Fix for charge parsing in PDB files, based on the patch by Nils <nils…

…@users.sf.net> Change-Id: I7414228850ac87880febdebfc6e912647638f2c6 Signed-off-by: John May <john.wilkinsonmay@gmail.com>
cdk · Feb 19, 2012 · 7c7248a · 7c7248a
1 parent e2eb007
commit 7c7248a
Showing 1 changed file with 12 additions and 2 deletions.
diff --git a/src/main/org/openscience/cdk/io/PDBReader.java b/src/main/org/openscience/cdk/io/PDBReader.java
@@ -671,9 +671,19 @@ private PDBAtom readAtom(String cLine, int lineLength) {
 //            oAtom.setSymbol((new String(cLine.substring(76, 78))).trim());
 //		}
 		if (lineLength >= 79) {
-            String frag = cLine.substring(78, 80).trim();
+			String frag;
+			if (lineLength >= 80) {
+				frag = cLine.substring(78, 80).trim();
+			} else {
+				frag = cLine.substring(78);
+			}
             if (frag.length() > 0) {
-                oAtom.setCharge(Double.parseDouble(frag));
+        		// see Format_v33_A4.pdf, p. 178
+            	if (frag.endsWith("-") || frag.endsWith("+")) {
+            		oAtom.setCharge(Double.parseDouble(new StringBuilder(frag).reverse().toString()));            		
+            	} else {
+            		oAtom.setCharge(Double.parseDouble(frag));
+                }
             }
 		}