class ColorButton(QToolButton):
def __init__(self, color, parent=None):
QToolButton.__init__(self, parent)
self.setIconSize(QSize(50, 25))
self.pix = QPixmap(self.iconSize())
self._color = QColor('#' + color)
self.pix.fill(self._color)
self.setIcon(QIcon(self.pix))
self.clicked.connect(self.choose_color)
@dynamic_property
def color(self):
def fget(self):
return self._color.name(QColor.HexRgb)[1:]
def fset(self, val):
self._color = QColor('#' + val)
return property(fget=fget, fset=fset)
def update_display(self):
self.pix.fill(self._color)
self.setIcon(QIcon(self.pix))
def choose_color(self):
c = QColorDialog.getColor(self._color, self, _('Choose color'))
if c.isValid():
self._color = c
self.update_display()
class ColorButton(QToolButton):
def __init__(self, color, parent=None):
QToolButton.__init__(self, parent)
self.setIconSize(QSize(50, 25))
self.pix = QPixmap(self.iconSize())
self._color = QColor('#' + color)
self.pix.fill(self._color)
self.setIcon(QIcon(self.pix))
self.clicked.connect(self.choose_color)
@property
def color(self):
return self._color.name(QColor.NameFormat.HexRgb)[1:]
@color.setter
def color(self, val):
self._color = QColor('#' + val)
def update_display(self):
self.pix.fill(self._color)
self.setIcon(QIcon(self.pix))
def choose_color(self):
c = QColorDialog.getColor(self._color, self, _('Choose color'))
if c.isValid():
self._color = c
self.update_display()
class MainWindow(QMainWindow, MainQtGui.Ui_MainWindow, QObject):
"""PyContact Application Main Window with timeline."""
def closeEvent(self, event):
"""Closing application when Exit on MainWindow is clicked."""
print("Closing Application")
event.accept()
QApplication.quit()
def __init__(self, parent=None):
self.config = None
self.analysis = None
self.maps = None
super(MainWindow, self).__init__(parent)
self.contacts = []
self.filteredContacts = []
self.setupUi(self)
self.setWindowTitle("PyContact")
# painter contains both labels and frame boxes for drawing
self.painter = Canvas()
self.scrollArea.setWidget(self.painter)
self.actionExportData.triggered.connect(self.pushExport)
self.actionLoad_Data.triggered.connect(self.loadDataPushed)
self.actionExport_Session.triggered.connect(self.exportSession)
self.actionImport_Session.triggered.connect(self.importSession)
self.actionShow_Info.triggered.connect(self.showDeveloperInfo)
# settings and filters
self.settingsView = PreferencesWidget()
self.settingsView.applySettingsButton.clicked.connect(
self.updateSettings)
self.applyFilterButton.clicked.connect(self.updateFilters)
# statistics
self.statisticsButton.clicked.connect(self.showStatistics)
# color picker
self.settingsView.pickColorButton.clicked.connect(self.showColorPicker)
self.customColor = QColor(230, 50, 0)
self.settingsView.pickColorButton.setStyleSheet(
"QWidget { background-color: %s }" % self.customColor.name())
# frames stride
posIntValidator = QIntValidator()
posIntValidator.setBottom(1)
self.frameStrideField.setValidator(posIntValidator)
# analysis button
self.analysisButton.clicked.connect(self.analyzeDataPushed)
# contact area button
self.actionContact_Area_Calculations.triggered.connect(
self.showContactAreaView)
# preferences
self.actionPreferences.triggered.connect(self.openPrefs)
