class BuildTab(QtWidgets.QFrame):
def __init__(self, hist, parent=None, previewer=None, settings=None):
super(BuildTab, self).__init__(parent)
#print "buildTab init in"
self.history = hist
self.mixModification = 0
self.wolffia = parent
self.allowUpdate = True
self.buildPreview = previewer
self.settings = settings
self.clipboard = None
self.prevSelection = None
self.prevShow = None
self.prevFixed = None
#widgets import
self.ui = Ui_buildTab()
self.ui.setupUi(self)
self.ui.structManager.setSortingEnabled(False)
px = QtGui.QPixmap()
self._WOLFFIA_OS = platform.system()
px.load(WOLFFIA_GRAPHICS + "hide.gif", format=None)
ico = QtGui.QIcon()
ico.addPixmap(px, state=QtGui.QIcon.On)
self.ui.structManager.horizontalHeaderItem(0).setIcon(ico)
px2 = QtGui.QPixmap()
px2.load(WOLFFIA_GRAPHICS + "pin16.png", format=None)
fixico = QtGui.QIcon()
fixico.addPixmap(px2, state=QtGui.QIcon.On)
self.ui.structManager.horizontalHeaderItem(1).setIcon(fixico)
#initialize editor
self.editor = PropertyEditor(self.buildPreview, self.history)
self.ui.editorLayout.addWidget(self.editor)
self.buildPreview.setBuildTab(self)
#initialize tool buttons
self.ui.removeButton.setIcon(QtGui.QIcon().fromTheme(
"edit-cut", QtGui.QIcon(str(WOLFFIA_GRAPHICS) + "edit-cut.png")))
self.ui.updateButton.setIcon(QtGui.QIcon().fromTheme(
"system-software-update",
QtGui.QIcon(str(WOLFFIA_GRAPHICS) + "system-software-update.png")))
self.ui.removeButton.setFlat(True)
self.ui.duplicateButton.setIcon(QtGui.QIcon().fromTheme(
"edit-paste",
QtGui.QIcon(str(WOLFFIA_GRAPHICS) + "edit-paste.png")))
self.ui.copyButton.setIcon(QtGui.QIcon().fromTheme(
"edit-copy", QtGui.QIcon(str(WOLFFIA_GRAPHICS) + "edit-copy.png")))
self.ui.saveWFMbutton.setIcon(QtGui.QIcon().fromTheme(
"document-save",
QtGui.QIcon(str(WOLFFIA_GRAPHICS) + "document-save.png")))
self.ui.addCustomButton.setIcon(QtGui.QIcon().fromTheme(
"document-open",
QtGui.QIcon(str(WOLFFIA_GRAPHICS) + "document-open.png")))
self.showCheckboxes = dict()
self.firstUpdate = True
#print "buildTab init out", QtGui.QWidget.keyboardGrabber ()
self.cMol = C_MOLECULE_CATALOG
def _checkFixedShiftModifier_(self, basePin, selected):
for i in range(self.ui.structManager.rowCount()):
if self.ui.structManager.cellWidget(i, 1) == basePin:
row = i
break
modifiers = QtGui.QApplication.keyboardModifiers()
if modifiers == QtCore.Qt.ShiftModifier and self.prevFixed != None:
if self.prevFixed[1] == selected:
if row < self.prevFixed[0]:
ind = list(range(row + 1, self.prevFixed[0] + 1))
else:
ind = list(range(self.prevFixed[0], row))
for i in ind:
pin = self.ui.structManager.cellWidget(i, 1)
#if selected: pin.setFixed(update=False)
if self.prevFixed[1]: pin.setFixed(update=False)
else: pin.setLoose(update=False)
self.prevFixed = [row, selected]
#self.buildPreview.update()
def _checkShowShiftModifier_(self, baseEye, selected):
#find row
for i in range(self.ui.structManager.rowCount()):
if self.ui.structManager.cellWidget(i, 0) == baseEye:
row = i
break
modifiers = QtGui.QApplication.keyboardModifiers()
if modifiers == QtCore.Qt.ShiftModifier and self.prevShow != None:
if self.prevShow[1] == selected:
if row < self.prevShow[0]:
ind = list(range(row, self.prevShow[0]))
else:
ind = list(range(self.prevShow[0] + 1, row))
for i in ind:
pin = self.ui.structManager.cellWidget(i, 0)
#if selected: pin.setShown(update=False)
if self.prevShow[1]: pin.setShown(update=False)
else: pin.setHidden(update=False)
self.prevShow = [row, selected]
#self.buildPreview.update()
#---------------------------------------------------------------
def on_structManager_cellPressed(self, i, j):
#print "on_structManager_cellPressed ", i,j
mouse_state = QtGui.qApp.mouseButtons()
if QtGui.qApp.mouseButtons() == QtCore.Qt.LeftButton:
#print "on_structManager_cellPressed ", QtGui.qApp.mouseButtons()==QtCore.Qt.LeftButton, mouse_state==QtCore.Qt.NoButton
QtGui.qApp.sendEvent(self.ui.structManager,
QtCore.QEvent(QtCore.QEvent.MouseButtonPress))
#self.ui.structManager.cellPressed.emit(i,j)
#activates the Structure Catalog
def on_molCatalog_itemActivated(self, item):
#print "on_molCatalog_itemActivated in"
