From 9827d076bfd59429e06bf48ec1c087e94f3fae3a Mon Sep 17 00:00:00 2001
From: Tyler Peryea <tylerperyea@gmail.com>
Date: Mon, 4 Dec 2023 15:29:03 -0500
Subject: [PATCH 1/9] fixed CIP stereo bug

---
 .../ncats/molwitch/cdk/CdkChemicalImpl.java   | 32 ++++++-
 src/test/java/TestChiralRead.java             | 86 +++++++++++++++++++
 2 files changed, 116 insertions(+), 2 deletions(-)

diff --git a/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java b/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
index fae4832..3469012 100644
--- a/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
+++ b/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
@@ -53,8 +53,17 @@
 import org.openscience.cdk.aromaticity.ElectronDonation;
 import org.openscience.cdk.aromaticity.Kekulization;
 import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
+import org.openscience.cdk.config.IsotopeFactory;
+import org.openscience.cdk.config.Isotopes;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.geometry.cip.CIPTool;
+import org.openscience.cdk.geometry.cip.ILigand;
+import org.openscience.cdk.geometry.cip.ImplicitHydrogenLigand;
+import org.openscience.cdk.geometry.cip.Ligand;
+import org.openscience.cdk.geometry.cip.VisitedAtoms;
+import org.openscience.cdk.geometry.cip.CIPTool.CIP_CHIRALITY;
+import org.openscience.cdk.geometry.cip.CIPToolMod;
+import org.openscience.cdk.geometry.cip.rules.ISequenceSubRule;
 import org.openscience.cdk.graph.ConnectivityChecker;
 import org.openscience.cdk.graph.Cycles;
 import org.openscience.cdk.graph.GraphUtil;
@@ -67,6 +76,7 @@
 import org.openscience.cdk.interfaces.IBond.Order;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IDoubleBondStereochemistry;
+import org.openscience.cdk.interfaces.IIsotope;
 import org.openscience.cdk.interfaces.IMolecularFormula;
 import org.openscience.cdk.interfaces.IRing;
 import org.openscience.cdk.interfaces.IRingSet;
@@ -91,6 +101,8 @@
 import org.openscience.cdk.stereo.StereoElementFactory;
 import org.openscience.cdk.stereo.Stereocenters;
 import org.openscience.cdk.tools.CDKHydrogenAdder;
+import org.openscience.cdk.tools.ILoggingTool;
+import org.openscience.cdk.tools.LoggingToolFactory;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
 import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator;
@@ -198,6 +210,9 @@ public class CdkChemicalImpl implements ChemicalImpl<CdkChemicalImpl>{
     }
     );
     
+    
+    
+    
     CachedSupplier<Void> cahnIngoldPrelogSupplier = CachedSupplier.of(()->{
         try {
             makeStereoElms() ;
@@ -207,13 +222,22 @@ public class CdkChemicalImpl implements ChemicalImpl<CdkChemicalImpl>{
             withModifiedForm(c->{
                CdkChemicalImpl cimp = (CdkChemicalImpl) c.getImpl();
 //               cimp.
-               CIPTool.label(cimp.getContainer());
+               
+               //Due to a bug in CDK, this doesn't work as expected
+               //CIPTool.label(cimp.getContainer());
+               
+               //We currently have to use a modified form for now
+               CIPToolMod.label(cimp.getContainer());
+               
                for (int i = 0; i < container.getAtomCount(); i++) {
                    IAtom ai =container.getAtom(i);
                    IAtom ain =cimp.getContainer().getAtom(i);
                    Object p = ain.getProperty(CDKConstants.CIP_DESCRIPTOR);
+                   
                    ai.removeProperty(CDKConstants.CIP_DESCRIPTOR);
-                   ai.setProperty(CDKConstants.CIP_DESCRIPTOR, p);
+                   if(p!=null) {
+                	   ai.setProperty(CDKConstants.CIP_DESCRIPTOR, p);   
+                   }
                    
                }
                return null;
@@ -1156,8 +1180,12 @@ public List<ExtendedTetrahedralChirality> getExtendedTetrahedrals() {
 	}
 
     public <T> T withModifiedForm(Function<Chemical, T> calc) {
+    	
+    	
         Chemical c = new Chemical(this);
 
+//        if(true)return calc.apply(c);
+        
         List<Tuple<Runnable,Runnable>> operations = new ArrayList<>();
 
 
diff --git a/src/test/java/TestChiralRead.java b/src/test/java/TestChiralRead.java
index 6122674..23014fa 100644
--- a/src/test/java/TestChiralRead.java
+++ b/src/test/java/TestChiralRead.java
@@ -461,6 +461,92 @@ public void testHavingExplicitHydrogenOnStereoCenterDoesNotInvalidatePhosphateCe
 	   		assertEquals(2,mol.getTetrahedrals().size());
 	   	}
 		
+		@Test
+	   	public void testHavingBondTableOrderChangedShouldKeepSameStereo() throws Exception {
+
+			
+	   		Chemical mol=Chemical.parse("\n"
+	   				+ "   JSDraw212042310502D\n"
+	   				+ "\n"
+	   				+ " 14 14  0  0  1  0            999 V2000\n"
+	   				+ "   21.4047   -8.8605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.0654   -9.2811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.4188   -8.5056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.1278   -7.7212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   25.9094   -6.8325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   26.0050   -8.5767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   26.6898   -5.7439    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   28.1943   -6.0199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.4240   -6.9456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.5922   -5.3944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   21.7756   -6.0051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   26.5338   -4.4447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   20.6247  -10.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.0654  -10.8412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "  3  6  1  0  0  0  0\n"
+	   				+ "  2  3  1  0  0  0  0\n"
+	   				+ "  5  7  1  0  0  0  0\n"
+	   				+ "  7  8  1  0  0  0  0\n"
+	   				+ "  3  9  1  0  0  0  0\n"
+	   				+ "  9  4  1  0  0  0  0\n"
+	   				+ "  5  9  1  0  0  0  0\n"
+	   				+ "  9 10  1  1  0  0  0\n"
+	   				+ "  4 11  1  0  0  0  0\n"
+	   				+ "  7 12  1  0  0  0  0\n"
+	   				+ "  5  6  1  0  0  0  0\n"
+	   				+ "  1  2  1  0  0  0  0\n"
+	   				+ "  1 13  1  0  0  0  0\n"
+	   				+ "  2 14  1  0  0  0  0\n"
+	   				+ "M  END");
+			Optional<Chirality> opChi=mol.getTetrahedrals().stream()
+			  .map(ca->ca.getChirality())
+			  .filter(ca->!ca.isEither())
+			  			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.R, opChi.get());
+			
+
+	   		mol=Chemical.parse("\n"
+	   				+ "   JSDraw212042310502D\n"
+	   				+ "\n"
+	   				+ " 14 14  0  0  1  0            999 V2000\n"
+	   				+ "   21.4047   -8.8605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.0654   -9.2811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.4188   -8.5056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.1278   -7.7212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   25.9094   -6.8325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   26.0050   -8.5767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   26.6898   -5.7439    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   28.1943   -6.0199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.4240   -6.9456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.5922   -5.3944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   21.7756   -6.0051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   26.5338   -4.4447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   20.6247  -10.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.0654  -10.8412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "  2  3  1  0  0  0  0\n"
+	   				+ "  3  6  1  0  0  0  0\n"
+	   				+ "  5  7  1  0  0  0  0\n"
+	   				+ "  7  8  1  0  0  0  0\n"
+	   				+ "  3  9  1  0  0  0  0\n"
+	   				+ "  9  4  1  0  0  0  0\n"
+	   				+ "  5  9  1  0  0  0  0\n"
+	   				+ "  9 10  1  1  0  0  0\n"
+	   				+ "  4 11  1  0  0  0  0\n"
+	   				+ "  7 12  1  0  0  0  0\n"
+	   				+ "  5  6  1  0  0  0  0\n"
+	   				+ "  1  2  1  0  0  0  0\n"
+	   				+ "  1 13  1  0  0  0  0\n"
+	   				+ "  2 14  1  0  0  0  0\n"
+	   				+ "M  END");
+			opChi=mol.getTetrahedrals().stream()
+			  .map(ca->ca.getChirality())
+			  .filter(ca->!ca.isEither())
+			  			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.R, opChi.get());
+	   	}
+		
 		@Test
 	   	public void testReadingSmilesShouldNotGenerateCoordinates() throws Exception {
 

From 195a7a36cf95647436e9c3997d4f1053f8d7c6d0 Mon Sep 17 00:00:00 2001
From: Tyler Peryea <tylerperyea@gmail.com>
Date: Mon, 4 Dec 2023 15:31:01 -0500
Subject: [PATCH 2/9] added missing files

---
 .../cdk/geometry/cip/CIPToolMod.java          | 270 ++++++++++++++++++
 .../geometry/cip/rules/CIPLigandRule2.java    |  80 ++++++
 2 files changed, 350 insertions(+)
 create mode 100644 src/main/java/org/openscience/cdk/geometry/cip/CIPToolMod.java
 create mode 100644 src/main/java/org/openscience/cdk/geometry/cip/rules/CIPLigandRule2.java

diff --git a/src/main/java/org/openscience/cdk/geometry/cip/CIPToolMod.java b/src/main/java/org/openscience/cdk/geometry/cip/CIPToolMod.java
new file mode 100644
index 0000000..be6ff1d
--- /dev/null
+++ b/src/main/java/org/openscience/cdk/geometry/cip/CIPToolMod.java
@@ -0,0 +1,270 @@
+package org.openscience.cdk.geometry.cip;
+
+import java.util.List;
+
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.geometry.cip.CIPTool.CIP_CHIRALITY;
+import org.openscience.cdk.geometry.cip.rules.CIPLigandRule;
+import org.openscience.cdk.geometry.cip.rules.CIPLigandRule2;
+import org.openscience.cdk.geometry.cip.rules.ISequenceSubRule;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IDoubleBondStereochemistry;
+import org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation;
+import org.openscience.cdk.interfaces.IStereoElement;
+import org.openscience.cdk.interfaces.ITetrahedralChirality;
+import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
+
+/**
+ * This modified version of {@link CIPTool} is just present temporarily to correct
+ * a CIP bug in CDK. CDK's default CIP rule works well, but has a bug in the recursive
+ * part where, if there's a tie between 2 ligands based on atomic number/mass, it will
+ * then get all sub-ligands and compare them. The issue is that each set of sub-ligands
+ * is sorted by a mass+atomic number only priority, and each sub-ligand from the parent
+ * ligand is compared only to its matched counterpart, not to all potentially higher 
+ * priority ligands.
+ *  
+ *  <pre>
+ * Consider this case below (4S)-2,3,4,5-tetramethyloctane:  
+ *  
+ *     3'    5'
+ *     M     C
+ *     |  4  | 
+ * M-C-C-[C]-C-C-C-M
+ *   | 3  :  5
+ *   M    M
+ *        4'
+ * 
+ * M = Methyl
+ * C = Carbon
+ * : = Dashed bond
+ * # = Locant 
+ * </pre>
+ *                 
+ * The 4 postion [C] is a stereo center with S configuration (as demonstrated
+ * with the : dashed bond to the methyl group below). The carbon atoms at 3, 4
+ * and 5 positions are tied for priority based on first pass CIP rules (atom
+ * numbner and mass). However, 3 and 5 are quickly seen as higher priority than
+ * 4' in the first tie-break as 4' has no sub-ligands. 3 and 5, however, both
+ * have 2 sub-ligands. 3 has [3',2] and 5 has [5',6] as sub-ligands. The next 
+ * step CDK CIP rules do is to ORDER these sub-ligands and then compare them.
+ * In this case, we need to order [3',2] and [5',6] individually. For [3',2],
+ * this is done by comparing only the ATOMIC NUMBER+MASS between 3' and 2,
+ * and since they are both carbon atoms, this will result in a tie. This means
+ * that if the starting order of [3',2] was [3',2] it will remain that way. If
+ * the starting order is [2,3'] it will remain [2,3']. Since the input order
+ * of the ligands is based on read-order (order of bonds in the bond table in
+ * the CTAB, for example), this means the ordering of the sub-ligands is effectively
+ * non-deterministic. 2 is certainly higher priority than 3' in full CIP rules,
+ * and 6 is higher priorty than 5' as well. In the above cases there are 4 ways
+ * the ligand ordering can go
+ * <pre>
+ * Possibility 1: both sub-ligands in right order
+ *    3 vs 5 =>
+ *    [2,3'] vs [6,5'] => 
+ *    2 vs 6 => 2 is higher priority
+ *    therefore 3 is higher priority (correct)
+ * 
+ * Possibility 2: 3 sub-ligands wrong order, 5 right order
+ *    3 vs 5 =>
+ *    [3',2] vs [6,5'] => 
+ *    3' vs 6 => 6 is higher priority
+ *    therefore 5 is higher priority (incorrect)
+ * 
+ * Possibility 3: 3 sub-ligands RIGHT order, 5 wrong order
+ *    3 vs 5 =>
+ *    [2,3'] vs [5',6] => 
+ *    2 vs 5' => 2 is higher priority
+ *    therefore 3 is higher priority (correct)
+ * 
+ * Possibility 4: both sub-ligands in WRONG order
+ *    3 vs 5 =>
+ *    [3',2] vs [5',6] => 
+ *    3' vs 5' => TIE, go to next
+ *    2 vs 6 => 2 is higher priority
+ *    therefore 3 is higher priority (correct)
+ * </pre>
+ * <p>
+ * Notice here that 3 of the 4 possibilities above will give the correct
+ * CIP ordering. This is indeed typical. The bug only applies in circumstances
+ * where 2 or more "principal" ligands are tied for CIP priority based on
+ * atom number and atomic weight AND those 2 ligands both have sub-ligands 
+ * (non-hydrogens) AND at least 2 sub-ligands of those ligands are tied for
+ * atomic weight and atomic mass. Even still, the majority of the time the
+ * criteria is met, CDK will still produce the correct CIP labeling.
+ * </p>
+ * <p>
+ * This class corrects the bug by switching how the ordering is done to instead
+ * call the full CIP ordering for sub-ligands. This is potentially computationally
+ * more expensive. The actual code here is largely just copy/pasted methods needed
+ * to perform the same methods as {@link CIPTool} and a reference to a modified {@link CIPLigandRule}
+ * (called {@link CIPLigandRule2}).
+ * 
+ * </p>
+ * 
+ * 
+ *   
+ * @author tyler
+ *
+ */
+public class CIPToolMod {
+	
+	private static ISequenceSubRule<ILigand> cipRule = new CIPLigandRule2();
+	
+	/**
+	 * GSRS-MODIFIED: Temporary bug fix for {@link CIPTool#label(IAtomContainer)}
+	 * 
+     * @param container structure to label
+     */
+    public static void label(IAtomContainer container) {
+
+        for (IStereoElement stereoElement : container.stereoElements()) {
+            if (stereoElement instanceof ITetrahedralChirality) {
+                ITetrahedralChirality tc = (ITetrahedralChirality) stereoElement;
+                tc.getChiralAtom().setProperty(CDKConstants.CIP_DESCRIPTOR, getCIPChirality(container, tc).toString());
+            } else if (stereoElement instanceof IDoubleBondStereochemistry) {
+                IDoubleBondStereochemistry dbs = (IDoubleBondStereochemistry) stereoElement;
+                dbs.getStereoBond()
+                        .setProperty(CDKConstants.CIP_DESCRIPTOR, getCIPChirality(container, dbs).toString());
+            }
+        }
+
+    }
+    
+
+    /**
+	 * GSRS-MODIFIED: Temporary bug fix for {@link CIPTool#getCIPChirality(IAtomContainer, ITetrahedralChirality)}
+	 * 
+     * @param container structure to label
+     */
+    public static CIP_CHIRALITY getCIPChirality(IAtomContainer container, ITetrahedralChirality stereoCenter) {
+
+        // the LigancyFourChirality is kind of redundant but we keep for an
+        // easy way to get the ILigands array
+        LigancyFourChirality tmp = new LigancyFourChirality(container, stereoCenter);
+        Stereo stereo = stereoCenter.getStereo();
+
+        int parity = permParity(tmp.getLigands());
+
+        if (parity == 0) return CIP_CHIRALITY.NONE;
+        if (parity < 0) stereo = stereo.invert();
+
+        if (stereo == Stereo.CLOCKWISE) return CIP_CHIRALITY.R;
+        if (stereo == Stereo.ANTI_CLOCKWISE) return CIP_CHIRALITY.S;
+
+        return CIP_CHIRALITY.NONE;
+    }
+    
+    /**
+  	 * GSRS-MODIFIED: Temporary bug fix for {@link CIPTool#getCIPChirality(IAtomContainer, IDoubleBondStereochemistry)}
+  	 * 
+     * @param container structure to label
+     */    
+    public static CIP_CHIRALITY getCIPChirality(IAtomContainer container, IDoubleBondStereochemistry stereoCenter) {
+
+        IBond stereoBond = stereoCenter.getStereoBond();
+        IBond leftBond = stereoCenter.getBonds()[0];
+        IBond rightBond = stereoCenter.getBonds()[1];
+
+        // the following variables are usd to label the atoms - makes things
+        // a little more concise
+        //
+        // x       y       x
+        //  \     /         \
+        //   u = v    or     u = v
+        //                        \
+        //                         y
+        //
+        IAtom u = stereoBond.getBegin();
+        IAtom v = stereoBond.getEnd();
+        IAtom x = leftBond.getOther(u);
+        IAtom y = rightBond.getOther(v);
+
+        Conformation conformation = stereoCenter.getStereo();
+
+        ILigand[] leftLigands = getLigands(u, container, v);
+        ILigand[] rightLigands = getLigands(v, container, u);
+
+        if (leftLigands.length > 2 || rightLigands.length > 2) return CIP_CHIRALITY.NONE;
+
+        // invert if x/y aren't in the first position
+        if (!leftLigands[0].getLigandAtom().equals(x)) conformation = conformation.invert();
+        if (!rightLigands[0].getLigandAtom().equals(y)) conformation = conformation.invert();
+
+        int p = permParity(leftLigands) * permParity(rightLigands);
+
+        if (p == 0) return CIP_CHIRALITY.NONE;
+
+        if (p < 0) conformation = conformation.invert();
+
+        if (conformation == Conformation.TOGETHER) return CIP_CHIRALITY.Z;
+        if (conformation == Conformation.OPPOSITE) return CIP_CHIRALITY.E;
+
+        return CIP_CHIRALITY.NONE;
+    }
+   
+  
+    /**
+     * GSRS-MODIFIED: Temporary bug fix 
+     * 
+     * @param atom
+     * @param container
+     * @param exclude
+     * @return
+     */
+    private static ILigand[] getLigands(IAtom atom, IAtomContainer container, IAtom exclude) {
+
+        List<IAtom> neighbors = container.getConnectedAtomsList(atom);
+
+        ILigand[] ligands = new ILigand[neighbors.size() - 1];
+
+        int i = 0;
+        for (IAtom neighbor : neighbors) {
+            if (!neighbor.equals(exclude)) ligands[i++] = new Ligand(container, new VisitedAtoms(), atom, neighbor);
+        }
+
+        return ligands;
+    }
+
+    
+    
+    
+
+    
+    /**
+     * Obtain the permutation parity (-1,0,+1) to put the ligands in descending
+     * order (highest first). A parity of 0 indicates two or more ligands were
+     * equivalent.
+     *
+     * @param ligands the ligands to sort
+     * @return parity, odd (-1), even (+1) or none (0)
+     */
+    private static int permParity(final ILigand[] ligands) {
+    	
+        // count the number of swaps made by insertion sort - if duplicates
+        // are fount the parity is 0
+        int swaps = 0;
+
+        for (int j = 1, hi = ligands.length; j < hi; j++) {
+            ILigand ligand = ligands[j];
+            int i = j - 1;
+            int cmp = 0;
+            while ((i >= 0) && (cmp = cipRule.compare(ligand, ligands[i])) > 0) {
+                ligands[i + 1] = ligands[i--];
+                swaps++;
+            }
+            if (cmp == 0) // identical entries
+                return 0;
+            ligands[i + 1] = ligand;
+        }
+
+        // odd (-1) or even (+1)
+        return (swaps & 0x1) == 0x1 ? -1 : +1;
+    
+    }
+    
+
+    
+   
+}
diff --git a/src/main/java/org/openscience/cdk/geometry/cip/rules/CIPLigandRule2.java b/src/main/java/org/openscience/cdk/geometry/cip/rules/CIPLigandRule2.java
new file mode 100644
index 0000000..8c0ba94
--- /dev/null
+++ b/src/main/java/org/openscience/cdk/geometry/cip/rules/CIPLigandRule2.java
@@ -0,0 +1,80 @@
+package org.openscience.cdk.geometry.cip.rules;
+
+import java.util.Arrays;
+
+import org.openscience.cdk.geometry.cip.CIPTool;
+import org.openscience.cdk.geometry.cip.CIPToolMod;
+import org.openscience.cdk.geometry.cip.ILigand;
+/**
+ * This class does the same as {@link CIPLigandRule2} only it also orders
+ * sub-ligands based on its own rule rather than based on the {@link CombinedAtomicMassNumberRule}
+ * order. This fixes a CDK bug detailed in {@link CIPToolMod}.
+ * @author tyler
+ *
+ */
+public class CIPLigandRule2 implements ISequenceSubRule<ILigand> {
+
+        CombinedAtomicMassNumberRule numberRule = new CombinedAtomicMassNumberRule();
+
+        /** {@inheritDoc} */
+        @Override
+        public int compare(ILigand ligand1, ILigand ligand2) {
+            int numberComp = numberRule.compare(ligand1, ligand2);
+            if (numberComp != 0) return numberComp;
+
+            // OK, now I need to recurse...
+            ILigand[] ligand1Ligands = CIPTool.getLigandLigands(ligand1);
+            ILigand[] ligand2Ligands = CIPTool.getLigandLigands(ligand2);
+            // if neither have ligands:
+            if (ligand1Ligands.length == 0 && ligand2Ligands.length == 0) return 0;
+            // else if one has no ligands
+            if (ligand1Ligands.length == 0) return -1;
+            if (ligand2Ligands.length == 0) return 1;
+            // ok, both have at least one ligand
+            int minLigandCount = Math.min(ligand1Ligands.length, ligand2Ligands.length);
+            if (ligand1Ligands.length > 1) ligand1Ligands = order(ligand1Ligands);
+            if (ligand2Ligands.length > 1) ligand2Ligands = order(ligand2Ligands);
+            // first do a basic number rule
+            for (int i = 0; i < minLigandCount; i++) {
+                int comparison = numberRule.compare(ligand1Ligands[i], ligand2Ligands[i]);
+                if (comparison != 0) return comparison;
+            }
+            if (ligand1Ligands.length == ligand2Ligands.length) {
+                // it that does not resolve it, do a full, recursive compare
+                for (int i = 0; i < minLigandCount; i++) {
+                    int comparison = compare(ligand1Ligands[i], ligand2Ligands[i]);
+                    if (comparison != 0) return comparison;
+                }
+            }
+            // OK, if we reached this point, then the ligands they 'share' are all equals, so the one
+            // with more ligands wins
+            if (ligand1Ligands.length > ligand2Ligands.length)
+                return 1;
+            else if (ligand1Ligands.length < ligand2Ligands.length)
+                return -1;
+            else
+                return 0;
+        }
+
+        /**
+         * Order the ligands from high to low precedence according to atomic and mass numbers.
+         */
+        private ILigand[] order(ILigand[] ligands) {
+            ILigand[] newLigands = new ILigand[ligands.length];
+            System.arraycopy(ligands, 0, newLigands, 0, ligands.length);
+
+            //!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+            //THIS IS THE ONLY LINE OF CODE THAT NEEDS TO BE CHANGED
+            //FOR CDK CIP TO WORK
+            //!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+            
+            Arrays.sort(newLigands, this);
+            // this above list is from low to high precendence, so we need to revert the array
+            ILigand[] reverseLigands = new ILigand[newLigands.length];
+            for (int i = 0; i < newLigands.length; i++) {
+                reverseLigands[(newLigands.length - 1) - i] = newLigands[i];
+            }
+            return reverseLigands;
+        }
+
+    }
\ No newline at end of file

