Round trip MF charge.

cdk · Oct 11, 2018 · 6819a15 · 6819a15
1 parent 156b407
commit 6819a15
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Showing 2 changed files with 29 additions and 2 deletions.
diff --git a/...mula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java b/...mula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java
@@ -230,6 +230,10 @@ public static String getString(IMolecularFormula formula, String[] orderElements
                                    boolean setOne, boolean setMassNumber) {
         StringBuilder  stringMF     = new StringBuilder();
         List<IIsotope> isotopesList = putInOrder(orderElements, formula);
+        Integer q = formula.getCharge();
+
+        if (q != null && q != 0)
+            stringMF.append('[');
 
         if (!setMassNumber) {
             int count = 0;
@@ -258,6 +262,20 @@ public static String getString(IMolecularFormula formula, String[] orderElements
             }
         }
 
+
+        if (q != null && q != 0) {
+            stringMF.append(']');
+            if (q > 0) {
+                if (q > 1)
+                    stringMF.append(q);
+                stringMF.append('+');
+            } else {
+                if (q < 1)
+                    stringMF.append(-q);
+                stringMF.append('-');
+            }
+        }
+
         return stringMF.toString();
     }
 
@@ -539,7 +557,7 @@ private static IMolecularFormula getMolecularFormula(String stringMF, boolean as
     private static final char MINUS  = '–';
     private static final String HYPHEN_STR = "-";
     private static final String MINUS_STR  = "–";
-    
+
     /**
      * add in a instance of IMolecularFormula the elements extracts form
      * molecular formula string. The string is immediately analyzed and a set of Nodes
@@ -707,7 +725,7 @@ private static String cleanMFfromCharge(String formula) {
         }
         return finalFormula;
     }
-    
+
     /**
      * Extract the charge given a molecular formula format [O3S]2-.
      *

diff --git a/.../src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java b/.../src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java
@@ -1363,4 +1363,13 @@ public void testMassNumberDisplayWithDefinedIsotopes() throws Exception {
         assertThat(MolecularFormulaManipulator.getString(mf, false, true),
             is("C7H3Br[81]BrO3"));
     }
+
+    @Test
+    public void testRoundTripCharge() {
+        String f = "[C3H7]+";
+        IMolecularFormula m =
+                MolecularFormulaManipulator.getMolecularFormula(f,
+                                                                SilentChemObjectBuilder.getInstance());
+        assertThat(MolecularFormulaManipulator.getString(m), is("[C3H7]+"));
+    }
 }