def __init__(self, key, appState, parent=None):
super(HomopolyEditor, self).__init__(parent, modal=1)
self.ui = Ui_HomopolyEditor()
self.ui.setupUi(self)
self.state = appState
self.type = key
#self.slideFactor = 50
#self.files = None
self.homopolPreview = MixtureViewer()
self.ui.viewerLayout.addWidget(self.homopolPreview)
self.ui.lengthDSpinner.setValue(self.DISPL[self.type][0])
self.ui.lengthDSpinner.setSingleStep(self.DISPL[self.type][0])
self.ui.lengthDSpinner.setMinimum(self.DISPL[self.type][0])
self.ui.lengthSlider.setValue(self.DISPL[self.type][0])
self.ui.lengthSlider.setTickInterval(self.DISPL[self.type][0])
self.ui.lengthSlider.setMinimum(self.DISPL[self.type][0])
self.ui.stackedWidget.setCurrentIndex(self.DISPL[self.type][1])
self.generateHomopol()
self.generateHomopol()
if __name__ != '__main__':
self.ui.saveButton.setHidden(True)
def __init__(self, parent=None, settings=None):
"""
Constructor for nanotube editor.
Parameters used:
parent : Window, widget or object that was used to call this dialogue
settings: Settings
"""
super(DiamondBuilder, self).__init__(parent, modal=1)
self.settings = settings
self.isAdded = False
self.files = None
# esto hay que arreglarlo!
self.history = History()
self.diamondPreview = MixtureViewer(self.history, self, None)
self.ui = Ui_DiamondEditor()
self.ui.setupUi(self)
self.ui.viewerLayout.addWidget(self.diamondPreview)
self.generateDimond()
if self.settings:
self.diamondPreview.setHighResolution(settings.highResolution)
self.diamondPreview.setLabeling(settings.showLabels)
self.diamondPreview.showAxes(settings.showAxes)
self.diamondPreview.showHelp(settings.showHelp)
self.ui.OKButton.setText("OK")
try:
self.setStyleSheet(open(WOLFFIA_STYLESHEET, 'r').read())
except:
print("WARNING: Could not read style specifications")
def __init__(self, key, appState, parent=None, settings=None):
"""
Constructor for homopolymer editor.
Parameters used:
parent : Window, widget or object that was used to call this dialogue
settings: Settings
"""
super(HomopolyEditor, self).__init__(parent, modal=1)
self.settings = settings
self.state = appState
self.type = key
self.files = None
self.isAdded = False
#esto hay que arreglarlo!
# Que hay que arreglar de aqui??? ~ Radames
self.history = History()
self.homopolPreview = MixtureViewer(self.history, self, None)
self.ui = Ui_HomopolyEditor()
self.ui.setupUi(self)
self.generateHomopol()
self.ui.viewerLayout.addWidget(self.homopolPreview)
self.ui.headerLabel.setText(str(self.type) + " Editor")
#self.ui.stackedWidget.setCurrentIndex (self.poly.STACK_INDEX)
self.ui.lengthDSpinner.setSingleStep(self.poly.DISPL)
self.ui.lengthDSpinner.setMinimum(self.poly.DISPL)
self.ui.lengthSlider.setTickInterval(self.poly.DISPL)
self.ui.lengthSlider.setMinimum(self.poly.DISPL)
self.ui.nSpinBox.setValue(2)
image = os.path.dirname(
os.path.realpath(__file__)) + "/images/" + self.poly.IMAGE
self.ui.diagram.setPixmap(
QtGui.QPixmap(QtCore.QString.fromUtf8(image)).scaledToHeight(
100, 1))
if self.settings != None:
self.homopolPreview.setHighResolution(self.settings.highResolution)
self.homopolPreview.setLabeling(self.settings.showLabels)
self.homopolPreview.showAxes(self.settings.showAxes)
self.homopolPreview.showHelp(settings.showHelp)
self.ui.okButton.setText("OK")
try:
self.setStyleSheet(open(WOLFFIA_STYLESHEET, 'r').read())
except:
print("WARNING: Could not read style specifications")
self.homopolPreview.update()
def __init__(self, parent=None, dropedPdb=None):
super(Load, self).__init__(parent, modal = 1)
print("Load dropedPdb=", dropedPdb)
#Dialog settings
self.uiLoad = Ui_Load()
self.uiLoad.setupUi(self)
self.history = History()
self.isAdded = False
self.history.currentState().reset()
#Viewer
print("Load setting viewer")
self.previewArea = MixtureViewer(self.history, self, None)
self.previewArea.showHelp(False)
self.uiLoad.moleculeViewerLayout.addWidget(self.previewArea)
#Mixture
print("Load setting getting mixture")
self.myMixture = self.history.currentState().getMixture()
self.mixAndRows = list()
#Table Settings
self.loadTable = self.uiLoad.tableWidget
self.loadTableRows = 0
self.equalMolecules = []
self.saveCheckBox = None
#Information Button Settings
self.uiLoad.hint.setFlat(True)
self.uiLoad.hint.setIcon(QtGui.QIcon().fromTheme("dialog-information", QtGui.QIcon(str(NANOCAD_BASE+"\\interface\\graphics\\") +"dialog-information.png")))
self.uiLoad.connectDataBaseButton.setFlat(True)
self.uiLoad.connectDataBaseButton.setIcon(QtGui.QIcon().fromTheme("network-server", QtGui.QIcon(str(NANOCAD_BASE+"\\interface\\graphics\\") +"dialog-information.png")))
#PDB droped from MixtureViewer
print("Load setting pdbDirectory")
self.pdbDirectory = dropedPdb
if self.pdbDirectory != None:
print("Load setting self.pdbDirectory != None")
self.uiLoad.lineEdit_1.setText(self.pdbDirectory)
print("Load animateClick")
self.uiLoad.loadButton.animateClick()
print("Load end")
class CelluloseEditor(QtGui.QDialog):
"""
Wolffia's dialogue to produce homopolymers.
