Add support for transglutaminase (tg) cross-linker.

proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/GetLinkerFactory.java

@@ -20,6 +20,7 @@
 import org.yeastrc.xlink.linkable_positions.linkers.DFDNB;
 import org.yeastrc.xlink.linkable_positions.linkers.ILinker;
 import org.yeastrc.xlink.linkable_positions.linkers.SulfoSMCC;
+import org.yeastrc.xlink.linkable_positions.linkers.Transglutaminase;
 
 public class GetLinkerFactory {
 
@@ -35,7 +36,10 @@ public class GetLinkerFactory {
 	public static final String BUILT_IN_LINKER_EDC = "edc";
 	public static final String BUILT_IN_LINKER_DFDNB = "dfdnb";
 	public static final String BUILT_IN_LINKER_SULFO_SMCC = "sulfo-smcc";
-	public static final String BUILD_INT_LINKER_DSSO = "dsso";
+	public static final String BUILD_IN_LINKER_DSSO = "dsso";
+
+	public static final String BUILD_IN_LINKER_TG = "tg";
+	public static final String BUILD_IN_LINKER_transglutaminase = "transglutaminase";
 
 	public static final String BUILT_IN_LINKER_BS3_STY = "bs3.sty";
 	public static final String BUILT_IN_LINKER_DSS_STY = "dss.sty";
@@ -53,6 +57,7 @@ public class GetLinkerFactory {
 	private static ILinker LINKER_DFDNB = new DFDNB();
 	private static ILinker LINKER_SULFO_SMCC = new SulfoSMCC();
 	private static ILinker LINKER_DSSO = new DSSO();
+	private static ILinker LINKER_TG = new Transglutaminase();
 
 	private static ILinker LINKER_DSS_STY = new DSS_STY();
 	private static ILinker LINKER_BS3_STY = new BS3_STY();
@@ -70,7 +75,10 @@ public class GetLinkerFactory {
 		linkers.put( BUILT_IN_LINKER_EDC, LINKER_EDC );
 		linkers.put( BUILT_IN_LINKER_DFDNB, LINKER_DFDNB );
 		linkers.put( BUILT_IN_LINKER_SULFO_SMCC, LINKER_SULFO_SMCC);
-		linkers.put( BUILD_INT_LINKER_DSSO, LINKER_DSSO);
+		linkers.put( BUILD_IN_LINKER_DSSO, LINKER_DSSO);
+
+		linkers.put( BUILD_IN_LINKER_TG, LINKER_TG );
+		linkers.put( BUILD_IN_LINKER_transglutaminase, LINKER_TG );
 
 		linkers.put( BUILT_IN_LINKER_BS3_STY, LINKER_BS3_STY );
 		linkers.put( BUILT_IN_LINKER_DSS_STY, LINKER_DSS_STY );

proxl_web_app/src_shared_code/org/yeastrc/xlink/linkable_positions/linkers/Transglutaminase.java

@@ -0,0 +1,61 @@
+package org.yeastrc.xlink.linkable_positions.linkers;
+
+import java.util.Collection;
+import java.util.HashSet;
+
+import org.yeastrc.xlink.utils.ProteinSequenceUtils;
+
+public class Transglutaminase implements ILinker {
+
+	@Override
+	public Collection<Integer> getLinkablePositions(String proteinSequence) throws Exception {
+
+		Collection<Integer> linkablePositions = ProteinSequenceUtils.getPositionsOfResidueForProteinSequence( proteinSequence, "K" );
+
+		linkablePositions.addAll( ProteinSequenceUtils.getPositionsOfResidueForProteinSequence( proteinSequence, "Q" ) );
+
+		return linkablePositions;		
+	}
+
+	@Override
+	public Collection<Integer> getLinkablePositions( String querySequence, String subjectSequence, int subjectPosition ) throws Exception {
+
+		String subjectResidue = subjectSequence.substring( subjectPosition - 1, subjectPosition );
+		Collection<Integer> linkablePositions = new HashSet<Integer>();
+
+		if( subjectResidue.equals( "K" ) ) {
+
+			// lysines interact with E, D, and C-terminus
+			linkablePositions.addAll( ProteinSequenceUtils.getPositionsOfResidueForProteinSequence( querySequence, "Q" ) );
+
+		} else if( subjectResidue.equals( "Q" ) ) {
+
+			// E and D interact with K and the two N-terminal residues
+			linkablePositions.addAll( ProteinSequenceUtils.getPositionsOfResidueForProteinSequence( querySequence, "K" ) );
+
+		}
+
+		return linkablePositions;
+	}
+
+
+	@Override
+	public double getLinkerLength() {
+		return 0;
+	}
+
+	@Override
+	public Collection<String> getCrosslinkFormulas() {
+
+		Collection<String> formulas = new HashSet<>();
+		formulas.add( "-NH3" );
+
+		return formulas;
+	}
+
+	@Override
+	public String getCrosslinkFormula(double mass) throws Exception {
+		return "-NH3";
+	}
+
+}