self.key = str(item.text(0))
self.parent = item.parent().text(0)
def moleculeDialog(self, dialog):
dialog.show()
dialog.exec_()
self.addMixture(dialog.getMixture())
self.buildPreview.update()
# Polymers
if self.key == "Polyaniline":
from interface.PANI.paniEditor import PANIBuilder
pani = PANIBuilder(self.history.currentState(),
self,
settings=self.settings)
moleculeDialog(self, pani)
elif self.key == "PEDOT":
from interface.PEDOT.pedotEditor import PEDOTBuilder
pedot = PEDOTBuilder(self.history.currentState(),
self,
settings=self.settings)
moleculeDialog(self, pedot)
elif self.key == "PSS":
from interface.PSS.pssEditor import PSSBuilder
pss = PSSBuilder(self.history.currentState(),
self,
settings=self.settings)
moleculeDialog(self, pss)
elif self.key == "Cellulose":
from interface.celluloseEditor.CelluloseEditor import CelluloseEditor
c = CelluloseEditor(self.history.currentState(),
self,
settings=self.settings)
moleculeDialog(self, c)
elif self.key == "ssDNA":
print("ssDNA is not yet implemented!")
elif self.parent == "Homopolymer":
from interface.homopolyEditor.HomopolyEditor import HomopolyEditor
homopol = HomopolyEditor(self.key,
self.history.currentState(),
settings=self.settings)
moleculeDialog(self, homopol)
# Carbon Allotropes
elif self.key == "swCNT":
from interface.nanotubeEditor.nanotubeEditor import NanotubeBuilder
cnt = NanotubeBuilder(self, self.settings)
moleculeDialog(self, cnt)
elif self.key == "Graphene":
from interface.grapheneEditor.grapheneEditor import GrapheneBuilder
graph = GrapheneBuilder(self, self.settings)
moleculeDialog(self, graph)
elif self.key == "Diamond":
from interface.diamondEditor.diamondEditor import DiamondBuilder
diamond = DiamondBuilder(self, self.settings)
moleculeDialog(self, diamond)
# Solvents
elif self.key == "THF":
from lib.chemicalGraph.molecule.solvent.THF import THF
self.addMolecule(THF())
elif self.key == "DMF":
from lib.chemicalGraph.molecule.solvent.DMF import DMF
self.addMolecule(DMF())
elif self.key == "Water":
from lib.chemicalGraph.molecule.solvent.WATER import WATER
self.addMolecule(WATER())
elif self.key == "Chloroform":
from lib.chemicalGraph.molecule.solvent.CLF import CLF
self.addMolecule(CLF())
elif self.key == "Chloroform (4 atoms)":
from lib.chemicalGraph.molecule.solvent.CLF4 import CLF4
self.addMolecule(CLF4())
elif self.key == "Hydrogen Peroxide":
from lib.chemicalGraph.molecule.solvent.H2O2 import H2O2
self.addMolecule(H2O2())
elif self.key == "Xylene":
from lib.chemicalGraph.molecule.solvent.Xylene import Xylene
self.addMolecule(Xylene())
elif self.key == "AcetoneAllH":
from lib.chemicalGraph.molecule.solvent.AcetoneAllH import AcetoneAllH
self.addMolecule(AcetoneAllH())
elif self.key == "AcetoneNoH":
from lib.chemicalGraph.molecule.solvent.AcetoneNoH import AcetoneNoH
self.addMolecule(AcetoneNoH())
# Surfactants
elif self.key == "SDS":
from lib.chemicalGraph.molecule.solvent.SDS import SDS
self.addMixture(SDS())
elif self.key == "SDBS":
from lib.chemicalGraph.molecule.solvent.SDBS import SDBS
self.addMixture(SDBS())
elif self.key == "PABA-Tetradecane":
from lib.chemicalGraph.molecule.solvent.PABA import PABA_Tetradecane
self.addMolecule(PABA_Tetradecane())
elif self.key == "PABA-Heptane":
from lib.chemicalGraph.molecule.solvent.PABA import PABA_Heptane
self.addMolecule(PABA_Heptane())
elif self.key == "PABA-Pentane":
from lib.chemicalGraph.molecule.solvent.PABA import PABA_Pentane
self.addMolecule(PABA_Pentane().changeResidues("PAB"))
# Ions
elif self.key == "Na":
from lib.chemicalGraph.molecule.solvent.Na import Na
self.addMolecule(Na())
else:
self.addMolecule(
Element(Element.nameToSymbol(self.key.split(' ')[0])))
self.update()
self.buildPreview.update()
def on_addCustomButton_pressed(self):
from interface.classifier.Load import Load
self.history.push()
loader = Load(self)
loader.show()
loader.exec_()
self.addMixture(loader.getMixture())
self.buildPreview.update()
self.update()
self.buildPreview.update()
def on_copyButton_pressed(self):
if not self.ui.copyButton.isFlat():
if (self.wolffia.simRunning):
message = QtGui.QMessageBox(
1, "Warning", "There's a simulation running right now.")