"""
# Class Fields:
# ui: stores reference to user interface
# files: [string, string], PDB and PSF filenames
# homopol: Mixture, an Homopolymer
# homopolPreview: MixtureViewer
def __init__(self, appState, parent=None, settings=None):
"""
Constructor for homopolymer editor.
Parameters used:
parent : Window, widget or object that was used to call this dialogue
settings: Settings
"""
super(CelluloseEditor, self).__init__(parent, modal=1)
self.settings = settings
self.state = appState
self.files = None
self.isAdded = False
#esto hay que arreglarlo!
# Que hay que arreglar de aqui??? ~ Radames
self.history = History()
self.homopolPreview = MixtureViewer(self.history, self, None)
self.ui = Ui_CelluloseEditor()
self.ui.setupUi(self)
self.generateCellulose()
self.ui.viewerLayout.addWidget(self.homopolPreview)
self.ui.headerLabel.setText("Cellulose Crystal Editor")
#self.ui.stackedWidget.setCurrentIndex (self.poly.STACK_INDEX)
self.ui.lengthDSpinner.setSingleStep(self.poly.DISPL)
self.ui.lengthDSpinner.setMinimum(self.poly.DISPL)
self.ui.lengthSlider.setTickInterval(self.poly.DISPL)
self.ui.lengthSlider.setMinimum(self.poly.DISPL)
self.ui.nSpinBox.setValue(2)
image = os.path.dirname(
os.path.realpath(__file__)) + "/images/" + self.poly.IMAGE
self.ui.diagram.setPixmap(
QtGui.QPixmap(QtCore.QString.fromUtf8(image)).scaledToHeight(
100, 1))
if self.settings != None:
self.homopolPreview.setHighResolution(self.settings.highResolution)
self.homopolPreview.setLabeling(self.settings.showLabels)
self.homopolPreview.showAxes(self.settings.showAxes)
self.homopolPreview.showHelp(settings.showHelp)
self.ui.okButton.setText("OK")
try:
self.setStyleSheet(open(WOLFFIA_STYLESHEET, 'r').read())
except:
print("WARNING: Could not read style specifications")
self.homopolPreview.update()
def generateCellulose(self):
n = self.ui.nSpinBox.value()
self.homopol = Mixture()
from chemicalGraph.molecule.polymer.Cellulose import Cellulose
if self.ui.buttonA.isChecked():
self.poly = Cellulose(n, 'a')
else:
self.poly = Cellulose(n, 'b')
self.homopol.add(self.poly)
self.history.currentState().reset()
self.history.currentState().addMixture(self.homopol)
self.homopolPreview.update()
def getMixture(self):
return self.history.currentState().getMixture()
# Signal managers
def on_nSpinBox_valueChanged(self):
self.generateCellulose()
length = self.poly.DISPL * self.ui.nSpinBox.value()
self.ui.lengthDSpinner.setValue(length)
self.ui.lengthSlider.setValue(length)
def on_lengthDSpinner_valueChanged(self):
n = round(self.ui.lengthDSpinner.value() / self.poly.DISPL)
self.ui.nSpinBox.setValue(n)
self.ui.lengthSlider.setValue(n * self.poly.DISPL)
def on_lengthSlider_sliderReleased(self):
n = int(self.ui.lengthSlider.value() / self.poly.DISPL)
self.ui.nSpinBox.setValue(n)
#---------------------------------------------------------------------
def on_buttonB_toggled(self, checked):
self.ui.buttonA.setChecked(not checked)
self.generateCellulose()
#---------------------------------------------------------------------
def on_buttonA_toggled(self, checked):
self.ui.buttonB.setChecked(not checked)
self.generateCellulose()
#---------------------------------------------------------------------
def on_button110_toggled(self, checked):
if checked:
self.ui.button100.setChecked(not checked)
self.ui.button010.setChecked(not checked)
self.update()
#---------------------------------------------------------------------
def on_button100_toggled(self, checked):
if checked:
self.ui.button110.setChecked(not checked)
self.ui.button010.setChecked(not checked)
self.update()
#---------------------------------------------------------------------
def on_button010_toggled(self, checked):
if checked:
self.ui.button100.setChecked(not checked)
self.ui.button110.setChecked(not checked)
self.update()
def on_okButton_pressed(self):
self.generateCellulose()
self.isAdded = True
self.close()
def on_cancelButton_pressed(self):
self.history.currentState().reset()
self.close()
def closeEvent(self, e):
if not self.isAdded:
self.history.currentState().updateMixture(Mixture())
def wheelEvent(self, e):
super(HomopolyEditor, self).wheelEvent(e)
class GrapheneBuilder(QtGui.QDialog):
"""
Wolffia's dialogue box to produce graphenes
"""
# Class Fields:
# ui: stores reference tu user interface
# files: [string, string], PDB and PSF filenames
# graphene: Mixture, a Graphene
# graphenePreview: MixtureViewer
def __init__(self, parent=None, settings=None):
"""
Constructor for graphene editor.
Parameters used:
parent : Window, widget or object that was used to call this dialogue
settings: Settings
"""
super(GrapheneBuilder, self).__init__(parent, modal=1)
self.ui = Ui_GrapheneEditor()
self.isAdded = False
self.settings = settings
self.history = History()
self.graphenePreview = MixtureViewer(self.history, self, None)
self.files = None
self.ui.setupUi(self)
self.ui.viewerLayout.addWidget(self.graphenePreview)
self.generateGraphene()
if self.settings:
self.graphenePreview.setHighResolution(
self.settings.highResolution)
self.graphenePreview.setLabeling(self.settings.showLabels)
self.graphenePreview.showAxes(self.settings.showAxes)
self.graphenePreview.showHelp(self.settings.showHelp)
self.ui.OKButton.setText("OK")
try:
self.setStyleSheet(open(WOLFFIA_STYLESHEET, 'r').read())
except:
print("WARNING: Could not read style specifications")
self.graphenePreview.update()
def generateGraphene(self):
n = self.ui.nSpinBox.value()
m = self.ui.mSpinBox.value()
grapheneLength = self.ui.grapheneLengthSpinBox.value()
self.history.currentState().reset()
self.history.currentState().addMolecule(Graphene(n, m, grapheneLength))
self.graphenePreview.update()
def getMixture(self):
return self.history.currentState().getMixture()
# Manages signals
def on_horizontalSlider_valueChanged(self, pos):
self.ui.grapheneLengthSpinBox.setValue(pos / 10.)
