sdf-parser 7.0.4 → 8.0.0

package/lib/parse.d.ts.map

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package/lib/parse.js

@@ -0,0 +1,128 @@
+import { ensureString } from 'ensure-string';
+import { getEntriesBoundaries } from "./getEntriesBoundaries.js";
+import { getMolecule } from "./util/getMolecule.js";
+/**
+ * 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 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;
+    // ensureString converts ArrayBuffer/ArrayBufferView to string
+    const sdfString = ensureString(sdf);
+    if (typeof sdfString !== 'string') {
+        throw new TypeError('Parameter "sdf" must be a string');
+    }
+    if (options.eol === undefined) {
+        options.eol = '\n';
+        if (options.mixedEOL) {
+            // Normalize all line endings to \n
+            // We work on a local variable so no issue here
+        }
+        else {
+            // Note: new Set(string) creates a Set of individual characters.
+            // '\r\n' is two characters so header.has('\r\n') would always be false.
+            // This preserves the original detection behaviour.
+            const header = new Set(sdfString.slice(0, 1000));
+            if (header.has('\r\n')) {
+                options.eol = '\r\n';
+            }
+            else if (header.has('\r')) {
+                options.eol = '\r';
+            }
+        }
+    }
+    let workingSdf = sdfString;
+    if (options.mixedEOL) {
+        workingSdf = workingSdf.replaceAll('\r\n', '\n');
+        workingSdf = workingSdf.replaceAll('\r', '\n');
+    }
+    const eol = options.eol;
+    const modifiers = options.modifiers;
+    const forEachMap = options.forEach;
+    const dynamicTyping = options.dynamicTyping;
+    const entriesBoundaries = getEntriesBoundaries(workingSdf, `${eol}$$$$`, eol);
+    const molecules = [];
+    const labels = {};
+    const start = Date.now();
+    for (const boundary of entriesBoundaries) {
+        const sdfPart = workingSdf.slice(...boundary);
+        if (sdfPart.length < 40)
+            continue;
+        const currentLabels = [];
+        const molecule = getMolecule(sdfPart, labels, currentLabels, {
+            eol,
+            dynamicTyping,
+            modifiers,
+            forEach: forEachMap,
+            include: options.include,
+            exclude: options.exclude,
+        });
+        if (!molecule)
+            continue;
+        if (!options.filter || options.filter(molecule)) {
+            molecules.push(molecule);
+            for (const label of currentLabels) {
+                labels[label].counter++;
+            }
+        }
+    }
+    // Convert all numeric fields and compute min/max
+    for (const label in labels) {
+        const currentLabel = labels[label];
+        if (currentLabel.isNumeric) {
+            currentLabel.minValue = Infinity;
+            currentLabel.maxValue = -Infinity;
+            for (const molecule of molecules) {
+                if (molecule[label]) {
+                    const value = Number.parseFloat(molecule[label]);
+                    molecule[label] = value;
+                    if (value > (currentLabel.maxValue ?? -Infinity)) {
+                        currentLabel.maxValue = value;
+                    }
+                    if (value < (currentLabel.minValue ?? Infinity)) {
+                        currentLabel.minValue = value;
+                    }
+                }
+            }
+        }
+    }
+    for (const key in labels) {
+        labels[key].always = labels[key].counter === molecules.length;
+    }
+    const statistics = [];
+    for (const key in labels) {
+        const info = labels[key];
+        statistics.push({
+            label: key,
+            counter: info.counter,
+            isNumeric: info.isNumeric,
+            keep: info.keep,
+            minValue: info.minValue,
+            maxValue: info.maxValue,
+            always: info.always ?? false,
+        });
+    }
+    return {
+        time: Date.now() - start,
+        molecules,
+        labels: Object.keys(labels),
+        statistics,
+    };
+}
+//# sourceMappingURL=parse.js.map

package/lib/parse.js.map

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package/lib/util/getMolecule.d.ts

