def test_toon_shading():
from chemlab.core.molecule import guess_bonds
cdb = ChemlabDB()
#mol = cdb.get('molecule', 'example.norbornene')
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
#v.widget.post_processing = FXAAEffect(v.widget)
#v.widget.post_processing = SSAOEffect(v.widget, kernel_size=64, kernel_radius=1.0, ssao_power=2.0)
v.widget.camera.autozoom(mol.r_array)
#sr = v.add_renderer(AtomRenderer, mol.r_array,
# mol.type_array, 'impostors',
# shading='toon')
#sr = v.add_renderer(AtomRenderer, mol.r_array,
# mol.type_array, 'polygons',
# shading='toon')
ar = v.add_renderer(BallAndStickRenderer,
mol.r_array,
mol.type_array,
guess_bonds(mol.r_array, mol.type_array),
shading='toon')
v.run()
def showmol(mol, style="ball-and-stick", width=300, height=300):
v = QtViewer()
w = v.widget
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)
# Make sure to finish everything
glBindTexture(w.textures["color"])
glActiveTexture(GL_TEXTURE0)
data = glGetTexImage(GL_TEXTURE_2D, 0, RGB, GL_UNSIGNED_BYTE)
# 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_pickers():
from chemlab.graphics.pickers import SpherePicker
from chemlab.io import datafile
mol = datafile('/home/gabriele/projects/LiCl/interface/loafintjc-heat/equilibrium.gro').read('system')
centers = [[0.0, 0.0, 0.0], [1.0, 0.0, 1.0]]
radii = np.array([1.0, 0.5])
colors = [[0, 255, 255, 100], [255, 255, 0, 100]]
centers = mol.r_array
radii = np.array([0.2]*mol.n_atoms)
colors = np.array([[0, 255, 255, 255]]*mol.n_atoms)
v = QtViewer()
sr = v.add_renderer(SphereImpostorRenderer, centers, radii, colors, transparent=False)
#sr = v.add_renderer(SphereImpostorRenderer, centers,
# radii*1.5, [[255, 255, 255, 50]]*mol.n_atoms, transparent=True)
sp = SpherePicker(v.widget, centers, radii)
def on_click(evt):
x, y = v.widget.screen_to_normalized(evt.x(), evt.y())
print sp.pick(x, y)
v.widget.clicked.connect(on_click)
v.run()
def test_glow():
from PySide import QtCore
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
v = QtViewer()
colors = np.array([(255, 0, 0, 255)]*mol.n_atoms)
colors[0][3] = 0
v.widget.camera.autozoom(mol.r_array)
sr = v.add_renderer(SphereImpostorRenderer, mol.r_array, [0.1]*mol.n_atoms,
colors)
ge = v.add_post_processing(GlowEffect)
#v.add_post_processing(GammaCorrectionEffect)
def changeglow():
#ge.radius = np.sin(time.time()*10.0) + 2.5
colors[0][3] = 255 * (np.sin(time.time()*10.0)*0.5 + 0.5)
sr.update_colors(colors)
v.widget.update()
timer = QtCore.QTimer()
timer.timeout.connect(changeglow)
timer.start(10)
v.run()
def showmol(mol, style='ball-and-stick',
width=300, height=300):
v = QtViewer()
w = v.widget
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)
# Make sure to finish everything
image = w.toimage(width, height)
b = BytesIO()
image.save(b, format='png')
data = b.getvalue()
# Cleanup
del v
del w
# Save as png
return ipy_Image(data=data)
def showsys(sys, width=400, height=400):
v = QtViewer()
w = v.widget
sr = v.add_renderer(AtomRenderer, sys.r_array, sys.type_array,
backend='impostors')
if sys.box_vectors is not None:
v.add_renderer(BoxRenderer, sys.box_vectors)
w.camera.autozoom(sys.r_array)
w.camera.orbit_y(3.14/4)
w.camera.orbit_x(3.14/4)
image = w.toimage(width, height)
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_toon_shading():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
from chemlab.graphics import colors
from chemlab.core.molecule import guess_bonds
cdb = ChemlabDB()
#mol = cdb.get('molecule', 'example.norbornene')
