Handle HCl, HF, HBr etc as though they were Cl-, F-, Br- etc.

johnmay · johnmay · commit e82085848ba4 · 2019-02-01T11:18:03.000Z
diff --git a/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptor.java b/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptor.java
@@ -1743,7 +1743,8 @@ private void calcGroup101_to_104(int i) {
         IAtom ai = atomContainer.getAtom(i);
         String s = ai.getSymbol();
 
-        if (ai.getFormalCharge() == -1) {
+        if (ai.getFormalCharge() == -1 ||
+            (ai.getFormalCharge() == 0 && isBondedToHydrogenOnly(ai))) {
             if (s.equals("F")) {
                 frags[101]++;
                 alogpfrag[i] = 101;
@@ -1762,6 +1763,11 @@ private void calcGroup101_to_104(int i) {
 
     }
 
+    private boolean isBondedToHydrogenOnly(IAtom ai) {
+        return ai.getBondCount() == 1 &&
+               ai.bonds().iterator().next().getOther(ai).getAtomicNumber() == 1;
+    }
+
     private void calcGroup106(int i) {
         // S in SH
         if (fragment[i].equals("SsSH")) {
