Merge pull request #30 from michaelmarty/v3

V3

.gitignore

@@ -45,7 +45,6 @@ Scripts/MTM/test_UniDec.py
 build.bat
 metaunidec/test_MUD.py
 unidec_bin/CDCReaderOld.exe
-unidec_modules/NanodiscBuilder.py
 unidec_modules/fft_test.py
 unidec_src/UniDec/compilewin.bat
 unidec_src/UniDec/UniDec.pdb
@@ -58,4 +57,11 @@ unidec_modules/Mass_Defect_Extracts.txt
 unidec_modules/Mass_Defect_Grid.txt
 unidec_modules/Total_1D_Mass_Defects.txt
 unidec_modules/Total_2D_Mass_Defects.txt
-unidec_modules/Mass_Defect_Extracts_xvals.txt
+unidec_modules/Mass_Defect_Extracts_xvals.txt
+unidec_modules/0_1D_Mass_Defects.txt
+unidec_modules/0_2D_Mass_Defects.txt
+unidec_modules/1_1D_Mass_Defects.txt
+unidec_modules/1_2D_Mass_Defects.txt
+unidec_modules/isolated_packages/spreadsheet.py
+unidec_src/UniDec/UniDec.VC.VC.opendb
+

GUniDec.py

@@ -1571,6 +1571,31 @@ def on_label_max_charge_states(self, e):
                                                     vlines=False, color=p.color)
         self.view.plot4.repaint()
 
+    def on_label_avg_charge_states(self, e):
+        charges = np.arange(self.eng.config.startz, self.eng.config.endz + 1)
+        if self.eng.config.adductmass > 0:
+            sign = "+"
+        else:
+            sign = "-"
+
+        self.view.plot4.textremove()
+        for i in range(0, self.eng.pks.plen):
+            p = self.eng.pks.peaks[i]
+            if p.ignore == 0:
+                if (not ud.isempty(p.mztab)) and (not ud.isempty(p.mztab2)):
+                    mztab = np.array(p.mztab)
+                    avgcharge = ud.weighted_avg(charges, mztab[:, 1])
+                    p.avgcharge = avgcharge
+                    pos = (p.mass + self.eng.config.adductmass * avgcharge) / avgcharge
+
+                    print("Mass:", p.mass, "Average Charge:", avgcharge)
+                    mztab = ud.datachop(mztab, np.amin(self.eng.data.data2[:, 0]), np.amax(self.eng.data.data2[:, 0]))
+                    self.view.plot4.plotadd(mztab[:, 0], mztab[:, 1], p.color)
+                    self.view.plot4.addtext(sign + str(np.round(avgcharge, 2)), pos, np.amax(mztab[:, 1]) + 0.07,
+                                            vlines=True, color=p.color)
+        self.view.plot4.repaint()
+        self.view.peakpanel.add_data(self.eng.pks, show="avgcharge")
+
     def on_plot_isotope_distribution(self, e=0):
         for i in range(0, self.eng.pks.plen):
             p = self.eng.pks.peaks[i]

Launcher.py

@@ -1,6 +1,6 @@
 import warnings
-warnings.simplefilter(action="ignore",category=FutureWarning)
 
+warnings.simplefilter(action="ignore", category=FutureWarning)
 
 import wx
 from unidec_modules.unidec_presbase import UniDecPres
@@ -13,6 +13,7 @@
 from metaunidec.meta_import_wizard.meta_import_wizard import ImportWizard as HDF5Wizard
 from metaunidec.ultrameta import DataCollector as UMDC
 import wx.py as py
+import sys
 
 
 class UniDecLauncher(UniDecPres):
@@ -34,6 +35,12 @@ def __init__(self, *args, **kwargs):
 
     def init(self, *args, **kwargs):
         self.view = Lview(self)
+        self.view.Bind(wx.EVT_CLOSE, self.on_close)
+
+    def on_close(self, e=None):
+        self.quit_application()
+        self.view.Destroy()
+        sys.exit()
 
 
 class Lview(wx.Frame):
@@ -51,13 +58,13 @@ def __init__(self, parent):
         button6 = wx.Button(panel, -1, "HDF5 Import Wizard\n\nImport Data into HDF5 for MetaUniDec")
         button7 = wx.Button(panel, -1, "UltraMeta Data Collector\n\nVisualize Multiple HDF5 Data Sets\nFit Trends")
 
