Fixed a null pointer exception from getAtomFromRecord

abradle · abradle · commit 8789bb5573b6 · 2016-08-15T09:52:54.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
@@ -454,7 +454,10 @@ private Map<Integer,Atom> getAtomFromRecord(String name, String altLoc, String r
 				if (g==null)
 					throw new StructureException("Could not find altLoc code "+altLoc+" in group "+resSeq+iCode+" of chain "+ chainID);
 			}
-			outMap.put(i,g.getAtom(name));
+			Atom a = g.getAtom(name);
+			if (a!=null){
+				outMap.put(i,a);
+			}
 		}
 		return outMap;
 	}

Original file line number	Diff line number	Diff line change
`@@ -454,7 +454,10 @@ private Map<Integer,Atom> getAtomFromRecord(String name, String altLoc, String r`
`454`	`454`	`if (g==null)`
`455`	`455`	`throw new StructureException("Could not find altLoc code "+altLoc+" in group "+resSeq+iCode+" of chain "+ chainID);`
`456`	`456`	`}`
`457`		`- outMap.put(i,g.getAtom(name));`
	`457`	`+ Atom a = g.getAtom(name);`
	`458`	`+ if (a!=null){`
	`459`	`+ outMap.put(i,a);`
	`460`	`+ }`
`458`	`461`	`}`
`459`	`462`	`return outMap;`
`460`	`463`	`}`