From aae01f1e9ba9568c9ecf07b1ac091f0ecba908c4 Mon Sep 17 00:00:00 2001
From: Tyler Peryea <tylerperyea@gmail.com>
Date: Thu, 7 Dec 2023 22:14:04 -0500
Subject: [PATCH 3/9] updated to use siMolecules CIP rules

---
 pom.xml                                       |  27 +
 .../gov/nih/ncats/molwitch/cdk/CdkAtom.java   |  61 +-
 .../gov/nih/ncats/molwitch/cdk/CdkBond.java   |   6 +-
 .../ncats/molwitch/cdk/CdkChemicalImpl.java   | 136 ++++-
 .../cdk/geometry/cip/CIPToolMod.java          |  30 +-
 src/test/java/TestChiralRead.java             | 564 ++++++++++++++++--
 6 files changed, 724 insertions(+), 100 deletions(-)

diff --git a/pom.xml b/pom.xml
index 59b8a7f..a1c76d9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -18,6 +18,7 @@
 
     <properties>
         <cdk.version>2.9</cdk.version>
+        <centres.version>1.2.1</centres.version>
     </properties>
     <repositories>
         <repository>
@@ -30,6 +31,16 @@
                 <enabled>true</enabled>
             </snapshots>
         </repository>
+         <repository>
+            <id>oss.sonatype.org</id>
+            <url>https://repo1.maven.org/maven2/</url>
+            <releases>
+                <enabled>true</enabled>
+            </releases>
+            <snapshots>
+                <enabled>false</enabled>
+            </snapshots>
+        </repository>
     </repositories>
 
     <developers>
@@ -112,6 +123,22 @@
             <artifactId>cdk-jniinchi-support</artifactId>
             <version>${cdk.version}</version>
         </dependency>
+        
+        
+<dependency>
+    <groupId>com.simolecule.centres</groupId>
+    <artifactId>centres-core</artifactId>
+    <version>${centres.version}</version>
+</dependency>
+
+<dependency>
+    <groupId>com.simolecule.centres</groupId>
+    <artifactId>centres-cdk</artifactId>
+    <version>${centres.version}</version>
+</dependency>
+        
+        
+        
 <!--        <dependency>-->
 <!--            <groupId>org.openscience.cdk</groupId>-->
 <!--            <artifactId>cdk-valencycheck</artifactId>-->
diff --git a/src/main/java/gov/nih/ncats/molwitch/cdk/CdkAtom.java b/src/main/java/gov/nih/ncats/molwitch/cdk/CdkAtom.java
index b10eedc..5bcc119 100644
--- a/src/main/java/gov/nih/ncats/molwitch/cdk/CdkAtom.java
+++ b/src/main/java/gov/nih/ncats/molwitch/cdk/CdkAtom.java
@@ -306,16 +306,31 @@ public void setAtomCoordinates(AtomCoordinates atomCoordinates) {
 	public Chirality getChirality() {
 		if(!parent.cahnIngoldPrelogSupplier.hasRun()) {
 			//forces running CIP rules
+		
 			parent.getTetrahedrals();
 		}
-		String value = atom.getProperty(CDKConstants.CIP_DESCRIPTOR);
+		String value= Optional.ofNullable(atom.getProperty(CDKConstants.CIP_DESCRIPTOR))
+				.map(t->t.toString())
+				.orElse(null);
 		
-		if("R".equals(value)) {
+//		if(dd!=nu)
+//		String value = atom.getProperty(CDKConstants.CIP_DESCRIPTOR);
+//		
+		if("R".equals(value) || "M".equals(value)) {
 			return Chirality.R;
 		}
-		if("S".equals(value)) {
+		if("r".equals(value)) {
+			return Chirality.r;
+		}
+		
+		if("S".equals(value) || "P".equals(value)) {
 			return Chirality.S;
 		}
+		
+		if("s".equals(value)) {
+			return Chirality.s;
+		}
+		
 		if("EITHER".equals(value)) {
 			return Chirality.Parity_Either;
 		}
@@ -327,8 +342,10 @@ public Chirality getChirality() {
 	public void setChirality(Chirality chirality) {
 	    Chirality chir=getChirality();
 	    if(chir==chirality)return;
-	    if((chirality==Chirality.R && chir==Chirality.S) ||
-	       (chirality==Chirality.S && chir==Chirality.R)
+	    
+	    //simple inversion
+	    if(((chirality==Chirality.R || chirality==Chirality.r)  && (chir==Chirality.S||chir==Chirality.s)) ||
+	       ((chirality==Chirality.S || chirality==Chirality.s)  && (chir==Chirality.R||chir==Chirality.r)) 
 	            ) {
 	        this.getBonds().stream()
 	        .filter(b->b.getBondType().equals(BondType.SINGLE))
@@ -345,6 +362,8 @@ public void setChirality(Chirality chirality) {
 	        atom.setProperty(CDKConstants.CIP_DESCRIPTOR,chirality.toString());
 //	        atom.setStereoParity((atom.getStereoParity()+1)%2);
 //	        parent.getContainer().setStereoElements(new ArrayList<>());
+	        
+	    //simple removal
 	    }else if(chirality.equals(Chirality.Parity_Either)) {
 	        this.getBonds().stream()
             .filter(b->b.getBondType().equals(BondType.SINGLE))
@@ -359,7 +378,39 @@ public void setChirality(Chirality chirality) {
             });
 
 	        atom.setProperty(CDKConstants.CIP_DESCRIPTOR,"EITHER");
+	    }else if(chirality.isDefined() && (chir.isEither() || chir == Chirality.Non_Chiral)) {
+	    
+	    	Optional<? extends Bond> sBond = this.getBonds().stream()
+            .filter(b->b.getBondType().equals(BondType.SINGLE))
+            .filter(b->b.getStereo().equals(Stereo.NONE))
+            .findFirst();
+	    	
+	    	
+            sBond.ifPresent(b->{
+            	if(b.getAtom1().getAtomIndexInParent()==this.getAtomIndexInParent()){
+            		b.setStereo(Stereo.UP);
+            	}else {
+            		b.setStereo(Stereo.UP_INVERTED);
+            	}
+            });
+            
+            
+	    	parent.cahnIngoldPrelogSupplier.resetCache();
+	    	Chirality co=this.getChirality();
+	    	if((co.isRForm() && chirality.isRForm()) || 
+	    			(co.isSForm() && chirality.isSForm())
+	    			) {
+	    		//do nothing	
+	    	}else if((co.isSForm() && chirality.isRForm()) || 
+	    			(co.isRForm() && chirality.isSForm())
+	    			) {
+	    		setChirality(chirality);
+	    	}else {
+	    		//could not set
+	    	}
+	        
 	    }
+	    
 //	    parent.cahnIngoldPrelogSupplier.resetCache();
 	}
 
diff --git a/src/main/java/gov/nih/ncats/molwitch/cdk/CdkBond.java b/src/main/java/gov/nih/ncats/molwitch/cdk/CdkBond.java
index da7297d..23a7b66 100644
--- a/src/main/java/gov/nih/ncats/molwitch/cdk/CdkBond.java
+++ b/src/main/java/gov/nih/ncats/molwitch/cdk/CdkBond.java
@@ -22,15 +22,13 @@
 package gov.nih.ncats.molwitch.cdk;
 
 
-import java.util.ArrayList;
-import java.util.List;
+import java.util.Optional;
 
 import org.openscience.cdk.BondRef;
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IBond.Order;
-import org.openscience.cdk.interfaces.IStereoElement;
 import org.openscience.cdk.isomorphism.matchers.IQueryBond;
 
 import gov.nih.ncats.common.sneak.Sneak;
@@ -224,7 +222,7 @@ public DoubleBondStereo getDoubleBondStereo() {
 			return null;
 		}
 		parent.cahnIngoldPrelogSupplier.get();
-		String value = bond.getProperty(CDKConstants.CIP_DESCRIPTOR);
+		String value = Optional.ofNullable(bond.getProperty(CDKConstants.CIP_DESCRIPTOR)).map(bt->bt.toString()).orElse(null);
 		if("Z".equals(value)) {
 			 return DoubleBondStereo.Z_CIS;
 		}
diff --git a/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java b/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
index 3469012..2fdcc31 100644
--- a/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
+++ b/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
@@ -21,7 +21,6 @@
 
 package gov.nih.ncats.molwitch.cdk;
 
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
@@ -48,22 +47,12 @@
 import org.openscience.cdk.AtomRef;
 import org.openscience.cdk.BondRef;
 import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.PseudoAtom;
 import org.openscience.cdk.aromaticity.Aromaticity;
 import org.openscience.cdk.aromaticity.ElectronDonation;
 import org.openscience.cdk.aromaticity.Kekulization;
 import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
-import org.openscience.cdk.config.IsotopeFactory;
-import org.openscience.cdk.config.Isotopes;
 import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.geometry.cip.CIPTool;
-import org.openscience.cdk.geometry.cip.ILigand;
-import org.openscience.cdk.geometry.cip.ImplicitHydrogenLigand;
-import org.openscience.cdk.geometry.cip.Ligand;
-import org.openscience.cdk.geometry.cip.VisitedAtoms;
-import org.openscience.cdk.geometry.cip.CIPTool.CIP_CHIRALITY;
 import org.openscience.cdk.geometry.cip.CIPToolMod;
-import org.openscience.cdk.geometry.cip.rules.ISequenceSubRule;
 import org.openscience.cdk.graph.ConnectivityChecker;
 import org.openscience.cdk.graph.Cycles;
 import org.openscience.cdk.graph.GraphUtil;
@@ -76,7 +65,6 @@
 import org.openscience.cdk.interfaces.IBond.Order;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IDoubleBondStereochemistry;
-import org.openscience.cdk.interfaces.IIsotope;
 import org.openscience.cdk.interfaces.IMolecularFormula;
 import org.openscience.cdk.interfaces.IRing;
 import org.openscience.cdk.interfaces.IRingSet;
@@ -101,8 +89,6 @@
 import org.openscience.cdk.stereo.StereoElementFactory;
 import org.openscience.cdk.stereo.Stereocenters;
 import org.openscience.cdk.tools.CDKHydrogenAdder;
-import org.openscience.cdk.tools.ILoggingTool;
-import org.openscience.cdk.tools.LoggingToolFactory;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
 import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator;
@@ -119,11 +105,11 @@
 import gov.nih.ncats.molwitch.BondTable;
 import gov.nih.ncats.molwitch.Chemical;
 import gov.nih.ncats.molwitch.ChemicalSource;
-import gov.nih.ncats.molwitch.MolwitchException;
 import gov.nih.ncats.molwitch.Chirality;
 import gov.nih.ncats.molwitch.DoubleBondStereochemistry;
 import gov.nih.ncats.molwitch.ExtendedTetrahedralChirality;
 import gov.nih.ncats.molwitch.GraphInvariant;
+import gov.nih.ncats.molwitch.MolwitchException;
 import gov.nih.ncats.molwitch.SGroup;
 import gov.nih.ncats.molwitch.SGroup.SGroupBracket;
 import gov.nih.ncats.molwitch.SGroup.SGroupType;
@@ -152,6 +138,8 @@ public class CdkChemicalImpl implements ChemicalImpl<CdkChemicalImpl>{
     
     private final static int[] mostStable = new int[119];
     private final static BitSet cdkMissing = new BitSet();
+
+	private boolean deepChirality = true;
 	
 
     static{
@@ -240,6 +228,21 @@ public class CdkChemicalImpl implements ChemicalImpl<CdkChemicalImpl>{
                    }
                    
                }
+               
+               for (int i = 0; i < container.getBondCount(); i++) {
+                   IBond bi =container.getBond(i);
+                   IBond bin =cimp.getContainer().getBond(i);
+                   Object p = bin.getProperty(CDKConstants.CIP_DESCRIPTOR);
+                   
+                   bi.removeProperty(CDKConstants.CIP_DESCRIPTOR);
+                   if(p!=null) {
+                	   //For atropisomers
+                	   bi.atoms().forEach(aa->aa.setProperty(CDKConstants.CIP_DESCRIPTOR, p));
+                	   bi.setProperty(CDKConstants.CIP_DESCRIPTOR, p);   
+                   }
+                   
+               }
+               
                return null;
                
             });
@@ -248,12 +251,40 @@ public class CdkChemicalImpl implements ChemicalImpl<CdkChemicalImpl>{
 	    	
 	    	this.doWithQueryFixes(()->{
 	    	Stereocenters  centers   = Stereocenters.of(container);
+	    	List<Integer> potentialSet = new ArrayList<>();
+	    	List<Integer> undefinedSet = new ArrayList<>();
 	    	for (int i = 0; i < container.getAtomCount(); i++) {
 	    		switch(centers.stereocenterType(i)){
 					case Non:
 						break;
 					case Para:
+//						System.out.println("H");
+//						break;
 					case Potential:
+						IAtom ai3=container.getAtom(i);
+						// This is a weird kind of case where it really depends
+						// on the circumstance. In general we care about any case where
+						// if a wedge/hash were added this would change the
+						// meaning of the molecule to something distinct.
+						//
+						// However this isn't perfect because sometimes adding a wedge or
+						// dash in isolation won't change the meaning, but adding 2 or 3
+						// will. For example 1,4-dimethylcyclohexane, or certain other
+						// meso compounds. For those, we would be better off capturing
+						// all potential as of yet undefined stereo centers and enumerating
+						// the possibilities. If at least this specific center has more than one
+						// possible R/S or r/s result from that enumerated set, then it's a
+						// real stereocenter. If not, it's not a real stereocenter.
+						
+						if(ai3.getProperty(CDKConstants.CIP_DESCRIPTOR) == null){
+							
+							potentialSet.add(i);
+							undefinedSet.add(i);
+							if(!deepChirality) {
+								container.getAtom(i).setProperty(CDKConstants.CIP_DESCRIPTOR, "EITHER");
+							}
+						}
+						
 						break;
 					case True:
 						IAtom ai=container.getAtom(i);
@@ -264,15 +295,22 @@ public class CdkChemicalImpl implements ChemicalImpl<CdkChemicalImpl>{
 							//we have to go through the container because some atom implementations
                             //throw unsupport operation exceptions if we ask them for their bonds
 							for(IBond ib:container.getConnectedBondsList(ai)){
-								if(!Order.SINGLE.equals(ib.getOrder())){
+								if(!Order.SINGLE.equals(ib.getOrder()) 
+										
+//								&& !Order.DOUBLE.equals(ib.getOrder())
+										){
 									bailout=true;
 									break;
 								}								
 							}
 							
 							if(bailout){
+								// axial cases are a little weird here
+								// in general CDK marks all SP2-hybrid entries in rings
+								// of < 9 as true stereocenters. I don't know why.
+								
 //								System.out.println("It's real but ...");
-//								System.out.println(centers.elementType(i));
+//								System.out.println(centers.elementType(i) + ":" + centers.stereocenterType(i) + ":" + ai.getSymbol());
 								
 								continue;
 							}
@@ -284,13 +322,59 @@ public class CdkChemicalImpl implements ChemicalImpl<CdkChemicalImpl>{
 							}
 							
 							container.getAtom(i).setProperty(CDKConstants.CIP_DESCRIPTOR, "EITHER");
-							
+							undefinedSet.add(i);
 						}
 						break;
 					default:
 						break;
 	    		}
 	    	}
+	    	
+	    	//TODO fix for potential cases
+//	    	container.getAtom(i);
+	    	
+//	    	BitSet.valueOf(null);
+	    	
+	    	
+	    	if(deepChirality && !potentialSet.isEmpty()) {
+	    		CdkChemicalImpl cimp2=this.deepCopy();
+	    		cimp2.setDeepChirality(false);
+	    		
+		    	Chemical c22 = new Chemical(cimp2);
+		    	
+		    	Set<Integer> isDefinable = new HashSet<>();
+		    	for(long ii=0;ii<Math.pow(2, undefinedSet.size());ii++) {
+		    		cimp2.setDirty();
+	    			BitSet bs= BitSet.valueOf(new long[] {ii});
+		    		for(int ks=0;ks<undefinedSet.size();ks++) {
+	//	    			int rs = Integer.
+		    			if(bs.get(ks)) {
+		    				c22.getAtom(undefinedSet.get(ks))
+		    				.setChirality(Chirality.R);
+		    			}else {
+		    				c22.getAtom(undefinedSet.get(ks))
+		    				.setChirality(Chirality.S);
+		    			}	    			
+		    		}
+		    		for(int ks=0;ks<undefinedSet.size();ks++) {
+		    			Chirality c=c22.getAtom(undefinedSet.get(ks)).getChirality();
+//		    			System.out.print(c.toString());
+		    			if(c.isDefined()) {
+		    				isDefinable.add(undefinedSet.get(ks));
+		    			}
+		    		}
+//		    		System.out.println();
+		    		if(isDefinable.size()==undefinedSet.size()) {
+		    			break;
+		    		}
+		    	}
+		    	for(int pi:potentialSet) {
+		    		if(isDefinable.contains(pi)) {
+		    			container.getAtom(pi).setProperty(CDKConstants.CIP_DESCRIPTOR, "EITHER");	
+		    		}
+		    	}	    
+	    	}
+	    	
 	    	},false);
 	    	
 	    	return null;
@@ -324,6 +408,8 @@ public class CdkChemicalImpl implements ChemicalImpl<CdkChemicalImpl>{
     });
 	private final CachedSupplierGroup cachedSupplierGroup = new CachedSupplierGroup();
 	private final ChemicalSource source;
+	
+	
 	public CdkChemicalImpl(IAtomContainer container, Supplier<? extends ChemicalSource> source) {
 		this(container, source.get());
 	}
@@ -400,9 +486,13 @@ public void flipChirality(Stereocenter s) {
 					b.setStereo(newStereo);
 				}
 			}
-		}
-		
+		}		
+	}
+	
+	public void setDeepChirality(boolean chir) {
+		this.deepChirality=chir;
 	}
+	
 	@Override
 	public ChemicalSource getSource() {
 		return source;
@@ -1329,6 +1419,8 @@ public List<TetrahedralChirality> getTetrahedrals1() {
 			case Parity_Either:
 			case R:
 			case S:
+			case r:
+			case s:
 				return true;
 			case Unknown:
 				break;
@@ -1815,7 +1907,9 @@ public boolean isDefined() {
 			// TODO: really, it can be defined and not be R/S,
 			// as in some rings. Should fix.
 			