# apply color button, outdated?
self.colorScheme = ColorScheme.bbsc
self.actionDefault.triggered.connect(self.loadDefault)
self.currentSelection1 = "-"
self.currentSelection2 = "-"
# setup of extra widgets
self.exportWidget = ExportTabWidget()
self.sasaView = SasaWidget()
self.statisticsView = None
self.analysis_state = False
self.vismode = False
self.visModeButton.setCheckable(True)
self.visModeButton.setChecked(False)
self.visModeButton.clicked.connect(self.switchedToVisMode)
self.vmdpanel = VMDControlPanel()
self.actionVMD_Remote_Control.triggered.connect(
self.showVMDControlPanel)
self.painter.clickedRowSignal.connect(self.updateVMDSelections)
self.painter.clickedColumnSignal.connect(self.updateVMDFrame)
self.updateSettings()
self.updateFilters()
# self.tableTest = Widget()
# self.tableTest.setGeometry(100, 100, 400, 400)
# self.tableTest.show()
# from ..db.DbReader import read_residue_db_all
# res = read_residue_db_all()
# residueList = [] # 1st: name, 2nd scpolarity
# for k in res:
# residueList.appen([k["name"], k["scpolarity"]])
self.actionDefault.setText("Load sample data")
def showVMDControlPanel(self):
"""Shows the VMD control panel, to remotely access VMD from PyContact."""
self.vmdpanel.show()
def showContactAreaView(self):
"""Shows the SASA computation panel."""
self.sasaView.show()
if self.analysis:
self.sasaView.setFilePaths(self.analysis.getFilePaths())
def switchedToVisMode(self):
"""Switch to vis mode, to show selected contacts directly in VMD."""
if self.visModeButton.isChecked():
self.vismode = True
# conversions with clicked frames are not allowed
self.frameStrideField.setText("1")
else:
self.vismode = False
self.painter.switchToVisMode(self.vismode)
self.updateSettings()
self.updateFilters()
@pyqtSlot()
def updateVMDSelections(self):
"""Updates the selected contact in VMD via the vmd panel."""
if self.vmdpanel.connected:
self.vmdpanel.updateSelections(
self.analysis.sel1text, self.analysis.sel2text,
[self.filteredContacts[self.painter.globalClickedRow]])
@pyqtSlot()
def updateVMDFrame(self):
"""Updates the selected frame in VMD via the vmd panel."""
if self.vmdpanel.connected:
self.vmdpanel.gotoVMDFrame(self.painter.clickedColumn)
def updateSelectionLabels(self, sel1, sel2):
"""Updates the current selection in the info labels."""
self.currentSelection1 = sel1
self.currentSelection2 = sel2
self.selection1label.setText(sel1)
self.selection2label.setText(sel2)
def importSession(self):
"""Imports a saved session from file."""
fnames = QFileDialog.getOpenFileNames(self, "Open file")
importfile = ""
for f in fnames[0]:
importfile = f
break
if importfile == "" or len(fnames) == 0:
return
self.contacts, arguments, trajArgs, self.maps, contactResults = DataHandler.importSessionFromFile(
importfile)
self.analysis = Analyzer(*arguments)
self.analysis.contactResults = contactResults
self.analysis.setTrajectoryData(*trajArgs)
self.analysis.finalAccumulatedContacts = self.contacts
self.sasaView.setFilePaths(*self.analysis.getFilePaths())
self.exportWidget.setFilePaths(*self.analysis.getFilePaths())
self.updateSelectionLabels(arguments[5], arguments[6])
self.updateSettings()
self.updateFilters()
def exportSession(self):
"""Exports the current session to file."""
fileName = QFileDialog.getSaveFileName(self, 'Export file')
filestring = fileName[0]
if filestring == "":
return
if self.contacts is not None and self.analysis is not None:
self.setInfoLabel("Exporting current session...")
