AlkylStructureFragmenter Implementation

src/main/java/de/unijena/cheminf/mortar/model/data/MoleculeDataModel.java

@@ -259,7 +259,8 @@ public boolean hasMoleculeUndergoneSpecificFragmentation(String aKey){
     public ImageView getStructure() {
         try {
             IAtomContainer tmpAtomContainer = this.getAtomContainer();
-            return new ImageView(DepictionUtil.depictImageWithZoomAndFillToFit(tmpAtomContainer, 1, this.getStructureImageWidth(), this.getStructureImageHeight(), true));
+            boolean tmpFillToFit = tmpAtomContainer.getAtomCount() > 6;
+            return new ImageView(DepictionUtil.depictImageWithZoomAndFillToFit(tmpAtomContainer, 1, this.getStructureImageWidth(), this.getStructureImageHeight(), tmpFillToFit));
         } catch (CDKException aCDKException) {
             Logger.getLogger(MoleculeDataModel.class.getName()).log(Level.SEVERE, aCDKException.toString(), aCDKException);
             return new ImageView(DepictionUtil.depictErrorImage(aCDKException.getMessage(), 250, 250));

src/main/java/de/unijena/cheminf/mortar/model/fragmentation/FragmentationService.java

@@ -24,10 +24,7 @@
 import de.unijena.cheminf.mortar.message.Message;
 import de.unijena.cheminf.mortar.model.data.FragmentDataModel;
 import de.unijena.cheminf.mortar.model.data.MoleculeDataModel;
-import de.unijena.cheminf.mortar.model.fragmentation.algorithm.ErtlFunctionalGroupsFinderFragmenter;
-import de.unijena.cheminf.mortar.model.fragmentation.algorithm.IMoleculeFragmenter;
-import de.unijena.cheminf.mortar.model.fragmentation.algorithm.ScaffoldGeneratorFragmenter;
-import de.unijena.cheminf.mortar.model.fragmentation.algorithm.SugarRemovalUtilityFragmenter;
+import de.unijena.cheminf.mortar.model.fragmentation.algorithm.*;
 import de.unijena.cheminf.mortar.model.settings.SettingsContainer;
 import de.unijena.cheminf.mortar.model.util.BasicDefinitions;
 import de.unijena.cheminf.mortar.model.util.ChemUtil;
@@ -153,6 +150,14 @@ public class FragmentationService {
      * Scaffold Generator
      */
     private IMoleculeFragmenter ScaffoldGF;
+    /**
+     * Alkyl Structure Fragmenter
+     */
+    private IMoleculeFragmenter AlkylSF;
+    /**
+     * Conjugated Pi System Fragmenter
+     */
+    private IMoleculeFragmenter ConjPiSysF;
     /**
      * List of  names of fragmentation algorithms that have already been run
      */
@@ -198,13 +203,17 @@ public class FragmentationService {
      */
     public FragmentationService(SettingsContainer aSettingsContainer){
         //Note: Every fragmenter class should only be added once to the array or there will be problems with setting persistence!
-        this.fragmenters = new IMoleculeFragmenter[3];
+        this.fragmenters = new IMoleculeFragmenter[5];
         this.ertlFGF = new ErtlFunctionalGroupsFinderFragmenter();
         this.fragmenters[0] = this.ertlFGF;
         this.sugarRUF = new SugarRemovalUtilityFragmenter();
         this.fragmenters[1] = this.sugarRUF;
         this.ScaffoldGF = new ScaffoldGeneratorFragmenter();
         this.fragmenters[2] = this.ScaffoldGF;
+        this.AlkylSF = new AlkylStructureFragmenter();
+        this.fragmenters[3] = this.AlkylSF;
+        this.ConjPiSysF = new ConjugatedPiSystemFragmenter();
+        this.fragmenters[4] = this.ConjPiSysF;
         //
         Objects.requireNonNull(aSettingsContainer, "aSettingsContainer must not be null");
         this.settingsContainer = aSettingsContainer;