-        sizer.Add(button1, (0,0),flag=wx.EXPAND)
-        sizer.Add(button2, (1,0),flag=wx.EXPAND)
-        sizer.Add(button3, (2,0),flag=wx.EXPAND)
-        sizer.Add(button4, (0,1),flag=wx.EXPAND)
+        sizer.Add(button1, (0, 0), flag=wx.EXPAND)
+        sizer.Add(button2, (1, 0), flag=wx.EXPAND)
+        sizer.Add(button3, (2, 0), flag=wx.EXPAND)
+        sizer.Add(button4, (0, 1), flag=wx.EXPAND)
         sizer.Add(button6, (2, 1), flag=wx.EXPAND)
         sizer.Add(button7, (1, 1), flag=wx.EXPAND)
-        sizer.Add(button5, (3,0),span=(1,2),flag=wx.EXPAND)
+        sizer.Add(button5, (3, 0), span=(1, 2), flag=wx.EXPAND)
 
         self.Bind(wx.EVT_BUTTON, self.button1, button1)
         self.Bind(wx.EVT_BUTTON, self.button2, button2)
@@ -78,7 +85,7 @@ def button1(self, e=None):
         app = GUniDec.UniDecApp()
         app.start()
 
-    def button2(self,e=None):
+    def button2(self, e=None):
         print("Launching Data Collector")
         app = wx.App(False)
         frame = datacollector.DataCollector(None, "Collect Data")
@@ -91,12 +98,12 @@ def button3(self, e=None):
         frame.Show()
         app.MainLoop()
 
-    def button4(self,e=None):
+    def button4(self, e=None):
         print("Launching MetaUniDec")
         app = mudpres.UniDecApp()
         app.start()
 
-    def button5(self,e=None):
+    def button5(self, e=None):
         print("Launching Scripting Shell")
         app = Shell()
         app.start()
@@ -108,7 +115,7 @@ def button6(self, e=None):
         frame.Show()
         app.MainLoop()
 
-    def button7(self,e=None):
+    def button7(self, e=None):
         print("Launching UltraMeta Data Collector")
         app = wx.App(False)
         frame = UMDC(None, "UltraMeta Data Collector")
@@ -123,12 +130,13 @@ def __init__(self, *args, **kwargs):
 
         self.shellwindow = py.shell.ShellFrame(self.shell, title="UniDecShell").Show()
 
-        #self.shell.Execute('app=UniDecApp()')
+        # self.shell.Execute('app=UniDecApp()')
         # self.shell.Execute('app.start()')
         # self.shellwindow.Center()
         # self.shell.setFocus()
         self.__wx_app.MainLoop()
 
+
 if __name__ == '__main__':
     # app2 = Shell()
     multiprocessing.freeze_support()

datacollector.py

@@ -121,7 +121,7 @@ def populate(self, listctrldata, colors=None):
             self.SetItemData(index, i)
             if colors is not None:
                 color = wx.Colour(int(round(colors[i][0] * 255)), int(round(colors[i][1] * 255)),
-                                  int(round(colors[i][2] * 255)) , alpha=255)
+                                  int(round(colors[i][2] * 255)), alpha=255)
                 self.SetItemBackgroundColour(index, col=color)
 
     def clear_list(self):
@@ -154,7 +154,7 @@ def __init__(self, parent, list_type="X", size=(200, 400)):
         wx.Panel.__init__(self, parent, -1, style=wx.WANTS_CHARS)
         id_value = wx.NewId()
         self.selection = []
-        self.list_type=list_type
+        self.list_type = list_type
         sizer = wx.BoxSizer(wx.VERTICAL)
         if list_type == "X":
             self.list = XValueListCtrl(self, id_value, size=size, style=wx.LC_REPORT | wx.BORDER_NONE)
@@ -388,7 +388,8 @@ def __init__(self, parent, title, config=None, pks=None, *args, **kwargs):
 
         self.runsizer = wx.BoxSizer(wx.HORIZONTAL)
         self.runsizer.Add(wx.StaticText(self.panel, label=" What to extract: "), 0, wx.ALIGN_CENTER_VERTICAL)
-        self.ctldata = wx.ComboBox(self.panel, value="Raw Data", choices=list(datachoices.values()), style=wx.CB_READONLY)
+        self.ctldata = wx.ComboBox(self.panel, value="Raw Data", choices=list(datachoices.values()),
+                                   style=wx.CB_READONLY)
         self.runsizer.Add(self.ctldata, 0, wx.EXPAND)
 
