Resolve off by one error in bug 489 by ensuring substring doesn't fail.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Jan 2, 2015 · 09ef737 · 09ef737
1 parent a25a2da
commit 09ef737
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Showing 3 changed files with 12,341 additions and 3 deletions.
diff --git a/storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java b/storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java
@@ -651,19 +651,19 @@ private PDBAtom readAtom(String cLine, int lineLength) {
             oAtom.setAtomTypeName(oAtom.getResName() + "." + rawAtomName);
         }
         if (lineLength >= 59) {
-            String frag = cLine.substring(54, 60).trim();
+            String frag = cLine.substring(54, Math.min(lineLength, 60)).trim();
             if (frag.length() > 0) {
                 oAtom.setOccupancy(Double.parseDouble(frag));
             }
         }
         if (lineLength >= 65) {
-            String frag = cLine.substring(60, 66).trim();
+            String frag = cLine.substring(60, Math.min(lineLength, 66)).trim();
             if (frag.length() > 0) {
                 oAtom.setTempFactor(Double.parseDouble(frag));
             }
         }
         if (lineLength >= 75) {
-            oAtom.setSegID(cLine.substring(72, 76).trim());
+            oAtom.setSegID(cLine.substring(72, Math.min(lineLength, 76)).trim());
         }
         //		if (lineLength >= 78) {
         //            oAtom.setSymbol((new String(cLine.substring(76, 78))).trim());

diff --git a/storage/pdb/src/test/java/org/openscience/cdk/io/PDBReaderTest.java b/storage/pdb/src/test/java/org/openscience/cdk/io/PDBReaderTest.java
@@ -590,4 +590,12 @@ public void test1D66() throws Exception {
 
     }
 
+    /**
+     * @cdk.bug 489
+     */
+    @Category(SlowTest.class)
+    @Test public void readFinalPump() throws Exception {
+        IChemFile chemFile = new PDBReader(getClass().getResourceAsStream("finalPump96.09.06.pdb")).read(new ChemFile());
+    }
+
 }