DataHandler.writeSessionToFile(filestring, self.analysis)
self.cleanInfoLabel()
else:
box = ErrorBox(ErrorMessages.NOEXPDATA)
box.exec_()
return
def loadDefault(self):
"""Loads the default session."""
self.contacts, arguments, trajArgs, self.maps, contactResults = \
DataHandler.importSessionFromFile(DEFAULTSESSION)
self.analysis = Analyzer(*arguments)
self.analysis.contactResults = contactResults
self.analysis.setTrajectoryData(*trajArgs)
self.analysis.finalAccumulatedContacts = self.contacts
self.sasaView.setFilePaths(*self.analysis.getFilePaths())
self.exportWidget.setFilePaths(*self.analysis.getFilePaths())
self.updateSelectionLabels(arguments[5], arguments[6])
self.updateSettings()
self.updateFilters()
def loadDataPushed(self):
"""Loads the trajectory data with the chosen initial parameters."""
self.config, result = FileLoaderDialog.getConfig()
if result == 1:
QApplication.processEvents()
self.setInfoLabel(
"Loading trajectory and running atomic contact analysis...")
nproc = int(self.settingsView.coreBox.value())
self.analysis = Analyzer(self.config.psf, self.config.dcd,
self.config.cutoff,
self.config.hbondcutoff,
self.config.hbondcutangle,
self.config.sel1text,
self.config.sel2text)
QApplication.processEvents()
try:
self.analysis.runFrameScan(nproc)
except:
box = ErrorBox(
"Error while loading data: Probably you specified an atom selection with 0 atoms or invalid input files."
)
box.exec_()
self.loadDataPushed()
self.setInfoLabel("%d frames loaded." %
len(self.analysis.contactResults))
self.updateSelectionLabels(self.config.sel1text,
self.config.sel2text)
self.sasaView.setFilePaths(*self.analysis.getFilePaths())
self.exportWidget.setFilePaths(*self.analysis.getFilePaths())
@pyqtSlot(float)
def updateAnalyzedFrames(self, value):
"""Handles the progress bar update."""
# print("Updating frames", value)
self.progressBar.setValue(100 * value)
QApplication.processEvents()
def setInfoLabel(self, txt):
"""Sets the Info label text."""
self.statusLabel.setText(txt)
def cleanInfoLabel(self):
"""Clears the Info label text."""
self.setInfoLabel("-")
def analyzeDataPushed(self):
"""Handles the Analyzer after the Accumulation maps have been set."""
if self.analysis is None:
box = ErrorBox(ErrorMessages.NODATA_PROMPTLOAD)
box.exec_()
return
self.maps, result = AnalysisDialog.getMapping()
if result == 1:
self.analysis.frameUpdate.connect(self.updateAnalyzedFrames)
self.setInfoLabel("Analyzing contacts...")
map1 = self.maps[0]
map2 = self.maps[1]
nproc = int(self.settingsView.coreBox.value())
self.contacts = self.analysis.runContactAnalysis(map1, map2, nproc)
self.progressBar.setValue(0)
self.setInfoLabel("Updating timeline...")
QApplication.processEvents()
self.updateSettings()
self.updateFilters()
self.cleanInfoLabel()
def updateSettings(self):
"""Updates the settings chosen from the settings view."""
if self.settingsView.bbscScoreRadioButton.isChecked():
self.colorScheme = ColorScheme.bbsc
elif self.settingsView.customColorRadioButton.isChecked():
self.colorScheme = ColorScheme.custom
self.painter.nsPerFrame = float(
self.settingsView.nsPerFrameField.text())
self.painter.threshold = float(self.settingsView.thresholdField.text())
self.painter.rendered = False
self.painter.colorScheme = self.colorScheme
self.painter.customColor = self.customColor
self.painter.repaint()
self.painter.update()
def updateFilters(self):
"""Updates the chosen filters in MainWindow."""