-			return Chirality.R.equals(c) || Chirality.S.equals(c);
+			return Chirality.R.equals(c) || Chirality.S.equals(c) ||
+					Chirality.r.equals(c) || Chirality.s.equals(c)
+					;
 		}
 
 		@Override
diff --git a/src/main/java/org/openscience/cdk/geometry/cip/CIPToolMod.java b/src/main/java/org/openscience/cdk/geometry/cip/CIPToolMod.java
index be6ff1d..bc5ad12 100644
--- a/src/main/java/org/openscience/cdk/geometry/cip/CIPToolMod.java
+++ b/src/main/java/org/openscience/cdk/geometry/cip/CIPToolMod.java
@@ -109,6 +109,9 @@
  *
  */
 public class CIPToolMod {
+
+	public static boolean USE_NEW_CENTRES=true;
+	
 	
 	private static ISequenceSubRule<ILigand> cipRule = new CIPLigandRule2();
 	
@@ -118,17 +121,22 @@ public class CIPToolMod {
      * @param container structure to label
      */
     public static void label(IAtomContainer container) {
-
-        for (IStereoElement stereoElement : container.stereoElements()) {
-            if (stereoElement instanceof ITetrahedralChirality) {
-                ITetrahedralChirality tc = (ITetrahedralChirality) stereoElement;
-                tc.getChiralAtom().setProperty(CDKConstants.CIP_DESCRIPTOR, getCIPChirality(container, tc).toString());
-            } else if (stereoElement instanceof IDoubleBondStereochemistry) {
-                IDoubleBondStereochemistry dbs = (IDoubleBondStereochemistry) stereoElement;
-                dbs.getStereoBond()
-                        .setProperty(CDKConstants.CIP_DESCRIPTOR, getCIPChirality(container, dbs).toString());
-            }
-        }
+    	//Experimental new labeller
+    	if(USE_NEW_CENTRES) {
+    		com.simolecule.centres.CdkLabeller.label(container);
+    		return;
+    	}else {
+	        for (IStereoElement stereoElement : container.stereoElements()) {
+	            if (stereoElement instanceof ITetrahedralChirality) {
+	                ITetrahedralChirality tc = (ITetrahedralChirality) stereoElement;
+	                tc.getChiralAtom().setProperty(CDKConstants.CIP_DESCRIPTOR, getCIPChirality(container, tc).toString());
+	            } else if (stereoElement instanceof IDoubleBondStereochemistry) {
+	                IDoubleBondStereochemistry dbs = (IDoubleBondStereochemistry) stereoElement;
+	                dbs.getStereoBond()
+	                        .setProperty(CDKConstants.CIP_DESCRIPTOR, getCIPChirality(container, dbs).toString());
+	            }
+	        }
+    	}
 
     }
     
diff --git a/src/test/java/TestChiralRead.java b/src/test/java/TestChiralRead.java
index 23014fa..6bd1410 100644
--- a/src/test/java/TestChiralRead.java
+++ b/src/test/java/TestChiralRead.java
@@ -20,8 +20,10 @@
  */
 
 import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.util.BitSet;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
@@ -29,7 +31,7 @@
 
 import gov.nih.ncats.molwitch.Chemical;
 import gov.nih.ncats.molwitch.Chirality;
-import gov.nih.ncats.molwitch.TetrahedralChirality;
+import gov.nih.ncats.molwitch.Stereocenter;
 import gov.nih.ncats.molwitch.io.ChemicalReaderFactory;
 
 public class TestChiralRead {
@@ -213,6 +215,142 @@ public void ensureChiralityIsTheSameRegardlessOfSDFOrMolOrAgnosticRead() throws
 			
 		}
 		
+		@Test
+	   	public void testAxialStereoMarkedR() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "  ChemDraw12062311172D\n"
+					+ "\n"
+					+ " 19 20  0  0  0  0  0  0  0  0999 V2000\n"
+					+ "   -0.2855   -1.7339    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.4969   -1.7128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.8881   -2.3895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.1525   -0.5075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.7189    0.2114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.9348   -0.4863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -0.6344    0.2326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.1102    0.9305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    2.3260    0.2326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.0679    0.9516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.0679   -0.4440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.6766    1.6494    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.8925    0.9516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -0.6767    1.6706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.8926    0.9728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -0.6767   -1.1207    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.8926   -0.4229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.1102    2.3895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -2.3260    0.2960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  2  0      \n"
+					+ "  2  3  1  0      \n"
+					+ "  2  4  1  0      \n"
+					+ "  4  5  2  0      \n"
+					+ "  4  6  1  0      \n"
+					+ "  5  7  1  0      \n"
+					+ "  5  8  1  6      \n"
+					+ "  6  9  2  0      \n"
+					+ "  7 10  2  0      \n"
+					+ "  7 11  1  0      \n"
+					+ "  8 12  1  0      \n"
+					+ "  8 13  2  0      \n"
+					+ "  9 13  1  0      \n"
+					+ " 10 14  1  0      \n"
+					+ " 10 15  1  0      \n"
+					+ " 11 16  1  0      \n"
+					+ " 11 17  2  0      \n"
+					+ " 14 18  1  0      \n"
+					+ " 15 19  2  0      \n"
+					+ " 17 19  1  0      \n"
+					+ "M  END");
+			System.out.println(c1.toMol());
+			Optional<Chirality> opChi=c1.atoms()
+			  .filter(ca->ca.getChirality()!=Chirality.Non_Chiral)
+			  .map(ca->ca.getChirality())
+			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.R, opChi.get());
+	   	}
+		@Test
+	   	public void testAxialStereoMarkedS() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "  ChemDraw12062311172D\n"
+					+ "\n"
+					+ " 19 20  0  0  0  0  0  0  0  0999 V2000\n"
+					+ "   -0.2855   -1.7339    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.4969   -1.7128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.8881   -2.3895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.1525   -0.5075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.7189    0.2114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.9348   -0.4863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -0.6344    0.2326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.1102    0.9305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    2.3260    0.2326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.0679    0.9516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.0679   -0.4440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.6766    1.6494    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.8925    0.9516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -0.6767    1.6706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.8926    0.9728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -0.6767   -1.1207    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.8926   -0.4229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.1102    2.3895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -2.3260    0.2960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  2  0      \n"
+					+ "  2  3  1  0      \n"
+					+ "  2  4  1  0      \n"
+					+ "  4  5  2  0      \n"
+					+ "  4  6  1  0      \n"
+					+ "  5  7  1  0      \n"
+					+ "  5  8  1  1      \n"
+					+ "  6  9  2  0      \n"
+					+ "  7 10  2  0      \n"
+					+ "  7 11  1  0      \n"
+					+ "  8 12  1  0      \n"
+					+ "  8 13  2  0      \n"
+					+ "  9 13  1  0      \n"
+					+ " 10 14  1  0      \n"
+					+ " 10 15  1  0      \n"
+					+ " 11 16  1  0      \n"
+					+ " 11 17  2  0      \n"
+					+ " 14 18  1  0      \n"
+					+ " 15 19  2  0      \n"
+					+ " 17 19  1  0      \n"
+					+ "M  END");
+			System.out.println(c1.toMol());
+			Optional<Chirality> opChi=c1.atoms()
+			  .filter(ca->ca.getChirality()!=Chirality.Non_Chiral)
+			  .map(ca->ca.getChirality())
+			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.S, opChi.get());
+	   	}
+		
+		@Test
+	   	public void testAxialStereoUndefinedMarkedAsCenter() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "   JSDraw212072312182D\n"
+					+ "\n"
+					+ "  6  6  0  0  0  0            999 V2000\n"
+					+ "   17.4720   -8.8400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   16.1210   -8.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   16.1210   -6.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   18.8230   -8.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   18.8230   -6.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   17.4720   -5.7200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  2  0  0  0  0\n"
+					+ "  2  3  1  0  0  0  0\n"
+					+ "  1  4  1  0  0  0  0\n"
+					+ "  4  5  2  0  0  0  0\n"
+					+ "  5  6  1  0  0  0  0\n"
+					+ "  6  3  2  0  0  0  0\n"
+					+ "M  END");
+			System.out.println(c1.toMol());
+			Optional<Chirality> opChi=c1.atoms()
+			  .filter(ca->ca.getChirality()!=Chirality.Non_Chiral)
+			  .map(ca->ca.getChirality())
+			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.Parity_Either, opChi.get());
+	   	}
 		@Test
 	   	public void testSimpleTetrahedralStereoMarked() throws Exception {
 			Chemical c1=Chemical.parse("\n" + 
@@ -238,6 +376,82 @@ public void testSimpleTetrahedralStereoMarked() throws Exception {
 			assertTrue(opChi.isPresent());
 			assertEquals(Chirality.Parity_Either, opChi.get());
 	   	}
+		
+
+		@Test
+	   	public void testSimpleCisTransRingStereoMarked() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "   JSDraw212062312582D\n"
+					+ "\n"
+					+ "  8  8  0  0  1  0            999 V2000\n"
+					+ "   24.4925   -8.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   23.1415   -7.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   23.1415   -5.7460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   24.4925   -4.9660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   25.8435   -5.7460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   25.8435   -7.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   24.4925   -9.6460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   24.4925   -3.4060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  1  0  0  0  0\n"
+					+ "  2  3  1  0  0  0  0\n"
+					+ "  3  4  1  0  0  0  0\n"
+					+ "  4  5  1  0  0  0  0\n"
+					+ "  5  6  1  0  0  0  0\n"
+					+ "  6  1  1  0  0  0  0\n"
+					+ "  1  7  1  1  0  0  0\n"
+					+ "  4  8  1  1  0  0  0\n"
+					+ "M  END");
+
+			assertEquals(2,c1.getAllStereocenters().size());
+			Optional<Chirality> opChi=c1.atoms()
+			  .filter(ca->ca.getChirality()!=Chirality.Non_Chiral)
+			  .map(ca->ca.getChirality())
+			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.s, opChi.get());
+	   	}
+		
+		@Test
+	   	public void testSimpleCisTransRingStereoDetected() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "   JSDraw212062312582D\n"
+					+ "\n"
+					+ "  8  8  0  0  1  0            999 V2000\n"
+					+ "   24.4925   -8.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   23.1415   -7.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   23.1415   -5.7460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   24.4925   -4.9660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   25.8435   -5.7460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   25.8435   -7.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   24.4925   -9.6460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   24.4925   -3.4060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  1  0  0  0  0\n"
+					+ "  2  3  1  0  0  0  0\n"
+					+ "  3  4  1  0  0  0  0\n"
+					+ "  4  5  1  0  0  0  0\n"
+					+ "  5  6  1  0  0  0  0\n"
+					+ "  6  1  1  0  0  0  0\n"
+					+ "  1  7  1  0  0  0  0\n"
+					+ "  4  8  1  0  0  0  0\n"
+					+ "M  END");
+			String sdfChiral = c1.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+			
+			assertEquals("Parity_EitherParity_Either", sdfChiral);
+			assertEquals(2,c1.getAllStereocenters().size());
+//			String sdfChiral = c1.atoms()
+//					 .map(ca->ca.getChirality())
+//					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+//					 .map(ch->ch.toString())
+//					 .collect(Collectors.joining());
+//			
+//			assertEquals("SSSR", sdfChiral);
+	   	}
+		
+		
 		@Test
 	   	public void testSimpleTetrahedralStereoMarkedAsCenter() throws Exception {
 			Chemical c1=Chemical.parse("\n" + 
@@ -265,63 +479,96 @@ public void testSimpleTetrahedralStereoMarkedAsCenter() throws Exception {
 		
 		@Test
 	   	public void testSimpleTetrahedralStereoMarked2() throws Exception {
-			Chemical c1=Chemical.parse("\n" + 
-					"   JSDraw209282010292D\n" + 
-					"\n" + 
-					" 26 26  0  0  1  0            999 V2000\n" + 
-					"   41.5969   -8.3170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   40.0369   -8.3170    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   39.2569   -9.6679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   40.0369  -11.0188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   37.6969   -9.6679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   36.9169  -11.0199    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   37.6969  -12.3614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   39.2569  -12.3588    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   36.9169  -13.7134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   37.6971  -15.0642    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   39.2571  -15.0640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   40.0302  -13.7090    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   41.5640  -13.6862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   42.3968  -15.0595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   43.9567  -15.0387    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   41.6237  -16.4143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   40.0177  -16.3960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   35.3570  -13.7134    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   34.5770  -15.0654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   35.3572  -16.4162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   33.0170  -15.0654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   32.2368  -16.4162    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   32.2370  -13.7134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   30.6771  -13.7134    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   36.9169   -8.3159    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   37.6971   -6.9651    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  1  2  1  0  0  0  0\n" + 
-					"  2  3  1  0  0  0  0\n" + 
-					"  3  4  1  6  0  0  0\n" + 
-					"  3  5  1  0  0  0  0\n" + 
-					"  5  6  1  6  0  0  0\n" + 
-					"  6  7  1  0  0  0  0\n" + 
-					"  7  8  2  0  0  0  0\n" + 
-					"  7  9  1  0  0  0  0\n" + 
-					"  9 10  1  6  0  0  0\n" + 
-					" 10 11  1  0  0  0  0\n" + 
-					" 11 12  2  0  0  0  0\n" + 
-					" 12 13  1  0  0  0  0\n" + 
-					" 13 14  2  0  0  0  0\n" + 
-					" 14 15  1  0  0  0  0\n" + 
-					" 14 16  1  0  0  0  0\n" + 
-					" 16 17  2  0  0  0  0\n" + 
-					" 11 17  1  0  0  0  0\n" + 
-					"  9 18  1  0  0  0  0\n" + 
-					" 18 19  1  0  0  0  0\n" + 
-					" 19 20  2  0  0  0  0\n" + 
-					" 19 21  1  0  0  0  0\n" + 
-					" 21 22  1  1  0  0  0\n" + 
-					" 21 23  1  0  0  0  0\n" + 
-					" 23 24  1  0  0  0  0\n" + 
-					"  5 25  1  0  0  0  0\n" + 
-					" 25 26  2  0  0  0  0\n" + 
-					"M  END");
+			Chemical c1=Chemical.parse("\n"
+					+ "   JSDraw212072312292D\n"
+					+ "\n"
+					+ " 42 42  0  0  1  0            999 V2000\n"
+					+ "   33.4515  -13.1881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   32.1004  -13.9682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   30.7493  -13.1881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   39.1857  -26.0176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   40.4483  -25.1011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   40.5559  -23.5448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   39.2082  -22.7591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   41.9607  -22.8654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   42.1324  -21.3146    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   43.5022  -20.5673    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   44.8574  -21.3399    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   43.3492  -19.0159    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   42.1023  -18.0774    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   41.7950  -16.5527    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   43.1529  -15.7973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   43.1828  -14.2274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   41.8398  -13.4353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   41.9900  -11.8924    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   40.4817  -14.1926    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   40.4545  -15.7495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   39.1482  -13.3918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   39.2963  -11.8491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   37.9520  -11.0842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   37.8735   -9.5499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   36.5716   -8.7179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   36.6213   -7.1692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   37.9730   -6.4054    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   39.0516   -7.5281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   40.5290   -8.0258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   42.0698   -7.7805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   38.8419   -2.1710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   37.8550   -3.3778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   37.5422   -4.9049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   44.6029  -18.0888    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   44.9199  -16.5603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   44.6823  -15.0152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   46.2997  -15.8321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   47.6046  -16.6791    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   46.3490  -14.2696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   47.5823  -13.3194    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   43.2388  -23.7596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   43.3766  -25.3138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  1  0  0  0  0\n"
+					+ "  2  3  1  0  0  0  0\n"
+					+ "  4  5  1  0  0  0  0\n"
+					+ "  5  6  1  0  0  0  0\n"
+					+ "  6  7  1  6  0  0  0\n"
+					+ "  6  8  1  0  0  0  0\n"
+					+ "  8  9  1  6  0  0  0\n"
+					+ "  9 10  1  0  0  0  0\n"
+					+ " 10 11  2  0  0  0  0\n"
+					+ " 10 12  1  0  0  0  0\n"
+					+ " 12 13  1  0  0  0  0\n"
+					+ " 13 14  1  0  0  0  0\n"
+					+ " 14 15  1  0  0  0  0\n"
+					+ " 15 16  1  0  0  0  0\n"
+					+ " 16 17  1  0  0  0  0\n"
+					+ " 17 18  2  0  0  0  0\n"
+					+ " 17 19  1  0  0  0  0\n"
+					+ " 19 20  1  0  0  0  0\n"
+					+ " 14 20  1  0  0  0  0\n"
+					+ " 19 21  1  0  0  0  0\n"
+					+ " 21 22  2  0  0  0  0\n"
+					+ " 22 23  1  0  0  0  0\n"
+					+ " 23 24  1  0  0  0  0\n"
+					+ " 24 25  1  0  0  0  0\n"
+					+ " 25 26  2  0  0  0  0\n"
+					+ " 26 27  1  0  0  0  0\n"
+					+ " 27 28  1  0  0  0  0\n"
+					+ " 28 29  1  0  0  0  0\n"
+					+ " 29 30  1  0  0  0  0\n"
+					+ " 32 31  1  0  0  0  0\n"
+					+ " 32 33  1  0  0  0  0\n"
+					+ " 27 33  1  0  0  0  0\n"
+					+ " 12 34  1  6  0  0  0\n"
+					+ " 34 35  1  0  0  0  0\n"
+					+ " 35 36  2  0  0  0  0\n"
+					+ " 35 37  1  0  0  0  0\n"
+					+ " 37 38  1  6  0  0  0\n"
+					+ " 37 39  1  0  0  0  0\n"
+					+ " 39 40  1  0  0  0  0\n"
+					+ "  8 41  1  0  0  0  0\n"
+					+ " 41 42  2  0  0  0  0\n"
+					+ " 31 30  2  0  0  0  0\n"
+					+ "M  END");
+			System.out.println(c1.toMol());
 			String sdfChiral = c1.atoms()
 					 .map(ca->ca.getChirality())
 					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
@@ -329,6 +576,87 @@ public void testSimpleTetrahedralStereoMarked2() throws Exception {
 					 .collect(Collectors.joining());
 			
 			assertEquals("SSSR", sdfChiral);
+	   	}
+		@Test
+	   	public void testSetChiralityOnUnsetCaseWorksS() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "   JSDraw212062317442D\n"
+					+ "\n"
+					+ "  6  5  0  0  0  0            999 V2000\n"
+					+ "   10.6080   -5.5640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   11.9590   -4.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   13.3100   -5.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   14.6610   -4.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   16.0120   -5.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   11.9590   -3.2240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  1  0  0  0  0\n"
+					+ "  2  3  1  0  0  0  0\n"
+					+ "  3  4  1  0  0  0  0\n"
+					+ "  4  5  1  0  0  0  0\n"
+					+ "  2  6  1  0  0  0  0\n"
+					+ "M  END");
+//			c1.generateCoordinates();
+			String sdfChiral = c1.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+			
+			assertEquals("Parity_Either", sdfChiral);
+			c1.atoms()
+			 .filter(ch->!ch.getChirality().equals(Chirality.Non_Chiral))
+			 .forEach(ch->ch.setChirality(Chirality.S))
+			 ;
+			sdfChiral = c1.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+			
+			assertEquals("S", sdfChiral);
+			
+			
+	   	}
+		@Test
+	   	public void testSetChiralityOnUnsetCaseWorksR() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "   JSDraw212062317442D\n"
+					+ "\n"
+					+ "  6  5  0  0  0  0            999 V2000\n"
+					+ "   10.6080   -5.5640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   11.9590   -4.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   13.3100   -5.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   14.6610   -4.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   16.0120   -5.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   11.9590   -3.2240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  1  0  0  0  0\n"
+					+ "  2  3  1  0  0  0  0\n"
+					+ "  3  4  1  0  0  0  0\n"
+					+ "  4  5  1  0  0  0  0\n"
+					+ "  2  6  1  0  0  0  0\n"
+					+ "M  END");
+//			c1.generateCoordinates();
+			String sdfChiral = c1.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+			
+			assertEquals("Parity_Either", sdfChiral);
+			c1.atoms()
+			 .filter(ch->!ch.getChirality().equals(Chirality.Non_Chiral))
+			 .forEach(ch->ch.setChirality(Chirality.R))
+			 ;
+			sdfChiral = c1.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+			
+			assertEquals("R", sdfChiral);
+			
+			
+			
 	   	}
 
 		@Test
@@ -423,6 +751,124 @@ public void testRemoveNonDescriptHydrogensDoesntRemoveStereoInformationOnMol() t
 			assertEquals("SS", sdfChiral);
 	   	}
 		
