From e708555cb4c4833f00bdf5ef1d8cf817c31dfe35 Mon Sep 17 00:00:00 2001
From: KaiLiCn <likaicnsh@gmail.com>
Date: Sun, 17 Dec 2023 18:25:15 -0500
Subject: [PATCH] Add Cysteine Carbamidomethylation for predicted spectra

---
 .idea/workspace.xml                                      | 8 ++++----
 .../java/PDVGUI/gui/utils/ImportPredictedDialog.java     | 9 +++++++--
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/.idea/workspace.xml b/.idea/workspace.xml
index fd1612a..1df4a37 100644
--- a/.idea/workspace.xml
+++ b/.idea/workspace.xml
@@ -9,8 +9,8 @@
   </component>
   <component name="ChangeListManager">
     <list default="true" id="0b0cca48-ec31-481b-94db-b982afc0e540" name="Default" comment="CLI mode debug.">
-      <change beforePath="$PROJECT_DIR$/pom.xml" beforeDir="false" afterPath="$PROJECT_DIR$/pom.xml" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/src/main/java/PDVGUI/gui/PDVMainClass.java" beforeDir="false" afterPath="$PROJECT_DIR$/src/main/java/PDVGUI/gui/PDVMainClass.java" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/src/main/java/PDVGUI/gui/utils/ImportPredictedDialog.java" beforeDir="false" afterPath="$PROJECT_DIR$/src/main/java/PDVGUI/gui/utils/ImportPredictedDialog.java" afterDir="false" />
     </list>
     <option name="SHOW_DIALOG" value="false" />
     <option name="HIGHLIGHT_CONFLICTS" value="true" />
@@ -350,7 +350,7 @@
       <recent name="E:\Work\PsmViewer\PDV\src\main\java" />
     </key>
   </component>
-  <component name="RunManager" selected="Application.GetPredictedOnline">
+  <component name="RunManager" selected="Application.PDVGUI">
     <configuration default="true" type="Applet">
       <option name="POLICY_FILE" value="$APPLICATION_HOME_DIR$/bin/appletviewer.policy" />
       <method v="2">
@@ -498,7 +498,7 @@
       <workItem from="1701642085572" duration="3000" />
       <workItem from="1702149679374" duration="3318000" />
       <workItem from="1702767788265" duration="1818000" />
-      <workItem from="1702839621322" duration="12307000" />
+      <workItem from="1702839621322" duration="12966000" />
     </task>
     <task id="LOCAL-00001" summary="File path debug.">
       <created>1527228400908</created>
diff --git a/src/main/java/PDVGUI/gui/utils/ImportPredictedDialog.java b/src/main/java/PDVGUI/gui/utils/ImportPredictedDialog.java
index 7b1301a..0fbb154 100644
--- a/src/main/java/PDVGUI/gui/utils/ImportPredictedDialog.java
+++ b/src/main/java/PDVGUI/gui/utils/ImportPredictedDialog.java
@@ -187,12 +187,17 @@ private String getModificationString(String originalMod) {
         String modificationString = "";
 
         if (modelListComboBox.getSelectedIndex() == 0 || modelListComboBox.getSelectedIndex() == 7) {
+            if (originalMod.contains("of C")){
+                if (Math.abs(ptmFactory.getPTM(originalMod).getMass() -57.021464) < 0.01) {
+                    modificationString = "[UNIMOD:4]";
+                }
+            }
             if (originalMod.contains("of M")){
-                if (Math.abs(ptmFactory.getPTM(originalMod).getMass() -15.994915) < 0.001) {
+                if (Math.abs(ptmFactory.getPTM(originalMod).getMass() -15.994915) < 0.01) {
                     modificationString = "[UNIMOD:35]";
                 }
             } if (originalMod.contains("of S") || originalMod.contains("of T") || originalMod.contains("of Y") || originalMod.contains("of STY")) {
-                if (Math.abs(ptmFactory.getPTM(originalMod).getMass() -79.966331) < 0.001) {
+                if (Math.abs(ptmFactory.getPTM(originalMod).getMass() -79.966331) < 0.01) {
                     modificationString = "[UNIMOD:21]";
                 }
             }