diff --git a/README.md b/README.md index 9aadabb9..5a8918e8 100644 --- a/README.md +++ b/README.md @@ -51,6 +51,8 @@ Thanks: - Sheneka Linton - Benjamin Russell ([benrr101](https://github.com/benrr101)) - Amanda Fisher +- Joshua Pouliot +- Peyton Kunselman - ChemAxon for providing MarvinSketch Java API. diff --git a/build.gradle b/build.gradle index 811317dc..017c834f 100644 --- a/build.gradle +++ b/build.gradle @@ -12,7 +12,11 @@ repositories { dirs 'libraries' } maven { - url "https://plugins.gradle.org/m2/" + url https://hub.chemaxon.com/artifactory + credentials { + username = pdk1750@rit.edu + password = AKCp5Zk9Ts3jqYHerpsqUpdsVsTM6dcf4JM5FNApA7zBd8K1objBHRgZRvTTTk2rPeF1PMYH6 + } } mavenCentral() } @@ -44,6 +48,8 @@ dependencies { //compile 'com.sun.media:jai_codec:1.0' //compile 'com.sun.media:jai_core:1.0' //compile '' + compile group: 'com.chemaxon', name: 'marvin-app', version: '17.+' + testCompile group: 'junit', name: 'junit', version: '4.+' } task wrapper(type: Wrapper) { diff --git a/gradle.properties b/gradle.properties new file mode 100644 index 00000000..e269fab7 --- /dev/null +++ b/gradle.properties @@ -0,0 +1,3 @@ +hubUser=pdk1750@rit.edu +hubPassword=AKCp5Zk9Ts3jqYHerpsqUpdsVsTM6dcf4JM5FNApA7zBd8K1objBHRgZRvTTTk2rPeF1PMYH6 +hubRepositoryUrl=https://hub.chemaxon.com/artifactory/libs-release diff --git a/libraries/InstallUninstallOleServer.vbs b/libraries/InstallUninstallOleServer.vbs deleted file mode 100644 index 1fff245a..00000000 --- a/libraries/InstallUninstallOleServer.vbs +++ /dev/null @@ -1,256 +0,0 @@ -' InstallUninstallOleServer.vbs -' VBScript to install/uninstall OLE Server registry settings -' author: Tamas Vertse, Viktor Hamori -' version: 04/20/2010 -' since: 12/14/2009 -Const HKEY_LOCAL_MACHINE = &H80000002 -Const REG_SZ = 1 -Const REG_EXPAND_SZ = 2 -Const REG_BINARY = 3 -Const REG_DWORD = 4 -Const REG_MULTI_SZ = 7 - -Const debugLevel = 0 -Dim ArgObj, dmsg -Dim sCommand, sTargetDirectory, sVersion - -Set shMain = CreateObject("WScript.Shell") -Set fso = CreateObject("Scripting.FileSystemObject") - -' Gets arguments -Set ArgObj = WScript.Arguments -If ArgObj.Count < 3 Then - WScript.Echo "Missing parameter" - WScript.Echo "Please us it as : '/I (Install) or /U (Uninstall)' 'Target path' 'Version'" - WScript.Quit 1 -End If - -sCommand = Trim(ArgObj.Item(0)) -sTargetDirectory = ArgObj.Item(1) -sVersion = ArgObj.Item(2) - -If UCase(sCommand) = "/I" Then - Call Install() -ElseIf UCase(sCommand) = "/U" Then - Call Uninstall() -Else - WScript.Echo "Invalid parameter (" & sCommand & ")" - WScript.Echo "Please us it as : '/I (Install) or /U (Uninstall)'" - WScript.Quit 1 -End If -WScript.Quit 0 - - -'----------------------------------------------------------------------- -' Installation scripts -'----------------------------------------------------------------------- - -' Install -Public Function Install() - - Call AddComponentReference() - Call SetRunningMode() - Wscript.Quit 0 -End Function - -' Uninstall -' Check if the program is running or not! -Public Function Uninstall() - Dim msg - msg = CheckMarvinProcess() - debugMsg msg - If msg <> "" Then - WScript.Echo "ERROR: Cannot uninstall Marvin because " & msg - WScript.Quit 1 - End If - Call DeleteComponentReference() - Call SetRunningMode() - - Wscript.Quit 0 -End Function - -'-------------------------------------------------------------------------- -' 64 bit support -'-------------------------------------------------------------------------- -Public Function Is64Bit() - -Const wbemFlagReturnImmediately = &H10 -Const wbemFlagForwardOnly = &H20 - - -Set objWMIService = GetObject("winmgmts:\\" & "." & "\root\CIMV2") -Set colItems = objWMIService.ExecQuery("SELECT AddressWidth FROM Win32_Processor", "WQL", _ -wbemFlagReturnImmediately + wbemFlagForwardOnly) - -Dim s -For Each objItem In colItems - s = objItem.AddressWidth -Next - -Is64Bit = cBool(CStr(s) = "64") - -End