+		@Test
+	   	public void testPsuedoStereocenterIsLowerCase() throws Exception {
+
+	   		Chemical mol=Chemical.parse("\n"
+	   				+ "   JSDraw212062315202D\n"
+	   				+ "\n"
+	   				+ " 10  9  0  0  1  0            999 V2000\n"
+	   				+ "   14.4560   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   15.8070   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   15.8070   -5.7720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   17.1580   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   18.5090   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   14.4560   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   13.1050   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   17.1580   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   20.0690   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   11.7540   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "  1  2  1  0  0  0  0\n"
+	   				+ "  2  3  1  1  0  0  0\n"
+	   				+ "  2  4  1  0  0  0  0\n"
+	   				+ "  4  5  1  0  0  0  0\n"
+	   				+ "  1  6  1  1  0  0  0\n"
+	   				+ "  1  7  1  0  0  0  0\n"
+	   				+ "  4  8  1  1  0  0  0\n"
+	   				+ "  5  9  1  0  0  0  0\n"
+	   				+ "  7 10  1  0  0  0  0\n"
+	   				+ "M  END");
+	   		mol= Chemical.parse(mol.toMol());
+	   			   		assertEquals(3,mol.getAllStereocenters().size());
+	   		String sdfChiral =mol.getAllStereocenters()
+	   		.stream()
+	   		.filter(Stereocenter::isDefined)
+			.map(Stereocenter::getCenterAtom)
+			.filter(a -> a.getChirality() != null)
+			.map(a->a.getChirality())
+			.map(ch->ch.toString())
+			 .collect(Collectors.joining());
+			
+			assertEquals("SrR", sdfChiral);
+	   	}
+		
+		@Test
+	   	public void testPsuedoStereocenterOnNonMesoNotFound() throws Exception {
+
+	   		Chemical mol=Chemical.parse("\n"
+	   				+ "   JSDraw212062315202D\n"
+	   				+ "\n"
+	   				+ " 10  9  0  0  1  0            999 V2000\n"
+	   				+ "   14.4560   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   15.8070   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   15.8070   -5.7720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   17.1580   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   18.5090   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   14.4560   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   13.1050   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   17.1580   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   20.0690   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   11.7540   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "  1  2  1  0  0  0  0\n"
+	   				+ "  2  3  1  1  0  0  0\n"
+	   				+ "  2  4  1  0  0  0  0\n"
+	   				+ "  4  5  1  0  0  0  0\n"
+	   				+ "  1  6  1  1  0  0  0\n"
+	   				+ "  1  7  1  0  0  0  0\n"
+	   				+ "  4  8  1  6  0  0  0\n"
+	   				+ "  5  9  1  0  0  0  0\n"
+	   				+ "  7 10  1  0  0  0  0\n"
+	   				+ "M  END");
+	   		mol= Chemical.parse(mol.toMol());
+	   		assertEquals(2,mol.getAllStereocenters().size());
+	   		String sdfChiral =mol.getAllStereocenters()
+							   	 .stream()
+							   	 .filter(Stereocenter::isDefined)
+								 .map(Stereocenter::getCenterAtom)
+								 .filter(a -> a.getChirality() != null)
+								 .map(a->a.getChirality())
+								 .map(ch->ch.toString())
+								 .collect(Collectors.joining());
+			
+			assertEquals("SS", sdfChiral);
+	   	}
+		
+		@Test
+	   	public void testPsuedoStereocenterIsDetected() throws Exception {
+
+	   		Chemical mol=Chemical.parse("\n"
+	   				+ "   JSDraw212062315202D\n"
+	   				+ "\n"
+	   				+ " 10  9  0  0  1  0            999 V2000\n"
+	   				+ "   14.4560   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   15.8070   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   15.8070   -5.7720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   17.1580   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   18.5090   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   14.4560   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   13.1050   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   17.1580   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   20.0690   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   11.7540   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "  1  2  1  0  0  0  0\n"
+	   				+ "  2  3  1  0  0  0  0\n"
+	   				+ "  2  4  1  0  0  0  0\n"
+	   				+ "  4  5  1  0  0  0  0\n"
+	   				+ "  1  6  1  0  0  0  0\n"
+	   				+ "  1  7  1  0  0  0  0\n"
+	   				+ "  4  8  1  0  0  0  0\n"
+	   				+ "  5  9  1  0  0  0  0\n"
+	   				+ "  7 10  1  0  0  0  0\n"
+	   				+ "M  END");
+	   		mol= Chemical.parse(mol.toMol());
+//	   		String sdfChiral = mol.atoms()
+//					 .map(ca->ca.getChirality())
+//					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+//					 .map(ch->ch.toString())
+//					 .collect(Collectors.joining());
+	   		assertEquals(3,mol.getAllStereocenters().size());
+	   	}
+		
 		@Test
 	   	public void testHavingExplicitHydrogenOnStereoCenterDoesNotInvalidatePhosphateCenter() throws Exception {
 

From cfaa46267f2d0d62e7caebb6ed8be31f2a9abab7 Mon Sep 17 00:00:00 2001
From: Tyler Peryea <tylerperyea@gmail.com>
Date: Thu, 7 Dec 2023 22:14:35 -0500
Subject: [PATCH 4/9] removed accidental file

---
 src/test/java/TestChiralRead.java | 1149 -----------------------------
 1 file changed, 1149 deletions(-)
 delete mode 100644 src/test/java/TestChiralRead.java

