def test_0():
t1 = load(get_fn('native2.xml'), top=get_fn('native2.pdb'))
t2 = load(get_fn('native2.pdb'))
t1.center_coordinates()
t2.center_coordinates()
yield lambda: eq(t1.xyz, t2.xyz)
yield lambda: eq(t1.unitcell_vectors, t2.unitcell_vectors)
def setup(self):
self.q_values = np.array([1.0, 2.0])
self.num_phi = 360
self.traj = trajectory.load(ref_file('ala2.pdb'))
self.num_shots = 2
# generate the tables file on disk, then re-open it
intensities = np.abs( np.random.randn(self.num_shots, len(self.q_values),
self.num_phi) / 100.0 + \
np.cos( np.linspace(0.0, 4.0*np.pi, self.num_phi) ) )
if os.path.exists('tmp_tables.h5'):
os.remove('tmp_tables.h5')
hdf = tables.File('tmp_tables.h5', 'w')
a = tables.Atom.from_dtype(np.dtype(np.float64))
node = hdf.createEArray(where='/', name='data',
shape=(0, len(self.q_values), self.num_phi),
atom=a, filters=io.COMPRESSION)
node.append(intensities)
hdf.close()
self.tables_file = tables.File('tmp_tables.h5', 'r+')
pi = self.tables_file.root.data
pm = np.random.binomial(1, 0.9, size=(len(self.q_values), self.num_phi))
k = 1.0
self.rings = xray.Rings(self.q_values, pi, k, pm)
return
def setup(self):
self.q_values = np.array([1.0, 2.0])
self.num_phi = 360
self.traj = trajectory.load(ref_file('ala2.pdb'))
self.num_shots = 2
self.rings = xray.Rings.simulate(self.traj, 1, self.q_values,
self.num_phi, self.num_shots) # 1 molec
def test_rm_com():
t = trajectory.load( ref_file('ala2.pdb') )
r = structure.remove_COM(t)
masses = [ a.element.mass for a in t.topology.atoms() ]
for i in range(t.n_frames):
assert_array_almost_equal(np.zeros(3), np.average(t.xyz[i,:,:], weights=masses, axis=0))
def setup(self):
self.q_values = np.array([1.0, 2.0])
self.num_phi = 360
self.traj = trajectory.load(ref_file('ala2.pdb'))
self.num_shots = 2
self.rings = xray.Rings.simulate(self.traj, 1, self.q_values,
self.num_phi,
self.num_shots) # 1 molec
def setup(self):
self.q_values = np.array([1.0, 2.0])
self.num_phi = 360
self.l = 50.0
self.d = xray.Detector.generic(spacing=0.4, l=self.l)
self.i = np.abs(np.random.randn(self.d.num_pixels))
self.t = trajectory.load(ref_file('ala2.pdb'))
self.shot = xray.Shotset(self.i, self.d)
def setup(self):
self.q_values = np.array([1.0, 2.0])
self.num_phi = 360
self.l = 50.0
self.d = xray.Detector.generic(spacing=0.4, l=self.l)
self.i = np.abs( np.random.randn(self.d.num_pixels) )
self.t = trajectory.load(ref_file('ala2.pdb'))
self.shot = xray.Shotset(self.i, self.d)
def test_rm_com():
t = trajectory.load( ref_file('ala2.pdb') )
r = structure.remove_COM(t)
masses = [ a.element.mass for a in t.topology.atoms() ]
for i in range(t.n_frames):
assert_array_almost_equal(np.zeros(3), np.average(t.xyz[i,:,:], weights=masses, axis=0))
def test_python_call(self):
print "testing python wrapper fxn..."
