def showMolecules(self):
tstep = self.animationSlider.value()
self.animationTime.setText("Time: %7.2f fs" % (tstep * self.dt))
self.mol.clear()
for geoms in self.geometries:
geom_time = geoms[min(tstep, len(geoms)-1)]
# atoms
atoms = []
for (Z,pos) in geom_time:
a = self.mol.addAtom()
a.pos = np.array(pos, dtype=float)
a.atomicNumber = Z
atoms.append(a)
# bond
C = XYZ.connectivity_matrix(geom_time)
Nat = len(geom_time)
for i in range(0, Nat):
for j in range(i+1,Nat):
if C[i,j] == 1:
bond = self.mol.addBond()
bond.setBegin(atoms[i])
bond.setEnd(atoms[j])
bond.order = 1
self.glWidget.mol = self.mol
self.glWidget.updateGeometry()
Avogadro.toPyQt(self.glWidget).update()
def load(self, row): mol = self.molFile.molecule(row) self.objects.append(mol) glWidget = self.newGLWidget() glWidget.molecule = mol mdiWindow = self.ui.mdiArea.addSubWindow(Avogadro.toPyQt(glWidget)) print glWidget print Avogadro.toPyQt(glWidget) mdiWindow.setWindowTitle(self.molFile.titles[row]) mdiWindow.show()
def test_engine(self):
engines = Avogadro.PluginManager.instance.identifiers(
Avogadro.PluginType.EngineType)
engine = Avogadro.PluginManager.instance.engine(
engines[0], Avogadro.toPyQt(self.glwidget))
self.assertNotEqual(engine, None)
self.glwidget.addEngine(engine)
self.glwidget.removeEngine(engine)
def load(self, row):
mol = self.molFile.molecule(row)
self.objects.append(mol)
glWidget = self.newGLWidget()
glWidget.molecule = mol
mdiWindow = self.ui.mdiArea.addSubWindow(Avogadro.toPyQt(glWidget))
mdiWindow.setWindowTitle(self.molFile.titles[row])
mdiWindow.show()
def __init__(self, ):
super(Main, self).__init__()
self.setupUi(self)
self.canvases = []
self.trajdirs = []
self.trajSelection.itemSelectionChanged.connect(self.changeTrajectory)
# load Trajectories
dyndir = "./"
if len(sys.argv) > 1:
dyndir = sys.argv[1]
self.dirBrowser.setText(dyndir)
self.dirBrowser.returnPressed.connect(self.fetchURL)
self.openButton.clicked.connect(self.openDirectory)
# plots
import matplotlib.pyplot as plt
cmap = plt.get_cmap('gnuplot')
self.colors = ['black', 'red', 'green', 'blue', 'k', 'm'
] + [cmap(f) for f in np.linspace(0.4, 1.0, 10)]
self.energiesAxis = self.addTab(self.energiesLayout)
self.coefficientsAxis = self.addTab(self.coefficientsLayout)
self.couplingsAxis = self.addTab(self.couplingsLayout)
self.currEnergyAxis = self.addTab(self.currEnergyLayout)
self.currStateAxis = self.addTab(self.currStateLayout)
self.populationsAxis = self.addTab(self.populationsLayout)
self.axes = [
self.energiesAxis, self.coefficientsAxis, self.couplingsAxis,
self.currEnergyAxis, self.currStateAxis
]
self.objects = []
# Window with geometries
self.glWidget = self.newGLWidget()
self.mol = Avogadro.molecules.addMolecule()
self.objects.append(self.mol)
self.glWidget.molecule = self.mol
self.viewerWidgetLayout.addWidget(Avogadro.toPyQt(self.glWidget))
#
self.animationSlider.valueChanged.connect(self.showMolecules)
self.loadTrajectories(dyndir)
#
self.pictureAorDiab = QtGui.QComboBox()
self.pictureAorDiab.addItems(["adiabatic", "local diabatic"])
self.pictureAorDiab.setToolTip(
"Choose whether energies and couplings should be shown in the adiabatic or the local diabatic picture."
