openchemlib 9.8.0 → 9.9.0

package/dist/openchemlib.d.ts

@@ -36,6 +36,39 @@ export interface MoleculeFromSmilesOptions {
   noStereo?: boolean;
 }
 
+interface FromMolfileOptions {
+  /**
+   * If set to 'superscript', it will add a ']' at the beginning of the custom label to be
+   * compatible with the way to represent superscript in OCL
+   * If set to 'normal', it will remove the ']' at the beginning of the custom label if present
+   * If set to 'auto', it will set normal for 'C' and superscript for everything else
+   * If not set, it will keep the label as is
+   * Default: undefined (keep as is)
+   * @default undefined
+   */
+  customLabelPosition?: 'normal' | 'superscript' | 'auto' | undefined;
+}
+
+interface ToMolfileOptions {
+  /**
+   * Include custom atom labels as A lines
+   */
+  includeCustomAtomLabelsAsALines?: boolean;
+  /**
+   * Include custom atom labels as V lines
+   */
+  includeCustomAtomLabelsAsVLines?: boolean;
+  /**
+   * If set to 'superscript', it will add a ']' at the beginning of the custom label to be
+   * compatible with the way to represent superscript in OCL
+   * If set to 'normal', it will remove the ']' at the beginning of the custom label if present
+   * If not set, it will keep the label as is
+   * Default: undefined (keep as is)
+   * @default undefined
+   */
+  customLabelPosition?: 'normal' | 'superscript' | 'auto' | undefined;
+}
+
 export interface AtomQueryFeatures {
   aromatic: boolean;
   notAromatic: boolean;
@@ -480,7 +513,7 @@ export declare class Molecule {
    * Parse the provided `molfile` and return a `Molecule`.
    * @param molfile - MDL Molfile string in V2000 or V3000
    */
-  static fromMolfile(molfile: string): Molecule;
+  static fromMolfile(molfile: string, options?: FromMolfileOptions): Molecule;
 
   /**
    * Parse the provided `molfile` and return an object with `Molecule` and map.
@@ -557,9 +590,13 @@ export declare class Molecule {
   toIsomericSmiles(options?: SmilesGeneratorOptions): string;
 
   /**
-   * Returns a MDL Molfile V2000 string.
+   * Returns a molfile V2000 with the possibility to add A and V lines to set custom atom labels
+   * Those fileds only exists in molfiles V2000
+   * @param molecule - the molecule to convert
+   * @param options - options to include A or V lines
+   * @returns the molfile as a string
    */
-  toMolfile(): string;
+  toMolfile(options?: ToMolfileOptions): string;
 
   /**
    * Returns a MDL Molfile V3000 string.

