def __init__(self):
mix = Mixture()
mix.loadWFM(WOLFFIA_WFY_DIR + "/PABApentane.wfm")
print(mix.molecules())
Molecule.__init__(self,
"PABA-Pentane",
molecule=mix.getMolecule("PABA-Pentane_1"))
self.changeResidues("PAB")
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)
class ShownMoleculesSet(set):
def __init__(self, mixture):
print("ShownMoleculesSet,__init__ caller=",
inspect.stack()[1]) #[3], mixture, type(mixture)
if isinstance(mixture, list):
self.mixture = Mixture()
for m in mixture:
self.mixture.add(m)
self.showAll()
else:
self.mixture = mixture
def show(self, mol):
#print "ShownMolecules show",mol
self.add(mol)
def showAll(self, mixture=None):
if mixture != None: self.addMolecules(mixture)
for mol in self.mixture:
self.add(mol)
def add(self, mol):
super(ShownMoleculesSet, self).add(self.mixture.getMolecule(mol))
def hide(self, mol):
self.discard(mol)
def remove(self, mol):
#print "ShownMoleculesSet remove ",mol
#try:
if isinstance(mol, Molecule):
super(ShownMoleculesSet, self).remove(mol)
else:
super(ShownMoleculesSet,
self).remove(self.mixture.getMolecule(mol))
#except:
#pass
def discard(self, mol):
super(ShownMoleculesSet, self).discard(self.mixture.getMolecule(mol))
'''
def discardFrom(self, molIDSet):
molset = set([ self.mixture.getMolecule(m) for m in molIDSet])
super(ShownMoleculesSet, self).difference(set(molSet))
'''
def duplicate(self, mol):
pass
def __deepcopy__(self, memo):
'''
Blocks deepcopy because it takes too long. Copy done manually in push()
'''
pass
def isShown(self, mol):
#print "isShown ", mol, mol in self.keys(), self[mol]
try:
return self.mixture.getMolecule(mol) in self
except:
return False
def shownList(self, mixture):
print("WARNING: ShownMoleculesSet deprecated.")
return list(self)
def addMolecules(self, mixture):
for mol in mixture:
self.add(mol)
def addDictionary(self, shDict):
'''
Adds information from a ShownMolecules object.
'''
for mol in shDict:
if shDict[mol]: self.add(mol)
def updateMixture(self, mixture):
self.intersection_update(
set([self.mixture.getMolecule(mol) for mol in mixture]))
self.mixture = mixture
def names(self):
return [self.mixture.getMoleculeID(molecule) for molecule in self]
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 NanoCADState(object):
def __init__(self, parent=None, filename=None, log=None):
#import inspect
#print "NanoCADState.init, caller=",inspect.stack()[1]
self.parent = parent
self.log = log
self.wolffiaVerion = WOLFFIA_VERSION
self.mixture = Mixture(mixName=WOLFFIA_DEFAULT_MIXTURE_NAME)
self.workingDir = WOLFFIA_DEFAULT_MIXTURE_LOCATION + "/"
self.drawer = None
self.simTabValues = None
self.minTabValues = None
self.shownMolecules = None
self.fixedMolecules = None
self.reset()
if not filename == None:
self.load(filename)
#print "NanoCADState__init__", self.forceFieldStorage.keys()
#-------------------------- methods ------------------------------------
def reset(self):
#self.forceFieldStorage = None
#self.mixture = Mixture(mixName = WOLFFIA_DEFAULT_MIXTURE_NAME)
self.mixture = Mixture(mixName=self.mixture.getMixtureName())
self.wolffiaVerion = WOLFFIA_VERSION
self.simTabValues = None
self.minTabValues = None
#self.mixture.setChanged()
#self.forceFieldStorage = dict()
#self.buildDir = WOLFFIA_DEFAULT_MIXTURE_LOCATION + "/" + self.mixture.getMixtureName()
#self.workingDir = os.getcwd()
self.drawer = Drawer()
self.shownMolecules = ShownMoleculesSet(self.mixture)
self.fixedMolecules = FixedMolecules()
#print "NanoCADState reset"
#--------------------------------------------------------------------
def save(self, filename=None, fileObject=None):
if fileObject != None:
f = fileObject
f.seek(0)
pickle.dump(self.__dict__, f)
else:
if filename == None:
#filename = WOLFFIA_DEFAULT_MIXTURE_LOCATION + "/" + WOLFFIA_DEFAULT_MIXTURE_NAME + ".wfy"
filename = self.getBuildDirectory(
) + "/" + self.getMixtureName() + ".wfy"
#print "History.save_ importing cPickle"
#print "History.save_ imported cPickle, starting to save"
#print "History.save_ self.getBuildDirectory(), self.getMixtureName() ", self.getBuildDirectory(), self.getMixtureName()
try:
f = open(filename, "w")
except IOError:
print(filename + ": File does not exist.")