def on_grapheneLengthSpinBox_valueChanged(self, val):
self.ui.horizontalSlider.setValue(int(float(val) * 10))
@QtCore.pyqtSlot()
def on_OKButton_pressed(self):
if self.settings:
self.generateGraphene()
#self.state.addMixture(self.graphene)
self.isAdded = True
self.close()
else:
from .GrapheneSaveDialog import GrapheneSaveDialog
self.generateGraphene()
ntDialog = GrapheneSaveDialog(self.graphene,
files=self.files,
parent=self)
ntDialog.show()
ntDialog.exec_()
self.files = ntDialog.getFileNames()
print(self.files)
@QtCore.pyqtSlot()
def on_previewButton_pressed(self):
self.generateGraphene()
@QtCore.pyqtSlot()
def on_cancelButton_pressed(self):
self.close()
def closeEvent(self, e):
if not self.isAdded:
self.history.currentState().updateMixture(Mixture())
class NanotubeBuilder(QtGui.QDialog):
"""
Wolffia's dialogue box to produce nanotubes.
"""
# Class Fields:
# ui: stores reference to user interface
# files: [string, string], PDB and PSF filenames
# tubes: Mixture, a Tube
# tubePreview: MixtureViewer
def __init__(self, parent=None, settings=None):
"""
Constructor for nanotube editor.
Parameters used:
parent : Window, widget or object that was used to call this dialogue
settings: Settings
"""
super(NanotubeBuilder, self).__init__(parent, modal=1)
self.settings = settings
self.isAdded = False
self.files = None
# esto hay que arreglarlo!
self.history = History()
self.tubePreview = MixtureViewer(self.history, self, None)
self.ui = Ui_NanotubeEditor()
self.ui.setupUi(self)
self.ui.viewerLayout.addWidget(self.tubePreview)
self.generateTubes()
self.ui.nSpinBox.setMaximum(200)
self.ui.mSpinBox.setMaximum(200)
if self.settings:
self.tubePreview.setHighResolution(settings.highResolution)
self.tubePreview.setLabeling(settings.showLabels)
self.tubePreview.showAxes(settings.showAxes)
self.tubePreview.showHelp(settings.showHelp)
self.ui.OKButton.setText("OK")
try:
self.setStyleSheet(open(WOLFFIA_STYLESHEET, 'r').read())
except:
print("WARNING: Could not read style specifications")
self.tubePreview.update()
def generateTubes(self):
n = self.ui.nSpinBox.value()
m = self.ui.mSpinBox.value()
tubeLength = self.ui.tubeLengthSpinBox.value()
self.history.currentState().reset()
self.history.currentState().addMolecule(Tube(n, m, tubeLength))
self.modified = False
def getMixture(self):
return self.history.currentState().getMixture()
# Signal managers
def on_horizontalSlider_valueChanged(self, pos):
self.ui.tubeLengthSpinBox.setValue(pos / 10.)
self.modified = True
def on_tubeLengthSpinBox_valueChanged(self, val):
self.ui.horizontalSlider.setValue(int(float(val) * 10))
self.modified = True
def on_mSpinBox_valueChanged(self, val):
if self.ui.armchairButton.isChecked():
self.ui.nSpinBox.setValue(self.ui.mSpinBox.value())
self.modified = True
# Toggles between the three different types of nanotube layouts
def on_armchairButton_toggled(self, selected):
if selected:
self.ui.nSpinBox.setValue(self.ui.mSpinBox.value())
self.ui.nSpinBox.setDisabled(True)
self.modified = True
def on_chiralButton_toggled(self, selected):
if selected:
self.ui.nSpinBox.setEnabled(True)
self.modified = True
def on_zigZagButton_toggled(self, selected):
if selected:
self.ui.nSpinBox.setValue(0)
self.ui.nSpinBox.setDisabled(True)
self.modified = True
@QtCore.pyqtSlot()
def on_cancelButton_pressed(self):
self.close()
@QtCore.pyqtSlot()
def on_OKButton_pressed(self):
if self.modified: self.generateTubes()
if self.settings:
self.isAdded = True
self.close()
else:
from .NanotubeSaveDialog import NanotubeSaveDialog
ntDialog = NanotubeSaveDialog(self.getMixture(),
files=self.files,
parent=self)
ntDialog.show()
ntDialog.exec_()
self.files = ntDialog.getFileNames()
print(self.files)
@QtCore.pyqtSlot()
def on_previewButton_pressed(self):
self.generateTubes()
self.tubePreview.update()
def closeEvent(self, e):
if not self.isAdded:
self.history.currentState().updateMixture(Mixture())
class HomopolyEditor(QtGui.QDialog):
# Class Fields:
# ui: stores reference tu user interface
# files: [string, string], PDF and PSF filenames
# homopol: Mixture, an Homopolymer
# homopolPreview: MixtureViewer
DISPL = {"PMMA": [3.7, 0], "PolyCYT": [6.0, 1]}
def __init__(self, key, appState, parent=None):
super(HomopolyEditor, self).__init__(parent, modal=1)
self.ui = Ui_HomopolyEditor()
self.ui.setupUi(self)
self.state = appState
self.type = key
#self.slideFactor = 50
#self.files = None
self.homopolPreview = MixtureViewer()
self.ui.viewerLayout.addWidget(self.homopolPreview)
self.ui.lengthDSpinner.setValue(self.DISPL[self.type][0])
self.ui.lengthDSpinner.setSingleStep(self.DISPL[self.type][0])
self.ui.lengthDSpinner.setMinimum(self.DISPL[self.type][0])
self.ui.lengthSlider.setValue(self.DISPL[self.type][0])
self.ui.lengthSlider.setTickInterval(self.DISPL[self.type][0])
self.ui.lengthSlider.setMinimum(self.DISPL[self.type][0])
self.ui.stackedWidget.setCurrentIndex(self.DISPL[self.type][1])
self.generateHomopol()
self.generateHomopol()
