def __init__(self, fileName=None):
super(MainWindow, self).__init__()
self.pixmappath = os.path.abspath(
os.path.dirname(__file__)) + '/pixmaps/'
print(self.pixmappath)
self.editor = MolEditWidget()
self.ptable = PTable()
self._fileName = None
self.initGUI(fileName=fileName)
self.ptable.atomtypeChanged.connect(self.setAtomTypeName)
def __init__(self, fileName=None, loglevel="WARNING"):
super(MainWindow, self).__init__()
self.pixmappath = os.path.abspath(
os.path.dirname(__file__)) + '/pixmaps/'
self.loglevels = [
"Critical", "Error", "Warning", "Info", "Debug", "Notset"
]
self.editor = MolEditWidget()
self.ptable = PTable()
self._fileName = None
self.initGUI(fileName=fileName)
self.ptable.atomtypeChanged.connect(self.setAtomTypeName)
self.editor.logger.setLevel(loglevel)
class MainWindow(QtWidgets.QMainWindow):
# Constructor function
def __init__(self, fileName=None, loglevel="WARNING"):
super(MainWindow, self).__init__()
self.pixmappath = os.path.abspath(
os.path.dirname(__file__)) + '/pixmaps/'
self.loglevels = [
"Critical", "Error", "Warning", "Info", "Debug", "Notset"
]
self.editor = MolEditWidget()
self.ptable = PTable()
self._fileName = None
self.initGUI(fileName=fileName)
self.ptable.atomtypeChanged.connect(self.setAtomTypeName)
self.editor.logger.setLevel(loglevel)
#Properties
@property
def fileName(self):
return self._fileName
@fileName.setter
def fileName(self, filename):
if filename != self._fileName:
self._fileName = filename
self.setWindowTitle(str(filename))
def initGUI(self, fileName=None):
self.setWindowTitle("A simple mol editor")
self.setWindowIcon(QIcon(self.pixmappath + 'appicon.svg.png'))
self.setGeometry(100, 100, 200, 150)
self.center = self.editor
self.center.setFixedSize(600, 600)
self.setCentralWidget(self.center)
self.fileName = fileName
self.filters = "MOL Files (*.mol *.mol);;Any File (*)"
self.SetupComponents()
self.infobar = QLabel("")
self.myStatusBar.addPermanentWidget(self.infobar, 0)
if self.fileName is not None:
self.logger.info("Loading model from %s" % self.fileName)
self.loadMolFile(fileName)
self.editor.sanitizeSignal.connect(self.infobar.setText)
self.show()
# Function to setup status bar, central widget, menu bar, tool bar
def SetupComponents(self):
self.myStatusBar = QStatusBar()
# self.molcounter = QLabel("-/-")
# self.myStatusBar.addPermanentWidget(self.molcounter, 0)
self.setStatusBar(self.myStatusBar)
self.myStatusBar.showMessage('Ready', 10000)
self.CreateActions()
self.CreateMenus()
self.CreateToolBars()
# Actual menu bar item creation
def CreateMenus(self):
self.fileMenu = self.menuBar().addMenu("&File")
self.toolMenu = self.menuBar().addMenu("&Tools")
self.atomtypeMenu = self.menuBar().addMenu("&AtomTypes")
self.bondtypeMenu = self.menuBar().addMenu("&BondTypes")
self.helpMenu = self.menuBar().addMenu("&Help")
self.fileMenu.addAction(self.openAction)
self.fileMenu.addAction(self.saveAction)
self.fileMenu.addAction(self.saveAsAction)
self.fileMenu.addSeparator()
self.fileMenu.addAction(self.exitAction)
self.toolMenu.addAction(self.selectAction)
self.toolMenu.addAction(self.addAction)
self.toolMenu.addAction(self.addBondAction)
self.toolMenu.addAction(self.replaceAction)
self.toolMenu.addAction(self.increaseChargeAction)
self.toolMenu.addAction(self.decreaseChargeAction)
self.toolMenu.addSeparator()
self.toolMenu.addAction(self.undoAction)
self.toolMenu.addSeparator()
self.toolMenu.addAction(self.removeAction)
#Atomtype menu
for action in self.atomActions:
self.atomtypeMenu.addAction(action)
self.specialatommenu = self.atomtypeMenu.addMenu("All Atoms")
