def test_multiple_post_processing():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
v = QtViewer()
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
#mol = datafile('/home/gabriele/projects/LiCl/interface/loafintjc-heat/equilibrium.gro').read('system')
sr = v.add_renderer(AtomRenderer,
mol.r_array,
mol.type_array,
'impostors',
shading='toon')
# Adding multiple post processing effects
v.add_post_processing(SSAOEffect)
v.add_post_processing(GammaCorrectionEffect, 2.0)
#v.add_post_processing(GammaCorrectionEffect, 2.0)
#v.add_post_processing(FXAAEffect)
v.run()
def test_wireframe_renderer():
from collections import defaultdict
from chemlab.db.cirdb import CirDB
v = QtViewer()
#v.widget.background_color = black
mol = Molecule([
Atom("O", [-0.499, 0.249, 0.0]),
Atom("H", [-0.402, 0.249, 0.0]),
Atom("H", [-0.532, 0.198, 0.10])
])
mol.bonds = np.array([[0, 1], [0, 2]])
mol = CirDB().get("molecule", "moronic acid")
ar = v.add_renderer(WireframeRenderer, mol.r_array, mol.type_array,
mol.bonds)
# Try without bonds
#ar2 = v.add_renderer(WireframeRenderer, mol.r_array + 0.5, mol.type_array, np.array([]))
v.run()
def test_unproject():
v = QtViewer()
vectors = [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]]
colors = [colors.blue, colors.blue]
ar = v.add_renderer(LineRenderer, vectors, colors)
def mouse_move(evt):
x,y = evt.x(), evt.y()
w = v.widget.width()
h = v.widget.height()
x, y = 2*float(x)/w - 1.0, 1.0 - 2*float(y)/h
start = v.widget.camera.unproject(x,y,-1.0)
print(x,y, 0.0)
print(start)
vectors[1] = [0.0, 0.0, 0.0]
vectors[0] = start
ar.update_positions(np.array(vectors))
v.widget.repaint()
v.mousePressEvent = mouse_move # Super Hack
v.run()
def test_cylinder_renderer():
bounds = np.array([[[-1.0, 0.0, 0.0], [-1.0, 1.0, 0.0]],
[[1.0, 0.0, 0.0], [1.0, 3.0, 0.0]],
[[1.0, 0.0, 0.0], [1.0, 0.0, 1.0]]])
radii = np.array([0.5, 0.3, 0.3])
colors = np.array([blue, orange, green])
# Test for speed
# random bounds
# n = 1000
#bounds = np.random.rand(n, 2, 3) * 10
#radii = np.random.rand(n)
#colors = np.array([blue] * n)
v = QtViewer()
import time
t0 = time.time()
ar = v.add_renderer(CylinderRenderer, bounds, radii, colors)
print time.time() - t0
#ar.update_bounds(bounds)
v.run()
def test_pickers():
from chemlab.graphics.pickers import SpherePicker, CylinderPicker
from chemlab.core.molecule import guess_bonds
from chemlab.io import datafile
#mol = datafile('tests/data/benzene.mol').read('molecule')
mol = ChemlabDB().get('molecule', 'example.water')
centers = mol.r_array
radii = np.array([0.05] * mol.n_atoms)
colors = np.array([[0, 255, 255, 255]] * mol.n_atoms)
bounds = mol.r_array.take(mol.bonds, axis=0)
b_radii = np.array([0.05] * mol.n_bonds)
b_colors = np.array([[0, 255, 255, 255]] * mol.n_bonds)
v = QtViewer()
#v.widget.camera.autozoom(mol.r_array)
sr = v.add_renderer(SphereImpostorRenderer,
centers,
radii * 1.2,
colors,
transparent=False)
cr = v.add_renderer(CylinderImpostorRenderer, bounds, b_radii, b_colors)
sp = SpherePicker(v.widget, centers, radii * 1.2)
cp = CylinderPicker(v.widget, bounds, b_radii)
def on_click(evt):
x, y = v.widget.screen_to_normalized(evt.x(), evt.y())
a_i, a_d = sp.pick(x, y)
b_i, b_d = cp.pick(x, y)
print 'A', a_d
print 'B', b_d
v.widget.clicked.connect(on_click)
v.run()
def test_offline():
# Api for PNG saving
v = QtViewer()
mol = cdb.get('molecule', 'example.norbornene')
sr = v.add_renderer(AtomRenderer,
mol.r_array,
mol.type_array,
'impostors',
shading='toon')
v.add_post_processing(SSAOEffect, kernel_size=128)
v.add_post_processing(FXAAEffect)
ne = v.add_post_processing(NoEffect)
v.widget.camera.autozoom(mol.r_array)
def dump():
image = v.widget.toimage(2048, 2048)
image.save("/tmp/hello.png")
os.system("eog /tmp/hello.png")
from PySide.QtCore import Qt
v.key_actions[Qt.Key_A] = dump
v.run()
def showmol(mol, style='ball-and-stick',
width=300, height=300):
v = QtViewer()
w = v.widget
w.initializeGL()
w.resize(width, height)
w.resizeGL(width, height)
if style == 'ball-and-stick':
bs = v.add_renderer(BallAndStickRenderer,
mol.r_array,
mol.type_array,
mol.bonds)
elif style == 'vdw':
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array,
backend='impostors')
w.camera.autozoom(mol.r_array)
w.paintGL()
# Make sure to finish everything
data = glReadPixels(0, 0, width, height, GL_RGB, GL_UNSIGNED_BYTE)
# Make pil image to save as png
image = pil_Image.fromstring('RGB', (width, height), data)
b = BytesIO()
image.save(b, format='png')
data = b.getvalue()
# Cleanup
del v
del w
# Save as png
return ipy_Image(data=data)
def test_box_renderer():
vectors = np.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]])
v = QtViewer()
ar = v.add_renderer(BoxRenderer, vectors, origin=np.array([-0.5, -0.5, -0.5]))
v.run()