if __name__ != '__main__':
self.ui.saveButton.setHidden(True)
def generateHomopol(self):
self.ui.headerLabel.setText(str(self.type) + " Editor")
n = self.ui.nSpinBox.value()
self.homopol = Mixture()
exec("from chemicalGraph.molecule.polymer." + str(self.type) +
" import " + str(self.type))
self.homopol.add(eval(str(self.type) + "(n)"))
self.homopolPreview.setMixture(self.homopol)
# Manages signals
def on_nSpinBox_valueChanged(self, value):
self.generateHomopol()
length = self.DISPL[self.type][0] * value
self.ui.lengthDSpinner.setValue(length)
self.ui.lengthSlider.setValue(length)
def on_lengthDSpinner_valueChanged(self, value):
n = int(math.floor(value / self.DISPL[self.type][0]))
self.ui.nSpinBox.setValue(n)
self.generateHomopol()
#self.ui.lengthSlider.setValue(value)
def on_lengthSlider_sliderMoved(self, value):
n = int(math.floor(value / self.DISPL[self.type][0]))
self.ui.nSpinBox.setValue(n)
self.generateHomopol()
self.ui.lengthDSpinner.setValue(value)
def on_okButton_pressed(self):
self.generateHomopol()
self.state.addMixture(self.homopol)
self.close()
'''
def on_saveButton_pressed(self):
from NanotubeSaveDialog import NanotubeSaveDialog
# generate tube
self.generateTubes()
ntDialog = NanotubeSaveDialog(self.tubes,files=self.files, parent=self)
ntDialog.show()
ntDialog.exec_()
self.files = ntDialog.getFileNames()
print self.files
'''
def on_cancelButton_pressed(self):
self.close()
class Load(QtGui.QDialog):
def __init__(self, parent=None, dropedPdb=None):
super(Load, self).__init__(parent, modal = 1)
print("Load dropedPdb=", dropedPdb)
#Dialog settings
self.uiLoad = Ui_Load()
self.uiLoad.setupUi(self)
self.history = History()
self.isAdded = False
self.history.currentState().reset()
#Viewer
print("Load setting viewer")
self.previewArea = MixtureViewer(self.history, self, None)
self.previewArea.showHelp(False)
self.uiLoad.moleculeViewerLayout.addWidget(self.previewArea)
#Mixture
print("Load setting getting mixture")
self.myMixture = self.history.currentState().getMixture()
self.mixAndRows = list()
#Table Settings
self.loadTable = self.uiLoad.tableWidget
self.loadTableRows = 0
self.equalMolecules = []
self.saveCheckBox = None
#Information Button Settings
self.uiLoad.hint.setFlat(True)
self.uiLoad.hint.setIcon(QtGui.QIcon().fromTheme("dialog-information", QtGui.QIcon(str(NANOCAD_BASE+"\\interface\\graphics\\") +"dialog-information.png")))
self.uiLoad.connectDataBaseButton.setFlat(True)
self.uiLoad.connectDataBaseButton.setIcon(QtGui.QIcon().fromTheme("network-server", QtGui.QIcon(str(NANOCAD_BASE+"\\interface\\graphics\\") +"dialog-information.png")))
#PDB droped from MixtureViewer
print("Load setting pdbDirectory")
self.pdbDirectory = dropedPdb
if self.pdbDirectory != None:
print("Load setting self.pdbDirectory != None")
self.uiLoad.lineEdit_1.setText(self.pdbDirectory)
print("Load animateClick")
self.uiLoad.loadButton.animateClick()
print("Load end")
def update(self):
self.previewArea.update()
return
mix = Mixture()
for i in range(self.loadTable.rowCount()):
#for j in range(3,6):
##print "Load update", self.loadTable.item(i,5).text(),self.loadTable.cellWidget(i,1).show
if self.loadTable.cellWidget(i,1).show:
mix.add(self.myMixture.getMolecule(str(self.loadTable.item(i,5).text())))
self.previewArea.setMixture(mix)
#-------------------------------------- Methods ------------------------------------
#loadPsfOrNot(): Asks the user if wants to change all the names of the molecules that are the same
def loadPsfOrNot(self,filename):
msg = QtGui.QMessageBox.question(self, 'Loading Fi\les...',
'Would you like to load the psf file associated with: '+filename+'?\n'+'\n NO, will imply to only read the pdb file.',
QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
return msg == QtGui.QMessageBox.Yes
#--------------------------------------
#changeNameOrNotMessage(): Asks the user if wants to change all the names of the molecules that are the same
def changeNameOrNotMessage(self):
msg = QtGui.QMessageBox.question(self, 'Change all Names...',
'Would you like to change all the names of the molecules with that color?',
QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
return msg == QtGui.QMessageBox.Yes
#--------------------------------------
#getLineEditInfo(): Gets the paths and constructs the Mixture
def getLineEditInfo(self):
# Gets paths
path_1 = str(self.uiLoad.lineEdit_1.displayText())
print("Load getLineEditInfo",path_1)
self.uiLoad.lineEdit_1.clear()
path_2 = str(self.uiLoad.lineEdit_2.displayText())
print("Load getLineEditInfo",path_2)
self.uiLoad.lineEdit_2.clear()
print("Load getLineEditInfo loadInfo")
self.loadInfo(path_1, path_2)
print("Load getLineEditInfo end")
#--------------------------------------
def loadInfo(self,path_1='',path_2= ''):
if path_1 != '' and path_2 == '':
try:
self.history.currentState().getMixture().load(path_1)
except:
QtGui.QMessageBox.warning(self,"Error 1 !!!","There is a problem loading the file " + path_1 + " in box 1.")
