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)
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)
def reset(self):
#print "PropertyEditor reset "
self.mixture = Mixture(None)
self.registry = dict()
#self.ident = None
self.resetBoxes()
self.setToolTip("Select molecules to activate.")
self.setEnabled(False)
self.update()
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 generateHomopol(self):
n = self.ui.nSpinBox.value()
self.homopol = Mixture()
exec("from chemicalGraph.molecule.polymer." + str(self.type) +
" import " + str(self.type))
self.poly = eval(str(self.type) + "(n)")
self.homopol.add(self.poly)
self.history.currentState().reset()
self.history.currentState().addMixture(self.homopol)
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 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()
def _processNextFrame(self):
"""
Gets next pybel Molecule and puts its Wolffia equivalent Mixture in self.currentMolecule.
Returns the next frame.
Assumes that _processFirstFrame() has been called earlier.
Raises whichever exception that pybel throws (probably StopIteration).
"""
self.currentMolecule = Mixture(self.currentMolecule) # copy mixture
mol = next(self.molIterator)
print("_processNextFrame", mol)
coordinates = []
for atom in mol.atoms:
coordinates.append(atom.coords)
self.currentMolecule.updateCoordinatesFromArray(coordinates)
return self.currentMolecule
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()
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)
def generatePolymer(self):
n = self.ui.nSpinBox.value()
m = self.ui.mSpinBox.value()
monomers = self.ui.monomersSpinBox.value()
self.pss = Mixture()
self.history.currentState().reset()
self.history.currentState().addMolecule(PSS(n, m, monomers))
self.pssPreview.update()
def on_addMixtureButton_pressed(self):
'''
Creates a new, nameless mixture on the QWidgetTree.
'''
self.loadTable.blockSignals(True)
newName, ok = QtGui.QInputDialog.getText(
self, 'Renaming a mixture', 'Enter the new name for the mixture:')
newName = str(newName).strip('\/\\')
if ok and newName and not newName.isspace():
for mixName in self.mixtures:
if mixName == newName:
QtGui.QMessageBox.information(
self, "Error", "That mixture name already exists",
QtGui.QMessageBox.Ok)
elif not ok:
return
else:
QtGui.QMessageBox.information(self, "Error", "Bad mixture name",
QtGui.QMessageBox.Ok)
return
from lib.chemicalGraph.Mixture import Mixture #@UnresolvedImport
self.wolffia.setDefaultTabs()
row = self.loadTable.rowCount()
self.loadTable.setRowCount(row + 1)
self.loadTable.setItem(row, 0, QtGui.QTableWidgetItem())
newTableWidgetItem = QtGui.QTableWidgetItem("")
self.loadTable.setItem(row, 0, newTableWidgetItem)
newTableWidgetItem.setFlags(QtCore.Qt.ItemIsEditable
| QtCore.Qt.ItemIsEnabled)
self.settings.setMixtureLocation(newName)
#print newName
self.history.currentState().setBuildDirectory(
self.settings.currentMixtureLocation())
self.wolffia.reset()
newMix = Mixture(mixName=newName)
for row in range(self.loadTable.rowCount()):
self.loadTable.item(row,
0).setBackgroundColor(QtGui.QColor("white"))
self.lastSelectedItem = newTableWidgetItem
newTableWidgetItem.setBackgroundColor(QtGui.QColor("blue"))
self.history.currentState().updateMixture(newMix)
self.history.currentState().setBuildDirectory(
self.settings.currentMixtureLocation())
self.history.currentState().save(
self.settings.currentMixtureLocation() + newMix.mixName + ".wfy")
self.wolffia.update()
self.mixtures.append(newName)
self.setTable()
self.loadTable.blockSignals(False)
class Cellulose(Polymer):
ALL_MONOMERS = Mixture()
ALL_MONOMERS.loadWFM(WOLFFIA_WFY_DIR + "/Cellulose.wfm")
print(ALL_MONOMERS.molecules())
IMAGE = "/Cellulose.png"
MONOMERS_MOLS={ 'Cs':ALL_MONOMERS.getMolecule('Cellulose_s_1'),\
'C_a_b':ALL_MONOMERS.getMolecule('Cellulose_b_1'),\
'C_a_e':ALL_MONOMERS.getMolecule('Cellulose_e_1'),\
'C_a_1':ALL_MONOMERS.getMolecule('Cellulose_1_1'),\
'C_a_s':ALL_MONOMERS.getMolecule('Cellulose_s_1'),\
'C_b_s':ALL_MONOMERS.getMolecule('CelluloseB_s_1'),\
'C_b_b':ALL_MONOMERS.getMolecule('CelluloseB_b_1'),\
'C_b_e':ALL_MONOMERS.getMolecule('CelluloseB_e_1'),\
'C_b_1':ALL_MONOMERS.getMolecule('CelluloseB_1_1')}
NUM_ATOMS_BACKBONE_MONOMER = MONOMERS_MOLS['C_a_b'].order()
END_ATOM = 2 #!!!