pickle.dump(self.__dict__, f)
f.close()
#print "NanoCADState.save, save sucessful", f.name
#--------------------------------------------------------------------------------
def writeFiles(self, filename=None):
from chemicalGraph.io.PRM import PRMError
if filename == None:
filename = self.getBuildDirectory() + "/" + self.getMixtureName()
#print "NanoCADState writeFiles,", filename
try:
self.getMixture().writeFiles(filename,
self.fixedMolecules.fixedList())
except:
raise
#--------------------------------------------------------------------------------
def packFiles(self, mixBaseFilename, filename, progressSignal=None):
import zipfile
if progressSignal != None: progressSignal.emit(0)
self.writeFiles(filename=mixBaseFilename)
if progressSignal != None: progressSignal.emit(50)
self.save(
) # .wfy saved because it may have changed w/r to the one when the MixtureBrowser was created
# .coor, .vel and .conf files preserve configuration of last run
#print "NanoCADState packFiles ", mixBaseFilename, filename
file1 = zipfile.ZipFile(filename, "w")
if progressSignal != None: progressSignal.emit(60)
#mixBaseFilename = str(self.settings.currentMixtureLocation()) + "/" + self.history.currentState().getMixtureName()
#mixBaseFilename = str(self.getBuildDirectory()) + "/" + self.getMixtureName()
#print "packFiles mixname", mixBaseFilename
#for name in glob.glob(str(self.settings.currentMixtureLocation()) + "/*"):
# file1.write(name, os.path.basename(name), zipfile.ZIP_DEFLATED)
extensionsNotPacked = ""
extensionsToPack = [
".prm", ".pdb", ".psf", ".wfy", ".conf", ".coor", ".vel", ".xsc"
]
progress = 60
for ext in extensionsToPack:
#if progress.wasCanceled(): break
confFilename = mixBaseFilename + ext
if not os.path.isfile(confFilename):
#print "packFiles confFilename NotPacked",confFilename
extensionsNotPacked += " " + ext
else:
file1.write(confFilename, os.path.basename(confFilename),
zipfile.ZIP_DEFLATED)
progress += 5
if progressSignal != None: progressSignal.emit(progress)
file1.close()
return extensionsNotPacked
#--------------------------------------------------------------------
def load(self, filename=None):
import pickle as pickle #Tremenda aportación por carlos cortés
#import inspect
#print "NanoCADState.load, caller1=",inspect.stack()[1]
#print "NanoCADState.load, caller2=",inspect.stack()[2]
#print "NanoCADState.load, caller3=",inspect.stack()[3]
if filename == None:
filename = WOLFFIA_DEFAULT_MIXTURE_LOCATION + "/" + WOLFFIA_DEFAULT_MIXTURE_NAME + ".wfy"
logger = logging.getLogger(self.__class__.__name__)
if hasattr(filename, 'read'): # new in v 1.132
logger.info("Loading state from " + str(filename.name))
filename.seek(0)
self.__dict__ = pickle.load(filename)
f = filename
else:
logger.info("Loading state from " + str(filename))
if not os.path.exists(filename):
self.reset()
self.save(filename)
return
#print "History.load_ importing cPickle"
#print "History.load_ imported cPickle, starting to load"
try:
f = open(filename, "r")
self.__dict__ = pickle.load(f)
f.close()
except Exception as e:
import traceback
traceback.print_exc()
#print "NanoCADState.load_ Exeption ", e, " when unpickling file."
from PyQt5 import QtGui
gui = QtWidgets.QErrorMessage.qtHandler()
QtWidgets.QErrorMessage.showMessage(
gui, "Error: could not open configuration file " +
filename + ".")
logger.warning("Error: could not open configuration file " +
filename + ".")