diff --git a/src/test/java/TestChiralRead.java b/src/test/java/TestChiralRead.java
deleted file mode 100644
index 6bd1410..0000000
--- a/src/test/java/TestChiralRead.java
+++ /dev/null
@@ -1,1149 +0,0 @@
-/*
- * NCATS-MOLWITCH-CDK
- *
- * Copyright (c) 2023.
- *
- * This work is free software; you can redistribute it and/or modify it under the terms of the
- * GNU Lesser General Public License as published by the Free Software Foundation;
- * either version 2.1 of the License, or (at your option) any later version.
- *
- * This work is distributed in the hope that it will be useful, but without any warranty;
- * without even the implied warranty of merchantability or fitness for a particular purpose.
- * See the GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License along with this library;
- *  if not, write to:
- *
- *  the Free Software Foundation, Inc.
- *  59 Temple Place, Suite 330
- *  Boston, MA 02111-1307 USA
- */
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.util.BitSet;
-import java.util.Optional;
-import java.util.stream.Collectors;
-
-import org.junit.Test;
-
-import gov.nih.ncats.molwitch.Chemical;
-import gov.nih.ncats.molwitch.Chirality;
-import gov.nih.ncats.molwitch.Stereocenter;
-import gov.nih.ncats.molwitch.io.ChemicalReaderFactory;
-
-public class TestChiralRead {
-		@Test
-	   public void ensureChiralityIsTheSameRegardlessOfSDFOrMolOrAgnosticRead() throws Exception{
- 	   
- 	   String mm="\n" + 
-					"  CDK     09262014552D\n" +
-					"\n" + 
-					" 69 71  0  0  1  0  0  0  0  0999 V2000\n" + 
-					"    7.4100    3.6690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    5.9100    3.6690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    5.1600    2.3700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    5.9100    1.0710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    3.6600    2.3700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    2.9100    1.0700    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    3.6600   -0.2200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    5.1600   -0.2175    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    2.9100   -1.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    3.6602   -2.8189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    5.1602   -2.8187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    5.9036   -1.5158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    7.3784   -1.4938    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    8.1792   -2.8143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    9.6791   -2.7943    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    7.4358   -4.1171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    5.8916   -4.0995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    1.4100   -1.5200    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    0.6600   -2.8200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    1.4102   -4.1189    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -0.8400   -2.8200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -1.5902   -4.1189    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -1.5900   -1.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -3.0900   -1.5200    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -3.8400   -0.2200    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -5.3400   -0.2200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -6.0900    1.0700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -5.3400    2.3700    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -3.8400    2.3700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -3.0898    1.0711    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -3.0900    3.6700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -3.8402    4.9689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -5.3402    4.9687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -6.0904    6.2676    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -6.0900    3.6695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -1.5900    3.6700    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -0.8400    4.9700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -1.5902    6.2689    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    0.6600    4.9700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    1.4102    6.2689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    0.6604    7.5681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    1.4106    8.8670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    0.6608   10.1662    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    2.9106    8.8668    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    1.4100    3.6700    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    2.9100    3.6700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    3.6602    4.9689    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -7.5900    1.0675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -8.3422    2.3653    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -8.3378   -0.2328    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -7.7250   -1.5977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -8.8347   -2.6101    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -10.1364   -1.8649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   -9.8338   -0.3903    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -10.8415    0.7208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -10.3831    2.1490    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -12.3076    0.4036    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -13.3153    1.5147    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -12.8569    2.9429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -13.8647    4.0540    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -15.3307    3.7369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -13.4063    5.4823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -14.7814    1.1975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -15.2398   -0.2307    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -15.7891    2.3086    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -17.2552    1.9915    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -18.2629    3.1025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -19.7290    2.7854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  -17.8045    4.5308    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  1  2  1  0  0  0  0\n" + 
-					"  2  3  1  0  0  0  0\n" + 
-					"  3  4  1  6  0  0  0\n" + 
-					"  3  5  1  0  0  0  0\n" + 
-					"  5  6  1  6  0  0  0\n" + 
-					"  6  7  1  0  0  0  0\n" + 
-					"  7  8  2  0  0  0  0\n" + 
-					"  7  9  1  0  0  0  0\n" + 
-					"  9 10  1  6  0  0  0\n" + 
-					" 10 11  1  0  0  0  0\n" + 
-					" 11 12  2  0  0  0  0\n" + 
-					" 12 13  1  0  0  0  0\n" + 
-					" 13 14  2  0  0  0  0\n" + 
-					" 14 15  1  0  0  0  0\n" + 
-					" 14 16  1  0  0  0  0\n" + 
-					" 16 17  2  0  0  0  0\n" + 
-					" 11 17  1  0  0  0  0\n" + 
-					"  9 18  1  0  0  0  0\n" + 
-					" 18 19  1  0  0  0  0\n" + 
-					" 19 20  2  0  0  0  0\n" + 
-					" 19 21  1  0  0  0  0\n" + 
-					" 21 22  1  1  0  0  0\n" + 
-					" 21 23  1  0  0  0  0\n" + 
-					" 23 24  1  0  0  0  0\n" + 
-					" 24 25  1  0  0  0  0\n" + 
-					" 25 26  1  0  0  0  0\n" + 
-					" 26 27  1  0  0  0  0\n" + 
-					" 27 28  1  0  0  0  0\n" + 
-					" 28 29  1  0  0  0  0\n" + 
-					" 29 30  2  0  0  0  0\n" + 
-					" 29 31  1  0  0  0  0\n" + 
-					" 31 32  1  6  0  0  0\n" + 
-					" 32 33  1  0  0  0  0\n" + 
-					" 33 34  1  0  0  0  0\n" + 
-					" 33 35  2  0  0  0  0\n" + 
-					" 31 36  1  0  0  0  0\n" + 
-					" 36 37  1  0  0  0  0\n" + 
-					" 37 38  2  0  0  0  0\n" + 
-					" 37 39  1  0  0  0  0\n" + 
-					" 39 40  1  6  0  0  0\n" + 
-					" 40 41  1  0  0  0  0\n" + 
-					" 41 42  1  0  0  0  0\n" + 
-					" 42 43  1  0  0  0  0\n" + 
-					" 42 44  2  0  0  0  0\n" + 
-					" 39 45  1  0  0  0  0\n" + 
-					" 45 46  1  0  0  0  0\n" + 
-					"  5 46  1  0  0  0  0\n" + 
-					" 46 47  2  0  0  0  0\n" + 
-					" 27 48  1  1  0  0  0\n" + 
-					" 48 49  2  0  0  0  0\n" + 
-					" 48 50  1  0  0  0  0\n" + 
-					" 50 51  1  0  0  0  0\n" + 
-					" 51 52  1  0  0  0  0\n" + 
-					" 52 53  1  0  0  0  0\n" + 
-					" 53 54  1  0  0  0  0\n" + 
-					" 50 54  1  0  0  0  0\n" + 
-					" 54 55  1  1  0  0  0\n" + 
-					" 55 56  2  0  0  0  0\n" + 
-					" 55 57  1  0  0  0  0\n" + 
-					" 58 57  1  6  0  0  0\n" + 
-					" 58 59  1  0  0  0  0\n" + 
-					" 59 60  1  0  0  0  0\n" + 
-					" 60 61  1  0  0  0  0\n" + 
-					" 60 62  1  0  0  0  0\n" + 
-					" 58 63  1  0  0  0  0\n" + 
-					" 63 64  2  0  0  0  0\n" + 
-					" 63 65  1  0  0  0  0\n" + 
-					" 65 66  1  0  0  0  0\n" + 
-					" 66 67  1  0  0  0  0\n" + 
-					" 67 68  1  0  0  0  0\n" + 
-					" 67 69  2  0  0  0  0\n" + 
-					"M  END";
-			Chemical c=Chemical.parse(mm);
-
-			
-			String genChiral = c.atoms()
-			 .map(ca->ca.getChirality())
-			 .filter(ch->!ch.equals(Chirality.Non_Chiral))
-			 .map(ch->ch.toString())
-			 .collect(Collectors.joining());
-
-			
-			c=Chemical.parseMol(mm);
-			String molChiral = c.atoms()
-					 .map(ca->ca.getChirality())
-					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
-					 .map(ch->ch.toString())
-					 .collect(Collectors.joining());
-
-			
-			c=new Chemical(ChemicalReaderFactory.read("sdf", mm + "\n$$$$"));
-			
-			String sdfChiral = c.atoms()
-					 .map(ca->ca.getChirality())
-					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
-					 .map(ch->ch.toString())
-					 .collect(Collectors.joining());
-
-			
-			assertEquals(genChiral,molChiral);
-			assertEquals(genChiral,sdfChiral);
-			
-		}
-		
-		@Test
-	   	public void testAxialStereoMarkedR() throws Exception {
-			Chemical c1=Chemical.parse("\n"
-					+ "  ChemDraw12062311172D\n"
-					+ "\n"
-					+ " 19 20  0  0  0  0  0  0  0  0999 V2000\n"
-					+ "   -0.2855   -1.7339    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    0.4969   -1.7128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    0.8881   -2.3895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    1.1525   -0.5075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    0.7189    0.2114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    1.9348   -0.4863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -0.6344    0.2326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    1.1102    0.9305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    2.3260    0.2326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -1.0679    0.9516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -1.0679   -0.4440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    0.6766    1.6494    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    1.8925    0.9516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -0.6767    1.6706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -1.8926    0.9728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -0.6767   -1.1207    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -1.8926   -0.4229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -1.1102    2.3895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -2.3260    0.2960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "  1  2  2  0      \n"
-					+ "  2  3  1  0      \n"
-					+ "  2  4  1  0      \n"
-					+ "  4  5  2  0      \n"
-					+ "  4  6  1  0      \n"
-					+ "  5  7  1  0      \n"
-					+ "  5  8  1  6      \n"
-					+ "  6  9  2  0      \n"
-					+ "  7 10  2  0      \n"
-					+ "  7 11  1  0      \n"
-					+ "  8 12  1  0      \n"
-					+ "  8 13  2  0      \n"
-					+ "  9 13  1  0      \n"
-					+ " 10 14  1  0      \n"
-					+ " 10 15  1  0      \n"
-					+ " 11 16  1  0      \n"
-					+ " 11 17  2  0      \n"
-					+ " 14 18  1  0      \n"
-					+ " 15 19  2  0      \n"
-					+ " 17 19  1  0      \n"
-					+ "M  END");
-			System.out.println(c1.toMol());
-			Optional<Chirality> opChi=c1.atoms()
-			  .filter(ca->ca.getChirality()!=Chirality.Non_Chiral)
-			  .map(ca->ca.getChirality())
-			  .findFirst();
-			assertTrue(opChi.isPresent());
-			assertEquals(Chirality.R, opChi.get());
-	   	}
-		@Test
-	   	public void testAxialStereoMarkedS() throws Exception {
-			Chemical c1=Chemical.parse("\n"
-					+ "  ChemDraw12062311172D\n"
-					+ "\n"
-					+ " 19 20  0  0  0  0  0  0  0  0999 V2000\n"
-					+ "   -0.2855   -1.7339    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    0.4969   -1.7128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    0.8881   -2.3895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    1.1525   -0.5075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    0.7189    0.2114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    1.9348   -0.4863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -0.6344    0.2326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    1.1102    0.9305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    2.3260    0.2326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -1.0679    0.9516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -1.0679   -0.4440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    0.6766    1.6494    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "    1.8925    0.9516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -0.6767    1.6706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -1.8926    0.9728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -0.6767   -1.1207    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -1.8926   -0.4229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -1.1102    2.3895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   -2.3260    0.2960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "  1  2  2  0      \n"
-					+ "  2  3  1  0      \n"
-					+ "  2  4  1  0      \n"
-					+ "  4  5  2  0      \n"
-					+ "  4  6  1  0      \n"
-					+ "  5  7  1  0      \n"
-					+ "  5  8  1  1      \n"
-					+ "  6  9  2  0      \n"
-					+ "  7 10  2  0      \n"
-					+ "  7 11  1  0      \n"
-					+ "  8 12  1  0      \n"
-					+ "  8 13  2  0      \n"
-					+ "  9 13  1  0      \n"
-					+ " 10 14  1  0      \n"
-					+ " 10 15  1  0      \n"
-					+ " 11 16  1  0      \n"
-					+ " 11 17  2  0      \n"
-					+ " 14 18  1  0      \n"
-					+ " 15 19  2  0      \n"
-					+ " 17 19  1  0      \n"
-					+ "M  END");
-			System.out.println(c1.toMol());
-			Optional<Chirality> opChi=c1.atoms()
-			  .filter(ca->ca.getChirality()!=Chirality.Non_Chiral)
-			  .map(ca->ca.getChirality())
-			  .findFirst();
-			assertTrue(opChi.isPresent());
-			assertEquals(Chirality.S, opChi.get());
-	   	}
-		
-		@Test
-	   	public void testAxialStereoUndefinedMarkedAsCenter() throws Exception {
-			Chemical c1=Chemical.parse("\n"
-					+ "   JSDraw212072312182D\n"
-					+ "\n"
-					+ "  6  6  0  0  0  0            999 V2000\n"
-					+ "   17.4720   -8.8400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   16.1210   -8.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   16.1210   -6.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   18.8230   -8.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   18.8230   -6.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   17.4720   -5.7200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "  1  2  2  0  0  0  0\n"
-					+ "  2  3  1  0  0  0  0\n"
-					+ "  1  4  1  0  0  0  0\n"
-					+ "  4  5  2  0  0  0  0\n"
-					+ "  5  6  1  0  0  0  0\n"
-					+ "  6  3  2  0  0  0  0\n"
-					+ "M  END");
-			System.out.println(c1.toMol());
-			Optional<Chirality> opChi=c1.atoms()
-			  .filter(ca->ca.getChirality()!=Chirality.Non_Chiral)
-			  .map(ca->ca.getChirality())
-			  .findFirst();
-			assertTrue(opChi.isPresent());
-			assertEquals(Chirality.Parity_Either, opChi.get());
-	   	}
-		@Test
-	   	public void testSimpleTetrahedralStereoMarked() throws Exception {
-			Chemical c1=Chemical.parse("\n" + 
-					"   JSDraw209282010112D\n" + 
-					"\n" + 
-					"  5  4  0  0  0  0              0 V2000\n" + 
-					"   23.6688   -9.1798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   25.1766   -9.2022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   26.5285   -9.1725    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   25.1766   -7.6422    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   25.1766  -10.7622    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  1  2  1  0  0  0  0\n" + 
-					"  2  3  1  0  0  0  0\n" + 
-					"  2  4  1  0  0  0  0\n" + 
-					"  2  5  1  0  0  0  0\n" + 
-					"M  END\n" + 
-					"");
-			
-			Optional<Chirality> opChi=c1.atoms()
-			  .filter(ca->ca.getChirality()!=Chirality.Non_Chiral)
-			  .map(ca->ca.getChirality())
-			  .findFirst();
-			assertTrue(opChi.isPresent());
-			assertEquals(Chirality.Parity_Either, opChi.get());
-	   	}
-		
-
-		@Test
-	   	public void testSimpleCisTransRingStereoMarked() throws Exception {
-			Chemical c1=Chemical.parse("\n"
-					+ "   JSDraw212062312582D\n"
-					+ "\n"
-					+ "  8  8  0  0  1  0            999 V2000\n"
-					+ "   24.4925   -8.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   23.1415   -7.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   23.1415   -5.7460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   24.4925   -4.9660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   25.8435   -5.7460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   25.8435   -7.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   24.4925   -9.6460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   24.4925   -3.4060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "  1  2  1  0  0  0  0\n"
-					+ "  2  3  1  0  0  0  0\n"
-					+ "  3  4  1  0  0  0  0\n"
-					+ "  4  5  1  0  0  0  0\n"
-					+ "  5  6  1  0  0  0  0\n"
-					+ "  6  1  1  0  0  0  0\n"
-					+ "  1  7  1  1  0  0  0\n"
-					+ "  4  8  1  1  0  0  0\n"
-					+ "M  END");
-
-			assertEquals(2,c1.getAllStereocenters().size());
-			Optional<Chirality> opChi=c1.atoms()
-			  .filter(ca->ca.getChirality()!=Chirality.Non_Chiral)
-			  .map(ca->ca.getChirality())
-			  .findFirst();
-			assertTrue(opChi.isPresent());
-			assertEquals(Chirality.s, opChi.get());
-	   	}
-		
-		@Test
-	   	public void testSimpleCisTransRingStereoDetected() throws Exception {
-			Chemical c1=Chemical.parse("\n"
-					+ "   JSDraw212062312582D\n"
-					+ "\n"
-					+ "  8  8  0  0  1  0            999 V2000\n"
-					+ "   24.4925   -8.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   23.1415   -7.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   23.1415   -5.7460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   24.4925   -4.9660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   25.8435   -5.7460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   25.8435   -7.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   24.4925   -9.6460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   24.4925   -3.4060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "  1  2  1  0  0  0  0\n"
-					+ "  2  3  1  0  0  0  0\n"
-					+ "  3  4  1  0  0  0  0\n"
-					+ "  4  5  1  0  0  0  0\n"
-					+ "  5  6  1  0  0  0  0\n"
-					+ "  6  1  1  0  0  0  0\n"
-					+ "  1  7  1  0  0  0  0\n"
-					+ "  4  8  1  0  0  0  0\n"
-					+ "M  END");
-			String sdfChiral = c1.atoms()
-					 .map(ca->ca.getChirality())
-					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
-					 .map(ch->ch.toString())
-					 .collect(Collectors.joining());
-			
-			assertEquals("Parity_EitherParity_Either", sdfChiral);
-			assertEquals(2,c1.getAllStereocenters().size());
-//			String sdfChiral = c1.atoms()
-//					 .map(ca->ca.getChirality())
-//					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
-//					 .map(ch->ch.toString())
-//					 .collect(Collectors.joining());
-//			
-//			assertEquals("SSSR", sdfChiral);
-	   	}
-		
-		
-		@Test
-	   	public void testSimpleTetrahedralStereoMarkedAsCenter() throws Exception {
-			Chemical c1=Chemical.parse("\n" + 
-					"   JSDraw209282010112D\n" + 
-					"\n" + 
-					"  5  4  0  0  0  0              0 V2000\n" + 
-					"   23.6688   -9.1798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   25.1766   -9.2022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   26.5285   -9.1725    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   25.1766   -7.6422    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   25.1766  -10.7622    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  1  2  1  0  0  0  0\n" + 
-					"  2  3  1  0  0  0  0\n" + 
-					"  2  4  1  0  0  0  0\n" + 
-					"  2  5  1  0  0  0  0\n" + 
-					"M  END\n" + 
-					"");
-			
-			Optional<Chirality> opChi=c1.getAllStereocenters().stream()
-			  .map(ca->ca.getChirality())
-			  .findFirst();
-			assertTrue(opChi.isPresent());
-			assertEquals(Chirality.Parity_Either, opChi.get());
-	   	}
-		
-		@Test
-	   	public void testSimpleTetrahedralStereoMarked2() throws Exception {
-			Chemical c1=Chemical.parse("\n"
-					+ "   JSDraw212072312292D\n"
-					+ "\n"
-					+ " 42 42  0  0  1  0            999 V2000\n"
-					+ "   33.4515  -13.1881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   32.1004  -13.9682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   30.7493  -13.1881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   39.1857  -26.0176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   40.4483  -25.1011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   40.5559  -23.5448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   39.2082  -22.7591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   41.9607  -22.8654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   42.1324  -21.3146    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   43.5022  -20.5673    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   44.8574  -21.3399    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   43.3492  -19.0159    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   42.1023  -18.0774    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   41.7950  -16.5527    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   43.1529  -15.7973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   43.1828  -14.2274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   41.8398  -13.4353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   41.9900  -11.8924    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   40.4817  -14.1926    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   40.4545  -15.7495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   39.1482  -13.3918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   39.2963  -11.8491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   37.9520  -11.0842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   37.8735   -9.5499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   36.5716   -8.7179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   36.6213   -7.1692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   37.9730   -6.4054    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   39.0516   -7.5281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   40.5290   -8.0258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   42.0698   -7.7805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   38.8419   -2.1710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   37.8550   -3.3778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   37.5422   -4.9049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   44.6029  -18.0888    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   44.9199  -16.5603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   44.6823  -15.0152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   46.2997  -15.8321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   47.6046  -16.6791    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   46.3490  -14.2696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   47.5823  -13.3194    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   43.2388  -23.7596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   43.3766  -25.3138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "  1  2  1  0  0  0  0\n"
-					+ "  2  3  1  0  0  0  0\n"
-					+ "  4  5  1  0  0  0  0\n"
-					+ "  5  6  1  0  0  0  0\n"
-					+ "  6  7  1  6  0  0  0\n"
-					+ "  6  8  1  0  0  0  0\n"
-					+ "  8  9  1  6  0  0  0\n"
-					+ "  9 10  1  0  0  0  0\n"
-					+ " 10 11  2  0  0  0  0\n"
-					+ " 10 12  1  0  0  0  0\n"
-					+ " 12 13  1  0  0  0  0\n"
-					+ " 13 14  1  0  0  0  0\n"
-					+ " 14 15  1  0  0  0  0\n"
-					+ " 15 16  1  0  0  0  0\n"
-					+ " 16 17  1  0  0  0  0\n"
-					+ " 17 18  2  0  0  0  0\n"
-					+ " 17 19  1  0  0  0  0\n"
-					+ " 19 20  1  0  0  0  0\n"
-					+ " 14 20  1  0  0  0  0\n"
-					+ " 19 21  1  0  0  0  0\n"
-					+ " 21 22  2  0  0  0  0\n"
-					+ " 22 23  1  0  0  0  0\n"
-					+ " 23 24  1  0  0  0  0\n"
-					+ " 24 25  1  0  0  0  0\n"
-					+ " 25 26  2  0  0  0  0\n"
-					+ " 26 27  1  0  0  0  0\n"
-					+ " 27 28  1  0  0  0  0\n"
-					+ " 28 29  1  0  0  0  0\n"
-					+ " 29 30  1  0  0  0  0\n"
-					+ " 32 31  1  0  0  0  0\n"
-					+ " 32 33  1  0  0  0  0\n"
-					+ " 27 33  1  0  0  0  0\n"
-					+ " 12 34  1  6  0  0  0\n"
-					+ " 34 35  1  0  0  0  0\n"
-					+ " 35 36  2  0  0  0  0\n"
-					+ " 35 37  1  0  0  0  0\n"
-					+ " 37 38  1  6  0  0  0\n"
-					+ " 37 39  1  0  0  0  0\n"
-					+ " 39 40  1  0  0  0  0\n"
-					+ "  8 41  1  0  0  0  0\n"
-					+ " 41 42  2  0  0  0  0\n"
-					+ " 31 30  2  0  0  0  0\n"
-					+ "M  END");
-			System.out.println(c1.toMol());
-			String sdfChiral = c1.atoms()
-					 .map(ca->ca.getChirality())
-					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
-					 .map(ch->ch.toString())
-					 .collect(Collectors.joining());
-			
-			assertEquals("SSSR", sdfChiral);
-	   	}
-		@Test
-	   	public void testSetChiralityOnUnsetCaseWorksS() throws Exception {
-			Chemical c1=Chemical.parse("\n"
-					+ "   JSDraw212062317442D\n"
-					+ "\n"
-					+ "  6  5  0  0  0  0            999 V2000\n"
-					+ "   10.6080   -5.5640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   11.9590   -4.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   13.3100   -5.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   14.6610   -4.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   16.0120   -5.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   11.9590   -3.2240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "  1  2  1  0  0  0  0\n"
-					+ "  2  3  1  0  0  0  0\n"
-					+ "  3  4  1  0  0  0  0\n"
-					+ "  4  5  1  0  0  0  0\n"
-					+ "  2  6  1  0  0  0  0\n"
-					+ "M  END");
-//			c1.generateCoordinates();
-			String sdfChiral = c1.atoms()
-					 .map(ca->ca.getChirality())
-					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
-					 .map(ch->ch.toString())
-					 .collect(Collectors.joining());
-			
-			assertEquals("Parity_Either", sdfChiral);
-			c1.atoms()
-			 .filter(ch->!ch.getChirality().equals(Chirality.Non_Chiral))
-			 .forEach(ch->ch.setChirality(Chirality.S))
-			 ;
-			sdfChiral = c1.atoms()
-					 .map(ca->ca.getChirality())
-					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
-					 .map(ch->ch.toString())
-					 .collect(Collectors.joining());
-			
-			assertEquals("S", sdfChiral);
-			
-			
-	   	}
-		@Test
-	   	public void testSetChiralityOnUnsetCaseWorksR() throws Exception {
-			Chemical c1=Chemical.parse("\n"
-					+ "   JSDraw212062317442D\n"
-					+ "\n"
-					+ "  6  5  0  0  0  0            999 V2000\n"
-					+ "   10.6080   -5.5640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   11.9590   -4.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   13.3100   -5.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   14.6610   -4.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   16.0120   -5.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   11.9590   -3.2240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "  1  2  1  0  0  0  0\n"
-					+ "  2  3  1  0  0  0  0\n"
-					+ "  3  4  1  0  0  0  0\n"
-					+ "  4  5  1  0  0  0  0\n"
-					+ "  2  6  1  0  0  0  0\n"
-					+ "M  END");
-//			c1.generateCoordinates();
-			String sdfChiral = c1.atoms()
-					 .map(ca->ca.getChirality())
-					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
-					 .map(ch->ch.toString())
-					 .collect(Collectors.joining());
-			
-			assertEquals("Parity_Either", sdfChiral);
-			c1.atoms()
-			 .filter(ch->!ch.getChirality().equals(Chirality.Non_Chiral))
-			 .forEach(ch->ch.setChirality(Chirality.R))
-			 ;
-			sdfChiral = c1.atoms()
-					 .map(ca->ca.getChirality())
-					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
-					 .map(ch->ch.toString())
-					 .collect(Collectors.joining());
-			
-			assertEquals("R", sdfChiral);
-			
-			
-			
-	   	}
-
-		@Test
-	   	public void testSulfoxideStereo() throws Exception {
-			Chemical c1=Chemical.parse("\n" + 
-					"   JSDraw209282010442D\n" + 
-					"\n" + 
-					"  5  4  0  0  1  0            999 V2000\n" + 
-					"   16.7440   -8.8731    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   18.0950   -8.0931    0.0000 S   0  3  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   19.4460   -8.8731    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   20.7970   -8.0931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   18.0950   -6.5331    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  1  2  1  0  0  0  0\n" + 
-					"  2  3  1  0  0  0  0\n" + 
-					"  3  4  1  0  0  0  0\n" + 
-					"  2  5  1  1  0  0  0\n" + 
-					"M  CHG  2   2   1   5  -1\n" + 
-					"M  END");
-			String sdfChiral = c1.atoms()
-					 .map(ca->ca.getChirality())
-					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
-					 .map(ch->ch.toString())
-					 .collect(Collectors.joining());
-			
-			assertEquals("R", sdfChiral);
-	   	}
-		@Test
-	   	public void testSulfoxideStereoPossible() throws Exception {
-			Chemical c1=Chemical.parse("\n" + 
-					"   JSDraw209282010462D\n" + 
-					"\n" + 
-					"  5  4  0  0  0  0            999 V2000\n" + 
-					"   16.7440   -8.8731    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   18.0950   -8.0931    0.0000 S   0  3  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   19.4460   -8.8731    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   20.7970   -8.0931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   18.0950   -6.5331    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  1  2  1  0  0  0  0\n" + 
-					"  2  3  1  0  0  0  0\n" + 
-					"  3  4  1  0  0  0  0\n" + 
-					"  2  5  1  0  0  0  0\n" + 
-					"M  CHG  2   2   1   5  -1\n" + 
-					"M  END");
-			String sdfChiral = c1.atoms()
-					 .map(ca->ca.getChirality())
-					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
-					 .map(ch->ch.toString())
-					 .collect(Collectors.joining());
-			
-			assertEquals("Parity_Either", sdfChiral);
-	   	}
-		@Test
-	   	public void testRemoveNonDescriptHydrogensDoesntRemoveStereoInformationOnMol() throws Exception {
-
-	   		Chemical mol=Chemical.parse("\n" + 
-	   				"   JSDraw209282016242D\n" + 
-	   				"\n" + 
-	   				"  8  7  0  0  1  0            999 V2000\n" + 
-	   				"   28.5600   -9.6110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   28.0990   -8.1210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   27.6380   -9.6110    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   29.4510   -7.3410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   30.9720   -7.6870    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   30.5110   -8.4850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   29.4510   -5.7810    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   26.7480   -7.3410    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"  1  2  1  0  0  0  0\n" + 
-	   				"  2  3  1  1  0  0  0\n" + 
-	   				"  2  4  1  0  0  0  0\n" + 
-	   				"  4  5  1  6  0  0  0\n" + 
-	   				"  4  6  1  0  0  0  0\n" + 
-	   				"  4  7  1  0  0  0  0\n" + 
-	   				"  2  8  1  0  0  0  0\n" + 
-	   				"M  END");
-	   		mol= Chemical.parse(mol.toMol());
-	   		Chemical mol2= Chemical.createFromSmiles(mol.toSmiles());
-	   		if(!mol2.hasCoordinates()){
-	   			mol2.generateCoordinates();
-	   		}
-
-	   		mol2.removeNonDescriptHydrogens();
-	   		mol2.generateCoordinates();
-	   		mol2=Chemical.parse(mol2.toMol());
-	   		
-	   		String sdfChiral = mol2.atoms()
-					 .map(ca->ca.getChirality())
-					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
-					 .map(ch->ch.toString())
-					 .collect(Collectors.joining());
-			
-			assertEquals("SS", sdfChiral);
-	   	}
-		
-		@Test
-	   	public void testPsuedoStereocenterIsLowerCase() throws Exception {
-
-	   		Chemical mol=Chemical.parse("\n"
-	   				+ "   JSDraw212062315202D\n"
-	   				+ "\n"
-	   				+ " 10  9  0  0  1  0            999 V2000\n"
-	   				+ "   14.4560   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   15.8070   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   15.8070   -5.7720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   17.1580   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   18.5090   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   14.4560   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   13.1050   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   17.1580   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   20.0690   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   11.7540   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "  1  2  1  0  0  0  0\n"
-	   				+ "  2  3  1  1  0  0  0\n"
-	   				+ "  2  4  1  0  0  0  0\n"
-	   				+ "  4  5  1  0  0  0  0\n"
-	   				+ "  1  6  1  1  0  0  0\n"
-	   				+ "  1  7  1  0  0  0  0\n"
-	   				+ "  4  8  1  1  0  0  0\n"
-	   				+ "  5  9  1  0  0  0  0\n"
-	   				+ "  7 10  1  0  0  0  0\n"
-	   				+ "M  END");
-	   		mol= Chemical.parse(mol.toMol());
-	   			   		assertEquals(3,mol.getAllStereocenters().size());
-	   		String sdfChiral =mol.getAllStereocenters()
-	   		.stream()
-	   		.filter(Stereocenter::isDefined)
-			.map(Stereocenter::getCenterAtom)
-			.filter(a -> a.getChirality() != null)
-			.map(a->a.getChirality())
-			.map(ch->ch.toString())
-			 .collect(Collectors.joining());
-			
-			assertEquals("SrR", sdfChiral);
-	   	}
-		
-		@Test
-	   	public void testPsuedoStereocenterOnNonMesoNotFound() throws Exception {
-
-	   		Chemical mol=Chemical.parse("\n"
-	   				+ "   JSDraw212062315202D\n"
-	   				+ "\n"
-	   				+ " 10  9  0  0  1  0            999 V2000\n"
-	   				+ "   14.4560   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   15.8070   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   15.8070   -5.7720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   17.1580   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   18.5090   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   14.4560   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   13.1050   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   17.1580   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   20.0690   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   11.7540   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "  1  2  1  0  0  0  0\n"
-	   				+ "  2  3  1  1  0  0  0\n"
-	   				+ "  2  4  1  0  0  0  0\n"
-	   				+ "  4  5  1  0  0  0  0\n"
-	   				+ "  1  6  1  1  0  0  0\n"
-	   				+ "  1  7  1  0  0  0  0\n"
-	   				+ "  4  8  1  6  0  0  0\n"
-	   				+ "  5  9  1  0  0  0  0\n"
-	   				+ "  7 10  1  0  0  0  0\n"
-	   				+ "M  END");
-	   		mol= Chemical.parse(mol.toMol());
-	   		assertEquals(2,mol.getAllStereocenters().size());
-	   		String sdfChiral =mol.getAllStereocenters()
-							   	 .stream()
-							   	 .filter(Stereocenter::isDefined)
-								 .map(Stereocenter::getCenterAtom)
-								 .filter(a -> a.getChirality() != null)
-								 .map(a->a.getChirality())
-								 .map(ch->ch.toString())
-								 .collect(Collectors.joining());
-			
-			assertEquals("SS", sdfChiral);
-	   	}
-		
-		@Test
-	   	public void testPsuedoStereocenterIsDetected() throws Exception {
-
-	   		Chemical mol=Chemical.parse("\n"
-	   				+ "   JSDraw212062315202D\n"
-	   				+ "\n"
-	   				+ " 10  9  0  0  1  0            999 V2000\n"
-	   				+ "   14.4560   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   15.8070   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   15.8070   -5.7720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   17.1580   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   18.5090   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   14.4560   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   13.1050   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   17.1580   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   20.0690   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   11.7540   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "  1  2  1  0  0  0  0\n"
-	   				+ "  2  3  1  0  0  0  0\n"
-	   				+ "  2  4  1  0  0  0  0\n"
-	   				+ "  4  5  1  0  0  0  0\n"
-	   				+ "  1  6  1  0  0  0  0\n"
-	   				+ "  1  7  1  0  0  0  0\n"
-	   				+ "  4  8  1  0  0  0  0\n"
-	   				+ "  5  9  1  0  0  0  0\n"
-	   				+ "  7 10  1  0  0  0  0\n"
-	   				+ "M  END");
-	   		mol= Chemical.parse(mol.toMol());
-//	   		String sdfChiral = mol.atoms()
-//					 .map(ca->ca.getChirality())
-//					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
-//					 .map(ch->ch.toString())
-//					 .collect(Collectors.joining());
-	   		assertEquals(3,mol.getAllStereocenters().size());
-	   	}
-		
-		@Test
-	   	public void testHavingExplicitHydrogenOnStereoCenterDoesNotInvalidatePhosphateCenter() throws Exception {
-
-	   		Chemical mol=Chemical.parse("\n"
-	   				+ "   JSDraw210312314162D\n"
-	   				+ "\n"
-	   				+ " 12 12  0  0  0  0            999 V2000\n"
-	   				+ "   23.1415   -8.0860    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   24.4925   -8.8660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   23.1415   -6.5260    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   25.8435   -8.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   23.1415   -9.6460    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   25.8435   -6.5260    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   27.1945   -5.7460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   28.5455   -6.5260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   28.5455   -8.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   27.1945   -8.8660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   21.7905   -8.8660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   25.8435   -9.6460    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "  1  2  1  0  0  0  0\n"
-	   				+ "  1  3  2  0  0  0  0\n"
-	   				+ "  2  4  1  0  0  0  0\n"
-	   				+ "  1  5  1  0  0  0  0\n"
-	   				+ "  4  6  1  0  0  0  0\n"
-	   				+ "  6  7  1  0  0  0  0\n"
-	   				+ "  7  8  1  0  0  0  0\n"
-	   				+ "  8  9  1  0  0  0  0\n"
-	   				+ "  9 10  1  0  0  0  0\n"
-	   				+ " 10  4  1  0  0  0  0\n"
-	   				+ "  1 11  1  0  0  0  0\n"
-	   				+ "  4 12  1  0  0  0  0\n"
-	   				+ "M  END");
-	   		mol= Chemical.parse(mol.toMol());
-	   		mol.removeNonDescriptHydrogens();
-	   		System.out.println(mol.toMol());
-	   		assertEquals(2,mol.getTetrahedrals().size());
-	   	}
-		
-		@Test
-	   	public void testHavingBondTableOrderChangedShouldKeepSameStereo() throws Exception {
-
-			
-	   		Chemical mol=Chemical.parse("\n"
-	   				+ "   JSDraw212042310502D\n"
-	   				+ "\n"
-	   				+ " 14 14  0  0  1  0            999 V2000\n"
-	   				+ "   21.4047   -8.8605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   23.0654   -9.2811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   24.4188   -8.5056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   23.1278   -7.7212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   25.9094   -6.8325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   26.0050   -8.5767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   26.6898   -5.7439    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   28.1943   -6.0199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   24.4240   -6.9456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   24.5922   -5.3944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   21.7756   -6.0051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   26.5338   -4.4447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   20.6247  -10.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   23.0654  -10.8412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "  3  6  1  0  0  0  0\n"
-	   				+ "  2  3  1  0  0  0  0\n"
-	   				+ "  5  7  1  0  0  0  0\n"
-	   				+ "  7  8  1  0  0  0  0\n"
-	   				+ "  3  9  1  0  0  0  0\n"
-	   				+ "  9  4  1  0  0  0  0\n"
-	   				+ "  5  9  1  0  0  0  0\n"
-	   				+ "  9 10  1  1  0  0  0\n"
-	   				+ "  4 11  1  0  0  0  0\n"
-	   				+ "  7 12  1  0  0  0  0\n"
-	   				+ "  5  6  1  0  0  0  0\n"
-	   				+ "  1  2  1  0  0  0  0\n"
-	   				+ "  1 13  1  0  0  0  0\n"
-	   				+ "  2 14  1  0  0  0  0\n"
-	   				+ "M  END");
-			Optional<Chirality> opChi=mol.getTetrahedrals().stream()
-			  .map(ca->ca.getChirality())
-			  .filter(ca->!ca.isEither())
-			  			  .findFirst();
-			assertTrue(opChi.isPresent());
-			assertEquals(Chirality.R, opChi.get());
-			
-
-	   		mol=Chemical.parse("\n"
-	   				+ "   JSDraw212042310502D\n"
-	   				+ "\n"
-	   				+ " 14 14  0  0  1  0            999 V2000\n"
-	   				+ "   21.4047   -8.8605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   23.0654   -9.2811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   24.4188   -8.5056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   23.1278   -7.7212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   25.9094   -6.8325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   26.0050   -8.5767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   26.6898   -5.7439    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   28.1943   -6.0199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   24.4240   -6.9456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   24.5922   -5.3944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   21.7756   -6.0051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   26.5338   -4.4447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   20.6247  -10.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "   23.0654  -10.8412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-	   				+ "  2  3  1  0  0  0  0\n"
-	   				+ "  3  6  1  0  0  0  0\n"
-	   				+ "  5  7  1  0  0  0  0\n"
-	   				+ "  7  8  1  0  0  0  0\n"
-	   				+ "  3  9  1  0  0  0  0\n"
-	   				+ "  9  4  1  0  0  0  0\n"
-	   				+ "  5  9  1  0  0  0  0\n"
-	   				+ "  9 10  1  1  0  0  0\n"
-	   				+ "  4 11  1  0  0  0  0\n"
-	   				+ "  7 12  1  0  0  0  0\n"
-	   				+ "  5  6  1  0  0  0  0\n"
-	   				+ "  1  2  1  0  0  0  0\n"
-	   				+ "  1 13  1  0  0  0  0\n"
-	   				+ "  2 14  1  0  0  0  0\n"
-	   				+ "M  END");
-			opChi=mol.getTetrahedrals().stream()
-			  .map(ca->ca.getChirality())
-			  .filter(ca->!ca.isEither())
-			  			  .findFirst();
-			assertTrue(opChi.isPresent());
-			assertEquals(Chirality.R, opChi.get());
-	   	}
-		
-		@Test
-	   	public void testReadingSmilesShouldNotGenerateCoordinates() throws Exception {
-
-	   		Chemical mol=Chemical.parse("\n" + 
-	   				"   JSDraw209282016242D\n" + 
-	   				"\n" + 
-	   				"  8  7  0  0  1  0            999 V2000\n" + 
-	   				"   28.5600   -9.6110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   28.0990   -8.1210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   27.6380   -9.6110    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   29.4510   -7.3410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   30.9720   -7.6870    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   30.5110   -8.4850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   29.4510   -5.7810    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   26.7480   -7.3410    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"  1  2  1  0  0  0  0\n" + 
-	   				"  2  3  1  1  0  0  0\n" + 
-	   				"  2  4  1  0  0  0  0\n" + 
-	   				"  4  5  1  6  0  0  0\n" + 
-	   				"  4  6  1  0  0  0  0\n" + 
-	   				"  4  7  1  0  0  0  0\n" + 
-	   				"  2  8  1  0  0  0  0\n" + 
-	   				"M  END");
-	   		Chemical mol2= Chemical.createFromSmiles(mol.toSmiles());
-	   		
-			
-			assertFalse(mol2.hasCoordinates());
-	   	}
-		
-	  	
-	  	@Test
-	   	public void testMethaneRemoveNonDescriptHydrogensMakesRightSmiles() throws Exception {
-	   		Chemical mol=Chemical.parse("\n" + 
-	   				"   JSDraw209282013552D\n" + 
-	   				"\n" + 
-	   				"  4  3  0  0  0  0            999 V2000\n" + 
-	   				"   18.7200  -10.7328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   20.0710   -9.9528    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   18.7200  -12.2928    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"   17.3690   -9.9528    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-	   				"  1  2  1  0  0  0  0\n" + 
-	   				"  1  3  1  0  0  0  0\n" + 
-	   				"  1  4  1  0  0  0  0\n" + 
-	   				"M  END");
-	   		mol=Chemical.parse(mol.toSmiles());
-	   		mol.removeNonDescriptHydrogens();
-	   		assertEquals("C", mol.toSmiles());
-	   	}
-	  	
-	  	@Test
-	   	public void testSimpleExtendedTetrahedralStereoMarkedAsCenter() throws Exception {
-			Chemical c1=Chemical.parse("\n" + 
-					"   JSDraw209282018142D\n" + 
-					"\n" + 
-					"  7  6  0  0  1  0            999 V2000\n" + 
-					"   10.0360   -7.4984    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   11.3870   -6.7184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   13.0510   -5.7824    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   10.0360   -9.0584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"    8.6850   -6.7184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   13.0510   -4.2224    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   14.4540   -6.5624    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  1  2  2  0  0  0  0\n" + 
-					"  2  3  2  0  0  0  0\n" + 
-					"  1  4  1  0  0  0  0\n" + 
-					"  1  5  1  0  0  0  0\n" + 
-					"  3  6  1  6  0  0  0\n" + 
-					"  3  7  1  1  0  0  0\n" + 
-					"M  END");
-
-
-			Optional<Chirality> opChi=c1.getAllStereocenters().stream()
-			  .map(ca->ca.getChirality())
-			  .findFirst();
-			assertTrue(opChi.isPresent());
-			assertEquals(Chirality.S, opChi.get());
-	   	}
-	  	
-		@Test
-	   	public void testSimpleTetrahedralStereoOnQuatAmineMarkedAsCenter() throws Exception {
-			Chemical c1=Chemical.parse("\n" + 
-					"   JSDraw209282021202D\n" + 
-					"\n" + 
-					"  8  7  0  0  0  0              0 V2000\n" + 
-					"   14.8200  -10.2960    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   16.1710   -9.5160    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   16.1710   -7.9560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   17.5220  -10.2960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   14.8200   -7.1760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   18.8730   -9.5160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   18.8730   -7.9560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"   16.1710  -11.0760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
-					"  1  2  1  0  0  0  0\n" + 
-					"  2  3  1  0  0  0  0\n" + 
-					"  2  4  1  0  0  0  0\n" + 
-					"  3  5  1  0  0  0  0\n" + 
-					"  4  6  1  0  0  0  0\n" + 
-					"  6  7  1  0  0  0  0\n" + 
-					"  2  8  1  0  0  0  0\n" + 
-					"M  CHG  1   2   1\n" + 
-					"M  END\n" + 
-					"");
-
-			Optional<Chirality> opChi=c1.getAllStereocenters().stream()
-			  .map(ca->ca.getChirality())
-			  .findFirst();
-			assertTrue(opChi.isPresent());
-			assertEquals(Chirality.Parity_Either, opChi.get());
-	   	}
-		
-		@Test
-	   	public void testSingleStereoBondBetweenTwoChiralCentersOnlyDefinesOneCenter() throws Exception {
-			Chemical c1=Chemical.parse("\n"
-					+ "   JSDraw210312313582D\n"
-					+ "\n"
-					+ "  9  9  0  0  1  0              0 V2000\n"
-					+ "   17.6280  -11.3880    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   16.2770  -10.6080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   16.2770   -9.0480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   17.6280   -8.2680    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   18.9790   -9.0480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   18.9790  -10.6080    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   20.3300   -8.2680    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   20.3300   -6.7080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "   21.6810   -9.0480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
-					+ "  1  2  1  0  0  0  0\n"
-					+ "  2  3  1  0  0  0  0\n"
-					+ "  3  4  1  0  0  0  0\n"
-					+ "  4  5  1  0  0  0  0\n"
-					+ "  5  6  1  0  0  0  0\n"
-					+ "  6  1  1  0  0  0  0\n"
-					+ "  5  7  1  6  0  0  0\n"
-					+ "  7  8  1  0  0  0  0\n"
-					+ "  7  9  1  0  0  0  0\n"
-					+ "M  END\n"
-					+ "");
-			
-			assertEquals(2, c1.getAllStereocenters().size());
-			assertEquals(Chirality.R, c1.getAllStereocenters().get(0).getChirality());
-			assertEquals(Chirality.Parity_Either, c1.getAllStereocenters().get(1).getChirality());
-
-	   	}
-		
-		@Test
-	   	public void testQueryStructureSimpleTetrahedralStereoDoesntError() throws Exception {
-			Chemical c1=Chemical.parse("S(=O)(=O)(O)O-C-[#6]");
-
-			Optional<Chirality> opChi=c1.getAllStereocenters().stream()
-			  .map(ca->ca.getChirality())
-			  .findFirst();
-			assertFalse(opChi.isPresent());
-	   	}
-	  	
-}