START_ATOM = 0
DISPL = 10.4
ANGLE = 0.
def __init__(self, numMonomers, type='b'):
# initialize base class
assert (numMonomers > 0)
molname = "Cellulose_" + type + "(" + str(numMonomers) + ")"
if numMonomers == 1: # only one monomer
#print "Cellulose ", self.MONOMERS_MOLS['P1'].bonds()
chain = ['C_' + type + '_1']
else:
chain = ['C_' + type + '_s']
for i in range(numMonomers - 2):
chain.append('C_' + type + '_b')
chain.append('C_' + type + '_e')
#print "Cellulose ", chain
Polymer.__init__(self, chain, molname)
self.type = type
# add FF parameters for monomer junctions
#self.getForceField().setAngle(('C','C','C'), 60., 0)
#self.getForceField().setAngle(('C','C','C'), 109.47, 1)
self.getForceField().setDihedral(('C100', 'O400', 'C400', 'C300'), 0.6,
0)
self.getForceField().setDihedral(('C100', 'O400', 'C400', 'C300'), 1,
1)
self.getForceField().setDihedral(('C100', 'O400', 'C400', 'C300'),
3.14, 2)
for atom in self:
self.getAtomAttributes(atom).getInfo().setResidue('CEL')
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):
Mixture.__init__(self, "SDS")
#print NANOCAD_PDB_DIR + "/Solvents/THF.pdb" , NANOCAD_PDB_DIR + "/Solvents/THF.psf"
self.load(NANOCAD_PDB_DIR + "/Surfactant/SDS.pdb" , NANOCAD_PDB_DIR + "/Surfactant/SDS.psf")
#print "SDS ff", _FORCE_FIELD._NONBONDED
#print "SDS a", NANOCAD_FORCE_FIELDS + "/SDS.prm"
p1, p2 = [self.getMolecule(p) for p in self.molecules()]
if p1.order() == 1:
p1.rename("NA")
SDS._FORCE_FIELD_NA = ForceField(p1, NANOCAD_FORCE_FIELDS + "/SDS.prm")
p1.setForceField(SDS._FORCE_FIELD_NA )
SDS._FORCE_FIELD_SDS = ForceField(p2, NANOCAD_FORCE_FIELDS + "/SDS.prm")
p2.setForceField(SDS._FORCE_FIELD_SDS )
else:
p2.rename("NA")
SDS._FORCE_FIELD_NA = ForceField(p2, NANOCAD_FORCE_FIELDS + "/SDS.prm")
p2.setForceField(SDS._FORCE_FIELD_NA )
SDS._FORCE_FIELD_SDS = ForceField(p1, NANOCAD_FORCE_FIELDS + "/SDS.prm")
p1.setForceField(SDS._FORCE_FIELD_SDS )
p1.copyChargesToForceField()
p2.copyChargesToForceField()
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)
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)
def closeEvent(self, e):
if not self.isAdded:
self.history.currentState().updateMixture(Mixture())
def __init2__(self,n,m,q):
super(Diamond,self).__init__(ident="Diamond")
allCells = Mixture()
allCells.loadWFM(WOLFFIA_WFY_DIR + "/diamond.wfm")
#print allCells.moleculeNames()
#print allCells.nodes()
cell = allCells.getMolecule(allCells.nodes()[0])
for x in range(n):
for y in range(m):
line = Molecule()
for z in range(q):
newCell = cell.copy()
newCell.moveBy([x*self._CELL_WIDTH_,y*self._CELL_WIDTH_,z*self._CELL_WIDTH_])
addAndJoin(line, newCell)
print "Diamond __init__",x,y
addAndJoin(self, line)
#print allCells.enclosingBox()
'''
#==========================================================================
#==========================================================================
if __name__ == '__main__':
d = Diamond(3, 3, 3)
print(d.edges())
d.writePDB("/home/jse/Desktop/Diamantito.pdb")
m = Mixture()
m.add(d)
m.save("/home/jse/Desktop/Diamantito.wfm")
def _processFirstFrame(self):
"""
Gets the first pybel Molecule and puts its Wolffia equivalent Mixture in self.currentMolecule.
