distance have to be looked up by element name, not atom name

andreasprlic · andreasprlic · commit 27988760a32f · 2016-06-10T16:08:49.000-07:00
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureUtil.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureUtil.java
@@ -250,7 +250,7 @@ public static Atom[] findLinkage(final Group group1, final Group group2,
 
 		if ( a1.getElement().isMetal() || a2.getElement().isMetal()){
 
-			MetalBondDistance defined = getMetalDistanceCutoff(a1.getName(),a2.getName());
+			MetalBondDistance defined = getMetalDistanceCutoff(a1.getElement().name(),a2.getElement().name());
 
 			if ( defined != null) {
 
diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java
@@ -88,15 +88,23 @@ public static String[][] setUpShortTest() {
 				{"3H8L", "AA0513"}, // CYS-S3H-CYS
 				{"1CAD", null}, // FE and 4 Cys, cross-link4
 
-				// Terbium
+				// Terbium cases
 				{"1NCZ", null},
 				{"3LTQ",null}, // has metalc,
-
 				{"4ESQ",null},
 				{"1TJB",null},
 				{"2V15",null},
 				{"2K61",null},
 
+				// iron bond to CYS
+				//{"1G20","AA0300"},
+
+				{"3CM6",null},
+				{"1W6Z",null},
+				//{"1Z2M",null}, distances are too big for the new cutoffs
+				{"2O6N",null},
+				{"1GA7",null},
+
 		};
 		return strucs;
 	}
