Added output of ITetrahedralChirality to InChI

Change-Id: Ie69b3b3e38790f2ab99f61c11738535dcc1b8cea Signed-off-by: John May <john.wilkinsonmay@gmail.com>
cdk · Sep 24, 2012 · 3c0d36b · 3c0d36b
1 parent 913c796
commit 3c0d36b
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diff --git a/src/main/org/openscience/cdk/inchi/InChIGenerator.java b/src/main/org/openscience/cdk/inchi/InChIGenerator.java
@@ -54,6 +54,9 @@
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IAtomParity;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IStereoElement;
+import org.openscience.cdk.interfaces.ITetrahedralChirality;
+import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 
 /**
@@ -366,6 +369,32 @@ else if (stereo == CDKConstants.UNSET) {
                         INCHI_STEREOTYPE.TETRAHEDRAL, p));
             }
         }
+        // Process tetrahedral stereo elements
+        for (IStereoElement stereoElem : atomContainer.stereoElements()) {
+        	if (stereoElem instanceof ITetrahedralChirality) {
+        		ITetrahedralChirality chirality = (ITetrahedralChirality)stereoElem;
+        		IAtom[] surroundingAtoms = chirality.getLigands();
+        		Stereo stereoType = chirality.getStereo();
+
+        		JniInchiAtom atC = (JniInchiAtom) atomMap.get(chirality.getChiralAtom());
+                JniInchiAtom at0 = (JniInchiAtom) atomMap.get(surroundingAtoms[0]);
+                JniInchiAtom at1 = (JniInchiAtom) atomMap.get(surroundingAtoms[1]);
+                JniInchiAtom at2 = (JniInchiAtom) atomMap.get(surroundingAtoms[2]);
+                JniInchiAtom at3 = (JniInchiAtom) atomMap.get(surroundingAtoms[3]);
+                INCHI_PARITY p = INCHI_PARITY.UNKNOWN;
+                if (stereoType == Stereo.ANTI_CLOCKWISE) {
+                    p = INCHI_PARITY.ODD;
+                } else if (stereoType == Stereo.CLOCKWISE) {
+                    p = INCHI_PARITY.EVEN;
+                } else {
+                    throw new CDKException("Unknown tetrahedral chirality");
+                }
+
+                JniInchiStereo0D jniStereo = new JniInchiStereo0D(atC, at0, at1, at2, at3,
+                        INCHI_STEREOTYPE.TETRAHEDRAL, p);
+                input.addStereo0D(jniStereo);
+        	}
+        }
 
         try {
             output = JniInchiWrapper.getInchi(input);

diff --git a/src/test/org/openscience/cdk/inchi/InChIGeneratorTest.java b/src/test/org/openscience/cdk/inchi/InChIGeneratorTest.java
@@ -25,7 +25,10 @@
 import org.openscience.cdk.*;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.ITetrahedralChirality;
 import org.openscience.cdk.interfaces.IBond.Order;
+import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
+import org.openscience.cdk.stereo.TetrahedralChirality;
 
 import javax.vecmath.Point2d;
 import javax.vecmath.Point3d;
@@ -629,4 +632,52 @@ public void testGetStandardInchiFromLandDAlanine3D() throws Exception {
             genD.getInchi()
         );
     }
+
+    @Test
+    public void testTetrahedralStereo() throws Exception {
+        // L-Alanine
+        IAtomContainer acL = new AtomContainer();
+        IAtom[] ligandAtoms = new IAtom[4];
+        IAtom a1 = new Atom("C");
+        IAtom a1H = new Atom("H");
+        ligandAtoms[0] = a1H;
+        IAtom a2 = new Atom("C");
+        ligandAtoms[1] = a2;
+        IAtom a3 = new Atom("N");
+        ligandAtoms[2] = a3;
+        IAtom a4 = new Atom("C");
+        ligandAtoms[3] = a4;
+        IAtom a5 = new Atom("O");
+        IAtom a6 = new Atom("O");
+        a1.setImplicitHydrogenCount(0);
+        a3.setImplicitHydrogenCount(2);
+        a4.setImplicitHydrogenCount(3);
+        a5.setImplicitHydrogenCount(1);
+        acL.addAtom(a1);
+        acL.addAtom(a1H);
+        acL.addAtom(a2);
+        acL.addAtom(a3);
+        acL.addAtom(a4);
+        acL.addAtom(a5);
+        acL.addAtom(a6);
+
+        acL.addBond(new Bond(a1, a1H, CDKConstants.BONDORDER_SINGLE));
+        acL.addBond(new Bond(a1, a2, CDKConstants.BONDORDER_SINGLE));
+        acL.addBond(new Bond(a1, a3, CDKConstants.BONDORDER_SINGLE));
+        acL.addBond(new Bond(a1, a4, CDKConstants.BONDORDER_SINGLE));
+        acL.addBond(new Bond(a2, a5, CDKConstants.BONDORDER_SINGLE));
+        acL.addBond(new Bond(a2, a6, CDKConstants.BONDORDER_DOUBLE));
+
+        ITetrahedralChirality chirality = new TetrahedralChirality(
+        	a1, ligandAtoms, Stereo.ANTI_CLOCKWISE
+        );
+        acL.addStereoElement(chirality);
+
+        InChIGenerator genL = getFactory().getInChIGenerator(acL);
+        Assert.assertEquals(INCHI_RET.OKAY, genL.getReturnStatus());
+        Assert.assertEquals(
+            "InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1",
+            genL.getInchi()
+        );
+    }
 }