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
#v.widget.post_processing = FXAAEffect(v.widget)
#v.widget.post_processing = SSAOEffect(v.widget, kernel_size=64, kernel_radius=1.0, ssao_power=2.0)
v.widget.camera.autozoom(mol.r_array)
#sr = v.add_renderer(AtomRenderer, mol.r_array,
# mol.type_array, 'impostors',
# shading='toon')
#sr = v.add_renderer(AtomRenderer, mol.r_array,
# mol.type_array, 'polygons',
# shading='toon')
ar = v.add_renderer(BallAndStickRenderer,
mol.r_array, mol.type_array,
guess_bonds(mol.r_array, mol.type_array),
shading='toon')
v.run()
def test_pickers():
from chemlab.graphics.pickers import SpherePicker, CylinderPicker
from chemlab.core.molecule import guess_bonds
#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_glow():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
from chemlab.graphics.postprocessing.glow import GlowEffect
from PySide import QtCore
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
#mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
colors = np.array([(255, 0, 0, 255)]*mol.n_atoms)
colors[0][3] = 0
v.widget.camera.autozoom(mol.r_array)
sr = v.add_renderer(SphereImpostorRenderer, mol.r_array, [0.1]*mol.n_atoms,
colors)
ge = v.add_post_processing(GlowEffect)
#v.add_post_processing(GammaCorrectionEffect)
def changeglow():
#ge.radius = np.sin(time.time()*10.0) + 2.5
colors[0][3] = 255 * (np.sin(time.time()*10.0)*0.5 + 0.5)
sr.update_colors(colors)
v.widget.update()
timer = QtCore.QTimer()
timer.timeout.connect(changeglow)
timer.start(10)
#v.add_post_processing(SSAOEffect, ssao_power = 5.0)
#v.add_post_processing(FXAAEffect)
#v.add_post_processing(GammaCorrectionEffect)
v.run()
def showsys(sys, width=400, height=400):
v = QtViewer()
w = v.widget
w.initializeGL()
w.resize(width, height)
w.resizeGL(width, height)
sr = v.add_renderer(AtomRenderer, sys.r_array, sys.type_array,
backend='impostors')
if sys.box_vectors is not None:
v.add_renderer(BoxRenderer, sys.box_vectors)
w.camera.autozoom(sys.r_array)
w.camera.orbit_y(3.14/4)
w.camera.orbit_x(3.14/4)
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 showsys(sys, width=400, height=400):
v = QtViewer()
w = v.widget
sr = v.add_renderer(AtomRenderer,
sys.r_array,
sys.type_array,
backend='impostors')
if sys.box_vectors is not None:
v.add_renderer(BoxRenderer, sys.box_vectors)
w.camera.autozoom(sys.r_array)
w.camera.orbit_y(3.14 / 4)
w.camera.orbit_x(3.14 / 4)
image = w.toimage(width, height)
b = BytesIO()
image.save(b, format='png')
data = b.getvalue()
# Cleanup
del v
del w
# Save as png
return ipy_Image(data=data)
def showmol(mol, style='ball-and-stick', width=300, height=300):
v = QtViewer()
w = v.widget
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)
# Make sure to finish everything
image = w.toimage(width, height)
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_cylinder_impostor_renderer():
from chemlab.graphics.renderers import CylinderImpostorRenderer
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])
bounds = np.array([[[0.0, 0.0, 0.0], [0.0, 1.0, 0.0]]])
radii = np.array([0.2])
colors = np.array([blue])
# Test for speed
# random bounds
#n = 50000
#bounds = np.random.rand(n, 2, 3) * 10
#radii = np.random.rand(n)/10.0
#colors = np.array([blue] * n)
import time
v = QtViewer()
t0 = time.time()
ar = v.add_renderer(CylinderImpostorRenderer, bounds, radii, colors)
#ar = v.add_renderer(CylinderRenderer, bounds, radii* 2.0, colors)
sr = v.add_renderer(SphereImpostorRenderer, bounds[:, 0], radii, colors)
sr = v.add_renderer(SphereImpostorRenderer, bounds[:, 1], radii, colors)