if not hasattr(self, "fixedMolecules"): # introduced in v 0.24
self.fixedMolecules = FixedMolecules()
if self.wolffiaVerion < "0.24-4":
self.simTabValues["pmeGridSp"] = 1.0
logger.info("Loaded mixture from version " + self.wolffiaVerion +
". Current version is " + WOLFFIA_VERSION)
if self.wolffiaVerion < "0.24-42":
#if True:
#print "YES, mixture=",self.getMixture().molecules()
for mol in self.getMixture():
#print "load ", self.getMixture().getMolecule(mol).getForceField()._NONBONDED
molecule = self.getMixture().getMolecule(mol)
self.getMixture().getMolecule(mol).copyChargesToForceField()
self.wolffiaVerion = "0.24-42"
#print "load ", self.getMixture().getMolecule(mol).getForceField()._NONBONDED
#else: print "NO"
if self.wolffiaVerion < "0.24-43":
temp = ShownMoleculesSet(self.getMixture())
temp.addDictionary(self.shownMolecules)
del self.shownMolecules
self.shownMolecules = temp
if self.wolffiaVerion < "0.24-44":
#print "History.load_ fixing self bonds"
for m in self.mixture: #remove bonds to self
molecule = self.mixture.getMolecule(m)
for atom in molecule:
if molecule.has_edge(atom, atom):
molecule.remove_edge(atom, atom)
#print "History.load_ self bonds removed"
# trick for backward compatibility
for mol in self.getMixture():
molecule = self.getMixture().getMolecule(mol)
#print "load inspecting ",molecule.__class__
if str(molecule.__class__)[-10:] == "Molecule\'>":
molecule.__class__ = Molecule
#print "molecule class changed", molecule.__class__
if self.wolffiaVerion < "1.13": # until further versions
# self.mixture.mixName should be the same as
# self.parent.settings.currentMixtureName.
print(
"History.load_ self.mixture.mixName should be the same as self.parent.settings.currentMixtureName"
)
try:
self.mixture.setMixtureName(
self.parent.settings.currentMixtureName)
except:
pass
if self.wolffiaVerion < "1.131": # fix for 1.13 did not work.
# self.parent.settings.currentMixtureName is being
# eliminated in this version.
print(
"History.load_ self.mixture.mixName should be the same as self.parent.settings.currentMixtureName"
)
try:
self.parent.settings.setMixtureLocation(
self.parent.settings.currentMixtureName)
del self.parent.settings.currentMixtureName
except:
pass
# other fixes ===========================
if self.shownMolecules == None:
self.shownMolecules = ShownMoleculesSet(self.getMixture())
# end other fixes ===========================
if self.wolffiaVerion < "1.31":
self.getMixture().upgrade(self.wolffiaVerion)
#from PyQt5 import QtGui
if self.wolffiaVerion < WOLFFIA_VERSION:
#QtGui.QMessageBox.information(self.parent,"Wolffia", "Simulation version updated from "+str(self.wolffiaVerion)+" to "+str(WOLFFIA_VERSION))
print("NANOCADState.load: Simulation version updated from " +
str(self.wolffiaVerion) + " to " + str(WOLFFIA_VERSION))
self.wolffiaVerion = WOLFFIA_VERSION
print("NanoCADState.load_ imported cPickle, load sucessful", f.name)
#print "History.load self.shownMolecules", self.shownMolecules
#self.shownMolecules.showAll()
#--------------------------------------------------------------------
# If progress != None, it is an object that responds to he folowing methods:
# .setLabelText("Removing collisions")
# .setRange(0,molNum)
# .setValue(0)
def fillBox(self,
solv,
molNum,
checkCollisions=False,
replaceCollisions=False,
applyPCBs=True,
progress=None):
import math, random
import numpy as np
from lib.chemicalGraph.molecule.solvent.Solvent import Solvent
solventMolecules = Solvent(solv) #.__class__)
remaining = -1 # to track removng collissions
totalDim = self.getDrawer().getBoxDimension()
boxmin = self.getDrawer().getCellOrigin()
boxmax = [
boxmin[0] + totalDim[0], boxmin[1] + totalDim[1],
boxmin[2] + totalDim[2]
]
#calculate the volume for a single solvent molecule
center = [0., 0., 0.]
pos = solv.massCenter()
solv.moveBy(
[center[0] - pos[0], center[1] - pos[1], center[2] - pos[2]])
#solvDiameter = solv.diameter()+ _SEPARATION_BETWEEN_SOLVENTS_
solvDiameter = math.pow(self.getDrawer().getBoxVolume() / molNum,
1. / 3.)
if solvDiameter == 0: return
row = math.floor(totalDim[1] / solvDiameter)
col = math.floor(totalDim[0] / solvDiameter)
dep = math.floor(totalDim[2] / solvDiameter)
progressMax = molNum
progressCount = 0
if progress != None:
progress.setLabelText("Adding solvent")
progress.setRange(0, molNum - 1)
progress.setValue(0)
solvRadius = solvDiameter / 2
newPos = solv.massCenter()
refCoor = boxmin
#boxmax[0] -= solvDiameter/2.