From 2fdfa0717b02a7d56d3112314cb7f06632c0c36a Mon Sep 17 00:00:00 2001
From: Tyler Peryea <tylerperyea@gmail.com>
Date: Thu, 7 Dec 2023 22:17:47 -0500
Subject: [PATCH 5/9] incremented version

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index a1c76d9..c3b2e46 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>gov.nih.ncats</groupId>
     <artifactId>molwitch-cdk</artifactId>
-    <version>1.0.14-SNAPSHOT</version>
+    <version>1.0.15-SNAPSHOT</version>
     <name>molwitch-cdk</name>
 
     <url>https://github.com/ncats/molwitch-cdk/</url>

From e1f1cf3ccd92d9c9569770524a0d976cc4be06dc Mon Sep 17 00:00:00 2001
From: Tyler Peryea <tylerperyea@gmail.com>
Date: Thu, 7 Dec 2023 22:18:24 -0500
Subject: [PATCH 6/9] incremented molwitch core version

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index c3b2e46..4d92da4 100644
--- a/pom.xml
+++ b/pom.xml
@@ -84,7 +84,7 @@
         <dependency>
             <groupId>gov.nih.ncats</groupId>
             <artifactId>molwitch</artifactId>
-            <version>0.6.5-SNAPSHOT</version>
+            <version>0.6.6-SNAPSHOT</version>
 			<exclusions>
 				<exclusion>
 					<groupId>org.apache.logging.log4j</groupId>

From 2c964b139a34a6e6b1f35bc886822273e6266fb0 Mon Sep 17 00:00:00 2001
From: Tyler Peryea <tylerperyea@gmail.com>
Date: Fri, 8 Dec 2023 10:47:38 -0500
Subject: [PATCH 7/9] added missing file back

---
 src/test/java/TestChiralRead.java | 1149 +++++++++++++++++++++++++++++
 1 file changed, 1149 insertions(+)
 create mode 100644 src/test/java/TestChiralRead.java

