feat: add method Molecule.getAtomQueryFeaturesObject

* wip: add getAtomQueryFeaturesObject

* create PlainJSObject class

* feat: add method Molecule.getAtomQueryFeaturesObject

---------

Co-authored-by: Michaël Zasso <targos@protonmail.com>

__tests__/__snapshots__/library.js.snap

@@ -100,6 +100,7 @@ exports[`prototype properties of Molecule 1`] = `
   "getAtomParity",
   "getAtomPi",
   "getAtomPreferredStereoBond",
+  "getAtomQueryFeaturesObject",
   "getAtomRadical",
   "getAtomRingBondCount",
   "getAtomRingCount",

__tests__/molecule.queryFeatures.test.js

@@ -0,0 +1,23 @@
+'use strict';
+
+const { Molecule } = require('../minimal');
+
+test('queryFeatures more than 2 neighbours', () => {
+  const molecule = Molecule.fromIDCode('eF@Hp[qp');
+
+  const firstQueryFeatures = molecule.getAtomQueryFeaturesObject(0);
+  expect(firstQueryFeatures.not0Neighbours).toBe(true);
+  expect(firstQueryFeatures.not1Neighbours).toBe(true);
+  expect(firstQueryFeatures.not2Neighbours).toBe(true);
+  expect(firstQueryFeatures.not3Neighbours).toBe(false);
+
+});
+
+test('queryFeatures exactly 2 hydrogens', () => {
+  const molecule = Molecule.fromIDCode('eF@Hp_Qh');
+  const firstQueryFeatures = molecule.getAtomQueryFeaturesObject(0);
+  expect(firstQueryFeatures.not0Hydrogen).toBe(true);
+  expect(firstQueryFeatures.not1Hydrogen).toBe(true);
+  expect(firstQueryFeatures.not2Hydrogen).toBe(false);
+  expect(firstQueryFeatures.not3Hydrogen).toBe(true);
+});

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

@@ -1,5 +1,6 @@
 package com.actelion.research.gwt.minimal;
 
+import com.actelion.research.gwt.minimal.MoleculeQueryFeatures;
 import java.util.HashMap;
 import java.util.Set;
 import java.util.Vector;
@@ -947,6 +948,11 @@ public int getAtomParity(int atom) {
   // return oclMolecule.getAtomQueryFeatures(atom);
   // }
 
+  public JavaScriptObject getAtomQueryFeaturesObject(int atom) {
+    return MoleculeQueryFeatures.getAtomQueryFeatures(oclMolecule, atom);
+  }
+
+
   public int getAtomRadical(int atom) {
     return oclMolecule.getAtomRadical(atom);
   }
@@ -1741,4 +1747,4 @@ public void setUnknownParitiesToExplicitlyUnknown() {
   public void setAssignParitiesToNitrogen(boolean b) {
     oclMolecule.setAssignParitiesToNitrogen(b);
   }
-}
+};

