feat: add possitility to generate smarts and kekule isomeric smiles

__tests__/__snapshots__/library.js.snap

@@ -296,6 +296,7 @@ exports[`prototype properties of Molecule 1`] = `
   "toMolfile",
   "toMolfileV3",
   "toSVG",
+  "toSmarts",
   "toSmiles",
   "translateCoords",
   "validate",

__tests__/molecule.js

@@ -2,7 +2,7 @@
 
 const fs = require('fs');
 
-const Molecule = require('../minimal').Molecule;
+const { Molecule } = require('../minimal');
 
 describe('from and to SMILES', () => {
   it.each(['C', 'COCOC', 'c1cc2cccc3c4cccc5cccc(c(c1)c23)c54'])(
@@ -34,8 +34,30 @@ describe('from and to SMILES', () => {
     const mol = Molecule.fromSmiles(input);
     expect(mol.toIsomericSmiles()).toBe(output);
   });
+
+  it('smiles options', () => {
+    const mol = Molecule.fromSmiles('C1=CC=CC=C1');
+    expect(mol.toSmiles()).toBe('C1(=CC=CC=C1)');
+    expect(mol.toIsomericSmiles()).toBe('c1ccccc1');
+    expect(mol.toIsomericSmiles({ kekulizedOutput: true })).toBe('C1=CC=CC=C1');
+    expect(mol.toIsomericSmiles({ createSmarts: true })).toBe('c1ccccc1');
+    mol.setAtomMapNo(0, 1);
+    expect(mol.toIsomericSmiles({ includeMapping: true })).toBe('c1cc[cH:1]cc1');
+
+    const fragment = Molecule.fromSmiles('C1=CC=CC=C1C');
+    fragment.setFragment(true);
+    fragment.setAtomicNo(6, 1)
+    expect(fragment.toIsomericSmiles({ createSmarts: true })).toBe('c1cc[c;!H0]cc1');
+  })
 });
 
+it('smarts options', () => {
+  const fragment = Molecule.fromSmiles('C1=CC=CC=C1C');
+  fragment.setFragment(true);
+  fragment.setAtomicNo(6, 1)
+  expect(fragment.toSmarts()).toBe('c1cc[c;!H0]cc1');
+})
+
 describe('Molecule', () => {
   it('medley', () => {
     const idcode =

package.json

@@ -70,6 +70,7 @@
   },
   "homepage": "https://github.com/cheminfo/openchemlib-js",
   "devDependencies": {
+    "@types/jest": "^29.5.12",
     "benchmark": "^2.1.4",
     "eslint": "^8.56.0",
     "eslint-config-cheminfo": "^9.1.1",

src/com/actelion/research/gwt/minimal/JSMolecule.java

@@ -82,11 +82,38 @@ public native Object getOCL()
   }-*/;
 
   public String toSmiles() {
+    // we still allow to old code that do not care about stereo features and provide another SMILES
     return new SmilesCreator().generateSmiles(oclMolecule);
   }
 
-  public String toIsomericSmiles(boolean includeAtomMapping) {
-    return new IsomericSmilesCreator(oclMolecule, includeAtomMapping).getSmiles();
+  public native String toIsomericSmiles(JavaScriptObject options)
+  /*-{
+    options = options || {}
+    var createSmarts = options.createSmarts === true;
+    var includeMapping = options.includeMapping === true;
+    var kekulizedOutput = options.kekulizedOutput === true;
+    return [email protected]::toIsomericSmilesInternal(ZZZ)(createSmarts, includeMapping, kekulizedOutput);
+  }-*/;
+
+  @JsIgnore
+  public String toIsomericSmilesInternal(boolean createSmarts, boolean includeMapping,
+      boolean kekulizedOutput) {
+    int mode = 0;
+    if (createSmarts) {
+      mode |= IsomericSmilesCreator.MODE_CREATE_SMARTS;
+    }
+    if (includeMapping) {
+      mode |= IsomericSmilesCreator.MODE_INCLUDE_MAPPING;
+    }
+    if (kekulizedOutput) {
+      mode |= IsomericSmilesCreator.MODE_KEKULIZED_OUTPUT;
+    }
+    return new IsomericSmilesCreator(oclMolecule, mode).getSmiles();
+  }
+
+  public String toSmarts() {
+    return new IsomericSmilesCreator(oclMolecule, IsomericSmilesCreator.MODE_CREATE_SMARTS)
+        .getSmiles();
   }
 
   public String toMolfile() {
@@ -293,7 +320,7 @@ public StereoMolecule getStereoMolecule() {
     return oclMolecule;
   }
 
-  // coming form Canonizer.java
+  // coming from Canonizer.java
   public static final int CANONIZER_CREATE_SYMMETRY_RANK = 1;
   public static final int CANONIZER_CONSIDER_DIASTEREOTOPICITY = 2;
   public static final int CANONIZER_CONSIDER_ENANTIOTOPICITY = 4;

types.d.ts

@@ -61,6 +61,24 @@ export interface IHoseCodesOptions {
   type: 0 | 1;
 }
 
+export interface ISmilesGeneratorOptions {
+  /**
+   * Whether to create SMILES with SMARTS capabilities.
+   * @default `false`
+   */
+  createSmarts?: boolean;
+  /**
+   * Whether to include mapping information (atomMapNo) in the SMILES.
+   * @default `false`
+   */
+  includeMapping?: boolean;
+  /**
+   * Should localisation of double bonds be attempted?
+   * @default `false`
+   */
+  kekulizedOutput?: boolean;
+}
+
 export interface Rectangle {
   /**
    * X-coordinate of the top-left corner.
@@ -93,6 +111,8 @@ export declare class Molecule {
 
   // based on JSMolecule.java you can do a regexp ".*static.* (int|long|double)(.*) = .*;" and replace with "$2: number;"
 
+  // bonds to represent aromaticity
+
   static CANONIZER_CREATE_SYMMETRY_RANK: number;
   static CANONIZER_CONSIDER_DIASTEREOTOPICITY: number;
   static CANONIZER_CONSIDER_ENANTIOTOPICITY: number;
@@ -437,7 +457,9 @@ export declare class Molecule {
 
   toSmiles(): string;
 
-  toIsomericSmiles(): string;
+  toSmarts(): string;
+
+  toIsomericSmiles(options?: ISmilesGeneratorOptions): string;
 
   /**
    * Returns a MDL Molfile V2000 string.
@@ -1302,7 +1324,7 @@ export declare class Molecule {
    * @param mapNo
    * @param autoMapped
    */
-  setAtomMapNo(atom: number, mapNo: number, autoMapped: boolean): void;
+  setAtomMapNo(atom: number, mapNo: number, autoMapped?: boolean): void;
 
   /**
    * Set atom to specific isotop or to have a natural isotop distribution