Returns the first frame.
Raises whichever exception that pybel throws (probably StopIteration).
"""
mol = next(self.molIterator)
chemicalGraphMixed = ChemicalGraph()
etable = openbabel.OBElementTable()
n = 0
for atom in mol.atoms:
atomType = atom.OBAtom.GetResidue().GetAtomID(atom.OBAtom)
symbol = etable.GetSymbol(atom.atomicnum)
coords = list(atom.coords)
name = etable.GetName(atom.atomicnum)
residue = atom.OBAtom.GetResidue().GetName()
psfType = atom.OBAtom.GetResidue().GetAtomID(atom.OBAtom).strip()
#print "_processFirstFrame: '" + psfType + "'"
charge = atom.partialcharge
mass = atom.atomicmass
if self.psf != None:
psfType = self.psf.getType(n)
charge = self.psf.getCharge(n)
mass = self.psf.getMass(n)
print("CoordinateFile _processFirstFrame charge ", charge)
ai = AtomInfo(atomType, symbol, psfType, charge, mass, 1, 1, 1, name, residue)
atr = AtomAttributes(ai, coords, [])
chemicalGraphMixed.add_node(n + 1, attrs=[atr])
n += 1
# add edges
print('_processFirstFrame add edges')
if self.psf != None:
for b in self.psf.bonds:
try: # avoids adding an edge twice
chemicalGraphMixed.add_edge(b)
except AdditionError:
pass
if len(mol.atoms) != len(self.psf.atoms):
raise MixtureError("Amount of atoms in " + self.fileName + " and psf File files are different (" + str(len(self.atoms)) + " vs " + str(len(self.psf.atoms)) + ").")
else:
for bond in openbabel.OBMolBondIter(mol.OBMol):
chemicalGraphMixed.add_edge([bond.GetBeginAtom().GetIdx(), bond.GetEndAtom().GetIdx()])
molecules = list(chemicalGraphMixed.connectedComponents())
self.currentMolecule = Mixture()
#print '_processFirstFrame Añadir'+ str(list(molecules)) + ' moléculas a mezcla: ',
if len(molecules) == 1:
self.currentMolecule.add(Molecule(self.mixtureName, molecule=molecules[0]))
else:
n = 0
for m in molecules:
self.currentMolecule.add(
Molecule(self.mixtureName + "(" + str(n) + ")", molecule=m),
checkForInconsistentNames=False)
n += 1
return self.currentMolecule
def closeEvent(self, e):
if not self.isAdded:
self.myMixture = Mixture()
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)
class PEDOT(Polymer):
ALL_MONOMERS = Mixture()
ALL_MONOMERS.loadWFM(WOLFFIA_WFY_DIR + "/PEDOT.wfm")
#print allMonomers.molecules()
BACKBONE_MONOMER_MOL = ALL_MONOMERS.getMolecule('PEDOT_1')
START_MONOMER_MOL = ALL_MONOMERS.getMolecule('PEDOT0_1')
END_MONOMER_MOL = ALL_MONOMERS.getMolecule('PEDOTF_1')
ONE_MONOMER_MOL = ALL_MONOMERS.getMolecule('PEDOT1_1')
IMAGE = "/PEDOT.png"
NUM_ATOMS_BACKBONE_MONOMER = BACKBONE_MONOMER_MOL.order()
NUM_ATOMS_START_MONOMER = START_MONOMER_MOL.order()
NUM_ATOMS_LAST_MONOMER = END_MONOMER_MOL.order()
END_ATOM = 2 #!!!
