def initialize(self):
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(protocols.vtkWebViewPortImageDelivery())
# Update authentication key to use
self.updateSecret(_WebMolecule.authKey)
# Create default pipeline (Only once for all the session)
if not self.view:
self.reader = vtk.vtkCMLMoleculeReader()
#self.reader.SetFileName('/home/cjh/work/VTKData/Data/porphyrin.cml')
self.mapper = vtk.vtkMoleculeMapper()
self.mapper.SetInputConnection(self.reader.GetOutputPort())
self.mapper.UseBallAndStickSettings()
self.actor = vtk.vtkActor()
self.actor.SetMapper(self.mapper)
self.renderer = vtk.vtkRenderer()
self.window = vtk.vtkRenderWindow()
self.window.AddRenderer(self.renderer)
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(self.window)
interactor.GetInteractorStyle().SetCurrentStyleToTrackballCamera()
self.renderer.AddActor(self.actor)
self.renderer.SetBackground(1, 1, 1)
# VTK Web application specific
_WebMolecule.view = self.window
self.Application.GetObjectIdMap().SetActiveObject(
"VIEW", self.window)
def create_structure(self):
import vtk # REQUIRES VTK < 9.0!!!
# molecule
mol = vtk.vtkMolecule()
# hardcoded structure CO2
a1 = mol.AppendAtom(6, 0.0, 0.0, 0.0)
a2 = mol.AppendAtom(8, 0.0, 0.0, -1.0)
a3 = mol.AppendAtom(8, 0.0, 0.0, 1.0)
mol.AppendBond(a2, a1, 1)
mol.AppendBond(a3, a1, 1)
# hardcoded cell, cubic 10x10x10
vector = vtk.vtkMatrix3x3()
vector.DeepCopy([10, 0, 0, 0, 10, 0, 0, 0, 10])
mol.SetLattice(vector)
# Change lattice origin so molecule is in the centre
mol.SetLatticeOrigin(vtk.vtkVector3d(-5.0, -5.0, -5.0))
# Create a mapper and actor
mapper = vtk.vtkMoleculeMapper()
mapper.SetInputData(mol)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
self.fbo.addActors([actor])
self.fbo.update()
def load(self, inchikey):
self.reader = vtk.vtkCMLMoleculeReader()
#self.reader.SetFileName('/home/cjh/work/VTKData/Data/porphyrin.cml')
self.mapper = vtk.vtkMoleculeMapper()
self.mapper.SetInputConnection(self.reader.GetOutputPort())
self.mapper.UseBallAndStickSettings()
self.actor = vtk.vtkActor()
self.actor.SetMapper(self.mapper)
self.renderer = vtk.vtkRenderer()
self.window = vtk.vtkRenderWindow()
self.window.AddRenderer(self.renderer)
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(self.window)
interactor.GetInteractorStyle().SetCurrentStyleToTrackballCamera()
self.renderer.AddActor(self.actor)
self.renderer.SetBackground(1, 1, 1)
# VTK Web application specific
_WebMolecule.view = self.window
# VTK Web application specific
_WebMolecule.view = self.window
self.Application.GetObjectIdMap().SetActiveObject("VIEW", self.window)
try:
path = converter.inchikey_to_cml_file(inchikey)
self.reader.SetFileName(path)
self.reader.Update()
bounds = [0, 0, 0, 0, 0, 0]
self.mapper.GetBounds(bounds)
os.remove(path)
self.renderer.ResetCamera(bounds)
self.renderer.GetActiveCamera().Zoom(1.5)
except:
print traceback.format_exc()
def main():
filename = get_program_parameters()
cml_source = vtk.vtkCMLMoleculeReader()
cml_source.SetFileName(filename)
molmapper = vtk.vtkMoleculeMapper()
molmapper.SetInputConnection(cml_source.GetOutputPort())
molmapper.UseBallAndStickSettings()
colors = vtk.vtkNamedColors()
actor = vtk.vtkActor()
actor.SetMapper(molmapper)
actor.GetProperty().SetDiffuse(.7)
actor.GetProperty().SetSpecular(.5)
actor.GetProperty().SetSpecularPower(20.0)
renderer = vtk.vtkRenderer()
renderer.AddActor(actor)
render_window = vtk.vtkRenderWindow()
render_window.AddRenderer(renderer)
render_window_interactor = vtk.vtkRenderWindowInteractor()
render_window_interactor.SetRenderWindow(render_window)
render_window.SetSize(640, 480)
render_window.Render()
renderer.GetActiveCamera().Zoom(2.0)
renderer.SetBackground(colors.GetColor3d("Silver"))
# Finally render the scene
render_window.SetMultiSamples(0)
render_window.GetInteractor().Initialize()
render_window.GetInteractor().Start()
atom_points.SetNumberOfPoints(nat)
vectors = vtk.vtkFloatArray()
vectors.SetNumberOfComponents(3)
vectors.SetNumberOfTuples(nat)
for i in range(nat):
a = coordinates[i]
atom_points.InsertPoint(i, a[0], a[1], a[2])
vectors.SetTuple(i, gradients[i])
grid = vtk.vtkUnstructuredGrid()
grid.SetPoints(atom_points)
grid.GetPointData().SetVectors(vectors)
molMapper = vtk.vtkMoleculeMapper()
molMapper.SetInputData(molecule)
molActor = vtk.vtkActor()
molActor.SetMapper(molMapper)
arrow = vtk.vtkArrowSource()
glyph = vtk.vtkGlyph3D()
glyph.SetInputData(grid)
glyph.SetSourceConnection(arrow.GetOutputPort())
glyph.SetScaleModeToScaleByVector()
glyph.SetScaleFactor(30.0)
glyphMapper = vtk.vtkPolyDataMapper()
glyphMapper.SetInputConnection(glyph.GetOutputPort())