def test_no_hydrogens():
traj = Trajectory.load(ref_file('ala2.pdb'))
num_molecules = 1
detector = xray.Detector.generic()
detector.beam.photons_scattered_per_shot = 1e3
I_noH = scatter.simulate_shot(traj, num_molecules, detector,
ignore_hydrogens=True,
dont_rotate=True)
I_wH = scatter.simulate_shot(traj, num_molecules, detector,
ignore_hydrogens=False,
dont_rotate=True)
assert not np.all(I_noH == I_wH)
# compute the differece -- we're not setting random numbers here so just
# looking at radially averaged stuff...
diff = np.sum(np.abs(I_noH - I_wH) / I_wH) / float(len(I_wH))
print diff
assert diff < 1.0, 'ignoring hydrogens makes too big of a difference...'
def test_py_cpu_smoke(self):
traj = Trajectory.load(ref_file('ala2.pdb'))
num_molecules = 1
detector = xray.Detector.generic()
detector.beam.photons_scattered_per_shot = 1e3
I = scatter.simulate_shot(traj, num_molecules, detector,
finite_photon=True)
# simple statistical sanity check
assert np.abs(I.sum() - detector.beam.photons_scattered_per_shot) < \
np.sqrt(detector.beam.photons_scattered_per_shot)*6.0
def test_python_call(self):
"""
Test the GPU scattering simulation interface (scatter.simulate)
"""
if not GPU: raise SkipTest
print "testing python wrapper fxn..."
traj = Trajectory.load(ref_file('ala2.pdb'))
num_molecules = 512
detector = xray.Detector.generic()
py_I = scatter.simulate_shot(traj, num_molecules, detector)
assert not np.all( py_I == 0.0 )
assert not np.isnan(np.sum( py_I ))
def __call__(self, trajectory):
"""
Return the system 'energy'.
Parameters
----------
"""
self._check_is_traj(trajectory)
energies = np.zeros(trajectory.n_frames)
for i in range(trajectory.n_frames):
prediction = scatter.simulate_shot(trajectory[i], 1, self.qxyz,
force_no_gpu=self._no_gpu,
device_id=self._device_id)
energies[i] = np.sum( np.square(prediction - self.intensities) /
(2.0 * self.sigma) ) / float(len(prediction))
return energies
test_system = 'ala' # 'ala' OR 'lyz'
prior = 'amber99min.xml'
num_moves = 1000
sigma = 1000.0 # hmmmm
# ------------------------------------------
if test_system == 'ala':
structure_file = 'ala2.pdb'
dtc = thor.Detector.generic()
elif test_system == 'lyz':
structure_file = '3lyz.clean.pdb'
dtc = thor.Detector.load('lcls_test.dtc')
else:
raise KeyError('no known test system: %s' % test_system)
starting_structure = mdtraj.load(structure_file)
qxyz = dtc.reciprocal
intensities = scatter.simulate_shot(starting_structure, 1, qxyz)
potential = cdi.CdiPotential(intensities, qxyz, sigma)
sampler = sample.MDMC(potential, prior, starting_structure.top,
starting_structure.xyz[0])
sampler.sample(num_moves, 'test_traj.h5')
t = mdtraj.load('test_traj.h5')
t.save_pdb('test_traj.pdb')
def _compute_Sq( self, traj, q_values, dont_rotate):
qxyz = self._get_qxyz_on_unit_sphere()
self.S_q = np.zeros( (self.q_values.shape[0], qxyz.shape[0]) )
for i,q in enumerate(self.q_values):
self.S_q[i,:] = simulate_shot(self.model, 1, q*qxyz, dont_rotate=dont_rotate, force_no_gpu=True)
self.S_q = self.S_q.reshape( self.n_q, self.n_theta, self.n_phi )
sigma = 1000.0 # hmmmm
# ------------------------------------------
if test_system == 'ala':
structure_file = 'ala2.pdb'
dtc = thor.Detector.generic()
elif test_system == 'lyz':
structure_file = '3lyz.clean.pdb'
dtc = thor.Detector.load('lcls_test.dtc')
else:
raise KeyError('no known test system: %s' % test_system)
starting_structure = mdtraj.load(structure_file)
qxyz = dtc.reciprocal
intensities = scatter.simulate_shot(starting_structure, 1, qxyz)
potential = cdi.CdiPotential(intensities, qxyz, sigma)
sampler = sample.MDMC(potential, prior,
starting_structure.top,
starting_structure.xyz[0])
sampler.sample(num_moves, 'test_traj.h5')
t = mdtraj.load('test_traj.h5')
t.save_pdb('test_traj.pdb')