START_ATOM = 21
DISPL = 3
ANGLE = 3.14
MONOMERS_MOLS={ 'Rs':ALL_MONOMERS.getMolecule('PEDOT0_1'),\
'Rb':ALL_MONOMERS.getMolecule('PEDOT_1'),\
'Re':ALL_MONOMERS.getMolecule('PEDOTF_1'),\
'Os':ALL_MONOMERS.getMolecule('PEDOTp0_1'),\
'Ob':ALL_MONOMERS.getMolecule('PEDOTp_1'),\
'Oe':ALL_MONOMERS.getMolecule('PEDOTpF_1'),\
'P1':ALL_MONOMERS.getMolecule('PEDOT1_1')}
def __init__(self, n, m, numMonomers):
# initialize base class
assert (n > 0 or m > 0)
molname = "PEDOT(" + str(n) + ", " + str(m) + ", " + str(
numMonomers) + ")"
baseChain = []
for i in range(n):
baseChain.append('Rb')
for i in range(m):
baseChain.append('Ob')
#for i in range(n):
# baseChain.append('Rb')
chain = []
for i in range(numMonomers):
chain += baseChain
if n > 0:
chain[0] = 'Rs'
chain[-1] = 'Re'
else:
chain[0] = 'Os'
chain[-1] = 'Oe'
Polymer.__init__(self, chain, molname)
# add FF parameters for monomer junctions
self.getForceField().setBond(('C', 'C'), 305., NonBond._EPSILON)
self.getForceField().setBond(('C', 'C'), 1.3750, NonBond._SIGMA)
self.getForceField().setBond(('C', 'C3'), 222.500, NonBond._EPSILON)
self.getForceField().setBond(('C', 'C3'), 1.5300, NonBond._SIGMA)
self.getForceField().setBond(('C3', 'C3'), 305.000, NonBond._EPSILON)
self.getForceField().setBond(('C3', 'C3'), 1.3750, NonBond._SIGMA)
self.getForceField().setAngle(('C', 'C3', 'S1'), 40., 0)
self.getForceField().setAngle(('C', 'C3', 'S1'), 120., 1)
self.getForceField().setAngle(('C', 'C3', 'C4'), 45.8, 0)
self.getForceField().setAngle(('C', 'C3', 'C4'), 120., 1)
self.getForceField().setAngle(('C3', 'C4', 'C4'), 51.8, 0)
self.getForceField().setAngle(('C3', 'C4', 'C4'), 107.5, 1)
self.getForceField().setAngle(('C3', 'C3', 'S1'), 40., 0)
self.getForceField().setAngle(('C3', 'C3', 'S1'), 120., 1)
self.getForceField().setAngle(('C3', 'C3', 'C4'), 45.8, 0)
self.getForceField().setAngle(('C3', 'C3', 'C4'), 120., 1)
self.getForceField().setDihedral(('C', 'C3', 'S1', 'C3'), 1.75, 0)
self.getForceField().setDihedral(('C', 'C3', 'S1', 'C3'), 2, 1)
self.getForceField().setDihedral(('C', 'C3', 'S1', 'C3'), 180, 2)
self.getForceField().setDihedral(('C3', 'S1', 'C3', 'C'), 1.75, 0)
self.getForceField().setDihedral(('C3', 'S1', 'C3', 'C'), 2, 1)
self.getForceField().setDihedral(('C3', 'S1', 'C3', 'C'), 180, 2)
self.getForceField().setDihedral(('C3', 'C3', 'S1', 'C3'), 1.75, 0)
self.getForceField().setDihedral(('C3', 'C3', 'S1', 'C3'), 2, 1)
self.getForceField().setDihedral(('C3', 'C3', 'S1', 'C3'), 180, 2)
self.getForceField().setDihedral(('C3', 'S1', 'C3', 'C3'), 1.75, 0)
self.getForceField().setDihedral(('C3', 'S1', 'C3', 'C3'), 2, 1)
self.getForceField().setDihedral(('C3', 'S1', 'C3', 'C3'), 180, 2)
class PSS(Polymer):
ALL_MONOMERS = Mixture()
ALL_MONOMERS.loadWFM(WOLFFIA_WFY_DIR + "/PSS.wfm")
'''
BACKBONE_MONOMER_MOL = ALL_MONOMERS.getMolecule('PSS_1')
START_MONOMER_MOL = ALL_MONOMERS.getMolecule('PSS0_1')
END_MONOMER_MOL = ALL_MONOMERS.getMolecule('PSSF_1')
ONE_MONOMER_MOL = ALL_MONOMERS.getMolecule('PSS1_1')
