Merge pull request #1330 from ghutchis/fix-nitrogen-valence

Adjust nitrogen valence determination
OpenChemistry · Sep 9, 2023 · 664ef1d · 664ef1d
2 parents 8970c8b + 1878545
commit 664ef1d
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/avogadro/core/mdlvalence_p.h b/avogadro/core/mdlvalence_p.h
@@ -97,7 +97,7 @@ static unsigned int atomValence(const unsigned char atomicNumber,
         case -1:
           return 2;
         case 0:
-          if (numBonds <= 3)
+          if (numBonds != 5)
             return 3;
           return 5;
         case 1:

diff --git a/tests/qtgui/hydrogentoolstest.cpp b/tests/qtgui/hydrogentoolstest.cpp
@@ -173,9 +173,10 @@ TEST(HydrogenToolsTest, valencyAdjustment_N)
   RWAtom N = mol.addAtom(7);
   int expectedAdjustment = 3;
   for (int i = 0; i < 8; ++i, --expectedAdjustment) {
-    if (i == 4) // neutral N can have 3 or 5 bonds in our valence model.
-      expectedAdjustment += 2;
-    EXPECT_EQ(expectedAdjustment, HydrogenTools::valencyAdjustment(N));
+    if (i == 5) // neutral N can have 3 or 5 bonds in our valence model.
+      EXPECT_EQ(0, HydrogenTools::valencyAdjustment(N));
+    else
+      EXPECT_EQ(expectedAdjustment, HydrogenTools::valencyAdjustment(N));
     mol.addBond(mol.addAtom(1), N, 1);
   }
 }