message.exec_()
else:
self.copy()
if not self.ui.removeButton.isFlat():
if (self.wolffia.simRunning):
message = QtGui.QMessageBox(
1, "Warning", "There's a simulation running right now.")
message.exec_()
else:
self.copy()
def on_catalogButton_pressed(self):
if not self.ui.catalogButton.isFlat():
selected = self.editor.selectedMolecules()
#print "SELCTEDDDDDD >>." , selected[0]
if (self.wolffia.simRunning):
message = QtGui.QMessageBox(
1, "Warning", "There's a simulation running right now.")
message.exec_()
elif selected == []:
QtGui.QMessageBox.warning(self, "Wolffia's warning",
"Please select a molecule.",
QtGui.QMessageBox.Ok)
return
else:
#print "on_catalogButton_pressed", self.ui.molCatalog.topLevelItemCount()
customTreeWidget = self.ui.molCatalog.topLevelItem(
self.ui.molCatalog.topLevelItemCount() - 1)
#print "on_catalogButton_pressed childCount", customTreeWidget.childCount ()
print("SELCTEDDDDDD >>.", selected)
mixtureToSave = Mixture()
print("mixtureToSave >>>>", mixtureToSave)
molName = ""
print("molName >>>>", molName)
for mol in selected:
print("mol >>>>", mol)
mixtureToSave.add(mol.copy(), True)
print("mixtureToSave agregados >>>>", mixtureToSave)
if molName == "":
molName = mol.molname()
else:
molName += ("-" + mol.molname())
print("SELECETEDDDD: ", selected, "mixtureToSave Final",
mixtureToSave)
print(
"############################################################"
)
#Pregunta el nombre de la molecula que quiere guardar en el catalogo
nameMolGUI = QtGui.QInputDialog(self)
nameMolGUI.setTextValue(str(selected[0]))
nameMol, ok = nameMolGUI.getText(self, "Custom Molecule",
"Set Molecule Name:", 0,
str(selected[0]))
print("value ", nameMol, " ok ", ok)
if ok:
#Guarda archivo en .cMolecule dentro de .wolffia
cMixFileName = "/" + nameMol + ".wfm"
cMixFileDir = WOLFFIA_DIR + C_MOLECULE_CATALOG + cMixFileName
if os.path.exists(cMixFileDir):
print("archivo existe", cMixFileDir)
nameMol = nameMol + "*"
cMixFileName = "/" + nameMol + ".wfm"
cMixFileDir = WOLFFIA_DIR + C_MOLECULE_CATALOG + cMixFileName
print("cMixFileDir>>>>>", cMixFileDir)
#Add a child to Custom Molecule in the Molecular Structure Catalog
nameQT = QtGui.QTreeWidgetItem()
nameQT.setText(0, nameMol)
customTreeWidget.addChild(nameQT)
#customTreeWidget.addChild(QtGui.QTreeWidgetItem())
print("NAMEMOL1", nameMol)
self.history.currentState().getMixture().save(cMixFileDir)
#Guarda archivo en .cMolecule dentro de .wolffia
#MixtureToSave are selected
#cMixtureToSave = Mixture("To save")
#Nombre del Archivo que se va a guardar es cMolName
#cMolName = str(nombre.textValue()) + ".wfm"
#for mol in selected:
# print "mol:", mol
# cMixtureToSave.add(mol.copy(), False)
#Directorio en donde se va a guardar es dirCmolName
#dirCmolName = self.settings.workingFolder + self.cMol
#try:
# print "TRYYYYYYYYYYYYyyyyy"
# basename = str(dirCmolName.path() + "/" + cMolName)
# print "basename" , basename
# mixtureToSave.writePDB(basename)
#except:
# QtGui.QMessageBox.warning(self, "Wolffia's warning", cMolName + " could not be saved.", QtGui.QMessageBox.Ok)
#print "cmolName >>>>>>>>>",cMolName, "directorio: >>>>>>", dirCmolName
#selected.writePDB(cMolName)
#print "SAVEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE "
#print ""
def on_catalogButton_pressed(self):
if not self.ui.removeButton.isFlat():
if (self.wolffia.simRunning):
message = QtGui.QMessageBox(
1, "Warning", "There's a simulation running right now.")
