def draw_molecule(molecule):
import mogli
mol = mogli.Molecule(positions=molecule.get_coordinates(),
atomic_numbers=molecule.get_atomic_numbers())
mogli.show(mol, bonds_param=1.5, title='Molecule')
def test_show():
"""
Show a molecule and close the window after 1 second.
"""
def alarm_handler(signal_number, stack_frame):
"""
Close the current GLFW window when called due to a SIGALRM.
"""
assert signal_number == signal.SIGALRM
window = glfw.get_current_context()
assert window is not None
glfw.set_window_should_close(window, True)
molecule = mogli.read('examples/dna.xyz')[0]
# Set the signal handler
signal.signal(signal.SIGALRM, alarm_handler)
# Set the alarm to 1 second (and check no previous alarm had been set)
assert signal.alarm(1) == 0
# Show the molecule (and open the GLFW window closed by the alarm handler)
mogli.show(molecule)
def test_show():
"""
Show a molecule and close the window after 1 second.
"""
def alarm_handler(signal_number, stack_frame):
"""
Close the current GLFW window when called due to a SIGALRM.
"""
assert signal_number == signal.SIGALRM
window = glfw.get_current_context()
assert window is not None
glfw.set_window_should_close(window, True)
molecule = mogli.read('examples/dna.xyz')[0]
# Set the signal handler
signal.signal(signal.SIGALRM, alarm_handler)
# Set the alarm to 1 second (and check no previous alarm had been set)
assert signal.alarm(1) == 0
# Show the molecule (and open the GLFW window closed by the alarm handler)
mogli.show(molecule)
"""
Example for interactively displaying a molecule using mogli
"""
import mogli
molecules = mogli.read('examples/dna.xyz')
for molecule in molecules:
mogli.show(molecule, bonds_param=1.15)
#PRZEKSZTALCA LISTE ATOMY W TEKST GOTOWY DO WKLEJENIA DO PLIKU
def dane(self):
tekst = str(N + 1) + "\n" + "linia komentarza"
for element in self.atomy:
tekst = (tekst + "\n" + str(element))
return tekst
#'{0:s},{1:f}x,{2:f}y,{3:f}z\n'.format('Ar',x[i],y[i],z)
def zapisz(self, nazwa_pliku):
fout = open(nazwa_pliku, "w+")
fout.write(self.dane())
fout.close()
p = populacja(h_max=1.4)
#parametry
h = p.h_max
V = m.pi * R * R * h
Va = (4 / 3) * m.pi * r**3
sigma = N * Va / V
#print(p.dane())
print("h =", h, "V =", 2 * m.pi * r * h, "sigma =", sigma)
p.zapisz("dane.xyz")
molecules = mogli.read('dane.xyz')
mogli.show(molecules[0], bonds_param=d_max)
self.atomy.append(a)
#PRZEKSZTALCA LISTE ATOMY W TEKST GOTOWY DO WKLEJENIA DO PLIKU
def dane(self):
tekst = str(N + 1) + "\n" + "linia komentarza"
for element in self.atomy:
tekst = (tekst + "\n" + str(element))
return tekst
def zapisz(self, nazwa_pliku):
fout = open(nazwa_pliku, "w+")
fout.write(self.dane())
fout.close()
p = populacja(h_max=1.4)
#parametry
h = p.h_max
V = m.pi * R * R * h
Va = (4 / 3) * m.pi * r**3
sigma = N * Va / V
#print(p.dane())
print("h =", h, "V =", 2 * m.pi * r * h, "sigma =", sigma)
p.zapisz("dane.xyz")
molecules = mogli.read('dane.xyz')
mogli.show(molecules[0], bonds_param=1)