Function -'-------------------------------------------------------------------------- - - - -'--------------------------------------------------------------------------- -' Registry manipulation -'--------------------------------------------------------------------------- -Public Function GetReferencePathRootSubkey() -Dim sKey - If Is64bit() then - sKey = "\Wow6432Node\ChemAxon\MarvinOLE" - Else - sKey = "\ChemAxon\MarvinOLE" - End if - GetReferencePathRootSubkey = sKey -End Function - -Public Function GetHKLMMarvinOLE() -' consider WOW64 bit registry usage - GetHKLMMarvinOLE = "SOFTWARE\ChemAxon\MarvinOLE" 'GetReferencePathRootSubkey() -End Function - -Public Function GetReferenceKey() - GetReferenceKey = Replace(sTargetDirectory, "\", "/") -End Function - -Public Function GetReferencePathRoot() - GetReferencePathRoot = GetHKLMMarvinOLE() & "\ReferenceFolders" -End Function - -Public Function GetReferencePath() -Dim sKey - sKey = "HKEY_LOCAL_MACHINE" & "\" & GetReferencePathRoot() & "\" & GetReferenceKey() - GetReferencePath = sKey -End Function - -Public Function GetRunningModePath() -Dim sKey - sKey = "HKEY_LOCAL_MACHINE" & "\" & GetHKLMMarvinOLE() & "\Settings\RunningMode" - GetRunningModePath = sKey -End Function - -Public Function ReadComponentReferenceCount() -Dim lValue, arrValueNames, arrValueTypes - - lValue = 0 - - sComputer = "." - - Set oReg=GetObject("winmgmts:{impersonationLevel=impersonate}!\\" & _ - sComputer & "\root\default:StdRegProv") - - call oReg.EnumValues( HKEY_LOCAL_MACHINE, GetReferencePathRoot(), arrValueNames, arrValueTypes) - On error resume next - lValue = UBound(arrValueNames) - LBound(arrValueNames) + 1 - - ReadComponentReferenceCount = lValue - -End Function - -Public Function ReadComponentReference() -Dim sValue - - On Error Resume Next - sValue = "" - sValue = CStr(shMain.RegRead(GetReferencePath())) - ReadComponentReference = sValue - -End Function - -Public Sub AddComponentReference() - - On error resume next - if not IsComponentKeyExists() then - on error goto 0 - Call shMain.RegWrite(GetReferencePath(), sVersion, "REG_SZ") - end if - -End Sub - -Public Function DeleteComponentReference() -Dim bRet - - On error resume next - bRet = False - if (IsComponentKeyExists()) then - Call shMain.RegDelete(GetReferencePath()) - bRet = True - end if - DeleteComponentReference = bRet -End Function - - -Public Function IsComponentKeyExists() -Dim sDummy - - IsComponentKeyExists = CBool(ReadComponentReference() <> "") - -End Function - -Public Sub SetRunningMode() -Dim lValue - - lValue = 0 ' Unknown mode - if (CLng(ReadComponentReferenceCount()) > 0) then - lValue = 1 ' JAVA mode - end if - - Call shMain.RegWrite(GetRunningModePath(), lValue, "REG_DWORD") - -End Sub -'----------------------------------------------------------------------- -' Running Process checking -'----------------------------------------------------------------------- - -Public Function CheckMarvinProcess() - Dim objWMIService, objProcess, colProcess - Dim strComputer - - strComputer = "." - - Set objWMIService = GetObject("winmgmts:" & "{impersonationLevel=impersonate}!\\" & strComputer & "\root\cimv2") - Set colProcess = objWMIService.ExecQuery ("Select * from Win32_Process") - CheckMarvinProcess = "" - For Each objProcess in colProcess - If UCase(objProcess.Name) = "MARVIN~1.EXE" Then - CheckMarvinProcess = "MARVIN~1.EXE is still running." - Exit For - End If - If UCase(objProcess.Name) = UCase("marvinOLEServer.exe") Then - CheckMarvinProcess = "marvinOLEServer.exe is still running." - Exit For - End If - If UCase(objProcess.Name) = "MARVINVIEW.EXE" Then - CheckMarvinProcess = "MarvinView.exe is still running." - Exit For - End If - If UCase(objProcess.Name) = "MARVINSKETCH.EXE" Then - CheckMarvinProcess = "MarvinSketch.exe is still running." - Exit For - End If - If UCase(objProcess.Name) = "MARVINSPACE.EXE" Then - CheckMarvinProcess = "MarvinSpace.exe is still running." - Exit For - End If - If UCase(objProcess.Name) = "LICENSEMANAGER.EXE" Then - CheckMarvinProcess = "LicenseManager.exe is still running." - Exit For - End If - If UCase(objProcess.Name) = UCase("instantjchem.exe") Then - CheckMarvinProcess = "instantjchem.exe is still running." - Exit For - End If - Next -End Function - -' Print debug messages -' msg the debug message -Public Function debugMsg(ByVal msg) - If (debugLevel > 0) Then - Wscript.Echo "[DEBUG]: " & msg - End If -End Function - diff --git a/libraries/MarvinBeans-alignment.jar b/libraries/MarvinBeans-alignment.jar deleted file mode 100644 index e855b912..00000000 Binary files a/libraries/MarvinBeans-alignment.jar and /dev/null differ diff --git a/libraries/MarvinBeans-beans.jar b/libraries/MarvinBeans-beans.jar deleted file mode 100644 index 81989673..00000000 Binary files a/libraries/MarvinBeans-beans.jar and /dev/null differ diff --git a/libraries/MarvinBeans-checkers.jar b/libraries/MarvinBeans-checkers.jar deleted file mode 100644 index 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/dev/null @@ -1,16 +0,0 @@ -@ECHO OFF - -REM -REM Install OLE server -REM Without parameter, display error message in popup -REM /c Run in silent/console mode, error messages are printed to the console -REM /w Run in silent/window mode, error messages are printed to the console - -FOR %%I in (%0) do cd /D %%~dpI - -if "%1" == "/w" ( - wscript.exe //NoLogo InstallUninstallOleServer.vbs /I %2 %3 -) else if "%1" == "/c" ( - cscript.exe //NoLogo InstallUninstallOleServer.vbs /I %2 %3 -) - diff --git a/libraries/jacob-1.15.jar b/libraries/jacob-1.15.jar deleted file mode 100644 index 6bdefa37..00000000 Binary files a/libraries/jacob-1.15.jar and /dev/null differ diff --git a/libraries/jacob-native-x64-1.15.jar b/libraries/jacob-native-x64-1.15.jar deleted file mode 100644 index b0bb6c3a..00000000 Binary files a/libraries/jacob-native-x64-1.15.jar and /dev/null differ diff --git a/libraries/jacob-native-x86-1.15.jar b/libraries/jacob-native-x86-1.15.jar deleted file mode 100644 index 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if "%1" == "/c" ( - cscript.exe //NoLogo InstallUninstallOleServer.vbs /U %2 %3 -) - diff --git a/libraries/wsdl4j-1.6.2.jar b/libraries/wsdl4j-1.6.2.jar deleted file mode 100644 index b9ffc36b..00000000 Binary files a/libraries/wsdl4j-1.6.2.jar and /dev/null differ diff --git a/libraries/xz-1.0.jar b/libraries/xz-1.0.jar deleted file mode 100644 index a848f16d..00000000 Binary files a/libraries/xz-1.0.jar and /dev/null differ diff --git a/src/main/java/MainWindows/MarvinTab.java b/src/main/java/MainWindows/MarvinTab.java index b09d1708..3e6a95bd 100644 --- a/src/main/java/MainWindows/MarvinTab.java +++ b/src/main/java/MainWindows/MarvinTab.java @@ -79,7 +79,7 @@ public JPanel createMainPanel() { private MSketchPane createSketchPane() { MSketchPane pane = new MSketchPane(createUserSettings()); - pane.setPreferredSize(new Dimension(900, 500)); + pane.setPreferredSize(new Dimension(1920, 1080)); return pane; } diff --git a/src/main/java/MassSpec/AminoAcidTranslator.java b/src/main/java/MassSpec/AminoAcidTranslator.java index eb3b6c9f..a3eb69a0 100644 --- a/src/main/java/MassSpec/AminoAcidTranslator.java +++ b/src/main/java/MassSpec/AminoAcidTranslator.java @@ -29,6 +29,13 @@ static public String translate(String inpt) { outpt += "Alanyl-"; } break; + case 'P': + if (i == inpt.length() - 1) { + outpt += "Proline"; + } else { + outpt += "Prolyl-"; + } + break; case 'G': if (i == inpt.length() - 1) { outpt += "Glycine"; diff --git a/src/main/java/MassSpec/Ion.java b/src/main/java/MassSpec/Ion.java index 62886615..1e784f2a 100644 --- a/src/main/java/MassSpec/Ion.java +++ b/src/main/java/MassSpec/Ion.java @@ -34,6 +34,7 @@ import java.awt.*; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.awt.event.MouseListener; import java.util.ArrayList; import java.io.