message.exec_()
else:
print("on_catalogButton_pressed",
self.ui.molCatalog.topLevelItemCount())
customTreeWidget = self.ui.molCatalog.topLevelItem(
self.ui.molCatalog.topLevelItemCount() - 1)
print("on_catalogButton_pressed childCount",
customTreeWidget.childCount())
selected = self.editor.selectedMolecules()
nombre = QtGui.QInputDialog(self)
nombre.setTextValue(str(selected[0]))
nombre.exec_()
customTreeWidget.addChild(
QtGui.QTreeWidgetItem([str(nombre.textValue())]))
def on_duplicateButton_pressed(self):
if not self.ui.duplicateButton.isFlat():
if (self.wolffia.simRunning):
message = QtGui.QMessageBox(
1, "Warning", "There's a simulation running right now.")
message.exec_()
else:
self.history.push()
self.duplicate()
self.buildPreview.update()
def on_removeButton_pressed(self):
#print "on_removeButton_pressed"
if not self.ui.removeButton.isFlat():
if (self.wolffia.simRunning):
message = QtGui.QMessageBox(
1, "Warning", "There's a simulation running right now.")
message.exec_()
else:
progress = QtGui.QProgressDialog(
"Removing...", QtCore.QString(), 0, 5, self,
QtCore.Qt.Dialog | QtCore.Qt.WindowTitleHint)
progress.setWindowModality(QtCore.Qt.WindowModal)
progress.setValue(1)
self.history.push()
progress.setValue(2)
self.remove()
progress.setValue(3)
self.editor.reset()
progress.setValue(4)
self.buildPreview.update()
#self.buildPreview.setMixture(self.history.currentState().getMixture())
progress.setValue(5)
progress.hide()
#-------------------------------------------------------------------------------
def on_saveWFMbutton_pressed(self, saveState=True):
#print "on_saveWFMbutton_pressed "
if not saveState: return
else:
mixFile = self.settings.currentMixtureLocation(
) + self.history.currentState().getMixtureName() + ".wfm"
d = WFileNameDialog(self, 'Save current Mixture',
self.settings.currentMixtureLocation(),
"Mixture file (*.wfm)")
if d.isReady():
filename = d.fullFilename()
#print "FILENAME = ", filename
#print "on_saveWFMbutton_pressed >>>>> ","\'"+filename[-4:]+"\'"
if filename[-4:] != ".wfm" and QtGui.QMessageBox.question(
self, "Wolffia's message",
"File does not end with .wfm. Add extension?", "Yes",
"No") == 0:
filename += ".wfm"
if os.path.exists(filename) and QtGui.QMessageBox.question(
self, "Wolffia's message", "File exists.",
"Overwrite", "Cancel") != 0:
return
self.history.currentState().getMixture().save(filename)
QtGui.QMessageBox.information(self, "Wolffia's message",
filename + " saved.",
QtGui.QMessageBox.Ok)
def on_saveButton_pressed2(self, saveFiles=True):
if not saveFiles: return
mixName = self.history.currentState().getMixtureName()
d = WDirectoryDialog(
self, 'Specify directory to save ' + mixName + ".pdb and " +
mixName + ".psf", self.settings.workingFolder)
if d.accepted():
basename = d.path() + "/" + mixName
import os
if not (os.path.exists(basename + ".pdb") or os.path.exists(
basename + ".psf")) or QtGui.QMessageBox.question(
self, "Wolffia's message", "File exists.", "Overwrite",
"Cancel") == 0:
mix = self.history.currentState().getMixture()
mix.writePDB(basename + ".pdb")
mix.writePSF(basename + ".psf")
QtGui.QMessageBox.information(
self, "Wolffia's message",
mixName + ".pdb and " + mixName + ".psf saved.",
QtGui.QMessageBox.Ok)
def on_saveButton_pressed3(self, saveFiles=True):
if not saveFiles: return
selected = self.editor.selectedMolecules()
#print "on_saveButton_pressed ", selected
if selected == []:
QtGui.QMessageBox.warning(
self, "Wolffia's warning",
"Could not determine the molecule to be saved.\nPlease select one.",
QtGui.QMessageBox.Ok)
return
mixtureToSave = Mixture("To save")
molName = ""
for mol in selected:
mixtureToSave.add(mol.copy(), False)
if molName == "":
molName = mol.molname()
else:
molName += ("-" + mol.molname())
d = WDirectoryDialog(
self, 'Specify directory to save ' + molName + ".pdb and " +
molName + ".psf", self.settings.workingFolder)
try:
if d.accepted():
basename = str(d.path() + "/" + molName)
#import os
if not (os.path.exists(basename + ".pdb") or os.path.exists(
basename + ".psf")) or QtGui.QMessageBox.question(
self, "Wolffia's message", "File exists.",
"Overwrite", "Cancel") == 0:
#mix = self.history.currentState().getMixture()
#print "on_saveButton_pressed ", basename
mixtureToSave.writePDB(basename + ".pdb")
mixtureToSave.writePSF(basename + ".psf")
QtGui.QMessageBox.information(
self, "Wolffia's message",
molName + ".pdb and " + molName + ".psf saved.",
QtGui.QMessageBox.Ok)
except:
QtGui.QMessageBox.warning(
self, "Wolffia's warning",