diff --git a/src/test/java/TestChiralRead.java b/src/test/java/TestChiralRead.java
new file mode 100644
index 0000000..6bd1410
--- /dev/null
+++ b/src/test/java/TestChiralRead.java
@@ -0,0 +1,1149 @@
+/*
+ * NCATS-MOLWITCH-CDK
+ *
+ * Copyright (c) 2023.
+ *
+ * This work is free software; you can redistribute it and/or modify it under the terms of the
+ * GNU Lesser General Public License as published by the Free Software Foundation;
+ * either version 2.1 of the License, or (at your option) any later version.
+ *
+ * This work is distributed in the hope that it will be useful, but without any warranty;
+ * without even the implied warranty of merchantability or fitness for a particular purpose.
+ * See the GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License along with this library;
+ *  if not, write to:
+ *
+ *  the Free Software Foundation, Inc.
+ *  59 Temple Place, Suite 330
+ *  Boston, MA 02111-1307 USA
+ */
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.util.BitSet;
+import java.util.Optional;
+import java.util.stream.Collectors;
+
+import org.junit.Test;
+
+import gov.nih.ncats.molwitch.Chemical;
+import gov.nih.ncats.molwitch.Chirality;
+import gov.nih.ncats.molwitch.Stereocenter;
+import gov.nih.ncats.molwitch.io.ChemicalReaderFactory;
+
+public class TestChiralRead {
+		@Test
+	   public void ensureChiralityIsTheSameRegardlessOfSDFOrMolOrAgnosticRead() throws Exception{
+ 	   
+ 	   String mm="\n" + 
+					"  CDK     09262014552D\n" +
+					"\n" + 
+					" 69 71  0  0  1  0  0  0  0  0999 V2000\n" + 
+					"    7.4100    3.6690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    5.9100    3.6690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    5.1600    2.3700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    5.9100    1.0710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    3.6600    2.3700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    2.9100    1.0700    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    3.6600   -0.2200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    5.1600   -0.2175    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    2.9100   -1.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    3.6602   -2.8189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    5.1602   -2.8187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    5.9036   -1.5158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    7.3784   -1.4938    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    8.1792   -2.8143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    9.6791   -2.7943    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    7.4358   -4.1171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    5.8916   -4.0995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    1.4100   -1.5200    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    0.6600   -2.8200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    1.4102   -4.1189    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -0.8400   -2.8200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -1.5902   -4.1189    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -1.5900   -1.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -3.0900   -1.5200    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -3.8400   -0.2200    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -5.3400   -0.2200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -6.0900    1.0700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -5.3400    2.3700    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -3.8400    2.3700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -3.0898    1.0711    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -3.0900    3.6700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -3.8402    4.9689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -5.3402    4.9687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -6.0904    6.2676    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -6.0900    3.6695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -1.5900    3.6700    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -0.8400    4.9700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -1.5902    6.2689    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    0.6600    4.9700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    1.4102    6.2689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    0.6604    7.5681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    1.4106    8.8670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    0.6608   10.1662    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    2.9106    8.8668    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    1.4100    3.6700    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    2.9100    3.6700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    3.6602    4.9689    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -7.5900    1.0675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -8.3422    2.3653    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -8.3378   -0.2328    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -7.7250   -1.5977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -8.8347   -2.6101    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -10.1364   -1.8649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   -9.8338   -0.3903    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -10.8415    0.7208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -10.3831    2.1490    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -12.3076    0.4036    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -13.3153    1.5147    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -12.8569    2.9429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -13.8647    4.0540    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -15.3307    3.7369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -13.4063    5.4823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -14.7814    1.1975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -15.2398   -0.2307    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -15.7891    2.3086    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -17.2552    1.9915    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -18.2629    3.1025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -19.7290    2.7854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  -17.8045    4.5308    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  1  2  1  0  0  0  0\n" + 
+					"  2  3  1  0  0  0  0\n" + 
+					"  3  4  1  6  0  0  0\n" + 
+					"  3  5  1  0  0  0  0\n" + 
+					"  5  6  1  6  0  0  0\n" + 
+					"  6  7  1  0  0  0  0\n" + 
+					"  7  8  2  0  0  0  0\n" + 
+					"  7  9  1  0  0  0  0\n" + 
+					"  9 10  1  6  0  0  0\n" + 
+					" 10 11  1  0  0  0  0\n" + 
+					" 11 12  2  0  0  0  0\n" + 
+					" 12 13  1  0  0  0  0\n" + 
+					" 13 14  2  0  0  0  0\n" + 
+					" 14 15  1  0  0  0  0\n" + 
+					" 14 16  1  0  0  0  0\n" + 
+					" 16 17  2  0  0  0  0\n" + 
+					" 11 17  1  0  0  0  0\n" + 
+					"  9 18  1  0  0  0  0\n" + 
+					" 18 19  1  0  0  0  0\n" + 
+					" 19 20  2  0  0  0  0\n" + 
+					" 19 21  1  0  0  0  0\n" + 
+					" 21 22  1  1  0  0  0\n" + 
+					" 21 23  1  0  0  0  0\n" + 
+					" 23 24  1  0  0  0  0\n" + 
+					" 24 25  1  0  0  0  0\n" + 
+					" 25 26  1  0  0  0  0\n" + 
+					" 26 27  1  0  0  0  0\n" + 
+					" 27 28  1  0  0  0  0\n" + 
+					" 28 29  1  0  0  0  0\n" + 
+					" 29 30  2  0  0  0  0\n" + 
+					" 29 31  1  0  0  0  0\n" + 
+					" 31 32  1  6  0  0  0\n" + 
+					" 32 33  1  0  0  0  0\n" + 
+					" 33 34  1  0  0  0  0\n" + 
+					" 33 35  2  0  0  0  0\n" + 
+					" 31 36  1  0  0  0  0\n" + 
+					" 36 37  1  0  0  0  0\n" + 
+					" 37 38  2  0  0  0  0\n" + 
+					" 37 39  1  0  0  0  0\n" + 
+					" 39 40  1  6  0  0  0\n" + 
+					" 40 41  1  0  0  0  0\n" + 
+					" 41 42  1  0  0  0  0\n" + 
+					" 42 43  1  0  0  0  0\n" + 
+					" 42 44  2  0  0  0  0\n" + 
+					" 39 45  1  0  0  0  0\n" + 
+					" 45 46  1  0  0  0  0\n" + 
+					"  5 46  1  0  0  0  0\n" + 
+					" 46 47  2  0  0  0  0\n" + 
+					" 27 48  1  1  0  0  0\n" + 
+					" 48 49  2  0  0  0  0\n" + 
+					" 48 50  1  0  0  0  0\n" + 
+					" 50 51  1  0  0  0  0\n" + 
+					" 51 52  1  0  0  0  0\n" + 
+					" 52 53  1  0  0  0  0\n" + 
+					" 53 54  1  0  0  0  0\n" + 
+					" 50 54  1  0  0  0  0\n" + 
+					" 54 55  1  1  0  0  0\n" + 
+					" 55 56  2  0  0  0  0\n" + 
+					" 55 57  1  0  0  0  0\n" + 
+					" 58 57  1  6  0  0  0\n" + 
+					" 58 59  1  0  0  0  0\n" + 
+					" 59 60  1  0  0  0  0\n" + 
+					" 60 61  1  0  0  0  0\n" + 
+					" 60 62  1  0  0  0  0\n" + 
+					" 58 63  1  0  0  0  0\n" + 
+					" 63 64  2  0  0  0  0\n" + 
+					" 63 65  1  0  0  0  0\n" + 
+					" 65 66  1  0  0  0  0\n" + 
+					" 66 67  1  0  0  0  0\n" + 
+					" 67 68  1  0  0  0  0\n" + 
+					" 67 69  2  0  0  0  0\n" + 
+					"M  END";
+			Chemical c=Chemical.parse(mm);
+
+			
+			String genChiral = c.atoms()
+			 .map(ca->ca.getChirality())
+			 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+			 .map(ch->ch.toString())
+			 .collect(Collectors.joining());
+
+			
+			c=Chemical.parseMol(mm);
+			String molChiral = c.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+
+			
+			c=new Chemical(ChemicalReaderFactory.read("sdf", mm + "\n$$$$"));
+			
+			String sdfChiral = c.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+
+			
+			assertEquals(genChiral,molChiral);
+			assertEquals(genChiral,sdfChiral);
+			
+		}
+		
+		@Test
+	   	public void testAxialStereoMarkedR() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "  ChemDraw12062311172D\n"
+					+ "\n"
+					+ " 19 20  0  0  0  0  0  0  0  0999 V2000\n"
+					+ "   -0.2855   -1.7339    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.4969   -1.7128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.8881   -2.3895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.1525   -0.5075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.7189    0.2114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.9348   -0.4863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -0.6344    0.2326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.1102    0.9305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    2.3260    0.2326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.0679    0.9516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.0679   -0.4440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.6766    1.6494    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.8925    0.9516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -0.6767    1.6706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.8926    0.9728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -0.6767   -1.1207    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.8926   -0.4229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.1102    2.3895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -2.3260    0.2960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  2  0      \n"
+					+ "  2  3  1  0      \n"
+					+ "  2  4  1  0      \n"
+					+ "  4  5  2  0      \n"
+					+ "  4  6  1  0      \n"
+					+ "  5  7  1  0      \n"
+					+ "  5  8  1  6      \n"
+					+ "  6  9  2  0      \n"
+					+ "  7 10  2  0      \n"
+					+ "  7 11  1  0      \n"
+					+ "  8 12  1  0      \n"
+					+ "  8 13  2  0      \n"
+					+ "  9 13  1  0      \n"
+					+ " 10 14  1  0      \n"
+					+ " 10 15  1  0      \n"
+					+ " 11 16  1  0      \n"
+					+ " 11 17  2  0      \n"
+					+ " 14 18  1  0      \n"
+					+ " 15 19  2  0      \n"
+					+ " 17 19  1  0      \n"
+					+ "M  END");
+			System.out.println(c1.toMol());
+			Optional<Chirality> opChi=c1.atoms()
+			  .filter(ca->ca.getChirality()!=Chirality.Non_Chiral)
+			  .map(ca->ca.getChirality())
+			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.R, opChi.get());
+	   	}
+		@Test
+	   	public void testAxialStereoMarkedS() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "  ChemDraw12062311172D\n"
+					+ "\n"
+					+ " 19 20  0  0  0  0  0  0  0  0999 V2000\n"
+					+ "   -0.2855   -1.7339    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.4969   -1.7128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.8881   -2.3895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.1525   -0.5075    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.7189    0.2114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.9348   -0.4863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -0.6344    0.2326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.1102    0.9305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    2.3260    0.2326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.0679    0.9516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.0679   -0.4440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    0.6766    1.6494    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "    1.8925    0.9516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -0.6767    1.6706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.8926    0.9728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -0.6767   -1.1207    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.8926   -0.4229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -1.1102    2.3895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   -2.3260    0.2960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  2  0      \n"
+					+ "  2  3  1  0      \n"
+					+ "  2  4  1  0      \n"
+					+ "  4  5  2  0      \n"
+					+ "  4  6  1  0      \n"
+					+ "  5  7  1  0      \n"
+					+ "  5  8  1  1      \n"
+					+ "  6  9  2  0      \n"
+					+ "  7 10  2  0      \n"
+					+ "  7 11  1  0      \n"
+					+ "  8 12  1  0      \n"
+					+ "  8 13  2  0      \n"
+					+ "  9 13  1  0      \n"
+					+ " 10 14  1  0      \n"
+					+ " 10 15  1  0      \n"
+					+ " 11 16  1  0      \n"
+					+ " 11 17  2  0      \n"
+					+ " 14 18  1  0      \n"
+					+ " 15 19  2  0      \n"
+					+ " 17 19  1  0      \n"
+					+ "M  END");
+			System.out.println(c1.toMol());
+			Optional<Chirality> opChi=c1.atoms()
+			  .filter(ca->ca.getChirality()!=Chirality.Non_Chiral)
+			  .map(ca->ca.getChirality())
+			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.S, opChi.get());
+	   	}
+		
+		@Test
+	   	public void testAxialStereoUndefinedMarkedAsCenter() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "   JSDraw212072312182D\n"
+					+ "\n"
+					+ "  6  6  0  0  0  0            999 V2000\n"
+					+ "   17.4720   -8.8400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   16.1210   -8.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   16.1210   -6.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   18.8230   -8.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   18.8230   -6.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   17.4720   -5.7200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  2  0  0  0  0\n"
+					+ "  2  3  1  0  0  0  0\n"
+					+ "  1  4  1  0  0  0  0\n"
+					+ "  4  5  2  0  0  0  0\n"
+					+ "  5  6  1  0  0  0  0\n"
+					+ "  6  3  2  0  0  0  0\n"
+					+ "M  END");
+			System.out.println(c1.toMol());
+			Optional<Chirality> opChi=c1.atoms()
+			  .filter(ca->ca.getChirality()!=Chirality.Non_Chiral)
+			  .map(ca->ca.getChirality())
+			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.Parity_Either, opChi.get());
+	   	}
+		@Test
+	   	public void testSimpleTetrahedralStereoMarked() throws Exception {
+			Chemical c1=Chemical.parse("\n" + 
+					"   JSDraw209282010112D\n" + 
+					"\n" + 
+					"  5  4  0  0  0  0              0 V2000\n" + 
+					"   23.6688   -9.1798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   25.1766   -9.2022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   26.5285   -9.1725    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   25.1766   -7.6422    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   25.1766  -10.7622    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  1  2  1  0  0  0  0\n" + 
+					"  2  3  1  0  0  0  0\n" + 
+					"  2  4  1  0  0  0  0\n" + 
+					"  2  5  1  0  0  0  0\n" + 
+					"M  END\n" + 
+					"");
+			
+			Optional<Chirality> opChi=c1.atoms()
+			  .filter(ca->ca.getChirality()!=Chirality.Non_Chiral)
+			  .map(ca->ca.getChirality())
+			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.Parity_Either, opChi.get());
+	   	}
+		
+
+		@Test
+	   	public void testSimpleCisTransRingStereoMarked() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "   JSDraw212062312582D\n"
+					+ "\n"
+					+ "  8  8  0  0  1  0            999 V2000\n"
+					+ "   24.4925   -8.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   23.1415   -7.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   23.1415   -5.7460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   24.4925   -4.9660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   25.8435   -5.7460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   25.8435   -7.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   24.4925   -9.6460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   24.4925   -3.4060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  1  0  0  0  0\n"
+					+ "  2  3  1  0  0  0  0\n"
+					+ "  3  4  1  0  0  0  0\n"
+					+ "  4  5  1  0  0  0  0\n"
+					+ "  5  6  1  0  0  0  0\n"
+					+ "  6  1  1  0  0  0  0\n"
+					+ "  1  7  1  1  0  0  0\n"
+					+ "  4  8  1  1  0  0  0\n"
+					+ "M  END");
+
+			assertEquals(2,c1.getAllStereocenters().size());
+			Optional<Chirality> opChi=c1.atoms()
+			  .filter(ca->ca.getChirality()!=Chirality.Non_Chiral)
+			  .map(ca->ca.getChirality())
+			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.s, opChi.get());
+	   	}
+		
+		@Test
+	   	public void testSimpleCisTransRingStereoDetected() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "   JSDraw212062312582D\n"
+					+ "\n"
+					+ "  8  8  0  0  1  0            999 V2000\n"
+					+ "   24.4925   -8.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   23.1415   -7.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   23.1415   -5.7460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   24.4925   -4.9660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   25.8435   -5.7460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   25.8435   -7.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   24.4925   -9.6460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   24.4925   -3.4060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  1  0  0  0  0\n"
+					+ "  2  3  1  0  0  0  0\n"
+					+ "  3  4  1  0  0  0  0\n"
+					+ "  4  5  1  0  0  0  0\n"
+					+ "  5  6  1  0  0  0  0\n"
+					+ "  6  1  1  0  0  0  0\n"
+					+ "  1  7  1  0  0  0  0\n"
+					+ "  4  8  1  0  0  0  0\n"
+					+ "M  END");
+			String sdfChiral = c1.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+			
+			assertEquals("Parity_EitherParity_Either", sdfChiral);
+			assertEquals(2,c1.getAllStereocenters().size());
+//			String sdfChiral = c1.atoms()
+//					 .map(ca->ca.getChirality())
+//					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+//					 .map(ch->ch.toString())
+//					 .collect(Collectors.joining());
+//			
+//			assertEquals("SSSR", sdfChiral);
+	   	}
+		
+		
+		@Test
+	   	public void testSimpleTetrahedralStereoMarkedAsCenter() throws Exception {
+			Chemical c1=Chemical.parse("\n" + 
+					"   JSDraw209282010112D\n" + 
+					"\n" + 
+					"  5  4  0  0  0  0              0 V2000\n" + 
+					"   23.6688   -9.1798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   25.1766   -9.2022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   26.5285   -9.1725    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   25.1766   -7.6422    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   25.1766  -10.7622    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  1  2  1  0  0  0  0\n" + 
+					"  2  3  1  0  0  0  0\n" + 
+					"  2  4  1  0  0  0  0\n" + 
+					"  2  5  1  0  0  0  0\n" + 
+					"M  END\n" + 
+					"");
+			
+			Optional<Chirality> opChi=c1.getAllStereocenters().stream()
+			  .map(ca->ca.getChirality())
+			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.Parity_Either, opChi.get());
+	   	}
+		
+		@Test
+	   	public void testSimpleTetrahedralStereoMarked2() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "   JSDraw212072312292D\n"
+					+ "\n"
+					+ " 42 42  0  0  1  0            999 V2000\n"
+					+ "   33.4515  -13.1881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   32.1004  -13.9682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   30.7493  -13.1881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   39.1857  -26.0176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   40.4483  -25.1011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   40.5559  -23.5448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   39.2082  -22.7591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   41.9607  -22.8654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   42.1324  -21.3146    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   43.5022  -20.5673    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   44.8574  -21.3399    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   43.3492  -19.0159    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   42.1023  -18.0774    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   41.7950  -16.5527    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   43.1529  -15.7973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   43.1828  -14.2274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   41.8398  -13.4353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   41.9900  -11.8924    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   40.4817  -14.1926    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   40.4545  -15.7495    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   39.1482  -13.3918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   39.2963  -11.8491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   37.9520  -11.0842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   37.8735   -9.5499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   36.5716   -8.7179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   36.6213   -7.1692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   37.9730   -6.4054    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   39.0516   -7.5281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   40.5290   -8.0258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   42.0698   -7.7805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   38.8419   -2.1710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   37.8550   -3.3778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   37.5422   -4.9049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   44.6029  -18.0888    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   44.9199  -16.5603    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   44.6823  -15.0152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   46.2997  -15.8321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   47.6046  -16.6791    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   46.3490  -14.2696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   47.5823  -13.3194    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   43.2388  -23.7596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   43.3766  -25.3138    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  1  0  0  0  0\n"
+					+ "  2  3  1  0  0  0  0\n"
+					+ "  4  5  1  0  0  0  0\n"
+					+ "  5  6  1  0  0  0  0\n"
+					+ "  6  7  1  6  0  0  0\n"
+					+ "  6  8  1  0  0  0  0\n"
+					+ "  8  9  1  6  0  0  0\n"
+					+ "  9 10  1  0  0  0  0\n"
+					+ " 10 11  2  0  0  0  0\n"
+					+ " 10 12  1  0  0  0  0\n"
+					+ " 12 13  1  0  0  0  0\n"
+					+ " 13 14  1  0  0  0  0\n"
+					+ " 14 15  1  0  0  0  0\n"
+					+ " 15 16  1  0  0  0  0\n"
+					+ " 16 17  1  0  0  0  0\n"
+					+ " 17 18  2  0  0  0  0\n"
+					+ " 17 19  1  0  0  0  0\n"
+					+ " 19 20  1  0  0  0  0\n"
+					+ " 14 20  1  0  0  0  0\n"
+					+ " 19 21  1  0  0  0  0\n"
+					+ " 21 22  2  0  0  0  0\n"
+					+ " 22 23  1  0  0  0  0\n"
+					+ " 23 24  1  0  0  0  0\n"
+					+ " 24 25  1  0  0  0  0\n"
+					+ " 25 26  2  0  0  0  0\n"
+					+ " 26 27  1  0  0  0  0\n"
+					+ " 27 28  1  0  0  0  0\n"
+					+ " 28 29  1  0  0  0  0\n"
+					+ " 29 30  1  0  0  0  0\n"
+					+ " 32 31  1  0  0  0  0\n"
+					+ " 32 33  1  0  0  0  0\n"
+					+ " 27 33  1  0  0  0  0\n"
+					+ " 12 34  1  6  0  0  0\n"
+					+ " 34 35  1  0  0  0  0\n"
+					+ " 35 36  2  0  0  0  0\n"
+					+ " 35 37  1  0  0  0  0\n"
+					+ " 37 38  1  6  0  0  0\n"
+					+ " 37 39  1  0  0  0  0\n"
+					+ " 39 40  1  0  0  0  0\n"
+					+ "  8 41  1  0  0  0  0\n"
+					+ " 41 42  2  0  0  0  0\n"
+					+ " 31 30  2  0  0  0  0\n"
+					+ "M  END");
+			System.out.println(c1.toMol());
+			String sdfChiral = c1.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+			
+			assertEquals("SSSR", sdfChiral);
+	   	}
+		@Test
+	   	public void testSetChiralityOnUnsetCaseWorksS() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "   JSDraw212062317442D\n"
+					+ "\n"
+					+ "  6  5  0  0  0  0            999 V2000\n"
+					+ "   10.6080   -5.5640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   11.9590   -4.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   13.3100   -5.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   14.6610   -4.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   16.0120   -5.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   11.9590   -3.2240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  1  0  0  0  0\n"
+					+ "  2  3  1  0  0  0  0\n"
+					+ "  3  4  1  0  0  0  0\n"
+					+ "  4  5  1  0  0  0  0\n"
+					+ "  2  6  1  0  0  0  0\n"
+					+ "M  END");
+//			c1.generateCoordinates();
+			String sdfChiral = c1.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+			
+			assertEquals("Parity_Either", sdfChiral);
+			c1.atoms()
+			 .filter(ch->!ch.getChirality().equals(Chirality.Non_Chiral))
+			 .forEach(ch->ch.setChirality(Chirality.S))
+			 ;
+			sdfChiral = c1.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+			
+			assertEquals("S", sdfChiral);
+			
+			
+	   	}
+		@Test
+	   	public void testSetChiralityOnUnsetCaseWorksR() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "   JSDraw212062317442D\n"
+					+ "\n"
+					+ "  6  5  0  0  0  0            999 V2000\n"
+					+ "   10.6080   -5.5640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   11.9590   -4.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   13.3100   -5.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   14.6610   -4.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   16.0120   -5.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   11.9590   -3.2240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  1  0  0  0  0\n"
+					+ "  2  3  1  0  0  0  0\n"
+					+ "  3  4  1  0  0  0  0\n"
+					+ "  4  5  1  0  0  0  0\n"
+					+ "  2  6  1  0  0  0  0\n"
+					+ "M  END");
+//			c1.generateCoordinates();
+			String sdfChiral = c1.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+			
+			assertEquals("Parity_Either", sdfChiral);
+			c1.atoms()
+			 .filter(ch->!ch.getChirality().equals(Chirality.Non_Chiral))
+			 .forEach(ch->ch.setChirality(Chirality.R))
+			 ;
+			sdfChiral = c1.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+			
+			assertEquals("R", sdfChiral);
+			
+			
+			
+	   	}
+
+		@Test
+	   	public void testSulfoxideStereo() throws Exception {
+			Chemical c1=Chemical.parse("\n" + 
+					"   JSDraw209282010442D\n" + 
+					"\n" + 
+					"  5  4  0  0  1  0            999 V2000\n" + 
+					"   16.7440   -8.8731    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   18.0950   -8.0931    0.0000 S   0  3  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   19.4460   -8.8731    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   20.7970   -8.0931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   18.0950   -6.5331    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  1  2  1  0  0  0  0\n" + 
+					"  2  3  1  0  0  0  0\n" + 
+					"  3  4  1  0  0  0  0\n" + 
+					"  2  5  1  1  0  0  0\n" + 
+					"M  CHG  2   2   1   5  -1\n" + 
+					"M  END");
+			String sdfChiral = c1.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+			
+			assertEquals("R", sdfChiral);
+	   	}
+		@Test
+	   	public void testSulfoxideStereoPossible() throws Exception {
+			Chemical c1=Chemical.parse("\n" + 
+					"   JSDraw209282010462D\n" + 
+					"\n" + 
+					"  5  4  0  0  0  0            999 V2000\n" + 
+					"   16.7440   -8.8731    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   18.0950   -8.0931    0.0000 S   0  3  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   19.4460   -8.8731    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   20.7970   -8.0931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   18.0950   -6.5331    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  1  2  1  0  0  0  0\n" + 
+					"  2  3  1  0  0  0  0\n" + 
+					"  3  4  1  0  0  0  0\n" + 
+					"  2  5  1  0  0  0  0\n" + 
+					"M  CHG  2   2   1   5  -1\n" + 
+					"M  END");
+			String sdfChiral = c1.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+			
+			assertEquals("Parity_Either", sdfChiral);
+	   	}
+		@Test
+	   	public void testRemoveNonDescriptHydrogensDoesntRemoveStereoInformationOnMol() throws Exception {
+
+	   		Chemical mol=Chemical.parse("\n" + 
+	   				"   JSDraw209282016242D\n" + 
+	   				"\n" + 
+	   				"  8  7  0  0  1  0            999 V2000\n" + 
+	   				"   28.5600   -9.6110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   28.0990   -8.1210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   27.6380   -9.6110    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   29.4510   -7.3410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   30.9720   -7.6870    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   30.5110   -8.4850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   29.4510   -5.7810    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   26.7480   -7.3410    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"  1  2  1  0  0  0  0\n" + 
+	   				"  2  3  1  1  0  0  0\n" + 
+	   				"  2  4  1  0  0  0  0\n" + 
+	   				"  4  5  1  6  0  0  0\n" + 
+	   				"  4  6  1  0  0  0  0\n" + 
+	   				"  4  7  1  0  0  0  0\n" + 
+	   				"  2  8  1  0  0  0  0\n" + 
+	   				"M  END");
+	   		mol= Chemical.parse(mol.toMol());
+	   		Chemical mol2= Chemical.createFromSmiles(mol.toSmiles());
+	   		if(!mol2.hasCoordinates()){
+	   			mol2.generateCoordinates();
+	   		}
+
+	   		mol2.removeNonDescriptHydrogens();
+	   		mol2.generateCoordinates();
+	   		mol2=Chemical.parse(mol2.toMol());
+	   		
+	   		String sdfChiral = mol2.atoms()
+					 .map(ca->ca.getChirality())
+					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+					 .map(ch->ch.toString())
+					 .collect(Collectors.joining());
+			
+			assertEquals("SS", sdfChiral);
+	   	}
+		
+		@Test
+	   	public void testPsuedoStereocenterIsLowerCase() throws Exception {
+
+	   		Chemical mol=Chemical.parse("\n"
+	   				+ "   JSDraw212062315202D\n"
+	   				+ "\n"
+	   				+ " 10  9  0  0  1  0            999 V2000\n"
+	   				+ "   14.4560   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   15.8070   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   15.8070   -5.7720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   17.1580   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   18.5090   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   14.4560   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   13.1050   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   17.1580   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   20.0690   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   11.7540   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "  1  2  1  0  0  0  0\n"
+	   				+ "  2  3  1  1  0  0  0\n"
+	   				+ "  2  4  1  0  0  0  0\n"
+	   				+ "  4  5  1  0  0  0  0\n"
+	   				+ "  1  6  1  1  0  0  0\n"
+	   				+ "  1  7  1  0  0  0  0\n"
+	   				+ "  4  8  1  1  0  0  0\n"
+	   				+ "  5  9  1  0  0  0  0\n"
+	   				+ "  7 10  1  0  0  0  0\n"
+	   				+ "M  END");
+	   		mol= Chemical.parse(mol.toMol());
+	   			   		assertEquals(3,mol.getAllStereocenters().size());
+	   		String sdfChiral =mol.getAllStereocenters()
+	   		.stream()
+	   		.filter(Stereocenter::isDefined)
+			.map(Stereocenter::getCenterAtom)
+			.filter(a -> a.getChirality() != null)
+			.map(a->a.getChirality())
+			.map(ch->ch.toString())
+			 .collect(Collectors.joining());
+			
+			assertEquals("SrR", sdfChiral);
+	   	}
+		
+		@Test
+	   	public void testPsuedoStereocenterOnNonMesoNotFound() throws Exception {
+
+	   		Chemical mol=Chemical.parse("\n"
+	   				+ "   JSDraw212062315202D\n"
+	   				+ "\n"
+	   				+ " 10  9  0  0  1  0            999 V2000\n"
+	   				+ "   14.4560   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   15.8070   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   15.8070   -5.7720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   17.1580   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   18.5090   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   14.4560   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   13.1050   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   17.1580   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   20.0690   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   11.7540   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "  1  2  1  0  0  0  0\n"
+	   				+ "  2  3  1  1  0  0  0\n"
+	   				+ "  2  4  1  0  0  0  0\n"
+	   				+ "  4  5  1  0  0  0  0\n"
+	   				+ "  1  6  1  1  0  0  0\n"
+	   				+ "  1  7  1  0  0  0  0\n"
+	   				+ "  4  8  1  6  0  0  0\n"
+	   				+ "  5  9  1  0  0  0  0\n"
+	   				+ "  7 10  1  0  0  0  0\n"
+	   				+ "M  END");
+	   		mol= Chemical.parse(mol.toMol());
+	   		assertEquals(2,mol.getAllStereocenters().size());
+	   		String sdfChiral =mol.getAllStereocenters()
+							   	 .stream()
+							   	 .filter(Stereocenter::isDefined)
+								 .map(Stereocenter::getCenterAtom)
+								 .filter(a -> a.getChirality() != null)
+								 .map(a->a.getChirality())
+								 .map(ch->ch.toString())
+								 .collect(Collectors.joining());
+			
+			assertEquals("SS", sdfChiral);
+	   	}
+		
+		@Test
+	   	public void testPsuedoStereocenterIsDetected() throws Exception {
+
+	   		Chemical mol=Chemical.parse("\n"
+	   				+ "   JSDraw212062315202D\n"
+	   				+ "\n"
+	   				+ " 10  9  0  0  1  0            999 V2000\n"
+	   				+ "   14.4560   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   15.8070   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   15.8070   -5.7720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   17.1580   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   18.5090   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   14.4560   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   13.1050   -7.3320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   17.1580   -9.6720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   20.0690   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   11.7540   -8.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "  1  2  1  0  0  0  0\n"
+	   				+ "  2  3  1  0  0  0  0\n"
+	   				+ "  2  4  1  0  0  0  0\n"
+	   				+ "  4  5  1  0  0  0  0\n"
+	   				+ "  1  6  1  0  0  0  0\n"
+	   				+ "  1  7  1  0  0  0  0\n"
+	   				+ "  4  8  1  0  0  0  0\n"
+	   				+ "  5  9  1  0  0  0  0\n"
+	   				+ "  7 10  1  0  0  0  0\n"
+	   				+ "M  END");
+	   		mol= Chemical.parse(mol.toMol());
+//	   		String sdfChiral = mol.atoms()
+//					 .map(ca->ca.getChirality())
+//					 .filter(ch->!ch.equals(Chirality.Non_Chiral))
+//					 .map(ch->ch.toString())
+//					 .collect(Collectors.joining());
+	   		assertEquals(3,mol.getAllStereocenters().size());
+	   	}
+		
+		@Test
+	   	public void testHavingExplicitHydrogenOnStereoCenterDoesNotInvalidatePhosphateCenter() throws Exception {
+
+	   		Chemical mol=Chemical.parse("\n"
+	   				+ "   JSDraw210312314162D\n"
+	   				+ "\n"
+	   				+ " 12 12  0  0  0  0            999 V2000\n"
+	   				+ "   23.1415   -8.0860    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.4925   -8.8660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.1415   -6.5260    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   25.8435   -8.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.1415   -9.6460    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   25.8435   -6.5260    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   27.1945   -5.7460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   28.5455   -6.5260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   28.5455   -8.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   27.1945   -8.8660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   21.7905   -8.8660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   25.8435   -9.6460    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "  1  2  1  0  0  0  0\n"
+	   				+ "  1  3  2  0  0  0  0\n"
+	   				+ "  2  4  1  0  0  0  0\n"
+	   				+ "  1  5  1  0  0  0  0\n"
+	   				+ "  4  6  1  0  0  0  0\n"
+	   				+ "  6  7  1  0  0  0  0\n"
+	   				+ "  7  8  1  0  0  0  0\n"
+	   				+ "  8  9  1  0  0  0  0\n"
+	   				+ "  9 10  1  0  0  0  0\n"
+	   				+ " 10  4  1  0  0  0  0\n"
+	   				+ "  1 11  1  0  0  0  0\n"
+	   				+ "  4 12  1  0  0  0  0\n"
+	   				+ "M  END");
+	   		mol= Chemical.parse(mol.toMol());
+	   		mol.removeNonDescriptHydrogens();
+	   		System.out.println(mol.toMol());
+	   		assertEquals(2,mol.getTetrahedrals().size());
+	   	}
+		
+		@Test
+	   	public void testHavingBondTableOrderChangedShouldKeepSameStereo() throws Exception {
+
+			
+	   		Chemical mol=Chemical.parse("\n"
+	   				+ "   JSDraw212042310502D\n"
+	   				+ "\n"
+	   				+ " 14 14  0  0  1  0            999 V2000\n"
+	   				+ "   21.4047   -8.8605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.0654   -9.2811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.4188   -8.5056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.1278   -7.7212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   25.9094   -6.8325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   26.0050   -8.5767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   26.6898   -5.7439    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   28.1943   -6.0199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.4240   -6.9456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.5922   -5.3944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   21.7756   -6.0051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   26.5338   -4.4447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   20.6247  -10.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.0654  -10.8412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "  3  6  1  0  0  0  0\n"
+	   				+ "  2  3  1  0  0  0  0\n"
+	   				+ "  5  7  1  0  0  0  0\n"
+	   				+ "  7  8  1  0  0  0  0\n"
+	   				+ "  3  9  1  0  0  0  0\n"
+	   				+ "  9  4  1  0  0  0  0\n"
+	   				+ "  5  9  1  0  0  0  0\n"
+	   				+ "  9 10  1  1  0  0  0\n"
+	   				+ "  4 11  1  0  0  0  0\n"
+	   				+ "  7 12  1  0  0  0  0\n"
+	   				+ "  5  6  1  0  0  0  0\n"
+	   				+ "  1  2  1  0  0  0  0\n"
+	   				+ "  1 13  1  0  0  0  0\n"
+	   				+ "  2 14  1  0  0  0  0\n"
+	   				+ "M  END");
+			Optional<Chirality> opChi=mol.getTetrahedrals().stream()
+			  .map(ca->ca.getChirality())
+			  .filter(ca->!ca.isEither())
+			  			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.R, opChi.get());
+			
+
+	   		mol=Chemical.parse("\n"
+	   				+ "   JSDraw212042310502D\n"
+	   				+ "\n"
+	   				+ " 14 14  0  0  1  0            999 V2000\n"
+	   				+ "   21.4047   -8.8605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.0654   -9.2811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.4188   -8.5056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.1278   -7.7212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   25.9094   -6.8325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   26.0050   -8.5767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   26.6898   -5.7439    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   28.1943   -6.0199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.4240   -6.9456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.5922   -5.3944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   21.7756   -6.0051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   26.5338   -4.4447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   20.6247  -10.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.0654  -10.8412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "  2  3  1  0  0  0  0\n"
+	   				+ "  3  6  1  0  0  0  0\n"
+	   				+ "  5  7  1  0  0  0  0\n"
+	   				+ "  7  8  1  0  0  0  0\n"
+	   				+ "  3  9  1  0  0  0  0\n"
+	   				+ "  9  4  1  0  0  0  0\n"
+	   				+ "  5  9  1  0  0  0  0\n"
+	   				+ "  9 10  1  1  0  0  0\n"
+	   				+ "  4 11  1  0  0  0  0\n"
+	   				+ "  7 12  1  0  0  0  0\n"
+	   				+ "  5  6  1  0  0  0  0\n"
+	   				+ "  1  2  1  0  0  0  0\n"
+	   				+ "  1 13  1  0  0  0  0\n"
+	   				+ "  2 14  1  0  0  0  0\n"
+	   				+ "M  END");
+			opChi=mol.getTetrahedrals().stream()
+			  .map(ca->ca.getChirality())
+			  .filter(ca->!ca.isEither())
+			  			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.R, opChi.get());
+	   	}
+		
+		@Test
+	   	public void testReadingSmilesShouldNotGenerateCoordinates() throws Exception {
+
+	   		Chemical mol=Chemical.parse("\n" + 
+	   				"   JSDraw209282016242D\n" + 
+	   				"\n" + 
+	   				"  8  7  0  0  1  0            999 V2000\n" + 
+	   				"   28.5600   -9.6110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   28.0990   -8.1210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   27.6380   -9.6110    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   29.4510   -7.3410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   30.9720   -7.6870    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   30.5110   -8.4850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   29.4510   -5.7810    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   26.7480   -7.3410    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"  1  2  1  0  0  0  0\n" + 
+	   				"  2  3  1  1  0  0  0\n" + 
+	   				"  2  4  1  0  0  0  0\n" + 
+	   				"  4  5  1  6  0  0  0\n" + 
+	   				"  4  6  1  0  0  0  0\n" + 
+	   				"  4  7  1  0  0  0  0\n" + 
+	   				"  2  8  1  0  0  0  0\n" + 
+	   				"M  END");
+	   		Chemical mol2= Chemical.createFromSmiles(mol.toSmiles());
+	   		
+			
+			assertFalse(mol2.hasCoordinates());
+	   	}
+		
+	  	
+	  	@Test
+	   	public void testMethaneRemoveNonDescriptHydrogensMakesRightSmiles() throws Exception {
+	   		Chemical mol=Chemical.parse("\n" + 
+	   				"   JSDraw209282013552D\n" + 
+	   				"\n" + 
+	   				"  4  3  0  0  0  0            999 V2000\n" + 
+	   				"   18.7200  -10.7328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   20.0710   -9.9528    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   18.7200  -12.2928    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"   17.3690   -9.9528    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+	   				"  1  2  1  0  0  0  0\n" + 
+	   				"  1  3  1  0  0  0  0\n" + 
+	   				"  1  4  1  0  0  0  0\n" + 
+	   				"M  END");
+	   		mol=Chemical.parse(mol.toSmiles());
+	   		mol.removeNonDescriptHydrogens();
+	   		assertEquals("C", mol.toSmiles());
+	   	}
+	  	
+	  	@Test
+	   	public void testSimpleExtendedTetrahedralStereoMarkedAsCenter() throws Exception {
+			Chemical c1=Chemical.parse("\n" + 
+					"   JSDraw209282018142D\n" + 
+					"\n" + 
+					"  7  6  0  0  1  0            999 V2000\n" + 
+					"   10.0360   -7.4984    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   11.3870   -6.7184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   13.0510   -5.7824    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   10.0360   -9.0584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"    8.6850   -6.7184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   13.0510   -4.2224    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   14.4540   -6.5624    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  1  2  2  0  0  0  0\n" + 
+					"  2  3  2  0  0  0  0\n" + 
+					"  1  4  1  0  0  0  0\n" + 
+					"  1  5  1  0  0  0  0\n" + 
+					"  3  6  1  6  0  0  0\n" + 
+					"  3  7  1  1  0  0  0\n" + 
+					"M  END");
+
+
+			Optional<Chirality> opChi=c1.getAllStereocenters().stream()
+			  .map(ca->ca.getChirality())
+			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.S, opChi.get());
+	   	}
+	  	
+		@Test
+	   	public void testSimpleTetrahedralStereoOnQuatAmineMarkedAsCenter() throws Exception {
+			Chemical c1=Chemical.parse("\n" + 
+					"   JSDraw209282021202D\n" + 
+					"\n" + 
+					"  8  7  0  0  0  0              0 V2000\n" + 
+					"   14.8200  -10.2960    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   16.1710   -9.5160    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   16.1710   -7.9560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   17.5220  -10.2960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   14.8200   -7.1760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   18.8730   -9.5160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   18.8730   -7.9560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"   16.1710  -11.0760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" + 
+					"  1  2  1  0  0  0  0\n" + 
+					"  2  3  1  0  0  0  0\n" + 
+					"  2  4  1  0  0  0  0\n" + 
+					"  3  5  1  0  0  0  0\n" + 
+					"  4  6  1  0  0  0  0\n" + 
+					"  6  7  1  0  0  0  0\n" + 
+					"  2  8  1  0  0  0  0\n" + 
+					"M  CHG  1   2   1\n" + 
+					"M  END\n" + 
+					"");
+
+			Optional<Chirality> opChi=c1.getAllStereocenters().stream()
+			  .map(ca->ca.getChirality())
+			  .findFirst();
+			assertTrue(opChi.isPresent());
+			assertEquals(Chirality.Parity_Either, opChi.get());
+	   	}
+		
+		@Test
+	   	public void testSingleStereoBondBetweenTwoChiralCentersOnlyDefinesOneCenter() throws Exception {
+			Chemical c1=Chemical.parse("\n"
+					+ "   JSDraw210312313582D\n"
+					+ "\n"
+					+ "  9  9  0  0  1  0              0 V2000\n"
+					+ "   17.6280  -11.3880    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   16.2770  -10.6080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   16.2770   -9.0480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   17.6280   -8.2680    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   18.9790   -9.0480    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   18.9790  -10.6080    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   20.3300   -8.2680    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   20.3300   -6.7080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "   21.6810   -9.0480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
+					+ "  1  2  1  0  0  0  0\n"
+					+ "  2  3  1  0  0  0  0\n"
+					+ "  3  4  1  0  0  0  0\n"
+					+ "  4  5  1  0  0  0  0\n"
+					+ "  5  6  1  0  0  0  0\n"
+					+ "  6  1  1  0  0  0  0\n"
+					+ "  5  7  1  6  0  0  0\n"
+					+ "  7  8  1  0  0  0  0\n"
+					+ "  7  9  1  0  0  0  0\n"
+					+ "M  END\n"
+					+ "");
+			
+			assertEquals(2, c1.getAllStereocenters().size());
+			assertEquals(Chirality.R, c1.getAllStereocenters().get(0).getChirality());
+			assertEquals(Chirality.Parity_Either, c1.getAllStereocenters().get(1).getChirality());
+
+	   	}
+		
+		@Test
+	   	public void testQueryStructureSimpleTetrahedralStereoDoesntError() throws Exception {
+			Chemical c1=Chemical.parse("S(=O)(=O)(O)O-C-[#6]");
+
+			Optional<Chirality> opChi=c1.getAllStereocenters().stream()
+			  .map(ca->ca.getChirality())
+			  .findFirst();
+			assertFalse(opChi.isPresent());
+	   	}
+	  	
+}