         self.runsizer.Add(wx.StaticText(self.panel, label=" Range:"), 0, wx.ALIGN_CENTER_VERTICAL)
@@ -406,7 +407,8 @@ def __init__(self, parent, title, config=None, pks=None, *args, **kwargs):
         self.ctlnorm2 = wx.CheckBox(self.panel, label="Normalize Extraction")
         self.runsizer.Add(self.ctlnorm2, 0, wx.EXPAND)
         self.runsizer.Add(wx.StaticText(self.panel, label=" How to extract: "), 0, wx.ALIGN_CENTER_VERTICAL)
-        self.ctlextract = wx.ComboBox(self.panel, value="Height", choices=list(extractchoices.values()), style=wx.CB_READONLY)
+        self.ctlextract = wx.ComboBox(self.panel, value="Height", choices=list(extractchoices.values()),
+                                      style=wx.CB_READONLY)
         self.runsizer.Add(self.ctlextract, 0, wx.EXPAND)
         self.runsizer.Add(wx.StaticText(self.panel, label=" Window:"), 0, wx.ALIGN_CENTER_VERTICAL)
         self.ctlwindow = wx.TextCtrl(self.panel, value="", size=(50, 20))
@@ -743,7 +745,8 @@ def update_get(self, e):
     def update_set(self, e):
         self.ctlprotmodel.SetValue(
             next((label for label, flag in list(modelchoices.items()) if flag == self.protflag), "test"))
-        self.ctlligmodel.SetValue(next((label for label, flag in list(modelchoices.items()) if flag == self.ligflag), "test"))
+        self.ctlligmodel.SetValue(
+            next((label for label, flag in list(modelchoices.items()) if flag == self.ligflag), "test"))
         self.dirinput.SetValue(self.directory)
         self.xpanel.list.populate(self.xvals)
         self.ypanel.list.populate(self.yvals)
@@ -1020,12 +1023,12 @@ def on_kd_fit(self, e):
             maxsites = int(self.maxsites)
         except (ValueError, TypeError):
             maxsites = 0
-        model = UniFit.KDmodel(self.numprot, self.numlig, np.transpose(self.extract),
-                               self.yvals[:, 2].astype(np.float64),
+        model = UniFit.KDmodel(np.transpose(self.extract), self.yvals[:, 2].astype(np.float64),
                                self.yvals[:, 1].astype(np.float64), nodelist, os.path.join(self.directory, "fits"),
-                               removeoutliers=outlierflag, plot1=self.plot2.subplot1, plot2=self.plot3.axes,
-                               plot3=self.plot3h, bootnum=self.bootstrap, prot=self.protflag, lig=self.ligflag,
-                               maxsites=maxsites)
+                               numtotprot=self.numprot, numtotlig=self.numlig, removeoutliers=outlierflag,
+                               plot1=self.plot2.subplot1,
+                               plot2=self.plot3.axes, plot3=self.plot3h, bootnum=self.bootstrap, maxsites=maxsites,
+                               prot=self.protflag, lig=self.ligflag)
         try:
             if self.bootstrap > 0:
                 np.savetxt(os.path.join(self.directory, "fits_boots.txt"), model.randfit)
@@ -1181,7 +1184,7 @@ def on_export(self, e):
             print("Grid is empty")
 
     def on_msms_norm(self, e):
-        dlg = wx.FileDialog(self, "Choose MS1 data file in x y list format", '', "", "*.*",)
+        dlg = wx.FileDialog(self, "Choose MS1 data file in x y list format", '', "", "*.*", )
         if dlg.ShowModal() == wx.ID_OK:
             filename = dlg.GetFilename()
             dirname = dlg.GetDirectory()

metaunidec/gui_elements/ud_cont_meta.py

@@ -224,7 +224,8 @@ def __init__(self, parent, config, pres, panel, iconfile):
         gbox2b.Add(sbs, (i, 0), span=(1, 2), flag=wx.EXPAND)
         i += 1
 
-        self.ctlisotopemode = wx.CheckBox(panel2b, label="Isotope Mode")
+        #self.ctlisotopemode = wx.CheckBox(panel2b, label="Isotope Mode")
+        self.ctlisotopemode = wx.Choice(panel2b, -1, size=(100, -1), choices=self.config.isotopechoices)
         gbox2b.Add(self.ctlisotopemode, (i, 0), flag=wx.ALIGN_CENTER_VERTICAL)
 
         self.ctlmanualassign = wx.CheckBox(panel2b, label="Manual Mode")
@@ -435,7 +436,7 @@ def import_config_to_gui(self):
             self.ctlmaxnativez.SetValue(str(self.config.nativezub))
             self.ctlpoolflag.SetSelection(self.config.poolflag)
             self.ctlmanualassign.SetValue(self.config.manualfileflag)
-            self.ctlisotopemode.SetValue(self.config.isotopemode)
+            self.ctlisotopemode.SetSelection(self.config.isotopemode)
             self.ctldatanorm.SetValue(self.config.datanorm)
             self.ctlorbimode.SetValue(self.config.orbimode)
             # self.ctlbintype.SetSelection(int(self.config.linflag))
@@ -547,7 +548,7 @@ def export_gui_to_config(self, e=None):
         self.config.crossover = ud.string_to_value(self.ctlcrossover.GetValue())
         self.config.numtot = ud.string_to_value(self.ctlnumtot.GetValue())
 