molName + ".pdb and " + molName + ".psf could not be saved.",
QtGui.QMessageBox.Ok)
#------------------------------------------------------------------------------------------
def on_updateButton_pressed(self):
#print "on_updateButton_pressed "
QtGui.QMessageBox.information(
self, "Wolffia's message",
"Updates can only be done from coordinate files\nproduced by simulations prepared with Wolffia.\nOther files will produce unexpected results..",
QtGui.QMessageBox.Ok)
d = WFileDialog(self,
'Specify coordinate file to load.',
self.settings.workingFolder,
filter="*.pdb *.coor")
if d.accepted():
self.history.push()
try:
self.history.currentState().mixture.updateCoordinates(
str(d.fullFilename()))
self.buildPreview.update()
QtGui.QMessageBox.information(self, "Wolffia's message",
"Coordinates updated.",
QtGui.QMessageBox.Ok)
except:
QtGui.QMessageBox.warning(self, "Wolffia's warning",
"Coordinates could not be updated.",
QtGui.QMessageBox.Ok)
self.history.back()
def on_structManager_itemChanged(self, wi):
#if isinstance(wi, myTableWidgetItem) and wi.name != "(no name)" and wi.isSelected():
if wi.column() == 2:
row = wi.row()
mol = str(self.ui.structManager.item(row, 4).text())
if str(wi.text()) == "":
wi.setText(
self.history.currentState().getMixture().getMolecule(
mol).molname())
elif mol[:8] == "SOLVENT(":
if wi.text() != self.history.currentState().getMixture(
).getMolecule(mol).molname():
nameLen = len(mol)
sepPos = mol.rfind("_")
for molecule in self.history.currentState().getMixture():
if mol[:sepPos] == molecule[:sepPos]:
with warnings.catch_warnings(record=True) as w:
#print "on_structManager_itemChanged",molecule,str(wi.text()),str(wi.text())+molecule[sepPos:]
self.history.currentState().getMixture(
).renameMolecule(molecule, str(wi.text()))
if len(w) > 0:
QtGui.QMessageBox.information(
self, "Error", str(w[-1].message))
self.update()
else:
#print "on_structManager_itemChanged changing molecule with id ", mol
#print "on_structManager_itemChanged", self.history.currentState().getMixture().getMolecule(mol).molname(), "->", str(wi.text()), " row=", row
if wi.text() != self.history.currentState().getMixture(
).getMolecule(mol).molname():
self.history.push()
with warnings.catch_warnings(record=True) as w:
self.history.currentState().getMixture(
).renameMolecule(mol, str(wi.text()))
if len(w) > 0:
QtGui.QMessageBox.information(self, "Error",
str(w[-1].message))
self.update()
#self.history.currentState().getMixture().getMolecule(mol).rename(str(wi.text()))
#print "on_structManager_itemChanged getMixture:",self.history.currentState().getMixture()
def on_structManager_cellClicked(self, row, col):
#update editor with selected molecule
#print "on_structManager_cellClicked",row,col
molecules = self.history.currentState().getMixture().moleculeIDs()
molecules.sort()
#mol = molecules[row]
mol = str(self.ui.structManager.item(row, 4).text())
#print "on_structManager_cellClicked",row,col,mol
if col == 0:
item = self.ui.structManager.itemAt(row, col)
#print "detecto"
elif col == 2:
#print "on_structManager_cellClicked B"
#selected = self.editor.setMolecule(self.history.currentState().getMixture().getMolecule(mol), str(mol), True)
m = self.history.currentState().getMixture().getMolecule(mol)
#print "on_structManager_cellClicked B2",m,mol
selected = self.editor.setMolecule(m, str(mol), True)
#print "on_structManager_cellClicked C", selected
# if shift key is pressed perform multiple selects
modifiers = QtGui.QApplication.keyboardModifiers()
if modifiers == QtCore.Qt.ShiftModifier and self.prevSelection != None:
if self.prevSelection[1] == selected:
if row < self.prevSelection[0]:
ind = list(range(row + 1, self.prevSelection[0]))
else:
ind = list(range(self.prevSelection[0] + 1, row))
for i in ind:
mol = str(self.ui.structManager.item(i, 4).text())
m = self.history.currentState().getMixture(
).getMolecule(mol)
if self.prevSelection[1]:
self.editor.removeSelection(m, str(mol))
else:
self.editor.setMolecule(m,
str(mol),
removeIfPresent=False)
self.prevSelection = [row, selected]
self.ui.removeButton.setFlat(False)
self.ui.duplicateButton.setFlat(self.clipboard == None
or len(self.clipboard) == 0)
self.ui.copyButton.setFlat(False)
self.ui.catalogButton.setFlat(False)
self.repaint()
self.buildPreview.update()
#print "on_structManager_cellClicked D"
#self.update()
#self.buildPreview.update()
return
@QtCore.pyqtSlot()
def on_saveButton_triggered(self, saveFiles=True):
if not saveFiles: return
d = WFileNameDialog(self, 'Save Files',
self.history.currentState().getBuildDirectory())