print(sys.exc_info())
elif not(path_2 == '') and path_1 == '':
try:
self.history.currentState().getMixture().load(path_2)
except:
QtGui.QMessageBox.warning(self,"Error 2 !!!","There is a problem loading the file " + path_2 + " in box 2.")
elif not(path_1 == '') and not(path_2 == ''):
if (path_1[len(path_1)-3]+path_1[len(path_1)-2]+path_1[len(path_1)-1]) == 'pdb' and (path_2[len(path_2)-3]+path_2[len(path_2)-2]+path_2[len(path_2)-1]) == 'psf':
try:
self.history.currentState().getMixture().load(path_1,path_2)
except Exception as e:
QtGui.QMessageBox.warning(self,"Error 3 !!!","There is a problem with the file."+str(e))
elif (path_1[len(path_1)-3]+path_1[len(path_1)-2]+path_1[len(path_1)-1]) == 'psf' and (path_2[len(path_2)-3]+path_2[len(path_2)-2]+path_2[len(path_2)-1]) == 'pdb':
try:
self.history.currentState().getMixture().load(path_2,path_1)
except Exception as e:
QtGui.QMessageBox.warning(self,"Error 4 !!!","There is a problem with the file."+str(e))
else:QtGui.QMessageBox.warning(self,"Error 5 !!!","There is a problem with the file.")
elif not(path_1 == '') and (path_1[len(path_1)-3]+path_1[len(path_1)-2]+path_1[len(path_1)-1]) == 'pdb':
filePath = None
#Search if the *.psf file associated with the *.pdb file exists in the same folder
for f in os.listdir(os.path.dirname(path_1)) :
path1 = os.path.basename(path_1)
if f == path1[0:len(path1)-2]+'s'+'f':
filePath = os.path.dirname(path_1)+'/'+f
#print "filePath",filePath
if not(filePath == None):
if self.loadPsfOrNot(f):
try:
self.history.currentState().getMixture().load(path_1,filePath)
except:
QtGui.QMessageBox.warning(self,"Error 6 !!!","There is a problem with the file.")
else:
try:
self.history.currentState().getMixture().load(path_1,None)
except:
QtGui.QMessageBox.warning(self,"Error 7 !!!","There is a problem with the file.")
else:
try:
self.history.currentState().getMixture().load(path_1,None)
except:
QtGui.QMessageBox.warning(self,"Error 8 !!!","There is a problem with the file.")
elif not(path_1 == '') and (path_1[len(path_1)-3]+path_1[len(path_1)-2]+path_1[len(path_1)-1]) == 'psf':
for f in os.listdir(os.path.dirname(path_1)) :
path1 = os.path.basename(path_1)
if f == path1[0:len(path1)-2]+'d'+'b':
filePath = os.path.dirname(path_1)+'/'+f
try:
self.history.currentState().getMixture().load(filePath,path_1)
except:
QtGui.QMessageBox.warning(self,"Error 9 !!!","There is a problem with the file.")
elif path_1 == '' and not(path_2 == '') and (path_2[len(path_2)-3]+path_2[len(path_2)-2]+path_2[len(path_2)-1]) == 'pdb':
filePath = None
for f in os.listdir(os.path.dirname(path_2)) :
path2 = os.path.basename(path_2)
if f == path2[0:len(path2)-2]+'s'+'f':
filePath = os.path.dirname(path_2)+'/'+f
if not(filePath == None):
if self.loadPsfOrNot(f):
try:
self.history.currentState().getMixture().load(path_2,filePath)
except:
QtGui.QMessageBox.warning(self,"Error 10 !!!","There is a problem with the file.")
else:
try:
self.history.currentState().getMixture().load(path_2,None)
except:
QtGui.QMessageBox.warning(self,"Error 11 !!!","There is a problem with the file.")
else:
try:
self.history.currentState().getMixture().load(path_2,None)
except:
QtGui.QMessageBox.warning(self,"Error 12 !!!","There is a problem with the file.")
elif path_1 == '' and not(path_2 == '') and (path_2[len(path_2)-3]+path_2[len(path_2)-2]+path_2[len(path_2)-1]) == 'psf':
for f in os.listdir(os.path.dirname(path_2)) :
path2 = os.path.basename(path_2)
if f == path2[0:len(path2)-2]+'d'+'b':
filePath = os.path.dirname(path_2)+'/'+f
try:
self.history.currentState().getMixture().load(filePath,path_2)
except:
QtGui.QMessageBox.warning(self,"Error 13 !!!","There is a problem with the file.")
else:QtGui.QMessageBox.warning(self,"Error 14 !!!","There is a problem with the file.**")
#This is how we can obtain the atoms...
