From d472f03c9addb7af5070194e9e30bd0a230b9c55 Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Mon, 13 May 2024 08:50:57 +0200
Subject: [PATCH] feat: add possitility to generate smarts and kekule isomeric
 smiles

We never documented  toIsomericSmiles(boolean) so I didn't do a breaking change
---
 __tests__/__snapshots__/library.js.snap       |  4 ++++
 __tests__/molecule.js                         | 17 ++++++++++++++++-
 .../research/gwt/minimal/JSMolecule.java      | 19 ++++++++++++++++---
 types.d.ts                                    |  9 +++++++--
 4 files changed, 43 insertions(+), 6 deletions(-)

diff --git a/__tests__/__snapshots__/library.js.snap b/__tests__/__snapshots__/library.js.snap
index 2199644b..eec44da4 100644
--- a/__tests__/__snapshots__/library.js.snap
+++ b/__tests__/__snapshots__/library.js.snap
@@ -296,6 +296,7 @@ exports[`prototype properties of Molecule 1`] = `
   "toMolfile",
   "toMolfileV3",
   "toSVG",
+  "toSmarts",
   "toSmiles",
   "translateCoords",
   "validate",
@@ -458,6 +459,9 @@ exports[`static properties of Molecule 1`] = `
   "CANONIZER_TIE_BREAK_FREE_VALENCE_ATOMS",
   "FISCHER_PROJECTION_LIMIT",
   "FISCHER_PROJECTION_RING_LIMIT",
+  "MODE_CREATE_SMARTS",
+  "MODE_INCLUDE_MAPPING",
+  "MODE_KEKULIZED_OUTPUT",
   "STEREO_ANGLE_LIMIT",
   "VALIDATION_ERRORS_STEREO",
   "VALIDATION_ERROR_AMBIGUOUS_CONFIGURATION",
diff --git a/__tests__/molecule.js b/__tests__/molecule.js
index 8343bf83..4762696a 100644
--- a/__tests__/molecule.js
+++ b/__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'])(
@@ -34,6 +34,21 @@ 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(Molecule.MODE_KEKULIZED_OUTPUT)).toBe('C1=CC=CC=C1');
+    expect(mol.toIsomericSmiles(Molecule.MODE_CREATE_SMARTS)).toBe('c1ccccc1');
+    mol.setAtomMapNo(0, 1);
+    expect(mol.toIsomericSmiles(Molecule.MODE_INCLUDE_MAPPING)).toBe('c1cc[cH:1]cc1');
+
+    const fragment = Molecule.fromSmiles('C1=CC=CC=C1C');
+    fragment.setFragment(true);
+    fragment.setAtomicNo(6, 1)
+    expect(fragment.toIsomericSmiles(Molecule.MODE_CREATE_SMARTS)).toBe('c1cc[c;!H0]cc1');
+  })
 });
 
 describe('Molecule', () => {
diff --git a/src/com/actelion/research/gwt/minimal/JSMolecule.java b/src/com/actelion/research/gwt/minimal/JSMolecule.java
index be61a958..e4010aec 100644
--- a/src/com/actelion/research/gwt/minimal/JSMolecule.java
+++ b/src/com/actelion/research/gwt/minimal/JSMolecule.java
@@ -82,11 +82,17 @@ 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 String toIsomericSmiles(int mode) {
+    return new IsomericSmilesCreator(oclMolecule, mode).getSmiles();
+  }
+
+  public String toSmarts() {
+    return new IsomericSmilesCreator(oclMolecule, IsomericSmilesCreator.MODE_CREATE_SMARTS)
+        .getSmiles();
   }
 
   public String toMolfile() {
@@ -293,7 +299,14 @@ public StereoMolecule getStereoMolecule() {
     return oclMolecule;
   }
 
-  // coming form Canonizer.java
+  // coming from IsomericSmilesCreator.java
+  public static final int MODE_CREATE_SMARTS = 1;
+  public static final int MODE_INCLUDE_MAPPING = 2;
+  public static final int MODE_KEKULIZED_OUTPUT = 4; // no lower case atom labels and single/double
+                                                     // bonds to represent aromaticity
+
+
+  // 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;
diff --git a/types.d.ts b/types.d.ts
index b0998879..7bf67701 100644
--- a/types.d.ts
+++ b/types.d.ts
@@ -93,6 +93,11 @@ export declare class Molecule {
 
   // based on JSMolecule.java you can do a regexp ".*static.* (int|long|double)(.*) = .*;" and replace with "$2: number;"
 
+  static MODE_CREATE_SMARTS = 1;
+  static MODE_INCLUDE_MAPPING = 2;
+  static MODE_KEKULIZED_OUTPUT = 4; // no lower case atom labels and single/double
+                                                     // bonds to represent aromaticity
+
   static CANONIZER_CREATE_SYMMETRY_RANK: number;
   static CANONIZER_CONSIDER_DIASTEREOTOPICITY: number;
   static CANONIZER_CONSIDER_ENANTIOTOPICITY: number;
@@ -435,7 +440,7 @@ export declare class Molecule {
    */
   getOCL(): any;
 
-  toSmiles(): string;
+  toSmiles(mode?: number): string;
 
   toIsomericSmiles(): string;
 
@@ -1302,7 +1307,7 @@ 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