#boxmax[1] -= solvDiameter/2.
#boxmax[2] -= solvDiameter/2.
if progress != None:
progress.setLabelText("Adding solvent")
progress.setRange(progressCount, progressMax)
progress.setValue(progressCount)
# lopps over a sequence of adding solvent and removing collisions
originalMolecules = self.getMixture().molecules()
originalCoords = self.getMixture().getAtomsCoordinatesAsArray()
solvRadius = solvDiameter / 2.0 + 1.5
#print "anadiendo... ", progressMax-progressCount
while progressCount < progressMax: # adds solvent
#random rotation for solvent atoms
rx = random.uniform(0, 360)
ry = random.uniform(0, 360)
rz = random.uniform(0, 360)
#random displacement for solvent atoms
rdx = random.uniform(boxmin[0], boxmax[0])
rdy = random.uniform(boxmin[1], boxmax[1])
rdz = random.uniform(boxmin[2], boxmax[2])
#generate new molecule and assign next position
mol = solv.copy()
mol.rotateDeg(rx, ry, rz)
newPos = np.array([[rdx, rdy, rdz]])
if checkCollisions:
atomDistances = euclidean_distances(originalCoords, newPos)
if np.min(atomDistances) > solvRadius:
#print 'fillBox: añadiendo', progressCount, np.min(atomDistances), newPos
mol.moveBy(list(newPos)[0])
#nodeName = self.addMolecule(mol, checkForInconsistentNames=False)
#self.shownMolecules.show(nodeName)
solventMolecules.addCoordinates(mol)
else:
#print 'fillBox: colision'
if replaceCollisions: progressCount -= 1
progressCount += 1
if progress != None: progress.setValue(progressCount)
del mol
# add solvent and rename with the given name
nodeName = self.addMolecule(solventMolecules,
checkForInconsistentNames=True)
self.shownMolecules.show(nodeName)
#print "fillBox ", mol.molname(),progressMax
solv.rename(solventMolecules.molname())
progressMax -= 1
#print "tiempo ", time.clock() - start
#print "Molecules after cleaning: ",mix.order()
def fillBoxBAK(self,
solv,
molNum,
checkCollisions=False,
replaceCollisions=False,
applyPCBs=True,
progress=None):
import math, random
remaining = -1 # to track removng collissions
totalDim = self.getDrawer().getBoxDimension()
boxmin = self.getDrawer().getCellOrigin()
boxmax = [
boxmin[0] + totalDim[0], boxmin[1] + totalDim[1],
boxmin[2] + totalDim[2]
]
#calculate the volume for a single solvent molecule
center = [0., 0., 0.]
pos = solv.massCenter()
solv.moveBy(
[center[0] - pos[0], center[1] - pos[1], center[2] - pos[2]])
#solvDiameter = solv.diameter()+ _SEPARATION_BETWEEN_SOLVENTS_
solvDiameter = math.pow(self.getDrawer().getBoxVolume() / molNum,
1. / 3.)
if solvDiameter == 0: return
row = math.floor(totalDim[1] / solvDiameter)
col = math.floor(totalDim[0] / solvDiameter)
dep = math.floor(totalDim[2] / solvDiameter)
progressMax = molNum
progressCount = 0
if progress != None:
progress.setLabelText("Adding solvent")
progress.setRange(0, molNum - 1)
progress.setValue(0)
solvRadius = solvDiameter / 2
newPos = solv.massCenter()
refCoor = boxmin
boxmax[0] -= solvDiameter / 2.
boxmax[1] -= solvDiameter / 2.
boxmax[2] -= solvDiameter / 2.