package/dist/openchemlib.debug.js

@@ -1288,6 +1288,127 @@ function init(OCL) {
   delete OCL.GenericUIHelper;
 }
 
+// lib/extend/utils/changeMolfileCustomLabelPosition.js
+function changeMolfileCustomLabelPosition(molecule, customLabelPosition) {
+  switch (customLabelPosition) {
+    case "superscript":
+      for (let i = 0; i < molecule.getAllAtoms(); i++) {
+        const customLabel = molecule.getAtomCustomLabel(i);
+        if (customLabel && !customLabel.startsWith("]")) {
+          molecule.setAtomCustomLabel(i, `]${customLabel}`);
+        }
+      }
+      break;
+    case "normal":
+      for (let i = 0; i < molecule.getAllAtoms(); i++) {
+        const customLabel = molecule.getAtomCustomLabel(i);
+        if (customLabel?.startsWith("]")) {
+          molecule.setAtomCustomLabel(i, customLabel.slice(1));
+        }
+      }
+      break;
+    case "auto":
+      for (let i = 0; i < molecule.getAllAtoms(); i++) {
+        const customLabel = molecule.getAtomCustomLabel(i);
+        if (customLabel) {
+          const atomLabel = molecule.getAtomLabel(i);
+          if (atomLabel === "C") {
+            if (customLabel.startsWith("]")) {
+              molecule.setAtomCustomLabel(i, customLabel.slice(1));
+            }
+          } else if (!customLabel.startsWith("]")) {
+            molecule.setAtomCustomLabel(i, `]${customLabel}`);
+          }
+        }
+      }
+      break;
+    case void 0:
+      break;
+    default:
+      break;
+  }
+}
+
+// lib/extend/extendFromMolfile.js
+function extendFromMolfile(Molecule2) {
+  const _fromMolfile = Molecule2.fromMolfile;
+  Molecule2.fromMolfile = function fromMolfile(molfile, options = {}) {
+    const { customLabelPosition } = options;
+    const molecule = _fromMolfile.call(this, molfile);
+    const lines = molfile.split("\n");
+    if (lines.length < 4 || !lines[3].includes("V2000")) {
+      return molecule;
+    }
+    const possibleLines = lines.slice(
+      4 + molecule.getAllAtoms() + molecule.getAllBonds()
+    );
+    for (let i = 0; i < possibleLines.length; i++) {
+      const line = possibleLines[i];
+      if (line.startsWith("A  ")) {
+        const atom = Number(line.slice(3));
+        const valueLine = possibleLines[i + 1]?.trim();
+        i++;
+        if (!Number.isNaN(atom) && atom <= molecule.getAllAtoms() && valueLine && !molecule.getAtomCustomLabel(atom - 1)) {
+          molecule.setAtomCustomLabel(atom - 1, valueLine);
+        }
+      }
+      if (line.startsWith("V  ")) {
+        const parts = line.split(" ").filter(Boolean);
+        if (parts.length >= 3) {
+          const atom = Number(parts[1]);
+          const label = parts.slice(2).join(" ");
+          if (!Number.isNaN(atom) && atom <= molecule.getAllAtoms() && !molecule.getAtomCustomLabel(atom - 1)) {
+            molecule.setAtomCustomLabel(atom - 1, label);
+          }
+        }
+      }
+    }
+    changeMolfileCustomLabelPosition(molecule, customLabelPosition);
+    return molecule;
+  };
+}
+
+// lib/extend/extendToMolfile.js
+function extendToMolfile(Molecule2) {
+  const _toMolfile = Molecule2.prototype.toMolfile;
+  Molecule2.prototype.toMolfile = function toMolfile(options = {}) {
+    let molecule = this.getCompactCopy();
+    const {
+      includeCustomAtomLabelsAsALines = false,
+      includeCustomAtomLabelsAsVLines = false,
+      customLabelPosition
+    } = options;
+    changeMolfileCustomLabelPosition(molecule, customLabelPosition);
+    const molfile = _toMolfile.call(this);
+    if (!includeCustomAtomLabelsAsALines && !includeCustomAtomLabelsAsVLines) {
+      return molfile;
+    }
+    const lines = molfile.split("\n");
+    if (lines.length < 4 || !lines[3].includes("V2000")) {
+      return molfile;
+    }
+    const newLines = [];
+    for (let i = 0; i < molecule.getAllAtoms(); i++) {
+      const label = molecule.getAtomCustomLabel(i);
+      if (label) {
+        const paddedAtomNumber = String(i + 1).padStart(3, " ");
+        if (includeCustomAtomLabelsAsALines) {
+          newLines.push(`A  ${paddedAtomNumber}`, label);
+        }
+        if (includeCustomAtomLabelsAsVLines) {
+          newLines.push(`V  ${paddedAtomNumber} ${label}`);
+        }
+      }
+    }
+    const mEndIndex = lines.findIndex((line) => line.startsWith("M  END"));
+    if (mEndIndex === -1) {
+      return molfile;
+    }
+    lines.splice(mEndIndex, 0, ...newLines);
+    return lines.join("\n");
+  };
+}
+
 // lib/extend/index.js
 function extendOCL(OCL) {
   const { ConformerGenerator: ConformerGenerator2, ForceFieldMMFF94: ForceFieldMMFF942, Molecule: Molecule2 } = OCL;
@@ -1313,6 +1434,8 @@ function extendOCL(OCL) {
       options.funcTol
     );
   };
+  extendFromMolfile(Molecule2);
+  extendToMolfile(Molecule2);
   function parseMoleculeFromText(text) {
     if (!text) {
       return null;
@@ -71020,7 +71143,7 @@ function getExports($wnd) {
   $sendStats("moduleStartup", "end");
   $gwt && $gwt.permProps && __gwtModuleFunction.__moduleStartupDone($gwt.permProps);
   const toReturn = $wnd["OCL"];
-  toReturn.version = "9.8.0";
+  toReturn.version = "9.9.0";
   return toReturn;
 }
 var isBrowserWindow = typeof window !== "undefined" && typeof window.document !== "undefined";
@@ -71164,8 +71287,8 @@ export {
 };
 /**
  * openchemlib - Manipulate molecules
- * @version v9.8.0
- * @date 2025-09-15T09:15:58.106Z
+ * @version v9.9.0
+ * @date 2025-10-07T16:21:21.464Z
  * @link https://github.com/cheminfo/openchemlib-js
  * @license BSD-3-Clause
 */