Merge pull request #35 from michaelmarty/v3

Version 4.1.0. Added biopolymer calculator. Updates to score. Various…

.gitignore

@@ -129,6 +129,8 @@ unidec_bin/Example Data/BSA_unidecfiles/BSA_chargedata.dat
 unidec_bin/Example Data/BSA_unidecfiles/BSA_chargedata_areas.dat
 unidec_bin/Example Data/BSA_unidecfiles/BSA_peakparam.dat
  /__pycache__/
+ __pycache__/
 unidec_bin/Example Data/GroEL HCD UniDec_unidecfiles/GroEL HCD UniDec_peak_areas.dat
+unidec_bin/mkl_intel_thread.dll
 
 

GUniDec.py

@@ -159,19 +159,19 @@ def on_open_file(self, filename, directory, skipengine=False, **kwargs):
             if self.eng.config.batchflag == 0:
                 self.view.plot1im.contourplot(self.eng.data.rawdata3, self.eng.config, xlab="m/z (Th)",
                                               ylab="Arrival Time (ms)", title="IM-MS Data")
-        #tstart = time.perf_counter()
+        # tstart = time.perf_counter()
         # Load Config to GUI
         self.import_config()
         self.view.SetStatusText("Ready", number=5)
-        #print("ImportConfig: %.2gs" % (time.perf_counter() - tstart))
+        # print("ImportConfig: %.2gs" % (time.perf_counter() - tstart))
         if False:
             try:
                 self.eng.unidec_imports(everything=False)
                 self.after_unidec_run()
             except:
                 pass
 
-        #print("ImportData: %.2gs" % (time.perf_counter() - tstart))
+        # print("ImportData: %.2gs" % (time.perf_counter() - tstart))
 
     def on_save_state(self, e=None, filenew=None):
         """
@@ -425,7 +425,7 @@ def on_pick_peaks(self, e=None):
             self.makeplot4(1)
 
         self.view.SetStatusText("Peak Pick Done", number=5)
-        #self.on_score()
+        self.on_score()
         pass
 
     def on_plot_peaks(self, e=None):
@@ -764,7 +764,7 @@ def on_delete(self, e=None):
         self.makeplot6(1)
         self.view.SetStatusText("Peak Change Done", number=5)
 
-    def on_charge_states(self, e=None):
+    def on_charge_states(self, e=None, mass=None):
         """
         Triggered by right click "plot charge states" on self.view.peakpanel.
         Plots a line with text listing the charge states of a specific peak.
@@ -776,7 +776,10 @@ def on_charge_states(self, e=None):
         else:
             sign = "-"
         charges = np.arange(self.eng.config.startz, self.eng.config.endz + 1)
-        peaksel = self.view.peakpanel.selection2[0]
+        if mass is None:
+            peaksel = self.view.peakpanel.selection2[0]
+        else:
+            peaksel = mass
         peakpos = (peaksel + charges * self.eng.config.adductmass) / charges
         boo1 = np.all([peakpos < self.eng.config.maxmz, peakpos > self.eng.config.minmz], axis=0)
         peakpos = peakpos[boo1]
@@ -1654,12 +1657,29 @@ def on_plot_isotope_distribution(self, e=0):
     def on_score(self, e=0):
         self.eng.dscore()
         self.view.peakpanel.add_data(self.eng.pks, show="dscore")
-        self.view.SetStatusText("Average Peaks Score: " + str(round(self.eng.pks.aps * 100, 2)), number=3)
+        self.view.SetStatusText("UniScore: " + str(round(self.eng.pks.uniscore * 100, 2)), number=3)
 
     def on_score2(self, e=0):
-        self.eng.filter_peaks()
+        defaultvalue = "40"
+        try:
+            defaultvalue = str(self.eng.fdrs[0, 1] * 100)
+        except:
+            pass
+        dialog = miscwindows.SingleInputDialog(self.view)
+        dialog.initialize_interface(title="Minimum DScore", message="Set Minimum DScore Value (%): ",
+                                    defaultvalue=defaultvalue)
+        dialog.ShowModal()
+
+        try:
+            minval = float(dialog.value)/100.
+        except:
+            print("Error with Score Input:", dialog.value)
+            minval = 0.4
+
+        print("Using DScore Cutoff (%): ", minval*100)
+        self.eng.filter_peaks(minscore=minval)
         self.view.peakpanel.add_data(self.eng.pks, show="dscore")
-        self.view.SetStatusText("Average Peaks Score: " + str(round(self.eng.pks.aps * 100, 2)), number=3)
+        self.view.SetStatusText("UniScore: " + str(round(self.eng.pks.uniscore * 100, 2)), number=3)
         self.makeplot2()
         self.makeplot4()
         self.makeplot6()
@@ -1671,9 +1691,20 @@ def on_score_window(self, e=0):
         sw.populate(self.eng.pks)
         pass
 
+    def on_score_label(self, e=0):
+        self.on_score()
+        offset = 0.08 * np.amax(self.eng.data.massdat[:, 1])
+        for p in self.eng.pks.peaks:
+            text = str(int(round(p.dscore * 100)))
+            self.view.plot2.addtext(text, p.mass, p.height + offset, vlines=False)
+
     # def on_remove_noise_points(self, e=0):
     #    self.on_dataprep_button(removenoise=True)
 
+    def on_score_FDR(self, e=0):
+        self.eng.estimate_FDR()
+
+
     def on_flip_mode(self, e=None):
         """
         Flips between MS and IM-MS mode

