From b7b6d78d88424de907a8bf0df07e0a0639f55f00 Mon Sep 17 00:00:00 2001
From: MaxR <60234321+Mila1004@users.noreply.github.com>
Date: Thu, 21 Nov 2024 16:59:34 +0100
Subject: [PATCH] WIP! bug with false fragment saturation after separation of
 double bonded carbon with ring structure;

---
 .../algorithm/AlkylStructureFragmenter.java        | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/main/java/de/unijena/cheminf/mortar/model/fragmentation/algorithm/AlkylStructureFragmenter.java b/src/main/java/de/unijena/cheminf/mortar/model/fragmentation/algorithm/AlkylStructureFragmenter.java
index 9c10350d..6bfe75d8 100644
--- a/src/main/java/de/unijena/cheminf/mortar/model/fragmentation/algorithm/AlkylStructureFragmenter.java
+++ b/src/main/java/de/unijena/cheminf/mortar/model/fragmentation/algorithm/AlkylStructureFragmenter.java
@@ -215,7 +215,8 @@ public class AlkylStructureFragmenter implements IMoleculeFragmenter{
      * Logger of this class.
      */
     private static final Logger logger = Logger.getLogger(AlkylStructureFragmenter.class.getName());
-
+    //WIP
+    private IAtomContainer builderInstanceAtomContainer;
     //</editor-fold>
     //
     //<editor-fold desc="Constructor">
@@ -606,6 +607,10 @@ public List<IAtomContainer> fragmentMolecule(IAtomContainer aMolecule)
         }
         //<editor-fold desc="Molecule Cloning, Property and Arrays Set" defaultstate="collapsed">
         IAtomContainer tmpClone = aMolecule.clone();
+        //WIP
+        this.builderInstanceAtomContainer = null;
+        this.builderInstanceAtomContainer = tmpClone.getBuilder().newInstance(IAtomContainer.class);
+        //IAtomContainer tmpBuilderAtomContainer = tmpClone.getBuilder().newInstance(IAtomContainer.class);
         int tmpPreFragmentationAtomCount = 0;
         for (IAtom tmpAtom: tmpClone.atoms()) {
             if (tmpAtom.getAtomicNumber() != 0) {
@@ -672,7 +677,7 @@ public List<IAtomContainer> fragmentMolecule(IAtomContainer aMolecule)
     //
     //</editor-fold>
     //
-    //<editor-fold desc="Private Methods" defaultstate="collapsed">
+    //<editor-fold desc="Protected Methods" defaultstate="collapsed">
 
     /**
      * Method to fill an IAtom array with the atoms of the input IAtomContainer
@@ -1047,7 +1052,9 @@ protected IAtomContainerSet extractFragments(IAtom[] anAtomArray, IBond[] aBondA
         Objects.requireNonNull(aBondArray);
         //<editor-fold desc="Extraction">
         IAtomContainerSet tmpExtractionSet = new AtomContainerSet();
-        IAtomContainer tmpRingFragmentationContainer = new AtomContainer();
+        //WIP
+        IAtomContainer tmpRingFragmentationContainer = this.builderInstanceAtomContainer.clone();
+        //IAtomContainer tmpRingFragmentationContainer = new AtomContainer();
         IAtomContainer tmpChainFragmentationContainer = new AtomContainer();
         IAtomContainer tmpIsolatedMultiBondsContainer = new AtomContainer();
         IAtomContainer tmpTertQuatCarbonContainer = new AtomContainer();
@@ -1094,6 +1101,7 @@ else if (tmpAtom.getProperty(AlkylStructureFragmenter.INTERNAL_ASF_DOUBLE_BOND_M
                             boolean tmpEnd = tmpDoubleToRingBond.getEnd().getProperty(AlkylStructureFragmenter.INTERNAL_ASF_RING_MARKER_KEY);
                             if (tmpBegin || tmpEnd) {
                                 tmpRingFragmentationContainer.addAtom(tmpAtom);
+                                //WIP
                                 //System.out.println("double bond to ring atom added");
                             } else {
                                 tmpIsolatedMultiBondsContainer.addAtom(tmpAtom);