bondsToHydrogens should be updated here.

johnmay · johnmay · commit 67c3c226d723 · 2019-01-10T13:11:32.000Z
diff --git a/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java b/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
@@ -790,6 +790,7 @@ public static IAtomContainer suppressHydrogens(IAtomContainer org) {
 
         for (final IBond bond : org.bonds()) {
             if (remaining > 0 && (hydrogens.contains(bond.getBegin()) || hydrogens.contains(bond.getEnd()))) {
+                bondsToHydrogens.add(bond);
                 remaining--;
                 continue;
             }

Original file line number	Diff line number	Diff line change
`@@ -790,6 +790,7 @@ public static IAtomContainer suppressHydrogens(IAtomContainer org) {`
`790`	`790`
`791`	`791`	`for (final IBond bond : org.bonds()) {`
`792`	`792`	`if (remaining > 0 && (hydrogens.contains(bond.getBegin()) \|\| hydrogens.contains(bond.getEnd()))) {`
	`793`	`+ bondsToHydrogens.add(bond);`
`793`	`794`	`remaining--;`
`794`	`795`	`continue;`
`795`	`796`	`}`