create branched fragments for CUSTOM

juliomarcopineda · Apr 17, 2018 · 2118496 · 2118496
1 parent ac7d469
commit 2118496
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Showing 2 changed files with 96 additions and 6 deletions.
diff --git a/peptideSerumStability/src/com/github/juliomarcopineda/FragmentAnalyzer.java b/peptideSerumStability/src/com/github/juliomarcopineda/FragmentAnalyzer.java
@@ -142,6 +142,19 @@ private void findBranchedAndCyclicFragments(Map<String, Double> fragmentWeights)
 
 			// Append the linkers to the fragment (DFBP or S or SS) to form branched fragments
 			switch (type) {
+				case CUSTOM:
+					// Skip if the fragment contains CUSTOM
+					if (fragmentWith1.contains(peptideSequence.length())) {
+						continue;
+					}
+
+					// Only append CUSTOM if the connection is not in the beginning
+					if (fragmentWith1.get(0) != connection1) {
+						sb1.append("#%");
+						fragmentWeights.put(sb1.toString(), calculateBranchedFragmentWeight(sb1.toString()));
+					}
+
+					break;
 				case DFBP:
 					// Skip if the fragment contains DFBP
 					if (fragmentWith1.contains(peptideSequence.length())) {
@@ -174,8 +187,6 @@ private void findBranchedAndCyclicFragments(Map<String, Double> fragmentWeights)
 					break;
 				case LINEAR:
 					break;
-				default:
-					break;
 			}
 
 			// Start building branched fragments using the linear fragment with the second connection
@@ -192,6 +203,15 @@ private void findBranchedAndCyclicFragments(Map<String, Double> fragmentWeights)
 				sb2.append(getPeptideStringRepresentation(fragmentWith1, type));
 				if (isValidBranchedFragment(afterConnection1, beforeConnection2)) {
 					switch (type) {
+						case CUSTOM:
+							// Skip if the fragment contains CUSTOM
+							if (fragmentWith2.contains(peptideSequence.length())) {
+								continue;
+							}
+
+							sb2.append("#%#" + getPeptideStringRepresentation(fragmentWith2, type));
+							fragmentWeights.put(sb2.toString(), calculateBranchedFragmentWeight(sb2.toString()));
+							break;
 						case DFBP:
 							// Skip if the fragment contains DFBP
 							if (fragmentWith2.contains(peptideSequence.length())) {
@@ -214,7 +234,7 @@ private void findBranchedAndCyclicFragments(Map<String, Double> fragmentWeights)
 							sb2.append("#" + getPeptideStringRepresentation(fragmentWith2, type));
 							fragmentWeights.put(sb2.toString(), calculateBranchedFragmentWeight(sb2.toString()));
 							break;
-						default:
+						case LINEAR:
 							break;
 					}
 				}
@@ -230,6 +250,19 @@ private void findBranchedAndCyclicFragments(Map<String, Double> fragmentWeights)
 
 			// Append the linkers (DFBP or S or SS) to form possible branched fragments
 			switch (type) {
+				case CUSTOM:
+					// Skip if linear fragment contains CUSTOM
+					if (fragmentWith2.contains(peptideSequence.length())) {
+						continue;
+					}
+
+					// Only append CUSTOM if connection is not in the end of the fragment
+					if (fragmentWith2.get(fragmentWith2.size() - 1) != connection2) {
+						sb1.append("#%");
+						fragmentWeights.put(sb1.toString(), calculateBranchedFragmentWeight(sb1.toString()));
+					}
+
+					break;
 				case DFBP:
 					// Skip if linear fragment contains DFBP
 					if (fragmentWith2.contains(peptideSequence.length())) {
@@ -258,7 +291,9 @@ private void findBranchedAndCyclicFragments(Map<String, Double> fragmentWeights)
 					}
 
 					break;
-				default:
+				case AMIDE:
+					break;
+				case LINEAR:
 					break;
 			}
 
@@ -276,6 +311,16 @@ private void findBranchedAndCyclicFragments(Map<String, Double> fragmentWeights)
 				sb2.append(getPeptideStringRepresentation(fragmentWith1, type));
 				if (isValidBranchedFragment(afterConnection1, beforeConnection2)) {
 					switch (type) {
+						case CUSTOM:
+							// Skip if fragment contains CUSTOM
+							if (fragmentWith1.contains(peptideSequence.length())) {
+								continue;
+							}
+
+							sb2.append("#%#" + getPeptideStringRepresentation(fragmentWith1, type));
+
+							fragmentWeights.put(sb2.toString(), calculateBranchedFragmentWeight(sb2.toString()));
+							break;
 						case DFBP:
 							// Skip if fragment contains DFBP
 							if (fragmentWith1.contains(peptideSequence.length())) {
@@ -301,8 +346,6 @@ private void findBranchedAndCyclicFragments(Map<String, Double> fragmentWeights)
 							break;
 						case LINEAR:
 							break;
-						default:
-							break;
 					}
 				}
 			}

diff --git a/peptideSerumStability/src/com/github/juliomarcopineda/tests/BranchedFragmentTest.java b/peptideSerumStability/src/com/github/juliomarcopineda/tests/BranchedFragmentTest.java
@@ -0,0 +1,47 @@
+package com.github.juliomarcopineda.tests;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
+import com.github.juliomarcopineda.FragmentAnalyzer;
+import com.github.juliomarcopineda.PeptideSerumStability;
+import com.github.juliomarcopineda.peptide.Peptide;
+import com.github.juliomarcopineda.peptide.PeptideType;
+
+/**
+ * This class prints out all the branched fragments for a peptide to check if the branched fragment builder 
+ * is working.
+ * 
+ * @author Julio Pineda
+ *
+ */
+public class BranchedFragmentTest {
+
+	public static void main(String[] args) {
+		Peptide peptide = new Peptide();
+
+		String peptideSequence = "CGYEQDPWGVRYWYGCKKKKB";
+		PeptideType type = PeptideType.CUSTOM;
+		double customWeight = 383.32;
+		List<Integer> connections = Arrays.asList(4, 19);
+		Map<Integer, List<Integer>> graph = PeptideSerumStability.createGraphStructure(peptideSequence, connections, type);
+
+		peptide.setSequence(peptideSequence);
+		peptide.setType(type);
+		peptide.setConnections(connections);
+		peptide.setCustomWeight(customWeight);
+		peptide.setGraph(graph);
+
+		FragmentAnalyzer analyzer = new FragmentAnalyzer(peptide);
+		analyzer.findAllFragments()
+			.measureAllFragmentWeights();
+
+		analyzer.getFragmentWeights()
+			.keySet()
+			.stream()
+			.filter(s -> s.contains("#"))
+			.forEach(System.out::println);
+	}
+
+}