if self.vismode is True:
self.frameStrideField.setText("1")
stride = int(self.frameStrideField.text())
if stride < 1:
stride = 1
QApplication.processEvents()
self.frameStrideField.setText(str(stride))
# print("stride: ", stride)
self.painter.merge = stride
self.painter.labelView.clean()
self.painter.showHbondScores = False
# total time filter
totalTimeActive = self.activeTotalTimeCheckbox.isChecked()
scoreActive = self.activeScoreCheckbox.isChecked()
sortingActive = self.activeSortingBox.isChecked()
onlyActive = self.onlyBoxActiveCheckbox.isChecked()
filterActive = (totalTimeActive or scoreActive or sortingActive
or onlyActive)
weightActive = False
# only filter given range
rangeFilterActive = self.filterRangeCheckbox.isChecked()
if len(self.contacts) > 0:
lower = int(self.lowerRangeField.text()) - 1
upper = self.upperRangeField.text()
if upper == "end":
upper = len(self.contacts[0].scoreArray)
else:
upper = int(upper)
if lower < 0:
lower = 0
self.painter.range = [lower, upper]
self.painter.rangeFilterActive = False
self.filteredContacts = copy.deepcopy(self.contacts)
# residue range filter
range_filter = RangeFilter("resrange")
self.filteredContacts = range_filter.filterByRange(
self.filteredContacts, self.residARangeField.text(),
self.residBRangeField.text(), AccumulationMapIndex.resid)
self.filteredContacts = range_filter.filterByRange(
self.filteredContacts, self.atomAIndexField.text(),
self.atomBIndexField.text(), AccumulationMapIndex.index)
# aminoacids name filter
name_filter = NameFilter("name")
self.filteredContacts = name_filter.filterContactsByName(
self.filteredContacts, self.residANameField.text(),
self.residBNameField.text(), AccumulationMapIndex.resname)
self.filteredContacts = name_filter.filterContactsByName(
self.filteredContacts, self.atomANameField.text(),
self.atomBNameField.text(), AccumulationMapIndex.name)
# range filter
if rangeFilterActive:
self.painter.rangeFilterActive = True
frameRangeFilter = FrameFilter("framer")
self.filteredContacts = frameRangeFilter.extractFrameRange(
self.filteredContacts, [lower, upper])
for c in self.filteredContacts:
c.setScores()
c.setContactType()
# weight functions
if weightActive:
if self.currentFunctionType == FunctionType.sigmoid:
print("sig weight")
x0 = float(self.sigX0Field.text())
L = float(self.sigLField.text())
k = float(self.sigKField.text())
y0 = float(self.sigY0Field.text())
sig = SigmoidWeightFunction(
"sig", np.arange(0, len(self.contacts[0].scoreArray),
1), x0, L, k, y0)
self.filteredContacts = sig.weightContactFrames(
self.filteredContacts)
elif self.currentFunctionType == FunctionType.rect:
x0 = float(self.rectX0Field.text())
x1 = float(self.rectX1Field.text())
h = float(self.rectHField.text())
y0 = float(self.rectY0Field.text())
rect = RectangularWeightFunction(
"rect",
np.arange(0, len(self.contacts[0].scoreArray), 1), x0,
x1, h, y0)
self.filteredContacts = rect.weightContactFrames(
self.filteredContacts)
elif self.currentFunctionType == FunctionType.linear:
y0 = float(self.linY0Field.text())
y1 = float(self.linY1Field.text())
lin = LinearWeightFunction(
"rect",
np.arange(0, len(self.contacts[0].scoreArray), 1), y0,
y1)
self.filteredContacts = lin.weightContactFrames(
self.filteredContacts)
# other filters
if filterActive:
if totalTimeActive:
operator = self.compareTotalTimeDropdown.currentText()
value = float(self.totalTimeField.text())
filter = TotalTimeFilter("tottime", operator, value)
self.filteredContacts = filter.filterContacts(
self.filteredContacts)
if scoreActive:
operator = self.compareScoreDropdown.currentText()
value = float(self.scoreField.text())
filter = ScoreFilter("score", operator, value,
self.meanDropdown.currentText())
self.filteredContacts = filter.filterContacts(
