Fix Test - ignore longer extended tetrahedral - could be a warning.

johnmay · egonw · commit 8c9e995735cb · 2021-12-18T10:07:39.000+01:00
diff --git a/base/core/src/main/java/org/openscience/cdk/stereo/ExtendedTetrahedral.java b/base/core/src/main/java/org/openscience/cdk/stereo/ExtendedTetrahedral.java
@@ -192,6 +192,28 @@ public IAtom[] findTerminalAtoms(IAtomContainer container) {
         return atoms;
     }
 
+    public static int getLength(IAtomContainer container, IAtom focus) {
+        int length = 0;
+        List<IBond> focusBonds = container.getConnectedBondsList(focus);
+        if (focusBonds.size() != 2)
+            throw new IllegalArgumentException("focus must have exactly 2 neighbors");
+        IAtom leftPrev  = focus;
+        IAtom rightPrev = focus;
+        IAtom left      = focusBonds.get(0).getOther(focus);
+        IAtom right     = focusBonds.get(1).getOther(focus);
+        IAtom tmp;
+        while (left != null && right != null) {
+            tmp = getOtherNbr(container, left, leftPrev);
+            leftPrev = left;
+            left     = tmp;
+            tmp = getOtherNbr(container, right, rightPrev);
+            rightPrev = right;
+            right     = tmp;
+            length++;
+        }
+        return 2*length;
+    }
+
     @Override
     protected IStereoElement<IAtom, IAtom> create(IAtom focus, List<IAtom> carriers,
                                                   int cfg) {
diff --git a/storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIGenerator.java b/storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIGenerator.java
@@ -419,6 +419,10 @@ private void generateInchiFromCDKAtomContainer(IAtomContainer atomContainer, boo
                 IAtom[] terminals = extendedTetrahedral.findTerminalAtoms(atomContainer);
                 IAtom[] peripherals = extendedTetrahedral.peripherals();
 
+                // InChI only supports length 2
+                if (ExtendedTetrahedral.getLength(atomContainer, focus) > 2)
+                    continue;
+
                 // InChI API is particualar about the input, each terminal atom
                 // needs to be present in the list of neighbors and they must
                 // be at index 1 and 2 (i.e. in the middle). This is true even
diff --git a/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorFactoryTest.java b/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorFactoryTest.java
@@ -185,7 +185,7 @@ public void dontIgnoreMajorIsotopes() throws CDKException {
     }
 
     // InChI only supports cumulenes of length 2 (CC=[C@]=CC) and 3
-    // (C/C=C=C=C=C/C) longer ones should be ignored
+    // (C/C=C=C=C/C) - longer ones should be ignored
     @Test
     public void longerExtendedTetrahedralsIgnored() throws Exception {
         SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());

Original file line number	Diff line number	Diff line change
`@@ -185,7 +185,7 @@ public void dontIgnoreMajorIsotopes() throws CDKException {`
`185`	`185`	`}`
`186`	`186`
`187`	`187`	`// InChI only supports cumulenes of length 2 (CC=[C@]=CC) and 3`
`188`		`- // (C/C=C=C=C=C/C) longer ones should be ignored`
	`188`	`+ // (C/C=C=C=C/C) - longer ones should be ignored`
`189`	`189`	`@Test`
`190`	`190`	`public void longerExtendedTetrahedralsIgnored() throws Exception {`
`191`	`191`	`SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());`