if d.isReady():
self.history.currentState().setMixtureName(d.mixname())
self.history.currentState().writeFiles(d.fullFilename())
mesg = self.history.currentState().getMixtureName(
) + '.pdb, ' + self.history.currentState().getMixtureName(
) + '.psf and ' + self.history.currentState().getMixtureName(
) + '.prm'
info = QtGui.QErrorMessage(self)
info.setModal(True) # blocks Wolffia
info.showMessage("The files " + mesg +
" have been successfully saved in " + d.path())
def on_showCheckbox(self, on):
print("on_showCheckbox", end=' ')
def addMolecule(self, mol, remember=True):
if mol != None:
self.editor.reset()
with warnings.catch_warnings(record=True) as w:
self.history.currentState().addMolecule(mol)
self.buildPreview.setMixture(
self.history.currentState().getMixture(), True)
#print "addMolecule len(w)",len(w)
if len(w) > 0:
QtGui.QMessageBox.information(self, "Error",
str(w[-1].message))
if remember: self.history.push()
def addMixture(self, mix, remember=True):
if mix != None:
for mol in mix:
self.addMolecule(mix.getMolecule(mol), False)
#self.history.currentState().addMixture(mix)
if remember: self.history.push()
def chosenMolecules(self):
count = self.ui.structManager.topLevelItemCount()
for i in range(count):
item = self.ui.structManager.itemAt(i, 1)
#print item.isChecked()
def copy(self):
selected = self.editor.selectedMolecules()
#print "copy ", selected
if selected == []:
errorgui = QtGui.QErrorMessage(self)
errorgui.setModal(True) # blocks Wolffia
errorgui.showMessage("Error: no molecule chosen.")
else:
self.clipboard = Mixture("Clipboard")
for mol in selected:
#print "copy", mol
#self.clipboard.add(self.history.currentState().getMixture().getMolecule(molname).copy(), False)
self.clipboard.add(mol.copy(), False)
#print "copy update<", self.editor.selected()
self.update()
#print "copy >", self.editor.selected()
def duplicate(self):
from sets import Set
#print "duplicate ", self.clipboard.molecules()
currentIDs = Set(self.history.currentState().getMixture().molecules())
try:
newMols = self.clipboard.copy()
newMols.moveBy([
random.uniform(0., 0.1),
random.uniform(0., 0.1),
random.uniform(0., 0.1)
])
self.history.currentState().getMixture().merge(newMols)
except:
errorgui = QtGui.QErrorMessage(self)
errorgui.setModal(True) # blocks Wolffia
errorgui.showMessage("Error: could not duplicate molecules.")
# select pasted molecules
newMols = Set(
self.history.currentState().getMixture().molecules()) - currentIDs
progressMax = len(newMols) - 1
progressCount = 0
progress = QtGui.QProgressDialog(
"Adding...", QtCore.QString(), 0, progressMax, self,
QtCore.Qt.Dialog | QtCore.Qt.WindowTitleHint)
progress.setWindowModality(QtCore.Qt.WindowModal)
#print "duplicate ", self.history.currentState().getMixture().molecules(),newMols
self.editor.reset()
for mol in newMols:
self.editor.setMolecule(
self.history.currentState().getMixture().getMolecule(mol), mol)
self.history.currentState().shownMolecules.show(mol)
progressCount += 1
progress.setValue(progressCount)
self.insertAllToManager()
progress.hide()
self.update()
def insertAllToManager(self):
from lib.chemicalGraph.molecule.solvent.Solvent import Solvent
start = time.clock()
#print "insertAllToManager ",self.history.currentState().getMixture().molecules()
self.mixModification = self.history.currentState().getMixture(
).getModificationTime()
#self.ui.structManager.setRowCount(len(self.history.currentState().mixture))
self.ui.structManager.setRowCount(0)
row = 0
solventShown = ShownSolvent()
shownMolecules = self.history.currentState().shownMolecules
molecules = self.history.currentState().getMixture().moleculeIDs()
#print "insertAllToManager ",molecules
#progress = QtGui.QProgressDialog("Storing...", "Abort", 0, len(molecules), self,QtCore.Qt.Dialog|QtCore.Qt.WindowTitleHint)
#progress.setWindowModality(QtCore.Qt.WindowModal)
#progress.setAutoClose(True)
#progress.setMinimumDuration(0)
self.ui.structManager.blockSignals(True)
molecules.sort()
molNum = 0
for molName in molecules:
#molName = self.history.currentState().getMixture().getMolecule(mol).molname()
#print "insertAllToManager ",ShownSolvent.isSolvent(molName),solventShown.isShown(molName)
if not ShownSolvent.isSolvent(molName) or not solventShown.isShown(
molName):
self.ui.structManager.setRowCount(row + 1)
#insert checkbox on column 1
checkBox = PreviewButton(self.history.currentState(),
self.buildPreview,
molname=str(molName),
parent=self,
initState=shownMolecules.isShown(
str(molName)),
editor=self.editor)
checkBox.setToolTip("Show or hide.")