'''
IMAGE = "/PSS.png"
MONOMERS_MOLS={ 'Rs':ALL_MONOMERS.getMolecule('PSSs_1'),\
'Rb':ALL_MONOMERS.getMolecule('PSS_1'),\
'Re':ALL_MONOMERS.getMolecule('PSSe_1'),\
'Os':ALL_MONOMERS.getMolecule('PSSns_1'),\
'Ob':ALL_MONOMERS.getMolecule('PSSn_1'),\
'Oe':ALL_MONOMERS.getMolecule('PSSne_1'),\
'P1':ALL_MONOMERS.getMolecule('PSS1_1')}
NUM_ATOMS_BACKBONE_MONOMER = MONOMERS_MOLS['Rb'].order()
'''
NUM_ATOMS_START_MONOMER = MONOMERS_MOLS[].order()
NUM_ATOMS_LAST_MONOMER = MONOMERS_MOLS[].order()
'''
END_ATOM = 2 #!!!
START_ATOM = 21
DISPL = 1.0
ANGLE = 3.14
def __init__(self, n, m, numMonomers):
# initialize base class
assert (n >= 0 or m >= 0 or numMonomers > 0)
molname = "PSS(" + str(n) + ", " + str(m) + ", " + str(
numMonomers) + ")"
if n == 0 and m == 0 and numMonomers == 1: # only one monomer
#print "PSS ", self.MONOMERS_MOLS['P1'].bonds()
chain = ['P1']
else:
baseChain = []
for i in range(n):
baseChain.append('Rb')
for i in range(m):
baseChain.append('Ob')
for i in range(n):
baseChain.append('Rb')
chain = []
for i in range(numMonomers):
chain += baseChain
if n > 0:
chain[0] = 'Rs'
chain[-1] = 'Re'
else:
chain[0] = 'Os'
chain[-1] = 'Oe'
#print "PSS ", chain
Polymer.__init__(self, chain, molname)
# add FF parameters for monomer junctions
self.getForceField().setAngle(('C', 'C', 'C'), 60., 0)
self.getForceField().setAngle(('C', 'C', 'C'), 109.47, 1)
self.getForceField().setDihedral(('C', 'C', 'C', 'C'), 1.4, 0)
self.getForceField().setDihedral(('C', 'C', 'C', 'C'), 3, 2)
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()
# Lists of densities and and names for output files
#densities = [100.0,0.90,0.80,0.70,0.60,0.50,0.40,0.30,0.20,0.10,0.05]
#d_names = ["100","09","08","07","06","05","04","03","02","01","005"]
densities = [0.05]
d_names = ["005"]
# Iterate through every density
for i in range(len(densities)):
# Density value
PABAratio = densities[i]
FileName = "Cellulose_PABA_Tetradecane_D" + d_names[i] + ".wfm"
# Define mixture
mixture = Mixture()
# Generate crystal minus last layer
monomer = Cellulose(POLY_LENGTH)
for j in range(VERTICAL_N - 1):
for i in range(HORIZONTAL_N):
newMonomer = monomer.copy()
newMonomer.moveBy([dx * i + dxz * (j % 2), dy * (i % 2), dz * j])
mixture.add(newMonomer)
print "layer " + str(j) + ", row " + str(i)
# Generate last layer
for i in range(HORIZONTAL_N):
newMonomer = monomer.copy()
newMonomer.moveBy([
dx * i + dxz * ((VERTICAL_N - 1) % 2), dy * (i % 2),
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)
class PropertyEditor(QtWidgets.QWidget):
def __init__(self, viewer, history):
super(PropertyEditor, self).__init__()
# set class fields
self.viewer = viewer
self.history = history
#widgets import
self.ui = Ui_propertyEditor()
self.ui.setupUi(self)
self.tree = self.ui.propertyTree
self.tree. setColumnWidth(0, 100)
self.tree. setColumnWidth(1, 140)
#initializes widgets on tree
self.xRotate = QtWidgets.QDoubleSpinBox(self.tree)
self.xRotate. setSingleStep (10.)