for atomnumber in self.ptable.ptable.keys():
atomname = self.ptable.ptable[atomnumber]["Symbol"]
self.specialatommenu.addAction(self.ptable.atomActions[atomname])
#Bondtype Menu
self.bondtypeMenu.addAction(self.singleBondAction)
self.bondtypeMenu.addAction(self.doubleBondAction)
self.bondtypeMenu.addAction(self.tripleBondAction)
self.bondtypeMenu.addSeparator()
#Bondtype Special types
self.specialbondMenu = self.bondtypeMenu.addMenu("Special Bonds")
for key in self.bondActions.keys():
self.specialbondMenu.addAction(self.bondActions[key])
#Help menu
self.helpMenu.addAction(self.aboutAction)
self.helpMenu.addSeparator()
self.helpMenu.addAction(self.aboutQtAction)
#Debug level sub menu
self.loglevelMenu = self.helpMenu.addMenu("Logging Level")
for loglevel in self.loglevels:
self.loglevelMenu.addAction(self.loglevelactions[loglevel])
def CreateToolBars(self):
self.mainToolBar = self.addToolBar('Main')
#Main action bar
self.mainToolBar.addAction(self.openAction)
self.mainToolBar.addAction(self.saveAction)
self.mainToolBar.addAction(self.saveAsAction)
self.mainToolBar.addSeparator()
self.mainToolBar.addAction(self.selectAction)
self.mainToolBar.addAction(self.addAction)
self.mainToolBar.addAction(self.addBondAction)
self.mainToolBar.addAction(self.replaceAction)
self.mainToolBar.addAction(self.rsAction)
self.mainToolBar.addAction(self.ezAction)
self.mainToolBar.addAction(self.increaseChargeAction)
self.mainToolBar.addAction(self.decreaseChargeAction)
self.mainToolBar.addSeparator()
self.mainToolBar.addAction(self.removeAction)
self.mainToolBar.addAction(self.clearCanvasAction)
#Bond types TODO are they necessary as can be toggled??
self.mainToolBar.addSeparator()
self.mainToolBar.addAction(self.undoAction)
#Side Toolbar
self.sideToolBar = QtWidgets.QToolBar(self)
self.addToolBar(QtCore.Qt.LeftToolBarArea, self.sideToolBar)
self.sideToolBar.addAction(self.singleBondAction)
self.sideToolBar.addAction(self.doubleBondAction)
self.sideToolBar.addAction(self.tripleBondAction)
self.sideToolBar.addSeparator()
for action in self.atomActions:
self.sideToolBar.addAction(action)
self.sideToolBar.addAction(self.openPtableAction)
def loadMolFile(self, filename):
self.fileName = filename
mol = Chem.MolFromMolFile(str(self.fileName),
sanitize=False,
strictParsing=False)
self.editor.mol = mol
self.statusBar().showMessage("File opened")
def openFile(self):
self.fileName, self.filterName = QFileDialog.getOpenFileName(
self, caption="Open MOL file", filter=self.filters)
self.loadMolFile(self.fileName)
def saveFile(self):
if self.fileName != None:
Chem.MolToMolFile(self.editor.mol, str(self.fileName))
else:
self.saveAsFile()
def saveAsFile(self):
self.fileName, self.filterName = QFileDialog.getSaveFileName(
self, filter=self.filters)
if (self.fileName != ''):
if self.fileName[-4:].upper() != ".MOL":
self.fileName = self.fileName + ".mol"
Chem.MolToMolFile(self.editor.mol, str(self.fileName))
# file = open(self.fileName, 'w')
# file.write(self.textEdit.toPlainText())
self.statusBar().showMessage("File saved", 2000)
def clearCanvas(self):
self.editor.clearAtomSelection()
self.editor.mol = None
self.fileName = None
self.statusBar().showMessage("Canvas Cleared")
def closeEvent(self, event):
self.editor.logger.debug("closeEvent triggered")
self.exitFile()
event.ignore()
def exitFile(self):
response = self.msgApp(
"Confirmation",
"This will quit the application. Do you want to Continue?")
if response == "Y":
self.ptable.close()
exit(
0) #TODO, how to exit qapplication from within class instance?