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

@@ -0,0 +1,83 @@
+package com.actelion.research.gwt.minimal;
+
+import com.actelion.research.chem.StereoMolecule;
+import com.actelion.research.chem.Molecule;
+import com.google.gwt.core.client.JavaScriptObject;
+
+class MoleculeQueryFeatures {
+  public static JavaScriptObject getAtomQueryFeatures(StereoMolecule oclMolecule, int atom) {
+    PlainJSObject moleculeQueryFeatures = PlainJSObject.create();
+
+    moleculeQueryFeatures.setPropertyBoolean("aromatic",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFAromatic) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("notAromatic",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNotAromatic) > 0);
+
+    moleculeQueryFeatures.setPropertyBoolean("notChain",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNotChain) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("not2RingBonds",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNot2RingBonds) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("not3RingBonds",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNot3RingBonds) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("not4RingBonds",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNot4RingBonds) > 0);
+
+    moleculeQueryFeatures.setPropertyBoolean("noMoreNeighbours",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNoMoreNeighbours) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("moreNeighbours",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFMoreNeighbours) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("matchStereo",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFMatchStereo) > 0);
+
+    moleculeQueryFeatures.setPropertyBoolean("not0PiElectrons",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNot0PiElectrons) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("not1PiElectrons",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNot1PiElectron) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("not2PiElectrons",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNot2PiElectrons) > 0);
+
+    moleculeQueryFeatures.setPropertyBoolean("not0Hydrogen",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNot0Hydrogen) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("not1Hydrogen",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNot1Hydrogen) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("not2Hydrogen",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNot2Hydrogen) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("not3Hydrogen",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNot3Hydrogen) > 0);
+
+    moleculeQueryFeatures.setPropertyBoolean("not0Neighbours",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNot0Neighbours) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("not1Neighbours",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNot0Neighbours) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("not2Neighbours",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNot2Neighbours) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("not3Neighbours",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNot3Neighbours) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("not4Neighbours",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNot4Neighbours) > 0);
+
+    moleculeQueryFeatures.setPropertyBoolean("notChargeNeg",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNotChargeNeg) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("notCharge0",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNotCharge0) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("noChargePos",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFNotChargePos) > 0);
+
+    moleculeQueryFeatures.setPropertyBoolean("ringSize0",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFRingSize0) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("ringSize3",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFRingSize3) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("ringSize4",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFRingSize4) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("ringSize5",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFRingSize5) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("ringSize6",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFRingSize6) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("ringSize7",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFRingSize7) > 0);
+    moleculeQueryFeatures.setPropertyBoolean("ringSizeLarge",
+        (oclMolecule.getAtomQueryFeatures(atom) & Molecule.cAtomQFRingSizeLarge) > 0);
+
+    return moleculeQueryFeatures;
+  }
+}

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

@@ -0,0 +1,23 @@
+package com.actelion.research.gwt.minimal;
+
+import com.google.gwt.core.client.JavaScriptObject;
+
+public class PlainJSObject extends JavaScriptObject {
+  protected PlainJSObject() {}
+
+  public static PlainJSObject create() {
+    return (PlainJSObject) JavaScriptObject.createObject().cast();
+  }
+
+  public native final void setPropertyString(String key, String value)/*-{
+    this[key] = value;
+  }-*/;
+
+  public native final void setPropertyInt(String key, int value)/*-{
+    this[key] = value;
+  }-*/;
+
+  public native final void setPropertyBoolean(String key, boolean value)/*-{
+    this[key] = value;
+  }-*/;
+}

types.d.ts

@@ -14,6 +14,40 @@ export interface IMoleculeFromSmilesOptions {
   noStereo?: boolean;
 }
 
+export interface AtomQueryFeatures {
+  aromatic: boolean;
+  notAromatic: boolean;
+  notChain: boolean;
+  not2RingBonds: boolean;
+  not3RingBonds: boolean;
+  not4RingBonds: boolean;
+  noMoreNeighbours: boolean;
+  moreNeighbours: boolean;
+  matchStereo: boolean;
+  not0PiElectrons: boolean;
+  not1PiElectrons: boolean;
+  not2PiElectrons: boolean;
+  not0Hydrogen: boolean;
+  not1Hydrogen: boolean;
+  not2Hydrogen: boolean;
+  not3Hydrogen: boolean;
+  not0Neighbours: boolean;
+  not1Neighbours: boolean;
+  not2Neighbours: boolean;
+  not3Neighbours: boolean;
+  not4Neighbours: boolean;
+  notChargeNeg: boolean;
+  notCharge0: boolean;
+  noChargePos: boolean;
+  ringSize0: boolean;
+  ringSize3: boolean;
+  ringSize4: boolean;
+  ringSize5: boolean;
+  ringSize6: boolean;
+  ringSize7: boolean;
+  ringSizeLarge: boolean;
+}
+
 export interface IMoleculeToSVGOptions extends IDepictorOptions {
   /**
    * Factor used to compute the size of text nodes.
@@ -905,6 +939,12 @@ export declare class Molecule {
    */
   getAtomLabel(atom: number): string;
 
+  /**
+   * Get the atomic query features as an object
+   * @param atom
+   */
+  getAtomQueryFeaturesObject(atom: number): AtomQueryFeatures;
+
   /**
    * The list of atoms that are allowed at this position during sub-structure
    * search. (or refused atoms, if atom query feature cAtomQFAny is set).