def unloadData(self):
self.loaded = False
self.helixLoaded = False
self.sheetLoaded = False
self.helixFileName = ""
self.sheetFileName = ""
BaseViewer.unloadData(self)
def loadSessionInfo(self, sessionManager, sessionProperties):
BaseViewer.loadSessionInfo(self, sessionManager, sessionProperties)
isoLevel = sessionManager.getProperty(sessionProperties, self.shortTitle, "ISO_LEVEL")
self.surfaceEditor.ui.histogram.setLowerValue(isoLevel)
maxIsoLevel = sessionManager.getProperty(sessionProperties, self.shortTitle, "MAX_ISO_LEVEL")
self.surfaceEditor.ui.histogram.setHigherValue(maxIsoLevel)
samplingInterval = sessionManager.getProperty(sessionProperties, self.shortTitle, "SAMPLING_INTERVAL")
#self.surfaceEditor.ui.horizontalSliderSampling.setValue(samplingInterval)
useDisplayRadius = sessionManager.getProperty(sessionProperties, self.shortTitle, "USE_DISPLAY_RADIUS")
self.surfaceEditor.ui.checkBoxUseRadius.setCheckState(useDisplayRadius)
displayRadius = sessionManager.getProperty(sessionProperties, self.shortTitle, "DISPLAY_RADIUS")
self.surfaceEditor.ui.spinBoxDisplayRadius.setValue(displayRadius)
surfaceViewing = sessionManager.getProperty(sessionProperties, self.shortTitle, "VIEWING_TYPE_SURFACE")
solidViewing = sessionManager.getProperty(sessionProperties, self.shortTitle, "VIEWING_TYPE_SOLID")
crossSectionViewing = sessionManager.getProperty(sessionProperties, self.shortTitle, "VIEWING_TYPE_CROSS_SECTION")
self.surfaceEditor.ui.radioButtonIsoSurface.setChecked(surfaceViewing)
self.surfaceEditor.ui.radioButtonSolid.setChecked(solidViewing)
self.surfaceEditor.ui.radioButtonCrossSection.setChecked(crossSectionViewing)
def unloadData(self):
#overwriting the function in base viewer
for chain in self.loadedChains:
del chain
chain = None
self.loadedChains = []
BaseViewer.unloadData(self)
def __init__(self, main, parent=None):
BaseViewer.__init__(self, main, parent)
self.title = "Skeleton"
self.shortTitle = "SKE"
self.app.themes.addDefaultRGB("Skeleton:Model:0", 180, 0, 0, 255)
self.app.themes.addDefaultRGB("Skeleton:Model:1", 200, 150, 0, 255)
self.app.themes.addDefaultRGB("Skeleton:Model:2", 0, 0, 0, 255)
self.app.themes.addDefaultRGB("Skeleton:BoundingBox", 255, 255, 255,
255)
self.isClosedMesh = False
self.twoWayLighting = True
self.lineThickness = 3
self.renderer = MeshRenderer()
self.renderer.setLineThickness(self.lineThickness)
self.createUI()
self.app.viewers["skeleton"] = self
self.volumeViewer = self.app.viewers["volume"]
self.initVisualizationOptions(ModelVisualizationForm(self.app, self))
self.visualizationOptions.ui.spinBoxThickness.setValue(
self.lineThickness)
self.visualizationOptions.ui.spinBoxThickness.setVisible(True)
self.visualizationOptions.ui.labelThickness.setVisible(True)
self.model2Visible = True
self.model3Visible = True
self.visualizationOptions.ui.checkBoxModelVisible.setText(
"Show curves colored:")
self.visualizationOptions.ui.checkBoxModel2Visible.setText(
"Show surfaces colored:")
self.visualizationOptions.ui.checkBoxModel2Visible.setVisible(True)
self.visualizationOptions.ui.pushButtonModel2Color.setVisible(True)
self.visualizationOptions.ui.checkBoxModel3Visible.setText(
"Show surface borders:")
self.visualizationOptions.ui.checkBoxModel3Visible.setVisible(True)
self.visualizationOptions.ui.pushButtonModel3Color.setVisible(True)
def emitElementClicked(self, hitStack, event):
print "emitElementClicked overridden: ", self.title, hitStack
print "self.displayStyle: ", self.displayStyle
if (self.displayStyle == self.DisplayStyleRibbon):
sseData = self.formatRibbonHitstack(hitStack)
self.emit(QtCore.SIGNAL("ribbonClicked (int, PyQt_PyObject, PyQt_PyObject, QMouseEvent)"), sseData[0], sseData[1], sseData[2], event)
else:
BaseViewer.emitElementClicked(self, hitStack, event)
def __init__(self, main, parent=None):
BaseViewer.__init__(self, main, parent)