print time.time() - t0
#ar = v.add_renderer(CylinderRenderer, bounds, radii, colors)
#ar.update_bounds(bounds)
v.run()
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()
def test_point_renderer():
'''To see if we're able to render a triangle'''
vertices = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [2.0, 0.0, 0.0]]
colors = [colors.blue] * 3
v = QtViewer()
tr = v.add_renderer(PointRenderer, vertices, colors)
v.run()
def test_line_renderer():
vectors = np.array([[0.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 1.0, 0.0], [0.0, 0.0, 1.0]])
colors = [blue, orange, orange, orange]
v = QtViewer()
ar = v.add_renderer(LineRenderer, vectors, colors)
v.run()
def test_line_renderer():
vectors = np.array([[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]])
colors = [colors.blue, colors.orange, colors.orange, colors.orange]
v = QtViewer()
ar = v.add_renderer(LineRenderer, vectors, colors)
v.run()
def test_point_renderer():
'''To see if we're able to render a triangle'''
vertices = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [2.0, 0.0, 0.0]]
colors = [colors.blue] * 3
v = QtViewer()
tr = v.add_renderer(PointRenderer, vertices, colors)
v.run()
def test_triangle_renderer():
'''To see if we're able to render a triangle'''
vertices = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [2.0, 0.0, 0.0]]
normals = [[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]
colors = [colors.blue]* 3
v = QtViewer()
tr = v.add_renderer(TriangleRenderer, vertices, normals, colors, shading='toon')
v.run()
def test_triangle_renderer():
'''To see if we're able to render a triangle'''
vertices = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [2.0, 0.0, 0.0]]
normals = [[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]
colors = [colors.blue]* 3
v = QtViewer()
tr = v.add_renderer(TriangleRenderer, vertices, normals, colors, shading='toon')
v.run()
def test_atom_renderer():
'''Simple rendering of atoms as spheres'''
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])])
v = QtViewer()
ar = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array)
v.run()
def test_atom_renderer():
'''Simple rendering of atoms as spheres'''
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])])
v = QtViewer()
ar = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array)
v.run()
def test_noeffect():
v = QtViewer()
centers = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [1.0, 0.0, 0.0]]
radii = [0.5, 0.1, 0.5]
colors_ = np.array([colors.orange, colors.blue, colors.forest_green])
sr = v.add_renderer(SphereImpostorRenderer, centers, radii, colors_)
v.widget.post_processing.append(NoEffect(v.widget))
v.run()
def test_point_fog():
'''To see if we're able to render a triangle'''
NPOINTS = 10000
vertices = (np.random.random((NPOINTS, 3)) - 0.5) * 3
colors = [colors.blue] * NPOINTS
v = QtViewer()
tr = v.add_renderer(PointRenderer, vertices, colors)
v.run()
def test_noeffect():
v = QtViewer()
centers = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [1.0, 0.0, 0.0]]
radii = [0.5, 0.1, 0.5]
colors_ = np.array([colors.orange, colors.blue, colors.forest_green])
sr = v.add_renderer(SphereImpostorRenderer, centers, radii, colors_)
v.widget.post_processing.append(NoEffect(v.widget))
v.run()
def test_point_fog():
'''To see if we're able to render a triangle'''
NPOINTS = 10000
vertices = (np.random.random((NPOINTS, 3))-0.5)*3
colors = [colors.blue] * NPOINTS
v = QtViewer()
tr = v.add_renderer(PointRenderer, vertices, colors)