)
self.pictureAorDiab.currentIndexChanged.connect(self.switchPicture)
self.picture = self.pictureAorDiab.currentText()
self.gridLayout.addWidget(self.pictureAorDiab, 1, 0)
def performAction(self, action, glwidget):
for i, engine in enumerate(glwidget.engines):
if engine.name == "Surfaces":
surfaceEngine = engine # This should work...
print "Name", engine.name # Bug, it gives nothing intelligible
print "Alias", engine.alias # Bug, same as before
print "Primitives", engine.primitiveTypes # Gives Surface, 3, Atoms etc...
print "index", i
cube = glwidget.molecule.addCube()
dim = array([5, 5, 5])
min = -array([10.0, 10.0, 10.0])
max = array([10.0, 10.0, 10.0])
cube.setLimits(min, max, dim)
data = []
for i in range(125):
data.append(sin(i / 5.0))
cube.setData(data)
mesh = glwidget.molecule.addMesh()
ID = mesh.id
mesh.cube = cube.id
iso = 1.0
mesh_gen = Avogadro.MeshGenerator()
initialized = mesh_gen.initialize(cube, mesh, iso)
mesh_gen.run()
Avogadro.toPyQt(mesh_gen).wait()
print "finished"
#settings = QSettings("mesh1Id", ID) This doesn't set values!!
settings = QSettings()
settings.setValue("mesh1Id", ID)
surfaceEngine.readSettings(settings)
surfaceEngine.enabled = True
glwidget.molecule.update()
def open(self):
filename = str(
QFileDialog.getOpenFileName(
self, 'Open', QDir.currentPath(),
'Chemistry files (*.cml *.sdf *.mol *.xyz)'))
self.molFile = Avogadro.OpenbabelWrapper.readFile(
filename, '', '', False)
self.connect(Avogadro.toPyQt(self.molFile), SIGNAL('ready()'), self,
SLOT('readThreadFinnished()'))
self.ui.statusbar.showMessage('Reading file...')
def performAction(self, action, glwidget):
for i,engine in enumerate(glwidget.engines):
if engine.name == "Surfaces":
surfaceEngine = engine # This should work...
print "Name",engine.name # Bug, it gives nothing intelligible
print "Alias",engine.alias # Bug, same as before
print "Primitives", engine.primitiveTypes # Gives Surface, 3, Atoms etc...
print "index",i
cube = glwidget.molecule.addCube()
dim = array([5,5,5])
min = -array([10.0,10.0,10.0])
max = array([10.0,10.0,10.0])
cube.setLimits(min,max,dim)
data = []
for i in range(125):
data.append(sin(i/5.0))
cube.setData(data)
mesh = glwidget.molecule.addMesh()
ID = mesh.id
mesh.cube = cube.id
iso = 1.0
mesh_gen = Avogadro.MeshGenerator()
initialized = mesh_gen.initialize(cube,mesh,iso)
mesh_gen.run()
Avogadro.toPyQt(mesh_gen).wait()
print "finished"
#settings = QSettings("mesh1Id", ID) This doesn't set values!!
settings = QSettings()
settings.setValue("mesh1Id", ID)
surfaceEngine.readSettings(settings)
surfaceEngine.enabled = True
glwidget.molecule.update()
def test_engine(self): engines = Avogadro.PluginManager.instance.identifiers(Avogadro.PluginType.EngineType) engine = Avogadro.PluginManager.instance.engine(engines[0], Avogadro.toPyQt(self.glwidget)) self.assertNotEqual(engine, None) self.glwidget.addEngine(engine) self.glwidget.removeEngine(engine)
def open(self):
filename = str(QFileDialog.getOpenFileName(self, 'Open', QDir.currentPath(),
'Chemistry files (*.cml *.sdf *.mol *.xyz)'))
self.molFile = Avogadro.MoleculeFile.readFile(filename, '', '', False)
self.connect(Avogadro.toPyQt(self.molFile), SIGNAL('ready()'), self, SLOT('readThreadFinnished()'))
self.ui.statusbar.showMessage('Reading file...')
def test_engine(self):
engine = Avogadro.PluginManager.instance.engine("Label", Avogadro.toPyQt(self.glwidget))
#engine = Avogadro.PluginManager.instance.engine("foo", N)
self.assertNotEqual(engine, None)
self.glwidget.addEngine(engine)
self.glwidget.removeEngine(engine)
