This is the most questionable change but believe to be a bug in InChI 1.03. Using JNI INCHI setting the chiral flag = on or off we get "rA:9n..." without it we get ""rA:9...". In JNA INCHI we always get "rA:9n..." - this molecule is not chiral so it seems odd that the setting would change anything. Since this is only a change in AuxInfo this is acceptable.

johnmay · egonw · commit 664390963b73 · 2021-12-18T10:07:39.000+01:00
diff --git a/storage/inchi/src/test/java/org/openscience/cdk/graph/invariant/InChINumbersToolsTest.java b/storage/inchi/src/test/java/org/openscience/cdk/graph/invariant/InChINumbersToolsTest.java
@@ -103,9 +103,9 @@ public void testGlycine_uSmiles() throws Exception {
     public void fixedH() throws Exception {
         SmilesParser parser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
         IAtomContainer atomContainer = parser.parseSmiles("N1C=NC2=CC=CC=C12");
-        String auxInfo = InChINumbersTools.auxInfo(atomContainer, INCHI_OPTION.FixedH, INCHI_OPTION.ChiralFlagON);
+        String auxInfo = InChINumbersTools.auxInfo(atomContainer, INCHI_OPTION.FixedH);
         String expected = "AuxInfo=1/1/" + "N:6,7,5,8,2,4,9,3,1/" + "E:(1,2)(3,4)(6,7)(8,9)/" + "F:7,6,8,5,2,9,4,1,3/"
-                + "rA:9NCNCCCCCC/" + "rB:s1;d2;s3;d4;s5;d6;s7;s1s4d8;/" + "rC:;;;;;;;;;";
+                + "rA:9nNCNCCCCCC/" + "rB:s1;d2;s3;d4;s5;d6;s7;s1s4d8;/" + "rC:;;;;;;;;;";
         assertThat(auxInfo, is(expected));
     }
 
