Sasa gui enhancement: issue #28

- added plot export
- added results export
- gui fixes -> resizing

PyContact/core/ContactAnalyzer.py

@@ -92,6 +92,9 @@ def getTrajectoryData(self):
                 self.type_array, self.segids, self.backbone, self.sel1text,
                 self.sel2text]
 
+    def getFilePaths(self):
+        return self.psf, self.dcd
+
     # find a string in s between the strings first and last
     @staticmethod
     def find_between(s, first, last):

PyContact/gui/Dialogues.py

@@ -5,6 +5,7 @@
 from PyQt5.QtGui import QDoubleValidator
 
 from ..core.LoadConfiguration import Configuration
+from PyContact.core.ContactAnalyzer import Analyzer
 from HelpButton import HelpButton
 
 
@@ -25,15 +26,15 @@ def __init__(self, parent=None):
 
         helpButton = HelpButton()
 
-        grid.addWidget(buttonPsf,0,0)
-        grid.addWidget(buttonDcd,0,1)
+        grid.addWidget(buttonPsf, 0, 0)
+        grid.addWidget(buttonDcd, 0, 1)
         buttons = QDialogButtonBox(
             QDialogButtonBox.Ok | QDialogButtonBox.Cancel,
             Qt.Horizontal, self)
         buttons.accepted.connect(self.accept)
         buttons.rejected.connect(self.reject)
-        grid.addWidget(buttons,1,0)
-        grid.addWidget(helpButton,2,0)
+        grid.addWidget(buttons, 1, 0)
+        grid.addWidget(helpButton, 2, 0)
 
     def pick_psf(self):
         psfname = QFileDialog.getOpenFileNames(self, "Open topology")

PyContact/gui/ErrorMessages.py

@@ -12,3 +12,5 @@ class ErrorMessages():
     RESID_REQUIRED = "Please analyze the trajectory with the resid box checked for both atom selections!"
 
     NOCONTACTS = "No data loaded or no filtered contacts available."
+
+    FILE_NOT_FOUND = "Attempt to load trajectory failed. File does not exist."

PyContact/gui/MainWindow.py

@@ -120,6 +120,8 @@ def showVMDControlPanel(self):
 
     def showContactAreaView(self):
         self.sasaView.show()
+        if self.analysis:
+            self.sasaView.setFilePaths(self.analysis.getFilePaths())
 
     def switchedToVisMode(self):
         if self.visModeButton.isChecked():
@@ -161,6 +163,7 @@ def importSession(self):
         self.analysis.contactResults = contactResults
         self.analysis.setTrajectoryData(*trajArgs)
         self.analysis.finalAccumulatedContacts = self.contacts
+        self.sasaView.setFilePaths(*self.analysis.getFilePaths())
         self.updateSelectionLabels(arguments[5], arguments[6])
         self.updateSettings()
         self.updateFilters()
@@ -186,6 +189,7 @@ def loadDefault(self):
         self.analysis.contactResults = contactResults
         self.analysis.setTrajectoryData(*trajArgs)
         self.analysis.finalAccumulatedContacts = self.contacts
+        self.sasaView.setFilePaths(*self.analysis.getFilePaths())
         self.updateSelectionLabels(arguments[5], arguments[6])
         self.updateSettings()
         self.updateFilters()

PyContact/gui/Plotters.py

@@ -196,3 +196,6 @@ def plot(self, x, y):
         self.axes.set_xlabel("x")
         self.axes.set_ylabel("f(x)")
         self.axes.xaxis.set_label_position('top')
+
+    def saveFigure(self, path, outputFormat):
+        self.fig.savefig(path + "." + outputFormat, format=outputFormat)

PyContact/gui/SasaWidgets.py

@@ -1,9 +1,10 @@
 from __future__ import print_function
 import sip
 import time
+import os
 
 
-from PyQt5.QtWidgets import QWidget, QProgressBar, QApplication
+from PyQt5.QtWidgets import QWidget, QProgressBar, QApplication, QFileDialog
 import MDAnalysis
 import numpy as np
 