v.run()
def test_text_ui():
v = QtViewer()
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])])
# To add some interaction to it
ar = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array, "impostors")
tr = v.add_ui(TextUI, 100, 100, 'Hello guys')
v.run()
def test_fxaa():
from chemlab.graphics.postprocessing.fxaa import FXAAEffect
v = QtViewer()
centers = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [1.0, 0.0, 0.0]]
radii = [0.5, 0.1, 0.5]
colors = np.array([orange, blue, forest_green])
sr = v.add_renderer(SphereImpostorRenderer, centers, radii, colors)
v.widget.post_processing.append(FXAAEffect(v.widget))
v.run()
def test_noeffect():
from chemlab.graphics.postprocessing import NoEffect
v = QtViewer()
centers = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [1.0, 0.0, 0.0]]
radii = [0.5, 0.1, 0.5]
colors = np.array([orange, blue, forest_green])
sr = v.add_renderer(SphereImpostorRenderer, centers, radii, colors)
v.widget.post_processing.append(NoEffect(v.widget))
v.run()
def test_camera_autozoom():
v = QtViewer()
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])])
s = datafile('tests/data/3ZJE.pdb').read('system')
# To add some interaction to it
ar = v.add_renderer(AtomRenderer, s.r_array, s.type_array, "impostors")
v.widget.camera.autozoom(s.r_array)
v.run()
def test_ssao():
cdb = ChemlabDB()
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
v.widget.post_processing.append(SSAOEffect(v.widget, kernel_size=16,
kernel_radius=3.0, ssao_power=2.7))
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array, 'impostors')
#ar = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array, [])
v.widget.camera.orbit_y(90)
v.run()
def test_camera_autozoom():
v = QtViewer()
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])])
from chemlab.io import datafile
s = datafile('tests/data/3ZJE.pdb').read('system')
# To add some interaction to it
ar = v.add_renderer(AtomRenderer, s.r_array, s.type_array, "impostors")
v.widget.camera.autozoom(s.r_array)
v.run()
def test_ssao():
cdb = ChemlabDB()
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
v.widget.post_processing.append(SSAOEffect(v.widget, kernel_size=16,
kernel_radius=3.0, ssao_power=2.7))
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array, 'impostors')
#ar = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array, [])
v.widget.camera.orbit_y(90)
v.run()
def test_cylinder_impostor_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([colors.blue, colors.orange, colors.green])
bounds = np.array([[[0.0, 0.0, 0.0], [0.0, 1.0, 0.0]]])
radii = np.array([0.2])
colors = np.array([colors.blue])
# Test for speed
# random bounds
#n = 50000
#bounds = np.random.rand(n, 2, 3) * 10
#radii = np.random.rand(n)/10.0
#colors = np.array([colors.blue] * n)
v = QtViewer()
ar = v.add_renderer(CylinderImpostorRenderer, bounds, radii, colors)
sr = v.add_renderer(SphereImpostorRenderer, bounds[:, 0], radii, colors)
sr = v.add_renderer(SphereImpostorRenderer, bounds[:, 1], radii, colors)
v.run()
# Test updates
ar.update_radii([0.1])
bounds[0, 0] -= 1.0
ar.update_bounds(bounds)
ar.update_colors([colors.green])
v.run()
# Test emptiness
ar.change_attributes([], [], [])
def test_point_fog():
'''To see if we're able to render a triangle'''
NPOINTS = 10000
vertices = (np.random.random((NPOINTS, 3))-0.5)*3
#vertices = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [2.0, 0.0, 0.0]]
blue = [[0, 255, 0, 125]]
colors = blue * NPOINTS
v = QtViewer()
tr = v.add_renderer(PointRenderer, vertices, colors)