#for m in self.history.currentState().getMixture().nodes():
#print "@Load:mixture",self.history.currentState().getMixture().getMolecule(m).nodes()
#print "myMixture",self.myMixture.order()
#--------------------------------------
#addCheckBox(): Adds a CheckBox into the column's cell to select the molecules that would be loaded
def addCheckBox(self,row,name):
#---CheckBox---
self.saveCheckBox = CheckBox(self,row,self.loadTable)
self.saveCheckBox.setObjectName(str(name+str(row)))
self.saveCheckBox.setCheckState(QtCore.Qt.Checked)
self.saveCheckBox.setFixedSize(25,25)
#---Cell---
self.loadTable.setCellWidget(row,0,self.saveCheckBox)
#--------------------------------------
#addButtonintoCell(): Adds a button into the column's cell to preview the molecules
def addButtonintoCell(self,row,name):
self.viewToolButton = PreviewButton(self.history.currentState(),
self.previewArea,parent=self.loadTable, molname=str(name),
initState=True)
#initState=self.history.currentState().shownMolecules.isShown(str(name)))
self.history.currentState().shownMolecules.show(str(name))
#QtCore.QObject.connect(self.viewToolButton, QtCore.SIGNAL('clicked()'), self.on_viewToolButton_clicked())
#self.viewToolButton.clicked.connect(self.on_viewToolButton_clicked)
self.viewToolButton.setObjectName(str(name))
self.viewToolButton.setFixedSize(25,25)
#---Cell---
self.loadTable.setCellWidget(row,1,self.viewToolButton)
#--------------------------------------
#showHideAllMessage(): Asks the user if wants to show/hide all the molecules painted with the same color
def loadMessage(self):
msg = QtGui.QMessageBox.information(self, 'Information...',
'This may take a while. Please be patient ... ',
QtGui.QMessageBox.Ok)
#--------------------------------------
#showHideAllMessage(): Asks the user if wants to show/hide all the molecules painted with the same color
def showHideAllMessage(self):
msg = QtGui.QMessageBox.question(self, 'Show or Hide...',
'Would you like to show/hide all the molecules with that color?',
QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
return msg == QtGui.QMessageBox.Yes
#--------------------------------------
#reviewIsomorphisms(): Verify graph's isomorphism between two graphs
def reviewIsomorphisms(self):
tempList = []
theColors = []
self.equalMolecules = []
row = -1
for c in range(0,self.myMixture.order()):
color = createColors()
theColors.append(color)
#Check equal molecules
remainingMols = list(self.myMixture)
for each in self.myMixture:
row = row + 1
searchList = list(remainingMols)
for theMol in searchList:
if self.myMixture.getMolecule(each) == self.myMixture.getMolecule(theMol):
tempList.append(theMol)
remainingMols.remove(theMol)
if len(tempList) > 0:
self.equalMolecules.append([tempList, None])
tempList = []
#creating colors
for c in range(0,len(self.equalMolecules)):
color = createColors()
self.equalMolecules[c][1] = color
#for molecule in self.equalMolecules[c][0]:
#self.myMixture.getMolecule(molecule).rename(molecule + str(c))
#************************************************
#addSelectAllCheckBox(): Create a checkBox to select all the molecules in the table
def addSelectAllCheckBox(self):
self.selectAllCheckBox = QtGui.QCheckBox()
self.deSelectAll = True
font = QtGui.QFont()
font.setPointSize(9)
self.selectAllCheckBox.setFont(font)
self.selectAllCheckBox.setText(QtGui.QApplication.translate("Load", "Select All", None, QtGui.QApplication.UnicodeUTF8))
self.selectAllCheckBox.setObjectName("selectAllCheckBox")
self.selectAllCheckBox.setCheckState(QtCore.Qt.Checked)
self.selectAllCheckBox.setTristate(on = False)
self.uiLoad.SelectAllLayout.addWidget(self.selectAllCheckBox)
self.connect(self.selectAllCheckBox, QtCore.SIGNAL('stateChanged(int)'), self.checkBoxState)
def checkBoxState(self, value):
if self.selectAllCheckBox.checkState() == QtCore.Qt.Checked:
for row in range(0,self.loadTableRows):
self.loadTable.cellWidget(row,0).setCheckState(QtCore.Qt.Checked)
elif self.selectAllCheckBox.checkState() == QtCore.Qt.Unchecked and self.deSelectAll == True:
for row in range(0,self.loadTableRows):
self.loadTable.cellWidget(row,0).setCheckState(QtCore.Qt.Unchecked)
elif self.selectAllCheckBox.checkState() == QtCore.Qt.Unchecked and self.deSelectAll == False:
self.deSelectAll = True
#************************************************
#addSelectAllCheckBox(): Create a checkBox to select all the molecules in the table
def addShowHideAllCheckBox(self):
self.showHideAllCheckBox = QtGui.QCheckBox()
#print "Entre aqui"
self.showAll = True
font = QtGui.QFont()
font.setPointSize(9)
self.showHideAllCheckBox.setFont(font)
self.showHideAllCheckBox.setText(QtGui.QApplication.translate("Load", "Show All", None, QtGui.QApplication.UnicodeUTF8))
self.showHideAllCheckBox.setObjectName("showHideAllCheckBox")
self.showHideAllCheckBox.setCheckState(QtCore.Qt.Checked)
self.showHideAllCheckBox.setTristate(on = False)
self.uiLoad.ShowAllLayout.addWidget(self.showHideAllCheckBox)
self.connect(self.showHideAllCheckBox, QtCore.SIGNAL('stateChanged(int)'), self.showHideAllState)
def showHideAllState(self, value):
if self.showHideAllCheckBox.checkState() == QtCore.Qt.Checked:
for row in range(0,self.loadTableRows):
self.loadTable.cellWidget(row,1).setShown()
#self.loadTable.cellWidget(row,1).click()
elif self.showHideAllCheckBox.checkState() == QtCore.Qt.Unchecked and self.showAll == True:
for row in range(0,self.loadTableRows):
self.loadTable.cellWidget(row,1).setHidden()
elif self.showHideAllCheckBox.checkState() == QtCore.Qt.Unchecked and self.showAll == False:
self.showAll = True
#*************************************************
#setTable(): Creates and show the table
