream.pipeThrough(new MolfileStream({ eol }));
+    for await (const entry of moleculeStream) {
+        const molecule = parseMolecule(entry, { eol, dynamicTyping });
+        if (!options.filter || options.filter(molecule)) {
+            yield molecule;
+        }
+    }
+}
+function parseMolecule(sdfPart, options) {
+    const { eol, dynamicTyping } = options;
+    const parts = sdfPart.split(`${eol}>`);
+    const molecule = {
+        molfile: parts.length > 0 && parts[0].length > 5 ? parts[0] + eol : '',
+    };
+    for (let j = 1; j < parts.length; j++) {
+        const lines = parts[j].split(eol);
+        const from = lines[0].indexOf('<');
+        const to = lines[0].indexOf('>');
+        const label = lines[0].slice(from + 1, to);
+        for (let k = 1; k < lines.length - 1; k++) {
+            if (molecule[label]) {
+                molecule[label] = `${molecule[label]}${eol}${lines[k]}`;
+            }
+            else {
+                molecule[label] = lines[k];
+            }
+        }
+        if (dynamicTyping) {
+            molecule[label] = parseString(molecule[label]);
+        }
+    }
+    return molecule;
+}
+//# sourceMappingURL=iterator.js.map

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package/lib/parse.d.ts

@@ -0,0 +1,105 @@
+/**
+ * A parsed SDF molecule entry. The `molfile` field contains the raw molfile
+ * string. Additional fields are populated from the SDF `> <field>` sections.
+ */
+export interface Molecule {
+    /** The raw V2000/V3000 molfile block. */
+    molfile: string;
+    [label: string]: any;
+}
+/**
+ * Options for the {@link parse} function.
+ */
+export interface ParseOptions {
+    /**
+     * Modifier functions applied to field values after parsing. The function
+     * receives the raw string value and may return a transformed value. Returning
+     * `undefined` or `null` removes the field from the molecule.
+     */
+    modifiers?: Record<string, (value: string) => unknown>;
+    /**
+     * Callback functions called for each field value. The callbacks are stored
+     * on the label info and available in statistics.
+     */
+    forEach?: Record<string, (value: unknown) => void>;
+    /**
+     * When `true`, numeric string values are automatically converted to numbers.
+     * @default true
+     */
+    dynamicTyping?: boolean;
+    /**
+     * End-of-line character. Auto-detected from the file content when not set.
+     * @default '\n'
+     */
+    eol?: string;
+    /**
+     * When `true`, normalises all `\r\n` and `\r` sequences to `\n` before
+     * parsing. Useful for SDF files with mixed or Windows-style line endings.
+     * @default false
+     */
+    mixedEOL?: boolean;
+    /**
+     * Only include fields whose names appear in this list.
+     * When combined with `exclude`, the field must satisfy both constraints.
+     */
+    include?: string[];
+    /**
+     * Exclude fields whose names appear in this list.
+     * When combined with `include`, the field must satisfy both constraints.
+     */
+    exclude?: string[];
+    /**
+     * A predicate function to filter molecules. Only molecules for which this
+     * function returns `true` are included in the result.
+     */
+    filter?: (molecule: Molecule) => boolean;
+}
+/**
+ * Statistics for a single SDF field label, as returned in
+ * {@link ParseResult.statistics}.
+ */
+export interface LabelStatistic {
+    /** Field label name. */
+    label: string;
+    /** Number of molecules that contain this field. */
+    counter: number;
+    /** Whether all parsed values are numeric. */
+    isNumeric: boolean;
+    /** Whether this field is included in the output (not excluded). */
+    keep: boolean;
+    /** Minimum numeric value, only set when `isNumeric` is `true`. */
+    minValue?: number;
+    /** Maximum numeric value, only set when `isNumeric` is `true`. */
+    maxValue?: number;
+    /** Whether every molecule in the result contains this field. */
+    always: boolean;
+}
+/**
+ * Return value of the {@link parse} function.
+ */
+export interface ParseResult {
+    /** Wall-clock time taken to parse, in milliseconds. */
+    time: number;
+    /** Parsed molecule entries. */
+    molecules: Molecule[];
+    /** Sorted list of all field label names found in the file. */
+    labels: string[];
+    /** Per-label statistics. */
+    statistics: LabelStatistic[];
+}
+/**
+ * Synchronously parse an SDF file into an array of molecule objects.
+ * @param sdf - The SDF content as a string, `ArrayBuffer`, or `ArrayBufferView`.
+ * @param options - Parsing options.
+ * @returns A {@link ParseResult} containing molecules and statistics.
+ * @example
+ * ```ts
+ * import { readFileSync } from 'node:fs';
+ * import { parse } from 'sdf-parser';
+ *
+ * const sdf = readFileSync('compounds.sdf', 'utf8');
+ * const { molecules, statistics } = parse(sdf);
+ * ```
+ */
+export declare function parse(sdf: unknown, options?: ParseOptions): ParseResult;
+//# sourceMappingURL=parse.d.ts.map