else:
self.editor.logger.debug("Abort closing")
# Function to show Diaglog box with provided Title and Message
def msgApp(self, title, msg):
userInfo = QMessageBox.question(self, title, msg,
QMessageBox.Yes | QMessageBox.No)
if userInfo == QMessageBox.Yes:
return "Y"
if userInfo == QMessageBox.No:
return "N"
self.close()
def aboutHelp(self):
QMessageBox.about(
self, "About Simple Molecule Editor",
"""A Simple Molecule Editor where you can edit molecules\nBased on RDKit! http://www.rdkit.org/ \nSome icons from http://icons8.com\n\nSource code: https://github.com/EBjerrum/rdeditor"""
)
def setAction(self):
sender = self.sender()
self.editor.setAction(sender.objectName())
self.myStatusBar.showMessage("Action %s selected" %
sender.objectName())
def setBondType(self):
sender = self.sender()
self.editor.setBondType(sender.objectName())
self.myStatusBar.showMessage("Bondtype %s selected" %
sender.objectName())
def setAtomType(self):
sender = self.sender()
self.editor.setAtomType(sender.objectName())
self.myStatusBar.showMessage("Atomtype %s selected" %
sender.objectName())
def setAtomTypeName(self, atomname):
self.editor.setAtomType(str(atomname))
self.myStatusBar.showMessage("Atomtype %s selected" % atomname)
def openPtable(self):
self.ptable.show()
def setLogLevel(self):
loglevel = self.sender().objectName().split(':')[-1].upper()
self.editor.logger.setLevel(loglevel)
# Function to create actions for menus
def CreateActions(self):
self.openAction = QAction(QIcon(self.pixmappath + 'open.png'),
'O&pen',
self,
shortcut=QKeySequence.Open,
statusTip="Open an existing file",
triggered=self.openFile)
self.saveAction = QAction(QIcon(self.pixmappath + '/icons8-Save.png'),
'S&ave',
self,
shortcut=QKeySequence.Open,
statusTip="Save file",
triggered=self.saveFile)
self.saveAsAction = QAction(QIcon(self.pixmappath +
'icons8-Save as.png'),
'S&ave As',
self,
shortcut=QKeySequence.Open,
statusTip="Save file as ..",
triggered=self.saveAsFile)
self.exitAction = QAction(QIcon(self.pixmappath +
'icons8-Shutdown.png'),
'E&xit',
self,
shortcut="Ctrl+Q",
statusTip="Exit the Application",
triggered=self.exitFile)
self.aboutAction = QAction(QIcon(self.pixmappath + 'about.png'),
'A&bout',
self,
statusTip="Displays info about text editor",
triggered=self.aboutHelp)
self.aboutQtAction = QAction(
"About &Qt",
self,
statusTip="Show the Qt library's About box",
triggered=QApplication.aboutQt)
self.openPtableAction = QAction(
QIcon(self.pixmappath + 'ptable.png'),
'O&pen Periodic Table',
self,
shortcut=QKeySequence.Open,
statusTip="Open the periodic table for atom type selection",
triggered=self.openPtable)
#Edit actions
self.actionActionGroup = QtWidgets.QActionGroup(self, exclusive=True)
self.selectAction = QAction(QIcon(self.pixmappath +
'icons8-Cursor.png'),
'S&elect',
self,
shortcut="Ctrl+S",
statusTip="Select Atoms",
triggered=self.setAction,
objectName="Select",
checkable=True)
self.actionActionGroup.addAction(self.selectAction)
self.addAction = QAction(QIcon(self.pixmappath + 'icons8-Edit.png'),
'A&dd',
self,
shortcut="Ctrl+A",
statusTip="Add Atoms",
triggered=self.setAction,
objectName="Add",
checkable=True)
self.actionActionGroup.addAction(self.addAction)
self.addBondAction = QAction(QIcon(self.pixmappath +
'icons8-Pinch.png'),
'Add B&ond',
self,
shortcut="Ctrl+B",
statusTip="Add Bond",
triggered=self.setAction,
objectName="Add Bond",
checkable=True)
self.actionActionGroup.addAction(self.addBondAction)
self.replaceAction = QAction(QIcon(self.pixmappath +
'icons8-Replace Atom.png'),
'R&eplace',
self,
shortcut="Ctrl+R",
statusTip="Replace Atom/Bond",
triggered=self.setAction,
objectName="Replace",
checkable=True)
self.actionActionGroup.addAction(self.replaceAction)
self.rsAction = QAction(QIcon(self.pixmappath + 'Change_R_S.png'),