def setTable(self):
self.reviewIsomorphisms()
#creates rows and columns
self.loadTable.setColumnCount(6)
self.loadTableRows = self.myMixture._len()
self.loadTable.setRowCount(self.loadTableRows)
item = QtGui.QTableWidgetItem()
self.loadTable.setHorizontalHeaderItem(0, item)
self.loadTable.horizontalHeaderItem(0).setText(QtGui.QApplication.translate("Load", "Save", None, QtGui.QApplication.UnicodeUTF8))
item = QtGui.QTableWidgetItem()
self.loadTable.setHorizontalHeaderItem(1, item)
self.loadTable.horizontalHeaderItem(1).setText(QtGui.QApplication.translate("Load", "Prev", None, QtGui.QApplication.UnicodeUTF8))
item = QtGui.QTableWidgetItem()
self.loadTable.setHorizontalHeaderItem(2, item)
self.loadTable.horizontalHeaderItem(2).setText(QtGui.QApplication.translate("Load", "Molecule Name", None, QtGui.QApplication.UnicodeUTF8))
item = QtGui.QTableWidgetItem()
self.loadTable.setHorizontalHeaderItem(3, item)
self.loadTable.horizontalHeaderItem(3).setText(QtGui.QApplication.translate("Load", "No. of Atoms", None, QtGui.QApplication.UnicodeUTF8))
item = QtGui.QTableWidgetItem()
item.setTextAlignment(0x0001)
self.loadTable.setHorizontalHeaderItem(4, item)
self.loadTable.horizontalHeaderItem(4).setText(QtGui.QApplication.translate("Load", "Atoms Found", None, QtGui.QApplication.UnicodeUTF8))
item = QtGui.QTableWidgetItem()
self.loadTable.setHorizontalHeaderItem(5, item)
self.loadTable.horizontalHeaderItem(5).setText(QtGui.QApplication.translate("Load", "Atom_ID", None, QtGui.QApplication.UnicodeUTF8))
row = 0
temp =[]
#Adding the molecule information into the rows
for eqCassInd in range(len(self.equalMolecules)):
for molName in self.equalMolecules[eqCassInd][0]:
for column in range(0,6):
item = QtGui.QTableWidgetItem()
self.loadTable.setItem(row, column, item)
if column == 0:
self.addCheckBox(row,molName)
self.loadTable.resizeColumnToContents(column)
elif column == 1:
self.addButtonintoCell(row,molName)
self.loadTable.resizeColumnToContents(column)
temp.append(molName)
temp.append(row)
self.mixAndRows.append(temp)
temp = []
elif column == 2:
newTableWidgetItem = myTableWidgetItem(self, self.myMixture.getMolecule(molName)._name, molName)
newTableWidgetItem.setBackgroundColor(self.equalMolecules[eqCassInd][1])
self.loadTable.setItem(row,column,newTableWidgetItem)
self.loadTable.resizeColumnToContents(column)
elif column == 3:
newitem = myTableWidgetItem(self,str(self.myMixture.getMolecule(molName).order()))
newitem.setFlags(QtCore.Qt.ItemIsEnabled)
self.loadTable.setItem(row, column, newitem)
self.loadTable.resizeColumnToContents(column)
elif column == 4:
molecule = self.myMixture.getMolecule(molName)
newitem = myTableWidgetItem(self,str(molecule.getElements()))
newitem.setFlags(QtCore.Qt.ItemIsEnabled)
self.loadTable.setItem(row, column, newitem)
self.loadTable.resizeColumnToContents(column)
elif column == 5:
newitem = QtGui.QTableWidgetItem(str(molName))
newitem.setFlags(QtCore.Qt.ItemIsEnabled)
self.loadTable.setItem(row, column, newitem)
self.loadTable.resizeColumnToContents(column)
row += 1
self.update()
#---------------- Dialog's signals -------------------
def on_Browse_1_pressed(self):
d = WFileDialog(self, 'Browse File','','')
if d.accepted():
filename = d.fullFilename()
if not os.path.exists(str(filename)):
QtGui.QMessageBox.information(self, "Wolffia's message", "Did not find file " + filename + ". File not loaded.", QtGui.QMessageBox.Ok)
return
self.uiLoad.lineEdit_1.setText(str(d.fullFilename()))
def on_Browse_2_pressed(self):
d = WFileDialog(self, 'Browse File','','')
if d.accepted():
filename = d.fullFilename()
if not os.path.exists(str(filename)):
QtGui.QMessageBox.information(self, "Wolffia's message", "Did not find file " + filename + ". File not loaded.", QtGui.QMessageBox.Ok)
return
self.uiLoad.lineEdit_2.setText(str(d.fullFilename()))
def on_hint_pressed(self):
from .AboutLoad import AboutLoad
about = AboutLoad(self)
about.show()
about.exec_()
def on_connectDataBaseButton_pressed(self):
#print"on_connectDataBaseButton_pressed"
from .ImportMolecules import ImportMolecules
importMoleculeDialog = ImportMolecules()
importMoleculeDialog.show()
importMoleculeDialog.exec_()
#print "PDB \n",importMoleculeDialog.getFileType()
if importMoleculeDialog.proceed():
try:
#print importMoleculeDialog.getMoleculeFile()
self.history.currentState().getMixture().load(None,None,importMoleculeDialog.getMoleculeFile(),importMoleculeDialog.getFileType(),importMoleculeDialog.inputName())
except Exception as err:
#print "Load on_connectDataBaseButton_pressed: There is a problem with the file ", importMoleculeDialog.getMoleculeFile()
QtGui.QMessageBox.warning(self,"Error 15 !!!","There is a problem with the file."+ err)
self.loadTable.clear()
self.loadTableRows = 0
self.mixAndRows = []
self.setTable()
if self.uiLoad.SelectAllLayout.isEmpty() and self.uiLoad.ShowAllLayout.isEmpty():
self.addSelectAllCheckBox()
self.addShowHideAllCheckBox()
self.previewArea.setMixture(self.history.currentState().getMixture())
def on_cancelButton_pressed(self):
#print "Load: Cancel Button: history",self.history.currentState()
self.close()
def on_loadButton_pressed(self,dropedPdb=None):
print("Load on_loadButton_pressed",dropedPdb)
if dropedPdb == None:
print("Load on_loadButton_pressed getLineEditInfo")
self.getLineEditInfo()
print("Load on_loadButton_pressed loadTable.clear")
self.loadTable.clear()
self.loadTableRows = 0
self.mixAndRows = []
print("Load on_loadButton_pressed setTable")
self.setTable()
if self.uiLoad.SelectAllLayout.isEmpty():
self.addSelectAllCheckBox()
self.addShowHideAllCheckBox()
print("Load on_loadButton_pressed previewArea.setMixture")