@@ -55,6 +56,8 @@ def __init__(self, parent=None):
         self.state = True
         self.name = None
         self.psf, self. dcd = "", ""
+        self.allSasas = []
+        self.totalFramesToProcess = 0
 
         sip.delete(self.sasaProgressBar)
         self.sasaProgressBar = PbWidget(total=100)
@@ -64,16 +67,48 @@ def __init__(self, parent=None):
         self.sasaProgressBar.setObjectName("sasaProgressBar")
         self.previewPlot = SimplePlotter(None, width=5, height=2, dpi=60)
         self.graphGridLayout.addWidget(self.previewPlot)
-        self.gridLayout.addWidget(self.sasaProgressBar, 7, 1, 1, 1)
+        self.gridLayout.addWidget(self.sasaProgressBar, 8, 1, 1, 2)
         self.calcSasaButton.clicked.connect(self.calculateSasa)
         self.loadDataButton.clicked.connect(self.loadData)
+        self.savePlotButton.clicked.connect(self.savePlot)
+        self.exportDataButton.clicked.connect(self.exportData)
         self.topoloader = TopoTrajLoaderDialog()
 
+    def setFilePaths(self, *argv):
+        self.psf = argv[0][0]
+        self.dcd = argv[0][1]
+
     def loadData(self):
         loadedData = self.topoloader.getConfig()
         self.psf = loadedData[0][0]
         self.dcd = loadedData[0][1]
 
+    def savePlot(self):
+        fileName = QFileDialog.getSaveFileName(self, 'Export Path')
+        if len(fileName[0]) > 0:
+            path, file_extension = os.path.splitext(fileName[0])
+            if file_extension == "":
+                file_extension = ".png"
+            file_extension = file_extension[1:]
+            try:
+                self.previewPlot.saveFigure(path, file_extension)
+            except ValueError:
+                box = ErrorBox("File format " + file_extension + " is not supported.\nPlease choose from eps, pdf, pgf,"
+                                                                 " png, ps, raw, rgba, svg, svgz. ")
+                box.exec_()
+
+    def exportData(self):
+        fileName = QFileDialog.getSaveFileName(self, 'Export Path')
+        if len(fileName[0]) > 0:
+            path, file_extension = os.path.splitext(fileName[0])
+            if file_extension == "":
+                file_extension = ".dat"
+
+            f = open(path + file_extension, "w")
+            for i in range(self.totalFramesToProcess):
+                f.write(str(i) + "\t" + str(self.allSasas[i]) + "\n")
+            f.close()
+
     def calculateSasa(self):
         print("calculate SASA")
 
@@ -92,7 +127,12 @@ def calculateSasa(self):
             e.exec_()
             return
 
-        u = MDAnalysis.Universe(self.psf, self.dcd)
+        try:
+            u = MDAnalysis.Universe(self.psf, self.dcd)
+        except IOError:
+            e = ErrorBox(ErrorMessages.FILE_NOT_FOUND)
+            e.exec_()
+            return
 
         probeRadius = 1.4
 
@@ -169,9 +209,8 @@ def calculateSasa(self):
         pool.join()
 
         self.state = False
-        all_sasas = []
         for r in results:
-            all_sasas.extend(r.get())
+            self.allSasas.extend(r.get())
 
         del radius
 
@@ -226,11 +265,11 @@ def calculateSasa(self):
             diff_list = []
             for sasa_value1, sasa_value2 in zip(all_sasas, all_sasas2):
                 diff_list.append(sasa_value1 - sasa_value2)
-            all_sasas = diff_list
+            self.allSasas = diff_list
 
         sip.delete(self.previewPlot)
         self.previewPlot = SimplePlotter(None, width=5, height=2, dpi=60)
-        self.previewPlot.plot(np.arange(0, trajLength, 1), all_sasas)
+        self.previewPlot.plot(np.arange(0, trajLength, 1), self.allSasas)
         self.previewPlot.axes.set_xlabel("frame")
         self.previewPlot.axes.set_ylabel(r'SASA [A$^\circ$^2]')
         self.graphGridLayout.addWidget(self.previewPlot)