update for 2VH3 TY2

andreasprlic · andreasprlic · commit 58c67432b9c0 · 2016-06-10T15:56:50.000-07:00
diff --git a/biojava-modfinder/src/main/resources/org/biojava/nbio/protmod/ptm_list.xml b/biojava-modfinder/src/main/resources/org/biojava/nbio/protmod/ptm_list.xml
@@ -4550,30 +4550,37 @@
 			</Component>
 			<Bond>
 				<Atom component="1">SG</Atom>
+				<!--<Atom component="8">*</Atom>-->
 				<Atom component="8">FE1,FE2,FE3,FE4,FE5,FE6,FE7,FE8</Atom>
 			</Bond>
 			<Bond>
 				<Atom component="2">SG</Atom>
+				<!--<Atom component="8">*</Atom>-->
 				<Atom component="8">FE1,FE2,FE3,FE4,FE5,FE6,FE7,FE8</Atom>
 			</Bond>
 			<Bond>
 				<Atom component="3">SG</Atom>
+				<!--<Atom component="8">*</Atom>-->
 				<Atom component="8">FE1,FE2,FE3,FE4,FE5,FE6,FE7,FE8</Atom>
 			</Bond>
 			<Bond>
 				<Atom component="4">SG</Atom>
+				<!--<Atom component="8">*</Atom>-->
 				<Atom component="8">FE1,FE2,FE3,FE4,FE5,FE6,FE7,FE8</Atom>
 			</Bond>
 			<Bond>
 				<Atom component="5">SG</Atom>
+				<!--<Atom component="8">*</Atom>-->
 				<Atom component="8">FE1,FE2,FE3,FE4,FE5,FE6,FE7,FE8</Atom>
 			</Bond>
 			<Bond>
 				<Atom component="6">SG</Atom>
+				<!--<Atom component="8">*</Atom>-->
 				<Atom component="8">FE1,FE2,FE3,FE4,FE5,FE6,FE7,FE8</Atom>
 			</Bond>
 			<Bond>
 				<Atom component="7">OG</Atom>
+				<!--<Atom component="8">*</Atom>-->
 				<Atom component="8">FE1,FE2,FE3,FE4,FE5,FE6,FE7,FE8</Atom>
 			</Bond>
 		</Condition>
@@ -7035,7 +7042,7 @@
 				<Id source="PDBCC">TY2</Id>
 			</Component>
 		   <Bond>
-		    	<Atom component="1">CE2,CE1</Atom>
+		    	<Atom component="1">CE2</Atom>
 			    <Atom component="2">NE2</Atom>
 		    </Bond>
 		</Condition>
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
@@ -27,9 +27,7 @@
 import junit.framework.TestCase;
 import org.biojava.nbio.protmod.ProteinModification;
 import org.biojava.nbio.protmod.ProteinModificationRegistry;
-import org.biojava.nbio.structure.ResidueNumber;
-import org.biojava.nbio.structure.Structure;
-import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -109,6 +107,9 @@ public static String[][] setUpShortTest() {
 				{"1ACD","AA0262"}, // test for CSD
 				{"1AA6","AA0022"} , // test for SEC
 
+				{"1WCT","AA0179"},
+				{"2VH3","AA0459"},
+
 		};
 		return strucs;
 	}
@@ -341,16 +342,35 @@ private void parserTest(String pdbId, String residId) throws IOException, Struct
 
 	private void parserTest(String pdbId, Set<ProteinModification> mods) throws IOException, StructureException {
 		Structure struc = TmpAtomCache.cache.getStructure(pdbId);
+/*
+ //needed for testing 1G20
+		if ( pdbId.equalsIgnoreCase("1G20")) {
+			Structure n = new StructureImpl();
+
+			n.addChain(struc.getPolyChainByPDB("A"));
+			n.addChain(struc.getPolyChainByPDB("B"));
+			for (Chain c : struc.getNonPolyChainsByPDB("A"))
+				n.addChain(c);
+
+			for (Chain c : struc.getNonPolyChainsByPDB("B"))
+				n.addChain(c);
+
+
+			struc = n;
+		}
+		*/
 
 		ProteinModificationIdentifier parser = new ProteinModificationIdentifier();
 		boolean recordUnidentifiable = false;
 		parser.setRecordUnidentifiableCompounds(recordUnidentifiable);
-//		parser.setbondLengthTolerance(2);
+		//parser.setbondLengthTolerance(2);
 
 		assertFalse(mods.isEmpty());
 
 		parser.identify(struc, mods);
 
+		//System.out.println(parser.getUnidentifiableModifiedResidues());
+
 		if ( parser.getIdentifiedModifiedCompound().isEmpty() ){
 			String msg = "Did not identify any modified compounds for " + pdbId;
 			logger.warn(msg);