self.ui.structManager.setCellWidget(row, 0, checkBox)
pin = FixedButton(self.history.currentState(),
self.buildPreview,
molname=str(molName),
parent=self,
initState=self.history.currentState().
fixedMolecules.isFixed(str(molName)))
pin.setToolTip("Fixes position of the molecule.")
self.ui.structManager.setCellWidget(row, 1, pin)
#print "insertAllToManager",str(self.history.currentState().mixture.getMolecule(molName)._name) , molecules
#insert molname on column 2
baseMolName = str(
self.history.currentState().mixture.getMolecule(
molName).molname())
#print "insertAllToManager creando item para ", baseMolName
#if isinstance(self.history.currentState().mixture.getMolecule(molName), Solvent):
# baseMolName += "(solvent)"
newitem = QtGui.QTableWidgetItem(baseMolName)
newitem.setFlags(QtCore.Qt.ItemIsEditable
| QtCore.Qt.ItemIsEnabled)
newitem.setToolTip(
"Click to select or double click to edit the name.")
self.ui.structManager.setItem(row, 2, newitem)
#print "insertAllToManager",self.editor.getId(),molName
if molName in self.editor.selectedNames():
newitem.setBackgroundColor(QtCore.Qt.green)
#insert atom count on column 3
newitem = QtGui.QTableWidgetItem(
str(self.history.currentState().mixture.getMolecule(
molName).order()))
newitem.setFlags(QtCore.Qt.ItemIsEnabled)
self.ui.structManager.setItem(row, 3, newitem)
#insert id on column 4
newitem = QtGui.QTableWidgetItem(str(molName))
newitem.setFlags(QtCore.Qt.ItemIsEnabled)
self.ui.structManager.setItem(row, 4, newitem)
row += 1
solventShown.setAsShown(molName)
#print "insertAllToManager solventShown.setAsShown(molName) ", solventShown.isShown(molName)
elif not ShownSolvent.isSolvent(molName):
self.history.currentState().shownMolecules.show(molName)
molNum += 1
#progress.setValue(molNum)
#self.buildPreview.setMixture(self.history.currentState().getMixture())
#self.chosenMolecules()
self.ui.structManager.blockSignals(False)
self.ui.removeButton.setFlat(len(self.editor) == 0)
#self.ui.duplicateButton.setFlat(self.editor.ident == None)
self.ui.copyButton.setFlat(len(self.editor) == 0)
self.ui.catalogButton.setFlat(len(self.editor) == 0)
self.ui.duplicateButton.setFlat(self.clipboard == None
or len(self.clipboard) == 0)
#self.ui.removeButton.setFlat(molNum == 0)
#self.ui.duplicateButton.setFlat(molNum == 0)
#progress.hide()
stop = time.clock()
#print "insertAllToManager time",stop-start
def showEvent(self, e):
#print "buildTab showEvent"
#start = time.clock()
#if self.firstUpdate:
# self.update()
# self.firstUpdate = False
self.update()
super(BuildTab, self).showEvent(e)
#print "buildTab showEvent time",time.clock()-start
def remove(self):
#print "remove"
self.copy()
selected = self.editor.selectedNames()
#print "BuildTab.remove ", selected
try:
self.history.currentState().removeMoleculesFrom(selected)
'''
for molname in selected:
self.history.currentState().removeMolecule(molname)
'''
#print "BuildTab.remove ", selected, " removed "
except:
#errorgui = QtGui.QErrorMessage(self)
#errorgui.setModal(True) # blocks Wolffia
#errorgui.showMessage("Error: could not delete molecule "
# + molname + "." )
logging.getLogger(self.__class__.__name__).warning(
"Could not delete molecules " + selected + ".")