self.xRotate. setRange (-360., 360.)
xRotateAt = self.tree.topLevelItem(1).child(0)
self.yRotate = QtWidgets.QDoubleSpinBox(self.tree)
self.yRotate. setSingleStep (10.)
self.yRotate. setRange (-360., 360.)
yRotateAt = self.tree.topLevelItem(1).child(1)
self.zRotate = QtWidgets.QDoubleSpinBox(self.tree)
self.zRotate. setSingleStep (10.)
self.zRotate. setRange (-360., 360.)
zRotateAt = self.tree.topLevelItem(1).child(2)
self.xMoveBy = QtWidgets.QDoubleSpinBox(self.tree)
self.xMoveBy. setSingleStep (0.5)
self.xMoveBy. setRange (-1000., 1000.)
xMoveByAt = self.tree.topLevelItem(2).child(0)
self.yMoveBy = QtWidgets.QDoubleSpinBox(self.tree)
self.yMoveBy. setSingleStep (0.5)
self.yMoveBy. setRange (-1000., 1000.)
yMoveByAt = self.tree.topLevelItem(2).child(1)
self.zMoveBy = QtWidgets.QDoubleSpinBox(self.tree)
self.zMoveBy. setSingleStep (0.5)
self.zMoveBy. setRange (-1000., 1000.)
zMoveByAt = self.tree.topLevelItem(2).child(2)
#adds widgets to tree
self.tree.setItemWidget(xRotateAt, 1, self.xRotate)
self.tree.setItemWidget(yRotateAt, 1, self.yRotate)
self.tree.setItemWidget(zRotateAt, 1, self.zRotate)
self.tree.setItemWidget(xMoveByAt, 1, self.xMoveBy)
self.tree.setItemWidget(yMoveByAt, 1, self.yMoveBy)
self.tree.setItemWidget(zMoveByAt, 1, self.zMoveBy)
#manages widget events
self.xRotate.valueChanged.connect(self.Rotate)
self.yRotate.valueChanged.connect(self.Rotate)
self.zRotate.valueChanged.connect(self.Rotate)
self.xMoveBy.valueChanged.connect(self.MoveBy)
self.yMoveBy.valueChanged.connect(self.MoveBy)
self.zMoveBy.valueChanged.connect(self.MoveBy)
self.tree.resizeColumnToContents(0)
self.tree.resizeColumnToContents(1)
#initialize tree window
self.reset()
def reset(self):
#print "PropertyEditor reset "
self.mixture = Mixture(None)
self.registry = dict()
#self.ident = None
self.resetBoxes()
self.setToolTip("Select molecules to activate.")
self.setEnabled(False)
self.update()
def update(self):
# update resistry
presentMolecules = self.history.currentState().getMixture().molecules()
#print "PropertyEditor update ",presentMolecules, self.registry
regKeys = list(self.registry.keys())
for regKey in regKeys:
if not regKey in presentMolecules:
if self.mixture.hasMoleculeID(regKey): self.mixture.remove(regKey)
self.registry.pop(regKey)
self.resetBoxes()
QtWidgets.QWidget.update(self)
def resetBoxes(self):
if len(self) == 0:
self.tree.topLevelItem(0).setText(1, "")
else:
self.tree.topLevelItem(0).setText(1, str(self))
self.dx = 0.
self.dy = 0.
self.dz = 0.
self.anglex = 0.
self.angley = 0.
self.anglez = 0.
self.xRotate.setValue(0.)
self.yRotate.setValue(0.)
self.zRotate.setValue(0.)
self.xMoveBy.setValue(0.)
self.yMoveBy.setValue(0.)
self.zMoveBy.setValue(0.)