v.run()
def test_point_fog():
'''To see if we're able to render a triangle'''
NPOINTS = 10000
vertices = (np.random.random((NPOINTS, 3)) - 0.5) * 3
#vertices = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [2.0, 0.0, 0.0]]
blue = [[0, 255, 0, 125]]
colors = blue * NPOINTS
v = QtViewer()
tr = v.add_renderer(PointRenderer, vertices, colors)
v.run()
def test_wireframe_renderer():
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_wireframe_renderer():
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_cylinder_impostor_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([colors.blue, colors.orange, colors.green])
bounds = np.array([[[0.0, 0.0, 0.0], [0.0, 1.0, 0.0]]])
radii = np.array([0.2])
colors = np.array([colors.blue])
# Test for speed
# random bounds
#n = 50000
#bounds = np.random.rand(n, 2, 3) * 10
#radii = np.random.rand(n)/10.0
#colors = np.array([colors.blue] * n)
v = QtViewer()
ar = v.add_renderer(CylinderImpostorRenderer, bounds, radii, colors)
sr = v.add_renderer(SphereImpostorRenderer, bounds[:, 0], radii, colors)
sr = v.add_renderer(SphereImpostorRenderer, bounds[:, 1], radii, colors)
v.run()
# Test updates
ar.update_radii([0.1])
bounds[0,0] -= 1.0
ar.update_bounds(bounds)
ar.update_colors([colors.green])
v.run()
# Test emptiness
ar.change_attributes([], [], [])
def test_gamma():
cdb = ChemlabDB()
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
v.widget.camera.orbit_y(3.14/3)
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array,
'impostors', shading='phong')
v.add_post_processing(SSAOEffect, ssao_power=4.0)
v.add_post_processing(GammaCorrectionEffect)
v.run()
def test_ball_and_stick_renderer():
from collections import defaultdict
from chemlab.io import datafile
from chemlab.db.cirdb import CirDB
v = QtViewer()
v.add_post_processing(SSAOEffect, kernel_radius=0.15)
#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")
mol = datafile('tests/data/3ZJE.pdb').read('molecule')
mol.bonds = find_bonds(mol)
ar = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array,
mol.bonds)
# Try without bonds
# ar2 = v.add_renderer(BallAndStickRenderer, mol.r_array + 0.5, mol.type_array, np.array([]))
v.run()
def test_ssao():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
v.widget.post_processing.append(SSAOEffect(v.widget, kernel_size=16, kernel_radius=3.0, ssao_power=2.7))
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array, 'impostors')
#ar = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array, [])
v.run()
def _image_molecule(self,
molecule,
ball_stick=False,
colorlist=[],
rotation=[0., 0., 0.],
width=300,
height=300,
zoom=1.,
lines=[],
linestyle='impostors'):
v = QtViewer()
w = v.widget
w.camera.orbit_z = MethodType(orbit_z, w.camera)
w.initializeGL()
if ball_stick:
r = v.add_renderer(BallAndStickRenderer,
molecule.r_array,
molecule.type_array,
molecule.bonds,
rgba_array=colorlist,
linestyle=linestyle)
else:
r = v.add_renderer(AtomRenderer,
molecule.r_array,
molecule.type_array,
rgba_array=colorlist)
for line in lines:
#line = [start_coord, end_coord, start_color, end_color, width, dashed]
#for some reason it didn't like unpacking them to named variables
v.add_renderer(LineRenderer, [line[0], line[1]],
[[str_to_colour(line[2]),
str_to_colour(line[3])]],
width=line[4],
dashed=line[5])
#v.add_post_processing(SSAOEffect)
w.camera.autozoom(molecule.r_array * 1. / zoom)
w.camera.orbit_x(rotation[0] * np.pi / 180.)
w.camera.orbit_y(rotation[1] * np.pi / 180.)
w.camera.orbit_z(rotation[2] * np.pi / 180.)