self.editor.reset()
self.update()
def repaint(self):
selected = self.editor.selectedNames()
for row in range(self.ui.structManager.rowCount()):
#print "repaint ", self.ui.structManager.item(row,4).text()
if self.ui.structManager.item(row, 4).text() in selected:
self.ui.structManager.item(row, 2).setBackgroundColor(
QtCore.Qt.green)
else:
self.ui.structManager.item(row, 2).setBackgroundColor(
QtCore.Qt.white)
def reset(self):
#print "buildTab reset in"
self.buildPreview.reset()
self.editor.reset()
self.prevSelection = None
self.prevShow = None
self.prevFixed = None
#print "buildTab reset out"
def update(self):
#start = time.clock()
#print "updating buldTab, mixture=", self.history.currentState().getMixture()
self.insertAllToManager()
#print "buildTab update insertAllToManager",time.clock()-start
#self.buildPreview.setMixture(self.history.currentState().getMixture())
self.mixModification = time.clock()
self.ui.structManager.resizeColumnToContents(0)
self.ui.structManager.resizeColumnToContents(1)
self.ui.structManager.resizeColumnToContents(2)
self.ui.structManager.resizeColumnToContents(3)
self.editor.update()
#self.buildPreview.update()
#self.wolffia.update()
#print "buildTab update time",time.clock()-start
self.repaint()
'''
def __init__(self, m, n, q):
diamondMix = Mixture()
diamondMix.loadWFM(WOLFFIA_WFY_DIR + "/diamond.wfm")
diamondCell = diamondMix.getMolecule('Diamond_1')
sal = Element("NA")
sal.moveBy([-1, -1, -1]) # put it out of the way
#'Crece' el diamante
tempMixture = Mixture()
for dm in range(m):
for dn in range(n):
for dq in range(q):
newCell = diamondCell.copy()
newCell.moveby([dm * 5.43, dn * 5.43, dq * 5.43])
tempMixture.add(newCell)
tempMixture.add(sal)
G = tempMixture.copy()
H = tempMixture.copy()
Coord = []
overlapAtoms = []
atomNeighbors = []
toEliminate = []
#Hace que las moleculas se conecten al atomo de Na y hace de la mezcla una molecula
for p, mol in enumerate(G):
molecule = G.getMolecule(mol)
for idx, atom1 in enumerate(molecule):
if molecule.getAttributes(
atom1).getInfo().getElement() == "NA":
molSal = mol
numMolecule = p
atomSal = molecule.atom(idx)
for p, mol in enumerate(G):
molecule = G.getMolecule(mol)
if p != numMolecule:
molC = mol
atomC = molecule.atom(1)
H.addBond([molSal, atomSal], [molC, atomC])
#Pone las coordenadas de la mezcla en una lista
for p, mol in enumerate(H):
molecule = H.getMolecule(mol)
for atom in molecule:
coordinates = molecule.getAttributes(atom).getCoord()
Coord.append(coordinates)
#Te da los atomos que estan en la misma posicion
for a, coord1 in enumerate(Coord):
#print a,coord1
for x, coord2 in enumerate(Coord):
if a < x and math.fabs(
coord1[0] - coord2[0]) < TOLERANCE and math.fabs(
coord1[1] - coord2[1]) < TOLERANCE and math.fabs(
coord1[2] - coord2[2]) < TOLERANCE:
overlapAtoms.append(a)
overlapAtoms.append(x)
toEliminate.append(x)
#Te dice los vecinos de los atomos
for mol in H:
molecule = H.getMolecule(mol)
for i in range(len(overlapAtoms) / 2):
vecinos = molecule.neighbors(overlapAtoms[2 * i + 1] + 1)
#atomNeighbors.append(overlapAtoms[2*i+1]+1)
atomNeighbors.append(vecinos)
G = H.copy()
for p, mol in enumerate(G):
molecule = G.getMolecule(mol)
for i, j in enumerate(atomNeighbors):
#print i, len(j), j[0]
mol1 = mol
atom1 = molecule.atom(overlapAtoms[2 * i])
#print atom1, "atomo 1", i
if len(j) == 1:
atom2 = molecule.atom(j[0] - 1)
#print j[0]
#print atom2, atom1
H.addBond([mol1, atom1], [mol1, atom2])
elif len(j) == 2:
atom2A = molecule.atom(j[0] - 1)
atom2B = molecule.atom(j[1] - 1)
H.addBond([mol1, atom1], [mol1, atom2A])
H.addBond([mol1, atom1], [mol1, atom2B])
#toEliminate.sort()
G = H.copy()
#print "a Eliminarse", toEliminate
toEliminate = sorted(set(toEliminate))
#Busca el indice del atomo Na
for p, mol in enumerate(G):
molecule = G.getMolecule(mol)
for idx, atom1 in enumerate(molecule):
if molecule.getAttributes(
atom1).getInfo().getElement() == "NA":
idxNa = idx + 1
#Elimina los atomos 'repetidos' y el atomo de Na
for p, mol in enumerate(G):
molecule = G.getMolecule(mol)
for i in reversed(toEliminate):
#print i+1
molecule.removeAtom(i + 1)
molecule.removeAtom(idxNa)
Molecule.__init__(self, "Diamond", next(G.moleculeGenerator()))
# Fix atom types
for atom in self:
N = len(self.neighbors(atom))
if N == 4:
self.getAtomAttributes(atom).getInfo().setType("C")
if N == 1:
self.getAtomAttributes(atom).getInfo().setType("C2")
if N == 2:
self.getAtomAttributes(atom).getInfo().setType("C3")
self.getForceField().setBond(('C', 'C'), 222., NonBond._EPSILON)
self.getForceField().setBond(('C', 'C'), 1.512, NonBond._SIGMA)