self.previewArea.setMixture(self.history.currentState().getMixture())
print("Load on_loadButton_pressed end")
def on_okButton_pressed(self):
if self.myMixture._len() == 0:
msg = QtGui.QMessageBox.warning(self, 'Warning',
'No molecule has been loaded!',QtGui.QMessageBox.Ok)
else:
progressMax = self.myMixture._len()
progressCount = 0
progress = QtGui.QProgressDialog("Loading mixture...", "Abort", 0, progressMax, self,QtCore.Qt.Dialog|QtCore.Qt.WindowTitleHint)
progress.setWindowModality(QtCore.Qt.WindowModal)
for row in range(0,self.myMixture._len()):
if progress.wasCanceled():
progress.hide()
self.history.currentState().reset()
self.myMixture = self.history.currentState().getMixture()
self.update()
self.close()
return
else:
#Delete unchecked molecules
if (self.loadTable.cellWidget(row,0).checkState()) == QtCore.Qt.Unchecked:
self.myMixture.remove(str(self.loadTable.item(row,5).text()))
#Add remaining molecules to the state
progressCount += 1
progress.setValue(progressCount)
self.isAdded = True
self.close()
def closeEvent(self, e):
if not self.isAdded:
self.myMixture = Mixture()
def getMixture(self): return self.myMixture
#------------- Table's signals ---------
def on_tableWidget_itemChanged(self, wi):
if isinstance(wi, myTableWidgetItem) and wi.name != "(no name)" and wi.isSelected():
self.loadTable.setItemSelected (wi, False)
multipleMolecules = False
for row in range(0,self.loadTable.rowCount()):
if not(self.loadTable.currentRow() == row) \
and self.loadTable.item(self.loadTable.currentRow(),2).backgroundColor() == self.loadTable.item(row,2).backgroundColor():
multipleMolecules = True
break
if multipleMolecules and self.changeNameOrNotMessage():
# changes names of all isomorphic molecules
selColor = wi.backgroundColor()
for eqClass in range(0,len(self.equalMolecules)):
if selColor == self.equalMolecules[eqClass][1]:
for mol in self.equalMolecules[eqClass][0]:
self.myMixture.getMolecule(mol)._name = str(wi.text())
self.setTable()
else:
mol = self.myMixture.getMolecule(wi.name)
mol._name = str(wi.text())
#--------------------------------------
#on_viewToolButton_clicked(): When a viewToolButton is clicked, the user can show/hide all the molecules painted with the same color
def on_viewToolButton_clicked(self):
#print "_mySignal"
value = self.viewToolButton.show
#print "@WWidget _mySignal value",value
multipleMolecules = False
#print "self.loaded.rowCount()",self.loadTable.rowCount()
for row in range(0,self.loadTable.rowCount()):
if not(self.viewToolButton.row == row) and self.loadTable.item(self.viewToolButton.row,2).backgroundColor() == self.loadTable.item(row,2).backgroundColor():
multipleMolecules = True
#print "multipleMolecules = True"
break
if isinstance(self, PreviewButton) and multipleMolecules and self.showHideAllMessage() :
selColor = self.loadTable.item(self.viewToolButton.row,2).backgroundColor()
for row in range(0,self.loadTable.rowCount()):
if selColor == self.loadTable.item(row,2).backgroundColor():
if value == True:
self.loadTable.cellWidget(row,1).setShown()
else:
self.loadTable.cellWidget(row,1).setHidden()
self.loadTable.showAll = False
self.loadTable.showHideAllCheckBox.setCheckState(QtCore.Qt.Unchecked)
else:
if value == False:
self.loadTable.showAll = False
self.loadTable.showHideAllCheckBox.setCheckState(QtCore.Qt.Unchecked)
class DiamondBuilder(QtGui.QDialog):
"""
Wolffia's dialogue box to produce nanotubes.
"""
# Class Fields:
# ui: stores reference to user interface
# files: [string, string], PDB and PSF filenames
# tubes: Mixture, a Tube
# diamondPreview: MixtureViewer
def __init__(self, parent=None, settings=None):
"""
Constructor for nanotube editor.
Parameters used:
parent : Window, widget or object that was used to call this dialogue
settings: Settings
"""
super(DiamondBuilder, self).__init__(parent, modal=1)
self.settings = settings
self.isAdded = False
self.files = None
# esto hay que arreglarlo!
self.history = History()
self.diamondPreview = MixtureViewer(self.history, self, None)
self.ui = Ui_DiamondEditor()
self.ui.setupUi(self)
self.ui.viewerLayout.addWidget(self.diamondPreview)
self.generateDimond()
if self.settings:
self.diamondPreview.setHighResolution(settings.highResolution)
self.diamondPreview.setLabeling(settings.showLabels)
self.diamondPreview.showAxes(settings.showAxes)
self.diamondPreview.showHelp(settings.showHelp)
self.ui.OKButton.setText("OK")
try:
self.setStyleSheet(open(WOLFFIA_STYLESHEET, 'r').read())
except:
print("WARNING: Could not read style specifications")
def generateDimond(self):
n = self.ui.nSpinBox.value()
m = self.ui.mSpinBox.value()
q = self.ui.qSpinBox.value()
self.history.currentState().reset()
self.history.currentState().addMolecule(Diamond(n, m, q))
self.diamondPreview.update()
self.modified = False
def getMixture(self):
return self.history.currentState().getMixture()
@QtCore.pyqtSlot()
def on_cancelButton_pressed(self):
self.close()
def on_nSpinBox_valueChanged(self, val):
self.modified = True
def on_mSpinBox_valueChanged(self, val):
self.modified = True
def on_qSpinBox_valueChanged(self, val):
self.modified = True
@QtCore.pyqtSlot()
def on_OKButton_pressed(self):
if self.settings:
if self.modified: self.generateDimond()
self.isAdded = True
self.close()
else:
from NanotubeSaveDialog import NanotubeSaveDialog
self.generateTubes()
ntDialog = NanotubeSaveDialog(self.tubes,
files=self.files,
parent=self)
ntDialog.show()
ntDialog.exec_()
self.files = ntDialog.getFileNames()
print(self.files)
@QtCore.pyqtSlot()
def on_previewButton_pressed(self):
self.generateDimond()
def closeEvent(self, e):
if not self.isAdded:
self.history.currentState().updateMixture(Mixture())