image = w.toimage(width, height)
# Cleanup
v.clear()
del v
del w
del r
return self._trim_image(image)
def test_fxaa():
centers = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [1.0, 0.0, 0.0]]
radii = [0.5, 0.1, 0.5]
colors_ = np.array([colors.orange, colors.blue, colors.forest_green])
vectors = np.array([[0.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 1.0, 0.0], [0.0, 0.0, 1.0]])
colors_ = [colors.blue, colors.orange, colors.orange, colors.orange]
v = QtViewer()
ar = v.add_renderer(LineRenderer, vectors, colors_)
#sr = v.add_renderer(SphereImpostorRenderer, centers, radii, colors)
v.widget.post_processing.append(FXAAEffect(v.widget, span_max=8.0,
reduce_mul=1/8.0,
reduce_min=1/128.0))
v.run()
def test_fxaa():
centers = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [1.0, 0.0, 0.0]]
radii = [0.5, 0.1, 0.5]
colors_ = np.array([colors.orange, colors.blue, colors.forest_green])
vectors = np.array([[0.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 1.0, 0.0], [0.0, 0.0, 1.0]])
colors_ = [colors.blue, colors.orange, colors.orange, colors.orange]
v = QtViewer()
ar = v.add_renderer(LineRenderer, vectors, colors_)
#sr = v.add_renderer(SphereImpostorRenderer, centers, radii, colors)
v.widget.post_processing.append(FXAAEffect(v.widget, span_max=8.0,
reduce_mul=1/8.0,
reduce_min=1/128.0))
v.run()
def test_ssao():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
v.widget.post_processing.append(
SSAOEffect(v.widget, kernel_size=16, kernel_radius=3.0,
ssao_power=2.7))
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array, 'impostors')
#ar = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array, [])
v.run()
def test_multiple_post_processing():
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_bond_renderer():
v = QtViewer()
v.widget.background_color = colors.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")
#radii_map = {"O": 0.03, "H": 0.03}
radii_map = defaultdict(lambda: 0.03)
br = v.add_renderer(BondRenderer, mol.bonds, mol.r_array,
mol.type_array, style='impostors')
ar = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array,
"impostors", radii_map = radii_map)
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 test_fxaa():
from chemlab.graphics.postprocessing.fxaa import FXAAEffect
centers = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [1.0, 0.0, 0.0]]
radii = [0.5, 0.1, 0.5]
colors = np.array([orange, blue, forest_green])
vectors = np.array([[0.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 1.0, 0.0], [0.0, 0.0, 1.0]])
colors = [blue, orange, orange, orange]
v = QtViewer()
ar = v.add_renderer(LineRenderer, vectors, colors)
#sr = v.add_renderer(SphereImpostorRenderer, centers, radii, colors)
v.widget.post_processing.append(FXAAEffect(v.widget, span_max=8.0,
reduce_mul=1/8.0,
reduce_min=1/128.0))
v.run()
def test_outline():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
from chemlab.graphics.postprocessing.outline import OutlineEffect
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
mol = datafile('tests/data/3ZJE.pdb').read('system')
#mol = datafile('tests/data/water.gro').read('system')
#mol = datafile('tests/data/benzene.mol').read('molecule')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array,
'impostors', shading='toon')
v.add_post_processing(OutlineEffect, 'depthonly')
v.add_post_processing(FXAAEffect)
v.add_post_processing(GammaCorrectionEffect)
v.run()
def test_fxaa():
from chemlab.graphics.postprocessing.fxaa import FXAAEffect
centers = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [1.0, 0.0, 0.0]]
radii = [0.5, 0.1, 0.5]
colors = np.array([orange, blue, forest_green])
vectors = np.array([[0.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 1.0, 0.0],