*; @@ -49,6 +50,7 @@ public class Ion extends ArrayList { private int xCoordinate = 0; private String sequence; Color color = Color.BLACK; + private String reverseSequence; /** * Adds the MassSpec.SpecAminoAcid to the end of the MassSpec.Ion. MassSpec.Ion adds its mass to @@ -89,9 +91,9 @@ public void displaySequence() { proteinSet.append( "Instructions: " + "\n" + - "\n To display the structure properly, go to Edit> Transformation > Flip> Flip Horizontally.\n \n" + + "\n To display the structure properly, right click and select Ungroup.\n \n" + "Note: The longer the sequence the more likely it is to display diagonally,"+ - "\n simply select all the atoms in the structure and move it where you would like it to be." + "\n Select everything. Click on Structure and select Clean 2D. \n" ); panel.add(proteinSet, BorderLayout.CENTER); @@ -101,7 +103,7 @@ public void displaySequence() { marvinButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - MarvinTab.getSketchPane().setMol(AminoAcidTranslator.translate(sequence)); + MarvinTab.getSketchPane().setMol(sequence); JBioFrameworkMain.getTabs().setSelectedIndex(4); frame.dispose(); } @@ -136,13 +138,20 @@ public void setMass(double mass) { public void setSequence(String sequence) { this.sequence = sequence; + + this.reverseSequence = new StringBuilder(sequence).reverse().toString(); } - // Gets the Sequence to be used in the Translator + // Gets the sequence to be used in the Translator public String getSequence() { return sequence; } + // Gets the reverseSequence to be used in the Translator + public String getReverseSequence() { + + return reverseSequence; + } /** * Used only by MassSpec.Spectrometer in RunAnalysis to set the charge of the ion to diff --git a/src/main/java/Utilities/ChargeCalculator.java b/src/main/java/Utilities/ChargeCalculator.java new file mode 100644 index 00000000..4cf072a1 --- /dev/null +++ b/src/main/java/Utilities/ChargeCalculator.java @@ -0,0 +1,99 @@ +package main.java.Utilities; + +import main.java.Electro2D.Electro2D; + +import javax.swing.JFrame; +import javax.swing.JTabbedPane; + +import java.io.*; +import java.io.BufferedReader; +import java.io.File; +import java.io.InputStreamReader; +import java.io.IOException; +import java.util.Hashtable; +import java.util.StringTokenizer; +import java.util.Vector; +import java.util.Scanner; +import javafx.application.Application; + +//Author Peyton Kunselman + +public class ChargeCalculator { + + + public static void main(String[] args) { + Scanner in = new Scanner(System.in); + System.out.print("pH = "); + double pH = in.nextDouble(); + System.out.print("sequence = "); + String sequence = in.next(); + + + double lowpH = 0, highpH = 14; + + int pLength = sequence.length(); + + double charge = 0; + + // n means that the amino acid is neutral + char type = 'n'; + + double pK = 0; + + + + + for (int a = 0; a < pLength; a++) { + switch (sequence.charAt(a)) { + case 'R': + type = 'b'; + pK = 12; + break; + case 'D': + type = 'a'; + pK = 4.05; + break; + case 'C': + type = 'a'; + pK = 9; + break; + case 'E': + type = 'a'; + pK = 4.75; + break;//pK = 4.45; break; + case 'H': + type = 'b'; + pK = 5.98; + break; + case 'K': + type = 'b'; + pK = 10; + break; + case 'Y': + type = 'a'; + pK = 10; + break; + default: + type = 'n'; + pK = 0; + break; + } + // calculates the charge for acids + if (type == 'a') { + charge += -1 / + (1 + Math.pow(10, pK - pH)); + } + // calculates the charge for the bases + if (type == 'b') { + charge += 1 / (1 + Math.pow(10, pH - pK)); + } + } + // this calculates the charge at the C terminus and adds it to the total charge + charge += -1 / + (1 + Math.pow(10, 3.2 - pH)); + + // this calculates the charge at the N terminus and adds it to the total charge + charge += 1 / (1 + Math.pow(10, pH -/*9.53*/8.2)); + System.out.println("Final charge: " + charge); + } +} \ No newline at end of file