#show molecule name in the editor
def setMolecule(self, molecule, ident, removeIfPresent=False):
'''
Returns True if the molecule ends up selected, False otherwise..
'''
from .BuildTab import ShownSolvent
#print "PropertyEditor setMolecule new", ident, self.registry
if ident not in self.registry:
if ShownSolvent.isSolvent(ident):
mixture = self.history.currentState().getMixture()
mixtureNames = mixture.molecules()
#print "PropertyEditor setMolecule SOLVENT(",mixtureNames
pos = ident.find(')')+1
for mol in mixtureNames:
if mol[:pos] == ident[:pos]:
self.registry[mol] = self.mixture.add(mixture.getMolecule(mol), False)
self.registry[mol] = mixture.getMolecule(mol)
else:
#print "PropertyEditor setMolecule adding", ident
self.registry[ident] = molecule
#print "PropertyEditor setMolecule adding to mixture", ident, self.mixture.molecules()
self.mixture.add(molecule, False)
#self.ident = ident
#self.ident = self.getId()
self.setToolTip("Manage molecules' positions.")
self.setEnabled(True)
return False
self.resetBoxes()
else:
#print "PropertyEditor setMolecule duplicate",ident, self.registry
if removeIfPresent:
if ShownSolvent.isSolvent(ident):
mixture = self.history.currentState().getMixture()
mixtureNames = mixture.molecules()
pos = ident.find(')')+1
for mol in mixtureNames:
#print "PropertyEditor removing ",ident[:pos], mol[:pos]
if mol[:pos] == ident[:pos]:
#print "PropertyEditor OK "
self.removeSelection(mixture.getMolecule(mol), mol)
else:
self.removeSelection(molecule, ident)
return True
#print "PropertyEditor setMolecule reseting"
#print "PropertyEditor setMolecule finished"
def removeSelection(self, molecule, ident):
if ident in self.registry:
self.mixture.remove(self.mixture.getMoleculeID(molecule))
self.registry.pop(ident)
#print "PropertyEditor removeSelection removed:",ident
if len(self.registry) == 0:
self.reset()
#print "PropertyEditor setMolecule reseting"
self.resetBoxes()
def hasSelections(self): return len(self.registry) > 0
def selectedMolecules(self):
#print "selectedMolecules ", self.registry
return list(self.registry.values())
def selectedNames(self):
#print "selectedMolecules ",self.registry
return list(self.registry.keys())
def __str__(self):
return str(list(self.registry.keys()))
def __len__(self):
return len(self.registry)
#show rotation values in the editor
def Rotate(self):
if self.mixture.order() > 0:
x = self.xRotate.value()
y = self.yRotate.value()
z = self.zRotate.value()
value = str(x) + " x " + str(y) + " x " + str(z)
self.tree.topLevelItem(1).setText(1, value)
center = self.mixture.center()
self.mixture.moveBy([-xx for xx in center])
#print "Rotate ", x-self.anglex,y-self.angley,z-self.anglez
self.mixture.rotateDeg(x-self.anglex,y-self.angley,z-self.anglez)
self.mixture.moveBy(center)
self.anglex = x
self.angley = y
self.anglez = z
self.history.currentState().getMixture().setChanged()
self.viewer.update()
else:
self.tree.topLevelItem(1).setText(1, "0 x 0 x 0")
def MoveBy(self):
x = self.xMoveBy.value()
y = self.yMoveBy.value()
z = self.zMoveBy.value()
value = str(x) + " x " + str(y) + " x " + str(z)
self.tree.topLevelItem(2).setText(1, value)
self.mixture.moveBy([x-self.dx,y-self.dy,z-self.dz])
self.dx = x
self.dy = y
self.dz = z
self.history.currentState().getMixture().setChanged()
self.viewer.update()
def getId(self):
return str(self.mixture.moleculeNames())
class CoordinateFile:
def __init__(self, mixtureFile, fileType=None, psfFile=None, mixtureName=None):
'''
Prepares file for reading molecules.
Raises MixtureError or whichever exception that pybel raises.