[0.0, 0.0, 1.0]])
colors = [blue, orange, orange, orange]
v = QtViewer()
ar = v.add_renderer(LineRenderer, vectors, colors)
#sr = v.add_renderer(SphereImpostorRenderer, centers, radii, colors)
v.widget.post_processing.append(
FXAAEffect(v.widget,
span_max=8.0,
reduce_mul=1 / 8.0,
reduce_min=1 / 128.0))
v.run()
def test_ball_and_stick_renderer():
from collections import defaultdict
from chemlab.io import datafile
from chemlab.db.cirdb import CirDB
v = QtViewer()
v.add_post_processing(SSAOEffect, kernel_radius = 0.15)
#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")
mol = datafile('tests/data/3ZJE.pdb').read('molecule')
mol.bonds = find_bonds(mol)
ar = v.add_renderer(BallAndStickRenderer, mol.r_array, mol.type_array, mol.bonds)
# Try without bonds
# ar2 = v.add_renderer(BallAndStickRenderer, mol.r_array + 0.5, mol.type_array, np.array([]))
v.run()
def test_glow():
from chemlab.db import ChemlabDB, CirDB
from chemlab.io import datafile
from chemlab.graphics.postprocessing.glow import GlowEffect
from PySide import QtCore
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
#mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
colors = np.array([(255, 0, 0, 255)] * mol.n_atoms)
colors[0][3] = 0
v.widget.camera.autozoom(mol.r_array)
sr = v.add_renderer(SphereImpostorRenderer, mol.r_array,
[0.1] * mol.n_atoms, colors)
ge = v.add_post_processing(GlowEffect)
#v.add_post_processing(GammaCorrectionEffect)
def changeglow():
#ge.radius = np.sin(time.time()*10.0) + 2.5
colors[0][3] = 255 * (np.sin(time.time() * 10.0) * 0.5 + 0.5)
sr.update_colors(colors)
v.widget.update()
timer = QtCore.QTimer()
timer.timeout.connect(changeglow)
timer.start(10)
#v.add_post_processing(SSAOEffect, ssao_power = 5.0)
#v.add_post_processing(FXAAEffect)
#v.add_post_processing(GammaCorrectionEffect)
v.run()
def test_glow():
from PySide import QtCore
cdb = ChemlabDB()
mol = cdb.get('molecule', 'example.norbornene')
v = QtViewer()
colors = np.array([(255, 0, 0, 255)] * mol.n_atoms)
colors[0][3] = 0
v.widget.camera.autozoom(mol.r_array)
sr = v.add_renderer(SphereImpostorRenderer, mol.r_array,
[0.1] * mol.n_atoms, colors)
ge = v.add_post_processing(GlowEffect)
#v.add_post_processing(GammaCorrectionEffect)
def changeglow():
#ge.radius = np.sin(time.time()*10.0) + 2.5
colors[0][3] = 255 * (np.sin(time.time() * 10.0) * 0.5 + 0.5)
sr.update_colors(colors)
v.widget.update()
timer = QtCore.QTimer()
timer.timeout.connect(changeglow)
timer.start(10)
v.run()
def test_gamma():
cdb = ChemlabDB()
mol = datafile('tests/data/3ZJE.pdb').read('system')
v = QtViewer()
v.widget.camera.autozoom(mol.r_array)
v.widget.camera.orbit_y(3.14/3)
sr = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array,
'impostors', shading='phong')
v.add_post_processing(SSAOEffect, ssao_power=4.0)
v.add_post_processing(GammaCorrectionEffect)
v.run()
def test_bond_renderer():
v = QtViewer()
v.widget.background_color = colors.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")
#radii_map = {"O": 0.03, "H": 0.03}
radii_map = defaultdict(lambda: 0.03)
br = v.add_renderer(BondRenderer,
mol.bonds,
mol.r_array,
mol.type_array,
style='impostors')
ar = v.add_renderer(AtomRenderer,
mol.r_array,
mol.type_array,
"impostors",
radii_map=radii_map)
v.run()
def test_pickers():
from chemlab.graphics.pickers import SpherePicker, CylinderPicker
from chemlab.core.molecule import guess_bonds
#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_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([colors.blue, colors.orange, colors.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()
t0 = time.time()
ar = v.add_renderer(CylinderRenderer, bounds, radii, colors)
print(time.time() - t0)
#ar.update_bounds(bounds)
v.run()