From 46f2577d961fac7b5fad4ef3f89b8662f13813e1 Mon Sep 17 00:00:00 2001
From: korffmo <modest@von-korff.net>
Date: Fri, 16 Feb 2024 18:43:18 +0100
Subject: [PATCH] added Flexophore functionality for synthon processing

---
 .../chem/descriptor/flexophore/DistHist.java  |  4 +-
 .../flexophore/PPNodeVizHelper.java           | 41 ++++++++++++++++++
 .../generator/CreatorMolDistHistViz.java      | 42 +++++++++++++++++--
 3 files changed, 81 insertions(+), 6 deletions(-)
 create mode 100644 src/main/java/com/actelion/research/chem/descriptor/flexophore/PPNodeVizHelper.java

diff --git a/src/main/java/com/actelion/research/chem/descriptor/flexophore/DistHist.java b/src/main/java/com/actelion/research/chem/descriptor/flexophore/DistHist.java
index f9f8dd4c..28d6fc34 100644
--- a/src/main/java/com/actelion/research/chem/descriptor/flexophore/DistHist.java
+++ b/src/main/java/com/actelion/research/chem/descriptor/flexophore/DistHist.java
@@ -224,10 +224,10 @@ public List<ClusterNode> getClusterCenter(int maxDistance){
 	}
 
 	/**
-	 * The distnce histograms are stored in a single array.
+	 * The distance histograms are stored in a single array.
 	 * @param indexAt1
 	 * @param indexAt2
-	 * @param arrHist
+	 * @param arrHist a deep copy is taken.
 	 */
 	public void setDistHist(int indexAt1, int indexAt2, byte [] arrHist) {
 		
diff --git a/src/main/java/com/actelion/research/chem/descriptor/flexophore/PPNodeVizHelper.java b/src/main/java/com/actelion/research/chem/descriptor/flexophore/PPNodeVizHelper.java
new file mode 100644
index 00000000..56d0cab5
--- /dev/null
+++ b/src/main/java/com/actelion/research/chem/descriptor/flexophore/PPNodeVizHelper.java
@@ -0,0 +1,41 @@
+package com.actelion.research.chem.descriptor.flexophore;
+
+import com.actelion.research.chem.Molecule3D;
+import com.actelion.research.chem.StereoMolecule;
+import com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/*
+ 
+
+ 
+ Created by Modest von Korff 
+ 16/02/2024
+ 
+ */
+public class PPNodeVizHelper {
+
+    public static PPNodeViz createWithoutCoordinates(SubGraphIndices sgi, int indexPPPoint, Molecule3D mol){
+        int [] arrIndexAtomFrag = sgi.getAtomIndices();
+        PPNodeViz ppNodeViz = new PPNodeViz();
+        ppNodeViz.setIndex(indexPPPoint);
+        for (int index : arrIndexAtomFrag) {
+            int interactionType = mol.getInteractionAtomType(index);
+            ppNodeViz.add(interactionType);
+            ppNodeViz.addIndexOriginalAtom(index);
+        }
+        return ppNodeViz;
+    }
+    public static List<PPNodeViz> createWithoutCoordinates(List<SubGraphIndices> liSubGraphIndices, Molecule3D mol){
+        List<PPNodeViz> liPPNodeViz = new ArrayList<>();
+        for (int i = 0; i < liSubGraphIndices.size(); i++) {
+            SubGraphIndices sgi = liSubGraphIndices.get(i);
+            PPNodeViz ppNodeViz = createWithoutCoordinates(sgi, i, mol);
+            liPPNodeViz.add(ppNodeViz);
+        }
+        return liPPNodeViz;
+    }
+
+}
diff --git a/src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/CreatorMolDistHistViz.java b/src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/CreatorMolDistHistViz.java
index 89b3e186..61b9e1e3 100644
--- a/src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/CreatorMolDistHistViz.java
+++ b/src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/CreatorMolDistHistViz.java
@@ -45,10 +45,7 @@
 import org.openmolecules.chem.conf.gen.ConformerGenerator;
 import org.openmolecules.chem.conf.gen.RigidFragmentCache;
 
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.List;
+import java.util.*;
 
 /**
  * CreatorMolDistHistViz
@@ -460,6 +457,43 @@ public static MolDistHistViz create(List<MultCoordFragIndex> liMultCoordFragInde
 
         return molDistHistViz;
 
+    }
+    public static MolDistHistViz createWithoutCoordinates(List<SubGraphIndices> liMultCoordFragIndex, Molecule3D molecule3D){
+
+        MolDistHistViz molDistHistViz = new MolDistHistViz(liMultCoordFragIndex.size(), molecule3D);
+
+        List<PPNodeViz> liPPNodeViz = new ArrayList<>();
+        for (int i = 0; i < liMultCoordFragIndex.size(); i++) {
+            SubGraphIndices sgi = liMultCoordFragIndex.get(i);
+
+            int [] arrIndexAtomFrag = sgi.getAtomIndices();
+
+            PPNodeViz ppNodeViz = new PPNodeViz();
+            ppNodeViz.setIndex(i);
+
+            for (int index : arrIndexAtomFrag) {
+                int interactionType = molecule3D.getInteractionAtomType(index);
+                ppNodeViz.add(interactionType);
+                ppNodeViz.addIndexOriginalAtom(index);
+            }
+            liPPNodeViz.add(ppNodeViz);
+        }
+
+        molDistHistViz.set(liPPNodeViz);
+
+        byte [] arrHistPercent = new byte [ConstantsFlexophoreGenerator.BINS_HISTOGRAM];
+        Arrays.fill(arrHistPercent, (byte)1);
+
+        for (int i = 0; i < liMultCoordFragIndex.size(); i++) {
+            for (int j = i+1; j < liMultCoordFragIndex.size(); j++) {
+                molDistHistViz.setDistHist(i,j,arrHistPercent);
+            }
+        }
+
+        molDistHistViz.realize();
+
+        return molDistHistViz;
+
     }
 
     private static Molecule3D createPharmacophorePoints(Molecule3D molecule3D, List<MultCoordFragIndex> liMultCoordFragIndex) {