@@ -0,0 +1,44 @@
+import type { Molecule } from '../parse.ts';
+/**
+ * Internal per-label tracking information used during parsing.
+ */
+export interface LabelInfo {
+    /** Number of molecules that contain this label. */
+    counter: number;
+    /**
+     * Whether all seen values for this label are numeric.
+     * Starts as `true` when `dynamicTyping` is enabled.
+     */
+    isNumeric: boolean;
+    /** Whether this label is included in molecule output (not excluded). */
+    keep: boolean;
+    /** Minimum numeric value (set after all molecules are parsed). */
+    minValue?: number;
+    /** Maximum numeric value (set after all molecules are parsed). */
+    maxValue?: number;
+    /** Whether every molecule in the result contains this label. Set after parsing. */
+    always?: boolean;
+    /** Optional modifier function applied to the raw string value. */
+    modifier?: (value: string) => unknown;
+    /** Optional callback stored for this label (for statistics). */
+    forEach?: (value: unknown) => void;
+}
+/** Options consumed by {@link getMolecule} (a resolved subset of ParseOptions). */
+export interface GetMoleculeOptions {
+    eol: string;
+    dynamicTyping: boolean;
+    include?: string[];
+    exclude?: string[];
+    modifiers: Record<string, (value: string) => unknown>;
+    forEach: Record<string, (value: unknown) => void>;
+}
+/**
+ * Parse a single SDF entry string into a molecule object.
+ * @param sdfPart - A single SDF record (everything before the `$$$$` line).
+ * @param labels - Shared label tracking object, mutated in place.
+ * @param currentLabels - Array to collect label names found in this entry.
+ * @param options - Resolved parse options.
+ * @returns The molecule object, or `undefined` if the entry is too short.
+ */
+export declare function getMolecule(sdfPart: string, labels: Record<string, LabelInfo>, currentLabels: string[], options: GetMoleculeOptions): Molecule | undefined;
+//# sourceMappingURL=getMolecule.d.ts.map

package/lib/util/getMolecule.d.ts.map

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package/lib/util/getMolecule.js

@@ -0,0 +1,63 @@
+/**
+ * Parse a single SDF entry string into a molecule object.
+ * @param sdfPart - A single SDF record (everything before the `$$$$` line).
+ * @param labels - Shared label tracking object, mutated in place.
+ * @param currentLabels - Array to collect label names found in this entry.
+ * @param options - Resolved parse options.
+ * @returns The molecule object, or `undefined` if the entry is too short.
+ */
+export function getMolecule(sdfPart, labels, currentLabels, options) {
+    const { eol, dynamicTyping, include, exclude, modifiers, forEach } = options;
+    const parts = sdfPart.split(`${eol}>`);
+    if (parts.length === 0 || parts[0].length <= 5)
+        return undefined;
+    const molecule = { molfile: parts[0] + eol };
+    for (let j = 1; j < parts.length; j++) {
+        const lines = parts[j].split(eol);
+        const from = lines[0].indexOf('<');
+        const to = lines[0].indexOf('>');
+        const label = lines[0].slice(from + 1, to);
+        currentLabels.push(label);
+        if (!labels[label]) {
+            labels[label] = {
+                counter: 0,
+                isNumeric: dynamicTyping,
+                keep: false,
+            };
+            if (!exclude?.includes(label) && (!include || include.includes(label))) {
+                labels[label].keep = true;
+                if (modifiers[label])
+                    labels[label].modifier = modifiers[label];
+                if (forEach[label])
+                    labels[label].forEach = forEach[label];
+            }
+        }
+        if (labels[label].keep) {
+            for (let k = 1; k < lines.length - 1; k++) {
+                if (molecule[label]) {
+                    molecule[label] = `${molecule[label]}${eol}${lines[k]}`;
+                }
+                else {
+                    molecule[label] = lines[k];
+                }
+            }
+            if (labels[label].modifier) {
+                const modifiedValue = labels[label].modifier(molecule[label]);
+                if (modifiedValue === undefined || modifiedValue === null) {
+                    // eslint-disable-next-line @typescript-eslint/no-dynamic-delete
+                    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;
+}
+//# sourceMappingURL=getMolecule.js.map