# add first molecule and rename solvent with the given name
mol = solv.copy()
mol.moveBy([
random.uniform(boxmin[0], boxmax[0]),
random.uniform(boxmin[1], boxmax[1]),
random.uniform(boxmin[2], boxmax[2])
])
nodeName = self.addMolecule(mol, checkForInconsistentNames=True)
self.shownMolecules.show(nodeName)
#print "fillBox ", mol.molname(),progressMax
solv.rename(mol.molname())
progressMax -= 1
if progress != None:
progress.setLabelText("Adding solvent")
progress.setRange(progressCount, progressMax)
progress.setValue(progressCount)
# lopps over a sequence of adding solvent and removing collisions
while progressCount < progressMax:
originalMolecules = self.getMixture().molecules()
#print "anadiendo... ", progressMax-progressCount
while progressCount < progressMax: # adds solvent
#random rotation for solvent atoms
rx = random.uniform(0, 360)
ry = random.uniform(0, 360)
rz = random.uniform(0, 360)
#random displacement for solvent atoms
rdx = random.uniform(boxmin[0], boxmax[0])
rdy = random.uniform(boxmin[1], boxmax[1])
rdz = random.uniform(boxmin[2], boxmax[2])
#generate new molecule and assign next position
mol = solv.copy()
mol.rotateDeg(rx, ry, rz)
newPos = [rdx, rdy, rdz]
mol.moveBy(newPos)
#mol.rename("SOLVENT("+mol.molname()+")")
nodeName = self.addMolecule(mol,
checkForInconsistentNames=False)
self.shownMolecules.show(nodeName)
progressCount += 1
if progress != None: progress.setValue(progressCount)
# remove collisions
if checkCollisions:
if progress != None:
progress.setLabelText("Removing collisions")
mix = self.getMixture()
collisions = mix.overlapingMolecules(originalMolecules,
pbc=self.getDrawer(),
applyPBCs=applyPCBs)
toRemove = set(collisions).difference(set(originalMolecules))
if remaining < 0: remaining = len(toRemove)
#print "remaining", remaining
#print "removiendo... ", len(toRemove)
#print "faltan... ", remaining-len(toRemove)
if progress != None:
progress.setRange(0, remaining)
progress.setValue(remaining - len(toRemove))
self.removeMoleculesFrom(toRemove)
if replaceCollisions: progressCount -= len(toRemove)
#print "tiempo ", time.clock() - start
#print "Molecules after cleaning: ",mix.order()
def getMixture(self):
return self.mixture
def getDrawer(self):
return self.drawer
def name(self):
return self.mixture.mixName
def getMixtureName(self):
return self.mixture.mixName
def getBuildDirectory(self):
#return self.buildDir # no longer used
try:
return self.workingDir
except:
self.workingDir = WOLFFIA_DEFAULT_MIXTURE_LOCATION + "/"
return self.workingDir
def getCurrentDirectory(self):
return self.getBuildDirectory()
def getSimTabValues(self):
return self.simTabValues
def updateMixture(self, mix):
#self.setChanged()
self.mixture = mix
self.shownMolecules.updateMixture(self.mixture)
self.fixedMolecules.updateMixture(self.mixture)
#for mol in self.mixture:
# print "mix @t NanoCADState",self.mixture.getMolecule(mol)._name
def addMixture(self, mix):
#print "History addMixture",mix
#self.mixture.merge(mix)
for mol in mix:
self.addMolecule(mix.getMolecule(mol))
def addMolecule(self, mol, checkForInconsistentNames=True):
print("NanoCADState addMolecule", mol)
molname = self.mixture.add(mol, checkForInconsistentNames)
self.shownMolecules.show(molname)
return molname
def removeMolecule(self, mol):
#import inspect
#print "NanoCADState.removeMolecule, caller=",inspect.stack()[1]
#self.forceFieldStorage = None
self.shownMolecules.remove(mol)
self.getMixture().remove(mol)
def removeMoleculesFrom(self, mols):
self.getMixture().removeFrom(mols)
self.updateMixture(self.getMixture())
#self.getMixture().removeFrom(mols)
def duplicateMolecule(self, mol):
newName = self.getMixture().duplicateMolecule(mol)
self.shownMolecules.show(newName)
def setMixtureName(self, n):
self.mixture.mixName = n
def setDrawer(self, dr):
self.drawer = dr
def setBuildDirectory(self, d):
#print "buildDirectory changed to, " , d
#self.buildDir = d # no longer used
self.workingDir = d
def setCurrentDirectory(self, d):
self.workingDir = d
def setSimTabValues(self, simVals):
self.simTabValues = simVals.copy()
def hasBox(self):
return self.drawer != None and self.drawer.hasCell()