traj = trajectory.load(ref_file('ala2.pdb'))
num_molecules = 512
detector = Detector.generic()
py_I = xray.simulate_shot(traj, num_molecules, detector, verbose=True)
def test_replicate():
if TRAVIS: raise SkipTest
cmd = 'replicate -i %s -n 10 -d 0.1 > /dev/null 2>&1' % ref_file('goldBenchMark.coor')
subprocess.check_call(cmd, shell=True)
if not os.path.exists('replicated.pdb'):
raise RuntimeError('no output produced')
else:
o = trajectory.load('replicated.pdb')
os.remove('replicated.pdb')
def test_solvate():
if not OPENMM: raise SkipTest
if TRAVIS: raise SkipTest
cmd = 'solvate -i %s > /dev/null 2>&1' % ref_file('ala2.pdb')
subprocess.check_call(cmd, shell=True)
if not os.path.exists('solvated.pdb'):
raise RuntimeError('no output produced')
else:
o = trajectory.load('solvated.pdb')
os.remove('solvated.pdb')
def setup(self):
self.t = trajectory.load(ref_file('ala2.pdb'))
# make a fake restraint array
self.restraint_array = np.zeros((2, 4))
self.restraint_array[0, :] = np.array([0, 5, 1.0, 1])
self.restraint_array[1, :] = np.array([4, 10, 10.0, 0])
self.dr = exptdata.DistanceRestraint(self.restraint_array)
def test_solvate():
if not OPENMM: raise SkipTest
if TRAVIS: raise SkipTest
cmd = 'solvate -i %s > /dev/null 2>&1' % ref_file('ala2.pdb')
subprocess.check_call(cmd, shell=True)
if not os.path.exists('solvated.pdb'):
raise RuntimeError('no output produced')
else:
o = trajectory.load('solvated.pdb')
os.remove('solvated.pdb')
def setup(self):
self.t = trajectory.load( ref_file('ala2.pdb') )
# make a fake restraint array
self.restraint_array = np.zeros((2,4))
self.restraint_array[0,:] = np.array([0, 5, 1.0, 1])
self.restraint_array[1,:] = np.array([4, 10, 10.0, 0])
self.dr = exptdata.DistanceRestraint(self.restraint_array)
def test_load_coor():
s = structure.load_coor( ref_file('goldBenchMark.coor') )
s.save('s.pdb')
t = trajectory.load('s.pdb')
assert_array_almost_equal(s.xyz, t.xyz, decimal=3)
for a in t.topology.atoms():
assert a.element.symbol == 'Au'
if os.path.exists('s.pdb'):
os.remove('s.pdb')
def test_load_coor():
s = structure.load_coor( ref_file('goldBenchMark.coor') )
s.save('s.pdb')
t = trajectory.load('s.pdb')
assert_array_almost_equal(s.xyz, t.xyz, decimal=3)
for a in t.topology.atoms():
assert a.element.symbol == 'Au'
if os.path.exists('s.pdb'):
os.remove('s.pdb')
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 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 setup(self):
self.q_values = np.array([1.0, 2.0])
self.num_phi = 360
self.l = 50.0
self.d = xray.Detector.generic(spacing=0.4, l=self.l)
self.t = trajectory.load(ref_file('ala2.pdb'))
self.num_shots = 2
intensities = np.abs(np.random.randn(self.num_shots, self.d.num_pixels))
io.saveh('tmp_tables.h5', data=intensities)
self.tables_file = tables.File('tmp_tables.h5')
self.i = self.tables_file.root.data
self.shot = xray.Shotset(self.i, self.d)
return
def setup(self):
self.d = xray.Detector.generic(spacing=0.3)
self.t = trajectory.load(ref_file('ala2.pdb'))
def test_m_confs():
# smoke test
t = trajectory.load( ref_file('ala2.pdb') )
m = structure.multiply_conformations(t, 10, 1.0)
#!/usr/bin/env python
import numpy as np
from odin import xray
from odin import _cpuscatter
from mdtraj import trajectory
import matplotlib.pyplot as plt
q_values = [1.4]
traj = trajectory.load('3LYZ.pdb')
xyzlist = traj.xyz[0]
atomic_numbers = np.array([ a.element.atomic_number for a in traj.topology.atoms() ])
b = xray.Beam(None, energy=10.) # same as was used to make reference.dtc
pol_q_grid = xray._q_grid_as_xyz(q_values, 360, b.k)
dtc = xray.load('reference.dtc')
dtc_q_grid = dtc.reciprocal
num_molecules = 1
rfloats = np.random.rand(num_molecules, 3)
pol_i = _cpuscatter.simulate(num_molecules, pol_q_grid, xyzlist,
atomic_numbers, rfloats=rfloats)
dtc_i = _cpuscatter.simulate(num_molecules, dtc_q_grid, xyzlist,
atomic_numbers, rfloats=rfloats)
def convert_dcd_xtc(pdb_name, dcd_name, xtc_name): t = trajectory.load(dcd_name, top=pdb_name) t.save(xtc_name)
def convert_dcd_xtc(pdb_name, dcd_name, xtc_name):
t = trajectory.load(dcd_name, top=pdb_name)
t.save(xtc_name)
import numpy as np
from odin import xray
from mdtraj import trajectory
import matplotlib.pyplot as plt
t = trajectory.load('reference/ala2.pdb')
dp = xray.Detector.generic_polar(q_lim=0.6)
xp = xray.Shot.simulate(t, 10, dp)
dc = xray.Detector.generic(spacing=0.6)
xc = xray.Shot.simulate(t, 10, dc)
# make sure it matches up decently with non-polar
ref = xc.I_ring(0.4)
pol = xp.I_ring(0.4)
ref = ref * (pol[0]/ref[0]) # scale them to be the same-ish
print np.abs(ref - pol) / ref
plt.figure()
plt.plot(ref, lw=2)
plt.plot(pol, lw=2)
plt.show()
def test_m_confs():
# smoke test
t = trajectory.load( ref_file('ala2.pdb') )
m = structure.multiply_conformations(t, 10, 1.0)
