'H+' is also okay

johnmay · johnmay · commit 07caf475cb71 · 2020-06-03T17:08:44.000+01:00
diff --git a/tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java b/tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java
@@ -750,9 +750,9 @@ private static IMolecularFormula getMolecularFormula(String stringMF, IMolecular
 
         // Extract charge from String when contains []X- format
         Integer charge = null;
-        if ((stringMF.contains("[") && stringMF.contains("]")) && (stringMF.contains("+") || stringMF.contains(HYPHEN_STR) || stringMF.contains(MINUS_STR))) {
+        if ((stringMF.contains("+") || stringMF.contains(HYPHEN_STR) || stringMF.contains(MINUS_STR))) {
             int pos = findChargePosition(stringMF);
-            if (pos >= 0) {
+            if (pos >= 0 && pos != stringMF.length()) {
                 charge = parseCharge(new CharIter(pos, stringMF));
                 stringMF = stringMF.substring(0, pos);
                 if (stringMF.charAt(0) == '[' &&
@@ -827,7 +827,6 @@ private static int findChargePosition(String formula) {
             pos--;
         if (pos == mark2 && formula.charAt(pos) != ']')
             pos = mark1; // not a charge CH3- we sucked up a number
-        if (pos == 0) return -1;
         return pos+1;
     }
 
diff --git a/tool/formula/src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java b/tool/formula/src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java
@@ -1481,5 +1481,6 @@ public void roundtrip(String mfStr, String expected) {
         roundtrip("[2]H2+", "[[2]H2]+");
         // +2 => 2+ with brackets
         roundtrip("[2H]2+2", "[[2]H2]2+");
+        roundtrip("H+", "[H]+");
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -1481,5 +1481,6 @@ public void roundtrip(String mfStr, String expected) {`
`1481`	`1481`	`roundtrip("[2]H2+", "[[2]H2]+");`
`1482`	`1482`	`// +2 => 2+ with brackets`
`1483`	`1483`	`roundtrip("[2H]2+2", "[[2]H2]2+");`
	`1484`	`+ roundtrip("H+", "[H]+");`
`1484`	`1485`	`}`
`1485`	`1486`	`}`