GUniDec.spec

@@ -12,9 +12,6 @@ import comtypes
 import encodings
 import zipimport
 from PyInstaller.utils.hooks import collect_data_files
-from sklearn.decomposition import PCA
-import sklearn.decomposition
-import sklearn
 from multiprocessing import freeze_support
 
 freeze_support()
@@ -55,11 +52,11 @@ zipdirectory = outputdir + "_" + date + ".zip"
 # Analysis of packages
 a = Analysis(['Launcher.py'],
              pathex=[os.getcwd()],
-             excludes=['pandas', 'IPython', 'Cython', 'statsmodels', 'pyopenms',
+             excludes=['pandas', 'IPython', 'Cython', 'statsmodels', 'pyopenms', 'sklearn',
                        'GdkPixbuf', 'PIL', 'pyQT4', 'pygobject', 'pygtk', 'pyside', 'PySide2', 'shiboken2', 'PyQt5'],
              hiddenimports=[  # 'plotly','
-                 'sklearn', 'sklearn.decomposition', 'sklearn.preprocessing', 'sklearn.utils', 'pytest', 'pluggy',
-                 'sklearn.utils.testing', 'sklearn.utils._cython_blas',
+                 # 'sklearn', 'sklearn.decomposition', 'sklearn.preprocessing', 'sklearn.utils', 'pytest', 'pluggy',
+                 # 'sklearn.utils.testing', 'sklearn.utils._cython_blas',
                  'scipy.special._ufuncs_cxx', 'scipy.linalg.cython_blas', 'scipy.linalg.cython_lapack',
                  'scipy._lib.messagestream',
                  'FileDialog', 'Dialog', 'encodings', 'encodings.__init__',
@@ -85,6 +82,7 @@ if system == "Windows":
     a.datas += [('readme.md', 'readme.md', 'DATA')]
     a.datas += [('LICENSE', 'LICENSE', 'DATA')]
     a.datas += [('libiomp5md.dll', 'unidec_bin\\libiomp5md.dll', 'DATA')]
+    a.datas += [('mkl_intel_thread.dll', 'unidec_bin\\mkl_intel_thread.dll', 'DATA')]
     a.datas += [('ucrtbase.dll', 'unidec_bin\\ucrtbase.dll', 'DATA')]
     a.datas += [('vcruntime140.dll', 'unidec_bin\\vcruntime140.dll', 'DATA')]
     a.datas += [('libmypfunc.dll', 'unidec_bin\\libmypfunc.dll', 'DATA')]
@@ -132,6 +130,15 @@ a.datas.extend(dir_files("unidec_bin\\Example Data", 'Example Data'))
 # grammar=os.path.join(os.path.dirname(lib2to3.__file__),'PatternGrammar.txt')
 # a.datas.extend([(os.path.join('lib2to3','PatternGrammar.txt'),grammar,'DATA')])
 
+from os import listdir
+from PyInstaller import compat
+
+mkldir = compat.base_prefix + "/Lib/site-packages/numpy/DLLs"
+# a.datas.extend(dir_files(mkldir, ''))
+#a.datas.extend(
+#    [(mkldir + "/" + mkl, '', 'DATA') for mkl in listdir(mkldir) if mkl.startswith('mkl_') or mkl.startswith('libio')])
+# for b in binaries:
+#    a.datas += b
 
 # Assemble and build
 pyz = PYZ(a.pure)
@@ -154,6 +161,8 @@ coll = COLLECT(exe,
 path = "C:\\Python\\UniDec3\\dist\\UniDec_Windows\\GUI_UniDec.exe"
 import subprocess
 
+print("Testing Software...", path)
+
 out = subprocess.call(path)
 
 if out != 0:

readme.md

@@ -112,7 +112,7 @@ we have provided the source code for the GUI and API.
 
 ### Python
 
-UniDec is currently compatible only with Python 2.7. There are several Python libraries that UniDec will depend on. 
+UniDec is currently compatible only with Python 3. There are several Python libraries that UniDec will depend on. 
 
 matplotlib
 numpy
@@ -124,6 +124,7 @@ networkx
 h5py
 multiplierz (Windows only, for Thermo RAW imports)
 pypubsub
+tornado
 
 All of these can be installed from the command line with (for example):
 
@@ -193,6 +194,26 @@ The main GUI class is GUniDec.UniDecApp.
 
 ## Change Log
 
+v.4.1.0
+
+Introduced **UniScore**. This will automatically score the quality of your peaks and the overall deconvolution. Various experimental features were also added with this to visualize and filter the scores. Some updates to the scoring algorithm from Version 4.0.2 to improve it.
+
+A good heuristic for UniScore and DScore values is:
+
+80-100: A (Excellent)
+
+60-80: B (Good)
+
+40-60: C (Fair)
+
+20-40: D (Poor)
+
+0-20: F (Almost certainly noise)
+
+Added **Calculator for getting masses from Protein/Peptide or RNA sequences**. This can be launched stand alone from the Experimental Menu or by right clicking on the Oligomer and Mass Tools Oligomer Builder box.  
+
+Fixed bug to now allow protein-protein oligomerization KD values to be measured with the Data Collector. Find out more on the [UniDec Wiki Page](https://github.com/michaelmarty/UniDec/wiki/Fitting-KDs-with-Data-Collector).
+
 v.4.0.2
 
 Switched UniDec to load processed data if it already exists.