'''
if fileType == None:
fileType = os.path.splitext(mixtureFile)[1][1:].strip() # get filename extension
if mixtureName == None:
mixtureName = os.path.basename(mixtureFile)
self.fileType = fileType
self.fileName = mixtureFile
self.mixtureName = mixtureName
print("CoordinateFile ", fileType)
if psfFile == None: self.psf = None
else: self.psf = PSF(psfFile)
self.__iter__()
def __iter__(self):
if self.fileType == "cc1":
from . import cc1
self.molIterator = cc1.readfile(self.fileName)
else:
self.molIterator = pybel.readfile(self.fileType, self.fileName)
self.currentMolecule = None
self.firstMolecule = True
return self
def _processFirstFrame(self):
"""
Gets the first pybel Molecule and puts its Wolffia equivalent Mixture in self.currentMolecule.
Returns the first frame.
Raises whichever exception that pybel throws (probably StopIteration).
"""
mol = next(self.molIterator)
chemicalGraphMixed = ChemicalGraph()
etable = openbabel.OBElementTable()
n = 0
for atom in mol.atoms:
atomType = atom.OBAtom.GetResidue().GetAtomID(atom.OBAtom)
symbol = etable.GetSymbol(atom.atomicnum)
coords = list(atom.coords)
name = etable.GetName(atom.atomicnum)
residue = atom.OBAtom.GetResidue().GetName()
psfType = atom.OBAtom.GetResidue().GetAtomID(atom.OBAtom).strip()
#print "_processFirstFrame: '" + psfType + "'"
charge = atom.partialcharge
mass = atom.atomicmass
if self.psf != None:
psfType = self.psf.getType(n)
charge = self.psf.getCharge(n)
mass = self.psf.getMass(n)
print("CoordinateFile _processFirstFrame charge ", charge)
ai = AtomInfo(atomType, symbol, psfType, charge, mass, 1, 1, 1, name, residue)
atr = AtomAttributes(ai, coords, [])
chemicalGraphMixed.add_node(n + 1, attrs=[atr])
n += 1
# add edges
print('_processFirstFrame add edges')
if self.psf != None:
for b in self.psf.bonds:
try: # avoids adding an edge twice
chemicalGraphMixed.add_edge(b)
except AdditionError:
pass
if len(mol.atoms) != len(self.psf.atoms):
raise MixtureError("Amount of atoms in " + self.fileName + " and psf File files are different (" + str(len(self.atoms)) + " vs " + str(len(self.psf.atoms)) + ").")
else:
for bond in openbabel.OBMolBondIter(mol.OBMol):
chemicalGraphMixed.add_edge([bond.GetBeginAtom().GetIdx(), bond.GetEndAtom().GetIdx()])
molecules = list(chemicalGraphMixed.connectedComponents())
self.currentMolecule = Mixture()
#print '_processFirstFrame Añadir'+ str(list(molecules)) + ' moléculas a mezcla: ',
if len(molecules) == 1:
self.currentMolecule.add(Molecule(self.mixtureName, molecule=molecules[0]))
else:
n = 0
for m in molecules:
self.currentMolecule.add(
Molecule(self.mixtureName + "(" + str(n) + ")", molecule=m),
checkForInconsistentNames=False)
n += 1
return self.currentMolecule
def _processNextFrame(self):
"""
Gets next pybel Molecule and puts its Wolffia equivalent Mixture in self.currentMolecule.
Returns the next frame.
Assumes that _processFirstFrame() has been called earlier.
Raises whichever exception that pybel throws (probably StopIteration).
"""
self.currentMolecule = Mixture(self.currentMolecule) # copy mixture
mol = next(self.molIterator)
print("_processNextFrame", mol)
coordinates = []
for atom in mol.atoms:
coordinates.append(atom.coords)
self.currentMolecule.updateCoordinatesFromArray(coordinates)
return self.currentMolecule
def __next__(self):
"""
Returns next frame if present.
Raises whichever exception that pybel throws (probably StopIteration).
"""
if self.firstMolecule:
self.firstMolecule = False
return self._processFirstFrame()
else: return self._processNextFrame()