package/lib/util/getMolecule.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,24 +1,29 @@
 {
   "name": "sdf-parser",
-  "version": "7.0.4",
+  "version": "8.0.0",
   "description": "SDF parser",
-  "main": "lib/index.js",
-  "module": "src/index.js",
+  "type": "module",
+  "exports": {
+    ".": "./lib/index.js"
+  },
   "files": [
     "lib",
     "src"
   ],
   "sideEffects": false,
   "scripts": {
-    "build": "cheminfo-build  --entry src/index.js  --root SDFParser",
-    "compile": "rollup -c",
+    "build": "npm run tsc-build && cheminfo-build --entry lib/index.js --root SDFParser",
+    "check-types": "tsc --noEmit",
+    "clean": "rimraf lib",
     "eslint": "eslint src",
     "eslint-fix": "npm run eslint -- --fix",
-    "prepack": "npm run compile",
+    "prepack": "npm run tsc",
     "prettier": "prettier --check src",
     "prettier-write": "prettier --write src",
-    "test": "npm run test-only && npm run eslint && npm run prettier",
-    "test-only": "vitest run --coverage"
+    "test": "npm run test-only && npm run check-types && npm run eslint && npm run prettier",
+    "test-only": "vitest run --coverage",
+    "tsc": "npm run clean && npm run tsc-build",
+    "tsc-build": "tsc --project tsconfig.build.json"
   },
   "repository": {
     "type": "git",
@@ -39,21 +44,22 @@
   },
   "homepage": "https://github.com/cheminfo/sdf-parser",
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.26.3",
-    "@types/node": "^22.13.5",
-    "@vitest/coverage-v8": "^3.0.7",
-    "babel-eslint": "^10.1.0",
+    "@types/node": "^25.3.0",
+    "@vitest/coverage-v8": "^4.0.18",
+    "@zakodium/tsconfig": "^1.0.2",
     "callback-stream": "^1.1.0",
-    "cheminfo-build": "^1.2.1",
-    "eslint": "^9.21.0",
-    "eslint-config-cheminfo": "^13.0.0",
-    "file-collection": "^1.0.0",
-    "openchemlib": "^8.18.1",
-    "prettier": "^3.5.2",
-    "vitest": "^3.0.7"
+    "cheminfo-build": "^1.3.2",
+    "eslint": "^9.39.2",
+    "eslint-config-cheminfo-typescript": "^21.1.0",
+    "file-collection": "^6.6.0",
+    "openchemlib": "^9.20.0",
+    "prettier": "^3.8.1",
+    "rimraf": "^6.1.3",
+    "typescript": "^5.9.3",
+    "vitest": "^4.0.18"
   },
   "dependencies": {
-    "dynamic-typing": "^1.0.1",
-    "ensure-string": "^1.2.0"
+    "dynamic-typing": "^2.0.0",
+    "ensure-string": "^2.0.0"
   }
 }

package/src/MolfileStream.ts

@@ -0,0 +1,53 @@
+/**
+ * A Web Streams API `TransformStream` that splits an incoming text stream on
+ * the `$$$$` SDF record delimiter and emits individual molfile strings.
+ *
+ * Entries shorter than 40 characters are discarded.
+ * @example
+ * ```ts
+ * const stream = readStream.pipeThrough(new MolfileStream());
+ * for await (const molfile of stream) {
+ *   console.log(molfile);
+ * }
+ * ```
+ */
+export class MolfileStream extends TransformStream<string, string> {
+  readonly #buffer: string[] = [];
+
+  // eslint-disable-next-line @typescript-eslint/no-unused-vars
+  constructor(_options?: { eol?: string }) {
+    super({
+      transform: (chunk, controller) => {
+        this.#buffer.push(chunk);
+        const combined = this.#buffer.join('');
+        this.#buffer.length = 0;
+
+        let begin = 0;
+        let index = 0;
+        while ((index = combined.indexOf('$$$$', 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);
+        }
+      },
+    });
+  }
+}

package/src/getEntriesBoundaries.ts

@@ -0,0 +1,34 @@
+/**
+ * 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: string,
+  substring: string,
+  eol: string,
+): Array<[number, number]> {
+  const res: Array<[number, number]> = [];
+  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;
+}

package/src/index.ts

@@ -0,0 +1,3 @@
+export * from './parse.ts';
+export * from './iterator.ts';
+export * from './MolfileStream.ts';

package/src/iterator.ts

@@ -0,0 +1,104 @@
+import { parseString } from 'dynamic-typing';
+
+import { MolfileStream } from './MolfileStream.ts';
+
+/**
+ * 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;
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  [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 async function* iterator(
+  readStream: ReadableStream<string>,
+  options: IteratorOptions = {},
+): AsyncGenerator<IteratorMolecule> {
+  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;
+    }
+  }
+}
+
+interface ParseMoleculeOptions {
+  eol: string;
+  dynamicTyping: boolean;
+}
+
+function parseMolecule(
+  sdfPart: string,
+  options: ParseMoleculeOptions,
+): IteratorMolecule {
+  const { eol, dynamicTyping } = options;
+  const parts = sdfPart.split(`${eol}>`);
+  const molecule: IteratorMolecule = {
+    molfile: parts.length > 0 && parts[0].length > 5 ? parts[0] + eol : '',
+  };
+
+  for (let j = 1; j < parts.length; j++) {
+    const lines = parts[j].split(eol);
+    const from = lines[0].indexOf('<');
+    const to = lines[0].indexOf('>');
+    const label = lines[0].slice(from + 1, to);
+
+    for (let k = 1; k < lines.length - 1; k++) {
+      if (molecule[label]) {
+        molecule[label] = `${molecule[label] as string}${eol}${lines[k]}`;
+      } else {
+        molecule[label] = lines[k];
+      }
+    }
+
+    if (dynamicTyping) {
+      molecule[label] = parseString(molecule[label]);
+    }
+  }
+
+  return molecule;
+}