-        self.config.isotopemode = int(self.ctlisotopemode.GetValue())
+        self.config.isotopemode = int(self.ctlisotopemode.GetSelection())
         self.config.datanorm = int(self.ctldatanorm.GetValue())
         self.config.orbimode = int(self.ctlorbimode.GetValue())
         self.config.manualfileflag = int(self.ctlmanualassign.GetValue())
@@ -658,7 +659,7 @@ def setup_tool_tips(self):
         self.ctlminnativez.SetToolTip(wx.ToolTip("Minimum offset from a native charge state"))
         self.ctlmaxnativez.SetToolTip(wx.ToolTip("Maximum offset from a native charge state"))
 
-        self.ctlisotopemode.SetToolTip(wx.ToolTip("Use isotopic distributions in deconvolution"))
+        self.ctlisotopemode.SetToolTip(wx.ToolTip("Use isotopic distributions in deconvolution.\nOutput either monoisotopic or average masses."))
         self.ctldatanorm.SetToolTip(wx.ToolTip("Normalize Data and Results"))
         self.ctlorbimode.SetToolTip(wx.ToolTip("Scale the intensity by dividing by the charge state"))
         self.ctlmanualassign.SetToolTip(wx.ToolTip("Use manual assignments. See Tools>Manual Assignment"))

metaunidec/mudstruct.py

@@ -111,7 +111,7 @@ def import_grids(self):
             grid3 = [grid2, grid]
             self.massgrid = np.transpose(grid3)
         except:
-            print("Mass Grid Warning:", grid.shape, sum.shape, len(grid)/len(sum))
+            print("Mass Grid Warning:", grid.shape, sum.shape)#, len(grid)/len(sum))
         # MZ Space
         axis = get_dataset(msdataset, "mz_axis")
         sum = get_dataset(msdataset, "mz_sum")
@@ -124,7 +124,7 @@ def import_grids(self):
             grid3 = [grid2, grid]
             self.mzgrid = np.transpose(grid3)
         except:
-            print("mz grid Warning:", grid.shape, sum.shape, len(grid)/len(sum))
+            print("mz grid Warning:", grid.shape, sum.shape)#, len(grid)/len(sum))
         hdf.close()
         return num
 

readme.md

@@ -192,6 +192,14 @@ The main GUI class is GUniDec.UniDecApp.
 
 ## Change Log
 
+v.3.1.1
+
+Expanded isotope mode to either output monoisotopic masses or average masses. 
+
+Added an experimental feature to plot average charge state for peaks in UniDec. 
+
+Bug fixes.
+
 v.3.1.0
 
 Added new parameter for Point Width Smooth. 

unidec_bin/Presets/Nanodiscs/DMPC.dat

@@ -4,6 +4,7 @@ numz 21
 endz 25
 startz 5
 zzsig 1.0
+psig 0
 mzsig 10
 psfun 0
 discreteplot 0

unidec_bin/Presets/Nanodiscs/DMPG.dat

@@ -4,6 +4,7 @@ numz 21
 endz 25
 startz 5
 zzsig 1.0
+psig 0
 mzsig 10
 psfun 0
 discreteplot 0

unidec_modules/MassDefectExtractor.py

@@ -18,9 +18,10 @@
 
 
 class MassDefectExtractorWindow(wx.Frame):
-    def __init__(self, parent, datalist, xarray, yarray, config=None):
+    def __init__(self, parent, datalist, xarray, yarray, config=None, xtype=0):
         wx.Frame.__init__(self, parent, title="Mass Defect")  # ,size=(-1,-1))
 
+        self.xtype=xtype
         if config is None:
             self.config = unidecstructure.UniDecConfig()
             self.config.initialize()
@@ -182,14 +183,12 @@ def on_extract(self, e=None):
         except Exception as e:
             print("Failed Data Export Extracts", e)
         self.make_ext_plots()
-        #self.fill_grid()
+        # self.fill_grid()
 
     def fill_grid(self):
         print(self.grid.shape)
         self.ss = spreadsheet.Spreadsheet(len(self.mdlist), len(self.ydat) + 1)
 
-
-
     def make_ext_plots(self):
         self.colormap = cm.get_cmap(ud.smartdecode(self.config.peakcmap), len(self.mdlist))
         if self.colormap is None:
@@ -272,7 +271,7 @@ def on_add_line(self, e):
         """
 
         for x in self.mdlist:
-            #print(x)
+            # print(x)
             try:
                 ylim = self.plot6.subplot1.get_ylim()
                 self.plot6.subplot1.plot((x, x), (ylim[0], ylim[1]), color=self.plot2.tickcolor)
@@ -302,6 +301,11 @@ def on_oligomer_tools(self, e):
             else:
                 nominalkmass = np.round(kmass)
             kmdefect = kmass - nominalkmass
+            if self.xtype == 0:
+                factor = 1.0
+            else:
+                factor = self.config.kendrickmass
+            kmdefect *= factor
             print(kmdefect)
             self.masslistbox.list.populate(kmdefect)