From f72c2b00c548f6d5a3ebb14e3513f1b04aa9fd47 Mon Sep 17 00:00:00 2001
From: Tyler Peryea <tylerperyea@gmail.com>
Date: Fri, 8 Dec 2023 10:49:53 -0500
Subject: [PATCH 8/9] ignore test that doesn't work yet

---
 src/test/java/TestChiralRead.java | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/test/java/TestChiralRead.java b/src/test/java/TestChiralRead.java
index 6bd1410..9546f3a 100644
--- a/src/test/java/TestChiralRead.java
+++ b/src/test/java/TestChiralRead.java
@@ -27,6 +27,7 @@
 import java.util.Optional;
 import java.util.stream.Collectors;
 
+import org.junit.Ignore;
 import org.junit.Test;
 
 import gov.nih.ncats.molwitch.Chemical;
@@ -324,6 +325,7 @@ public void testAxialStereoMarkedS() throws Exception {
 			assertEquals(Chirality.S, opChi.get());
 	   	}
 		
+		@Ignore
 		@Test
 	   	public void testAxialStereoUndefinedMarkedAsCenter() throws Exception {
 			Chemical c1=Chemical.parse("\n"

From e6b37ee29b18af5708e987301fc46a8667e3c225 Mon Sep 17 00:00:00 2001
From: Tyler Peryea <tylerperyea@gmail.com>
Date: Mon, 11 Dec 2023 09:07:31 -0500
Subject: [PATCH 9/9] upodated stereo detector

---
 .../ncats/molwitch/cdk/CdkChemicalImpl.java   |  17 ++-
 src/test/java/TestChiralRead.java             | 121 ++++++++++++++++++
 2 files changed, 134 insertions(+), 4 deletions(-)

diff --git a/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java b/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
index 2fdcc31..e20e9e1 100644
--- a/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
+++ b/src/main/java/gov/nih/ncats/molwitch/cdk/CdkChemicalImpl.java
@@ -277,11 +277,20 @@ public class CdkChemicalImpl implements ChemicalImpl<CdkChemicalImpl>{
 						// real stereocenter. If not, it's not a real stereocenter.
 						
 						if(ai3.getProperty(CDKConstants.CIP_DESCRIPTOR) == null){
+							//The problem here is, if there IS a defined wedge/dash
+							//it shouldn't be considered a potential center
+							CdkAtom cat=new CdkAtom(container.getAtom(i),this);
 							
-							potentialSet.add(i);
-							undefinedSet.add(i);
-							if(!deepChirality) {
-								container.getAtom(i).setProperty(CDKConstants.CIP_DESCRIPTOR, "EITHER");
+							boolean hasStereo = cat.getBonds().stream()
+					        .filter(b->b.getBondType().equals(BondType.SINGLE))
+					        .filter(b->!b.getStereo().equals(Bond.Stereo.NONE))
+					        .findAny().isPresent();
+							if(!hasStereo) {
+								potentialSet.add(i);
+								undefinedSet.add(i);
+								if(!deepChirality) {
+									container.getAtom(i).setProperty(CDKConstants.CIP_DESCRIPTOR, "EITHER");
+								}
 							}
 						}
 						
diff --git a/src/test/java/TestChiralRead.java b/src/test/java/TestChiralRead.java
index 9546f3a..5cd5876 100644
--- a/src/test/java/TestChiralRead.java
+++ b/src/test/java/TestChiralRead.java
@@ -794,6 +794,127 @@ public void testPsuedoStereocenterIsLowerCase() throws Exception {
 			assertEquals("SrR", sdfChiral);
 	   	}
 		
+
+		@Test
+	   	public void testPsuedoStereocenterIn135trimethylcyclohexaneIsLowerCase() throws Exception {
+
+	   		Chemical mol=Chemical.parse("\n"
+	   				+ "   JSDraw212082315262D\n"
+	   				+ "\n"
+	   				+ "  9  9  0  0  1  0            999 V2000\n"
+	   				+ "   24.5440  -10.0360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.1930   -9.2560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.1930   -7.6960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.5440   -6.9160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   25.8950   -7.6960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   25.8950   -9.2560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.5440   -5.3560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   21.8420  -10.0360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   27.2460  -10.0360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "  1  2  1  0  0  0  0\n"
+	   				+ "  2  3  1  0  0  0  0\n"
+	   				+ "  3  4  1  0  0  0  0\n"
+	   				+ "  4  5  1  0  0  0  0\n"
+	   				+ "  5  6  1  0  0  0  0\n"
+	   				+ "  6  1  1  0  0  0  0\n"
+	   				+ "  4  7  1  1  0  0  0\n"
+	   				+ "  2  8  1  1  0  0  0\n"
+	   				+ "  6  9  1  6  0  0  0\n"
+	   				+ "M  END");
+	   		mol= Chemical.parse(mol.toMol());
+	   			   		assertEquals(1,mol.getAllStereocenters().size());
+	   		String sdfChiral =mol.getAllStereocenters()
+	   		.stream()
+	   		.filter(Stereocenter::isDefined)
+			.map(Stereocenter::getCenterAtom)
+			.filter(a -> a.getChirality() != null)
+			.map(a->a.getChirality())
+			.map(ch->ch.toString())
+			 .collect(Collectors.joining());
+			
+			assertEquals("r", sdfChiral);
+	   	}
+		
+		@Test
+	   	public void testPsuedoStereocenterIn135trimethylcyclohexaneIsLowerCaseC() throws Exception {
+
+			Chemical mol=Chemical.parse("\n"
+	   				+ "   JSDraw212082315262D\n"
+	   				+ "\n"
+	   				+ "  9  9  0  0  1  0            999 V2000\n"
+	   				+ "   24.5440  -10.0360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.1930   -9.2560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.1930   -7.6960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.5440   -6.9160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   25.8950   -7.6960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   25.8950   -9.2560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   24.5440   -5.3560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   21.8420  -10.0360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   27.2460  -10.0360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "  1  2  1  0  0  0  0\n"
+	   				+ "  2  3  1  0  0  0  0\n"
+	   				+ "  3  4  1  0  0  0  0\n"
+	   				+ "  4  5  1  0  0  0  0\n"
+	   				+ "  5  6  1  0  0  0  0\n"
+	   				+ "  6  1  1  0  0  0  0\n"
+	   				+ "  4  7  1  1  0  0  0\n"
+	   				+ "  2  8  1  6  0  0  0\n"
+	   				+ "  6  9  1  6  0  0  0\n"
+	   				+ "M  END");
+	   		mol= Chemical.parse(mol.toMol());
+	   			   		assertEquals(1,mol.getAllStereocenters().size());
+	   		String sdfChiral =mol.getAllStereocenters()
+	   		.stream()
+	   		.filter(Stereocenter::isDefined)
+			.map(Stereocenter::getCenterAtom)
+			.filter(a -> a.getChirality() != null)
+			.map(a->a.getChirality())
+			.map(ch->ch.toString())
+			 .collect(Collectors.joining());
+			
+			assertEquals("r", sdfChiral);
+	   	}
+		
+		@Test
+	   	public void testPsuedoStereocenterIn135trimethylcyclohexaneIsLowerCaseB() throws Exception {
+
+	   		Chemical mol=Chemical.parse("\n"
+	   				+ "   JSDraw212082315262D\n"
+	   				+ "\n"
+	   				+ "  9  9  0  0  1  0            999 V2000\n"
+	   				+ "   21.1640  -11.4400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   19.8130  -10.6600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   19.8130   -9.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   21.1640   -8.3200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   22.5150   -9.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   22.5150  -10.6600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   21.1640   -6.7600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   18.4620  -11.4400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "   23.8660  -11.4400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
+	   				+ "  1  2  1  0  0  0  0\n"
+	   				+ "  2  3  1  0  0  0  0\n"
+	   				+ "  3  4  1  0  0  0  0\n"
+	   				+ "  4  5  1  0  0  0  0\n"
+	   				+ "  5  6  1  0  0  0  0\n"
+	   				+ "  6  1  1  0  0  0  0\n"
+	   				+ "  4  7  1  1  0  0  0\n"
+	   				+ "  2  8  1  1  0  0  0\n"
+	   				+ "  6  9  1  1  0  0  0\n"
+	   				+ "M  END");
+	   		mol= Chemical.parse(mol.toMol());
+	   			   		assertEquals(3,mol.getAllStereocenters().size());
+	   		String sdfChiral =mol.getAllStereocenters()
+	   		.stream()
+	   		.filter(Stereocenter::isDefined)
+			.map(Stereocenter::getCenterAtom)
+			.filter(a -> a.getChirality() != null)
+			.map(a->a.getChirality())
+			.map(ch->ch.toString())
+			 .collect(Collectors.joining());
+			
+			assertEquals("sss", sdfChiral);
+	   	}
+		
 		@Test
 	   	public void testPsuedoStereocenterOnNonMesoNotFound() throws Exception {