self.filteredContacts)
if sortingActive:
key = self.sortingKeyDropdown.currentText()
descending = SortingOrder.mapping[
self.sortingOrderDropdown.currentText()]
sorter = Sorting("sorting", key, descending)
sorter.setThresholdAndNsPerFrame(
float(self.settingsView.thresholdField.text()),
float(self.settingsView.nsPerFrameField.text()))
self.filteredContacts = sorter.sortContacts(
self.filteredContacts)
if onlyActive:
key = self.selectOnlyToolbox.currentText()
only = OnlyFilter("only", key, 0)
self.filteredContacts = only.filterContacts(
self.filteredContacts)
if key == "hbonds":
self.painter.showHbondScores = True
self.painter.contacts = self.filteredContacts
self.painter.rendered = False
self.painter.repaint()
self.painter.update()
if len(self.filteredContacts) == 0:
self.painter.labelView.clean()
else:
# no weight or filters
self.painter.showHbondScores = False
self.painter.contacts = self.filteredContacts
self.painter.rendered = False
self.painter.repaint()
self.painter.update()
# Update data for export
self.exportWidget.setContacts(self.filteredContacts)
if self.maps is not None:
self.exportWidget.setMaps(self.maps[0], self.maps[1])
self.exportWidget.setMapLabels(self.analysis.sel1text,
self.analysis.sel2text)
self.exportWidget.setThresholdAndNsPerFrame(self.painter.threshold,
self.painter.nsPerFrame)
def openPrefs(self):
"""Opens the preferences panel."""
self.settingsView.show()
def showStatistics(self):
"""Shows general statistics of the analyzed data over all frames."""
if len(self.contacts) == 0 or self.contacts is None:
box = ErrorBox(ErrorMessages.NOSCORES_PROMPTANALYSIS)
box.exec_()
return
self.statisticsView = Statistics(self.contacts)
self.statisticsView.showNormal()
def showDeveloperInfo(self):
"""Shows information about the contributing authors."""
d = QDialog()
grid = QGridLayout()
d.setLayout(grid)
info = QLabel("Developers: Maximilian Scheurer and Peter Rodenkirch")
info2 = QLabel(
"Departments: TCBG, University of Illinois at Urbana-Champaign; BZH Heidelberg University"
)
mail = QLabel(
"Contact: [email protected], [email protected]"
)
copyright = QLabel("Version 1.0, May 2017")
grid.addWidget(info, 0, 0)
grid.addWidget(info2, 1, 0)
grid.addWidget(mail, 2, 0)
grid.addWidget(copyright, 3, 0)
d.setWindowTitle("Developer Info")
d.resize(150, 80)
d.setWindowModality(Qt.ApplicationModal)
d.exec_()
def pushExport(self):
"""Opens the export panel."""
self.exportWidget.valueUpdated.connect(self.handleExportUpdate)
self.exportWidget.setContacts(self.filteredContacts)
if self.maps is not None:
self.exportWidget.setMaps(self.maps[0], self.maps[1])
self.exportWidget.setMapLabels(self.analysis.sel1text,
self.analysis.sel2text)
self.exportWidget.setThresholdAndNsPerFrame(self.painter.threshold,
self.painter.nsPerFrame)
self.exportWidget.show()
@QtCore.Slot(str, str)
def handleExportUpdate(self, fileName, fileType):
"""Handles the paint event after the export of the current view has been initiated."""
print("test")
if fileType == "PNG":
if len(fileName) > 0:
print("Saving current view to ", fileName)
currentView = self.painter.grab()
currentView.save(fileName)
elif fileType == "SVG":
if len(fileName) > 0:
print("Saving current view to ", fileName)
generator = QSvgGenerator()
generator.setFileName(fileName)
generator.setSize(self.painter.size())
generator.setViewBox(self.painter.rect())
self.painter.renderContact(generator)
self.painter.rendered = False
self.painter.repaint()
self.painter.update()
def showColorPicker(self):
"""Shows a color picker for the current view."""
col = QColorDialog.getColor()
self.customColor = col
if col.isValid():
self.settingsView.pickColorButton.setStyleSheet(
"QWidget { background-color: %s }" % self.customColor.name())