Update Pharos3D. Flexophore and PheSA for enumerated products are now…

… calculated in one rush.
Actelion · Sep 9, 2024 · bf123e4 · bf123e4
1 parent 9f876b8
commit bf123e4
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Showing 2 changed files with 35 additions and 2 deletions.
diff --git a/src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerFlexophore.java b/src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerFlexophore.java
@@ -98,8 +98,11 @@ public class DescriptorHandlerFlexophore implements IDescriptorHandlerFlexophore
 
 	protected static final int MIN_NUM_ATOMS = 6;
 
-	// 250
-	public static final int NUM_CONFORMATIONS = 250;
+	/**
+	 *
+	 * 06.09.2024 Set to 200 to be aligned with PheSA
+	 */
+	public static final int NUM_CONFORMATIONS = 200;
 
 	public static final int MAX_NUM_SOLUTIONS = 1000;
 
@@ -384,6 +387,7 @@ public MolDistHistViz createVisualDescriptorSingleConf(ConformerSet conformerSet
 		return mdhv;
 	}
 
+
 	public MolDistHist createDescriptor(Object mol) {
 		StereoMolecule fragBiggest = (StereoMolecule)mol;
 
@@ -456,6 +460,10 @@ public MolDistHistViz createVisualDescriptor(StereoMolecule fragBiggest) {
 		return mdhv;
 	}
 
+	public MolDistHistViz createVisualDescriptor(ConformerSet cs){
+		return creatorMolDistHistViz.createFromConformerSet(cs);
+	}
+
 	public Exception getRecentException() {
 		return recentException;
 	}

diff --git a/...ava/com/actelion/research/chem/descriptor/flexophore/generator/CreatorMolDistHistViz.java b/...ava/com/actelion/research/chem/descriptor/flexophore/generator/CreatorMolDistHistViz.java
@@ -37,6 +37,8 @@
 import com.actelion.research.calc.ArrayUtilsCalc;
 import com.actelion.research.calc.ThreadMaster;
 import com.actelion.research.chem.*;
+import com.actelion.research.chem.conf.Conformer;
+import com.actelion.research.chem.conf.ConformerSet;
 import com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore;
 import com.actelion.research.chem.descriptor.flexophore.*;
 import com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphExtractor;
@@ -210,6 +212,29 @@ public MolDistHistViz createMultipleConformations(StereoMolecule molOrig, int nC
         MolDistHistViz mdhv = create(liMultCoordFragIndex, molViz);
         return mdhv;
     }
+    public MolDistHistViz createFromConformerSet(ConformerSet conformerSet)  {
+
+        Molecule3D mol = new Molecule3D(conformerSet.iterator().next().toMolecule());
+        mol.ensureHelperArrays(Molecule.cHelperRings);
+        InteractionAtomTypeCalculator.setInteractionTypes(mol);
+
+        List<SubGraphIndices> liSGI = getSubGraphIndices(mol);
+        List<MultCoordFragIndex> liMultCoordFragIndex = new ArrayList<>();
+        for (SubGraphIndices subGraphIndices : liSGI) {
+            liMultCoordFragIndex.add(new MultCoordFragIndex(subGraphIndices.getAtomIndices()));
+        }
+
+        Iterator<Conformer> it = conformerSet.iterator();
+        while (it.hasNext()){
+            Conformer c = it.next();
+            Molecule3D molConf = new Molecule3D(c.toMolecule());
+            molConf.ensureHelperArrays(Molecule.cHelperRings);
+            calcFragmentCenter(molConf, liMultCoordFragIndex);
+        }
+
+        Molecule3D molViz = createPharmacophorePoints(mol, liMultCoordFragIndex);
+        return create(liMultCoordFragIndex, molViz);
+    }
 
     public List<SubGraphIndices> getSubGraphIndices(Molecule3D molInPlace){
         //