self.title = "Secondary Structure Element"
self.shortTitle = "SSE"
self.app.themes.addDefaultRGB("Secondary Structure Element:Model:0", 0,
180, 0, 255)
self.app.themes.addDefaultRGB("Secondary Structure Element:Model:1",
120, 185, 255, 255)
self.app.themes.addDefaultRGB("Secondary Structure Element:Model:2",
120, 185, 255, 255)
self.app.themes.addDefaultRGB(
"Secondary Structure Element:BoundingBox", 255, 255, 255, 255)
self.isClosedMesh = False
self.helixFileName = ""
self.sheetFileName = ""
self.currentMatch = None
self.showBox = False
self.helixLoaded = False
self.sheetLoaded = False
self.renderer = SSERenderer()
self.correspondenceEngine = SSECorrespondenceEngine()
self.createUI()
self.selectEnabled = True
self.app.viewers["sse"] = self
self.model2Visible = True
self.model3Visible = False
self.initVisualizationOptions(ModelVisualizationForm(self.app, self))
self.visualizationOptions.ui.checkBoxModelVisible.setText(
"Show helices colored:")
self.visualizationOptions.ui.checkBoxModel2Visible.setText(
"Show sheets colored:")
self.visualizationOptions.ui.checkBoxModel2Visible.setVisible(True)
self.visualizationOptions.ui.pushButtonModel2Color.setVisible(True)
self.visualizationOptions.ui.checkBoxModel3Visible.setText(
"Show skeleton sheets colored:")
self.visualizationOptions.ui.checkBoxModel3Visible.setVisible(False)
self.visualizationOptions.ui.pushButtonModel3Color.setVisible(False)
self.connect(
self,
QtCore.SIGNAL(
'elementSelected (int, int, int, int, int, int, QMouseEvent)'),
self.updateCurrentMatch)
self.connect(self.app.viewers["volume"],
QtCore.SIGNAL('modelLoaded()'),
self.updateActionsAndMenus)
self.connect(self.app.viewers["volume"],
QtCore.SIGNAL('modelUnloaded()'),
self.updateActionsAndMenus)
self.connect(self, QtCore.SIGNAL('modelLoaded()'),
self.updateActionsAndMenus)
self.connect(self, QtCore.SIGNAL('modelUnloaded()'),
self.updateActionsAndMenus)
self.selectedObjects = []
self.correspondences = []
def emitElementMouseOver(self, hitStack, event):
if (self.displayStyle == self.DisplayStyleRibbon):
sseData = self.formatRibbonHitstack(hitStack)
self.emit(
QtCore.SIGNAL(
"ribbonMouseOver (int, PyQt_PyObject, PyQt_PyObject, QMouseEvent)"
), sseData[0], sseData[1], sseData[2], event)
else:
BaseViewer.emitElementMouseOver(self, hitStack, event)
def loadSessionInfo(self, sessionManager, sessionProperties):
BaseViewer.loadSessionInfo(self, sessionManager, sessionProperties)
self.helixLoaded = sessionManager.getProperty(sessionProperties, self.shortTitle, "HELIX_LOADED")
if self.helixLoaded:
self.helixFileName = sessionManager.getProperty(sessionProperties, self.shortTitle, "HELIX_FILE")
self.loadHelixDataFromFile(self.helixFileName)
self.sheetLoaded = sessionManager.getProperty(sessionProperties, self.shortTitle, "SHEET_LOADED")
if self.sheetLoaded:
self.sheetFileName = sessionManager.getProperty(sessionProperties, self.shortTitle, "SHEET_FILE")
self.loadSheetDataFromFile(self.sheetFileName)
def emitElementClicked(self, hitStack, event):
if (self.app.viewers["calpha"].displayStyle ==
self.app.viewers["calpha"].DisplayStyleRibbon):
if (self.app.mainCamera.mouseRightPressed and hitStack[0] == 0):
self.emit(
QtCore.SIGNAL(
"SSERightClicked(PyQt_PyObject, PyQt_PyObject, QMouseEvent)"
), hitStack[0], hitStack[1], event)
else:
BaseViewer.emitElementClicked(self, hitStack, event)
def __init__(self, main, parent=None):
BaseViewer.__init__(self, main, parent)
self.title = "Volume"
self.shortTitle = "VOL"
self.app.themes.addDefaultRGB("Volume:Model:0", 180, 180, 180, 150) #rgba color: default alpha used to be 255 for opaque
self.app.themes.addDefaultRGB("Volume:Model:1", 180, 180, 180, 150)
self.app.themes.addDefaultRGB("Volume:Model:2", 180, 180, 180, 150)
self.app.themes.addDefaultRGB("Volume:BoundingBox", 255, 255, 255, 255)
self.renderer = VolumeRenderer()
self.loaded = False
self.createUI()