'T&oggle R/S',
self,
shortcut="Ctrl+o",
statusTip="Toggle Stereo Chemistry",
triggered=self.setAction,
objectName="RStoggle",
checkable=True)
self.actionActionGroup.addAction(self.rsAction)
self.ezAction = QAction(QIcon(self.pixmappath + 'Change_E_Z.png'),
'Toggle &E/Z',
self,
shortcut="Ctrl+E",
statusTip="Toggle Bond Stereo Chemistry",
triggered=self.setAction,
objectName="EZtoggle",
checkable=True)
self.actionActionGroup.addAction(self.ezAction)
self.removeAction = QAction(QIcon(self.pixmappath +
'icons8-Cancel.png'),
'D&elete',
self,
shortcut="Ctrl+D",
statusTip="Delete Atom or Bond",
triggered=self.setAction,
objectName="Remove",
checkable=True)
self.actionActionGroup.addAction(self.removeAction)
self.increaseChargeAction = QAction(QIcon(self.pixmappath +
'icons8-Increase Font.png'),
'I&ncrease Charge',
self,
shortcut="Ctrl++",
statusTip="Increase Atom Charge",
triggered=self.setAction,
objectName="Increase Charge",
checkable=True)
self.actionActionGroup.addAction(self.increaseChargeAction)
self.decreaseChargeAction = QAction(QIcon(self.pixmappath +
'icons8-Decrease Font.png'),
'D&ecrease Charge',
self,
shortcut="Ctrl+-",
statusTip="Decrease Atom Charge",
triggered=self.setAction,
objectName="Decrease Charge",
checkable=True)
self.actionActionGroup.addAction(self.decreaseChargeAction)
self.addAction.setChecked(True)
#BondTypeActions
self.bondtypeActionGroup = QtWidgets.QActionGroup(self, exclusive=True)
self.singleBondAction = QAction(QIcon(self.pixmappath +
'icons8-Single.png'),
'S&ingle Bond',
self,
shortcut="Ctrl+S",
statusTip="Set bondtype to SINGLE",
triggered=self.setBondType,
objectName="SINGLE",
checkable=True)
self.bondtypeActionGroup.addAction(self.singleBondAction)
self.doubleBondAction = QAction(QIcon(self.pixmappath +
'icons8-Double.png'),
'Double Bond',
self,
shortcut="Ctrl+S",
statusTip="Set bondtype to DOUBLE",
triggered=self.setBondType,
objectName="DOUBLE",
checkable=True)
self.bondtypeActionGroup.addAction(self.doubleBondAction)
self.tripleBondAction = QAction(QIcon(self.pixmappath +
'icons8-Triple.png'),
'Triple Bond',
self,
shortcut="Ctrl+S",
statusTip="Set bondtype to TRIPLE",
triggered=self.setBondType,
objectName="TRIPLE",
checkable=True)
self.bondtypeActionGroup.addAction(self.tripleBondAction)
self.singleBondAction.setChecked(True)
#Build dictionary of ALL available bondtypes in RDKit
self.bondActions = {}
for key in self.editor.bondtypes.keys():
action = QAction('%s' % key,
self,
statusTip="Set bondtype to %s" % key,
triggered=self.setBondType,
objectName=key,
checkable=True)
self.bondtypeActionGroup.addAction(action)
self.bondActions[key] = action
#Replace defined actions
self.bondActions["SINGLE"] = self.singleBondAction
self.bondActions["DOUBLE"] = self.doubleBondAction
self.bondActions["TRIPLE"] = self.tripleBondAction
#Misc Actions
self.undoAction = QAction(QIcon(self.pixmappath + 'prev.png'),
'U&ndo',
self,
shortcut="Ctrl+U",
statusTip="Undo/Redo changes to molecule",
triggered=self.editor.undo,
objectName="undo")
self.clearCanvasAction = QAction(QIcon(self.pixmappath +
'icons8-Trash.png'),
'C&lear Canvas',
self,
shortcut="Ctrl+X",
statusTip="Clear Canvas (no warning)",
triggered=self.clearCanvas,
objectName="Clear Canvas")
#Atom Actions in actiongroup, reuse from ptable widget
self.atomActions = []
for atomname in [
"H", "B", "C", "N", "O", "F", "P", "S", "Cl", "Br", "I"
]:
action = self.ptable.atomActions[atomname]
if action.objectName() == "C":
action.setChecked(True)
self.atomActions.append(action)
self.loglevelactions = {}
for key in self.loglevels:
self.loglevelactions[key] = QAction(
key,
self,
statusTip="Set logging level to %s" % key,
triggered=self.setLogLevel,
objectName="loglevel:%s" % key)