Corrections in readme and wiki code added to test class;

README.md

@@ -18,7 +18,7 @@ An open implementation of the [Ertl algorithm for functional group identificatio
 ## Description
 The algorithm for automated functional groups detection and extraction of organic molecules developed by Dr Peter Ertl 
 is implemented on the basis of the [Chemistry Development Kit (CDK)](https://github.com/cdk/cdk). <br/>
-The open reimplementation named ErtlFunctionalGroupsFinder is described in a [scientific article](https://doi.org/10.1186/s13321-019-0361-8). <br/>
+This open reimplementation named ErtlFunctionalGroupsFinder is described in a [scientific article](https://doi.org/10.1186/s13321-019-0361-8). <br/>
 <br>ErtlFunctionalGroupsFinder is also available in the open Java rich client application MORTAR ('MOlecule fRagmenTation fRamework')
 where <i>in silico</i> molecule fragmentation can be easily conducted on a given data set and the results visualised
 ([MORTAR GitHub repository](https://github.com/FelixBaensch/MORTAR), [MORTAR article preprint](https://doi.org/10.26434/chemrxiv-2022-zgg8s)).
@@ -79,9 +79,12 @@ be pre-installed.
 
 # Acknowledgments
 Project team: Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny.<br/>
-The authors like to thank Peter Ertl for describing his algorithm in a way that allowed easy re-implementation. 
+<br>
+Logo: [Kohulan Rajan](https://github.com/Kohulan) <br>
+<br>
+The authors thank Peter Ertl for describing his algorithm in a way that allowed easy re-implementation. 
 This is not always the case. We also thank him for valuable discussions. 
-We appreciate help from Egon Willighagen and John Mayfield with the CDK integration 
+<br>We appreciate help from Egon Willighagen and John Mayfield with the CDK integration 
 and from Felix Bänsch for unbiased release testing.
 
 # References
@@ -96,4 +99,4 @@ and from Felix Bänsch for unbiased release testing.
 * [Steinbeck C, Han Y, Kuhn S, Horlacher O, Luttmann E, Willighagen EL. The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics. J Chem Inform Comput Sci. 2003;43(2):493-500.](https://dx.doi.org/10.1021%2Fci025584y) <br/>
 * [Steinbeck C, Hoppe C, Kuhn S, Floris M, Guha R, Willighagen EL. Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics. Curr Pharm Des. 2006; 12(17):2111-2120.](https://doi.org/10.2174/138161206777585274) <br/>
 * [May JW and Steinbeck C. Efficient ring perception for the Chemistry Development Kit. J. Cheminform. 2014; 6:3.](https://dx.doi.org/10.1186%2F1758-2946-6-3) <br/>
-* [Willighagen EL, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, Kuhn S, Pluska T, Rojas-Chertó M, Spjuth O, Torrance G, Evelo CT, Guha R, Steinbeck C, The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J Cheminform. 2017; 9:33.](https://doi.org/10.1186/s13321-017-0220-4)
+* [Willighagen EL, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, Kuhn S, Pluskal T, Rojas-Chertó M, Spjuth O, Torrance G, Evelo CT, Guha R, Steinbeck C, The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. J Cheminform. 2017; 9:33.](https://doi.org/10.1186/s13321-017-0220-4)

src/test/java/org/openscience/cdk/tools/test/ErtlFunctionalGroupsFinderTest.java

@@ -38,6 +38,8 @@
 import org.openscience.cdk.isomorphism.Pattern;
 import org.openscience.cdk.isomorphism.VentoFoggia;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.smiles.SmiFlavor;
+import org.openscience.cdk.smiles.SmilesGenerator;
 import org.openscience.cdk.smiles.SmilesParser;
 import org.openscience.cdk.tools.ErtlFunctionalGroupsFinder;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
@@ -198,6 +200,38 @@ public void testFind20() throws Exception {
         testFind(moleculeSmiles, expectedFGs);
     }
 
+    /**
+     * Example code to be used in the GitHub wiki of the project.
+     *
+     * @throws Exception if anything goes wrong
+     * @author Jonas Schaub
+     */
+    @Test
+    public void gitHubWikiTest() throws Exception {
+        //Prepare input
+        SmilesParser tmpSmiPar = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IAtomContainer tmpInputMol = tmpSmiPar.parseSmiles("C[C@@H]1CN(C[C@H](C)N1)C2=C(C(=C3C(=C2F)N(C=C(C3=O)C(=O)O)C4CC4)N)F"); //PubChem CID 5257
+        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(tmpInputMol);
+        Aromaticity tmpAromaticity = new Aromaticity(ElectronDonation.cdk(), Cycles.cdkAromaticSet());
+        tmpAromaticity.apply(tmpInputMol);
+        //Identify functional groups
+        ErtlFunctionalGroupsFinder tmpEFGF = new ErtlFunctionalGroupsFinder(); //default: generalization turned on
+        List<IAtomContainer> tmpFunctionalGroupsList = tmpEFGF.find(tmpInputMol);
+        SmilesGenerator tmpSmiGen = new SmilesGenerator(SmiFlavor.Canonical | SmiFlavor.UseAromaticSymbols);
+        for (IAtomContainer tmpFunctionalGroup : tmpFunctionalGroupsList) {
+            String tmpSmilesString = tmpSmiGen.create(tmpFunctionalGroup);
+            System.out.println(tmpSmilesString);
+        }
+        //non-generalized functional groups
+        System.out.println("----------------");
+        tmpEFGF = new ErtlFunctionalGroupsFinder(ErtlFunctionalGroupsFinder.Mode.NO_GENERALIZATION);
+        tmpFunctionalGroupsList = tmpEFGF.find(tmpInputMol);
+        for (IAtomContainer tmpFunctionalGroup : tmpFunctionalGroupsList) {
+            String tmpSmilesString = tmpSmiGen.create(tmpFunctionalGroup);
+            System.out.println(tmpSmilesString);
+        }
+    }
+
     private void testFind(String moleculeSmiles, String[] fGStrings) throws Exception {
         testFind(moleculeSmiles, fGStrings, new Aromaticity(ElectronDonation.daylight(), Cycles.all()));
     }