self.app.viewers["volume"] = self
self.initVisualizationOptions(ModelVisualizationForm(self.app, self))
def getSessionInfo(self, sessionManager):
info = BaseViewer.getSessionInfo(self, sessionManager)
info.extend(sessionManager.getRemarkLines(self.shortTitle, "HELIX_LOADED", self.helixLoaded))
info.extend(sessionManager.getRemarkLines(self.shortTitle, "HELIX_FILE", self.helixFileName))
info.extend(sessionManager.getRemarkLines(self.shortTitle, "SHEET_LOADED", self.sheetLoaded))
info.extend(sessionManager.getRemarkLines(self.shortTitle, "SHEET_FILE", self.sheetFileName))
return info
def getSessionInfo(self, sessionManager):
info = BaseViewer.getSessionInfo(self, sessionManager)
info.extend(
sessionManager.getRemarkLines(
self.shortTitle, "ISO_LEVEL",
self.surfaceEditor.ui.histogram.lowerValue()))
info.extend(
sessionManager.getRemarkLines(
self.shortTitle, "MAX_ISO_LEVEL",
self.surfaceEditor.ui.histogram.higherValue()))
info.extend(
sessionManager.getRemarkLines(
self.shortTitle, "SAMPLING_INTERVAL",
self.surfaceEditor.getSamplingValue()))
info.extend(
sessionManager.getRemarkLines(
self.shortTitle, "DISPLAY_RADIUS",
self.surfaceEditor.ui.spinBoxDisplayRadius.value()))
info.extend(
sessionManager.getRemarkLines(
self.shortTitle, "VIEWING_TYPE_SURFACE",
self.surfaceEditor.ui.radioButtonIsoSurface.isChecked()))
info.extend(
sessionManager.getRemarkLines(
self.shortTitle, "VIEWING_TYPE_SOLID",
self.surfaceEditor.ui.radioButtonSolid.isChecked()))
info.extend(
sessionManager.getRemarkLines(
self.shortTitle, "VIEWING_TYPE_CROSS_SECTION",
self.surfaceEditor.ui.radioButtonCrossSection.isChecked()))
info.extend(
sessionManager.getRemarkLines(
self.shortTitle, "USE_DISPLAY_RADIUS",
self.surfaceEditor.ui.checkBoxUseRadius.checkState()))
return info
def __init__(self, main, parent=None):
BaseViewer.__init__(self, main, parent)
self.title = "C-Alpha"
self.shortTitle = "CAL"
self.app.themes.addDefaultRGB("C-Alpha:Atom", 170, 170, 0, 255)
self.app.themes.addDefaultRGB("C-Alpha:Bond", 120, 120, 170, 255)
self.app.themes.addDefaultRGB("C-Alpha:Helix", 0, 255, 0, 255)
self.app.themes.addDefaultRGB("C-Alpha:Strand", 128, 255, 255, 255)
self.app.themes.addDefaultRGB("C-Alpha:Loop", 255, 128, 0, 255)
self.app.themes.addDefaultRGB("C-Alpha:Carbon", 200, 200, 200, 255)
self.app.themes.addDefaultRGB("C-Alpha:Nitrogen", 0, 0, 255, 255)
self.app.themes.addDefaultRGB("C-Alpha:Oxygen", 255, 0, 0, 255)
self.app.themes.addDefaultRGB("C-Alpha:Sulphur", 255, 255, 0, 255)
self.app.themes.addDefaultRGB("C-Alpha:BoundingBox", 255, 255, 255,
255)
self.isClosedMesh = False
self.centerOnRMB = True
self.selectEnabled = True
self.renderer = CAlphaRenderer()
self.displayStyle = self.DisplayStyleBackbone
self.renderer.setDisplayStyle(self.displayStyle)
self.main_chain = Chain('', self.app)
self.structPred = None
self.createUI()
self.app.viewers["calpha"] = self
self.atomsVisible = True
self.bondsVisible = True
self.helicesVisible = True
self.strandsVisible = True
self.loopsVisible = True
#self.interpSegments = 10 # the number of segments interpolated per calpha atom when rendering ribbon diagrams
#self.ribbonSlices = 10 # the number of slices used to render each segment of a ribbon diagram
self.initVisualizationOptions(AtomVisualizationForm(self.app, self))
self.loadedChains = []
self.ribbonMouseMapping = {}
self.ribbonMouseMapping[0] = {}
self.ribbonMouseMapping[1] = {}
self.ribbonMouseMapping[2] = {}
#self.connect(self, QtCore.SIGNAL("elementSelected (int, int, int, int, int, int, QMouseEvent)"), self.centerOnSelectedAtoms)
self.connect(
self,
QtCore.SIGNAL(
"elementClicked (int, int, int, int, int, int, QMouseEvent)"),
self.processElementClick)
def clearSelection(self):
BaseViewer.clearSelection(self)
self.main_chain.setSelection([], None, None, None)
self.emitAtomSelectionUpdated(self.main_chain.getSelection())