From 9f9974d186765642cdc93dbd206f3b6e5ea29b52 Mon Sep 17 00:00:00 2001
From: Luc Patiny <lpatiny@users.noreply.github.com>
Date: Sun, 13 Aug 2023 17:50:20 +0200
Subject: [PATCH] feat: add getFinalRanks (#171)

---
 __tests__/__snapshots__/library.js.snap       |  1 +
 __tests__/molecule.js                         | 43 ++++++++++++++++++-
 .../research/gwt/minimal/JSMolecule.java      |  9 +++-
 types.d.ts                                    |  9 ++++
 4 files changed, 60 insertions(+), 2 deletions(-)

diff --git a/__tests__/__snapshots__/library.js.snap b/__tests__/__snapshots__/library.js.snap
index 03f01370..13639bcd 100644
--- a/__tests__/__snapshots__/library.js.snap
+++ b/__tests__/__snapshots__/library.js.snap
@@ -142,6 +142,7 @@ exports[`prototype properties of Molecule 1`] = `
   "getElectronValenceCorrection",
   "getExcludedNeighbourCount",
   "getExplicitHydrogens",
+  "getFinalRanks",
   "getFisherProjectionParity",
   "getFragmentAtoms",
   "getFragmentNumbers",
diff --git a/__tests__/molecule.js b/__tests__/molecule.js
index 12c255d5..a0f75a36 100644
--- a/__tests__/molecule.js
+++ b/__tests__/molecule.js
@@ -116,7 +116,7 @@ describe('Molecule', () => {
     expect(mol.getChiralText()).toBe('this enantiomer');
   });
 
-  it.skip('getCanonizedIDCode', () => {
+  it('getCanonizedIDCode', () => {
     let idcode = 'didH@@RYm^Fh@BHx@';
     let mol = Molecule.fromIDCode(idcode);
     expect(
@@ -138,6 +138,47 @@ describe('Molecule', () => {
     ).toBe(idcode);
   });
 
+  it('getFinalRanks', () => {
+    const molecule = Molecule.fromSmiles('CCC');
+    molecule.setAtomicNo(0, 8)
+    const atoms = [];
+    const ranks = [...molecule.getFinalRanks()];
+    for (let i = 0; i < molecule.getAllAtoms(); i++) {
+      atoms.push(molecule.getAtomLabel(i), ranks[i]);
+    }
+    expect(atoms).toStrictEqual(['O', 3, 'C', 2, 'C', 1])
+    const molecule2 = Molecule.fromSmiles('CCC');
+    molecule2.setAtomicNo(2, 8)
+    const atoms2 = [];
+    const ranks2 = [...molecule2.getFinalRanks()];
+    for (let i = 0; i < molecule2.getAllAtoms(); i++) {
+      atoms2.push(molecule2.getAtomLabel(i), ranks2[i]);
+    }
+    expect(atoms2).toStrictEqual(['C', 1, 'C', 2, 'O', 3])
+  })
+
+  it('getFinalRanks of xMolecule', () => {
+    const molecule = Molecule.fromSmiles('CCCO');
+    const xAtomicNumber = Molecule.getAtomicNoFromLabel(
+      'X',
+      Molecule.cPseudoAtomX,
+    );
+    molecule.addImplicitHydrogens();
+    for (let i = 0; i < molecule.getAllAtoms(); i++) {
+      // hydrogens are not taken into account during canonization, we need to change them with an atom with a valence of 1
+      if (molecule.getAtomicNo(i) === 1) {
+        molecule.setAtomicNo(i, xAtomicNumber);
+      }
+    }
+
+    const ranks = [...molecule.getFinalRanks()];
+    expect(ranks).toStrictEqual([
+      3, 1, 2, 4, 11,
+      10, 9, 5, 6, 7,
+      8, 12
+    ])
+  })
+
   it('should have a method that returns the OCL object', () => {
     const molecule = Molecule.fromSmiles('C');
     const OCL = molecule.getOCL();
diff --git a/src/com/actelion/research/gwt/minimal/JSMolecule.java b/src/com/actelion/research/gwt/minimal/JSMolecule.java
index 41e70bb0..27a250c1 100644
--- a/src/com/actelion/research/gwt/minimal/JSMolecule.java
+++ b/src/com/actelion/research/gwt/minimal/JSMolecule.java
@@ -153,6 +153,13 @@ public String getCanonizedIDCode(int flag) {
     return canonizer.getIDCode();
   }
 
+
+
+  public int[] getFinalRanks(int flag) {
+    Canonizer canonizer = new Canonizer(oclMolecule, flag);
+    return canonizer.getFinalRank();
+  }
+
   public native JavaScriptObject getIDCodeAndCoordinates()
   /*-{
   	return {
@@ -249,7 +256,7 @@ private void addImplicitHydrogens(int atomNumber) {
 
   @JsIgnore
   public static JSMolecule fromSmiles(String smiles, boolean createCoordinates,
-  boolean readStereoFeatures) throws Exception {
+      boolean readStereoFeatures) throws Exception {
     SmilesParser parser = new SmilesParser();
     JSMolecule mol = new JSMolecule();
     parser.parse(mol.oclMolecule, smiles.getBytes(), createCoordinates, readStereoFeatures);
diff --git a/types.d.ts b/types.d.ts
index b8ef325c..ff18d364 100644
--- a/types.d.ts
+++ b/types.d.ts
@@ -463,8 +463,17 @@ export declare class Molecule {
     options?: IMoleculeToSVGOptions,
   ): string;
 
+  /**
+   * Get an ID code for the molecule
+   * @param flag
+   */
   getCanonizedIDCode(flag: number): string;
 
+  /**
+   * Returns the canonic numbering of the atoms.
+   */
+  getFinalRanks(flag: number): number[];
+
   /**
    * Returns an object with both the ID code and coordinates of the molecule.
    */