def test_traj_split(self):
traj1 = traj.TimeSeries(distraj=[1, 2, 3], dt=1.)
traj2 = traj.TimeSeries(distraj=[3, 2, 1], dt=2.)
trajs = [traj1, traj2]
self.filepath = msm_lib.traj_split(data=trajs, lagt=10)
self.assertIsInstance(self.filepath, str)
self.assertTrue(os.path.exists(self.filepath))
os.remove(self.filepath) # clean temp file
def setUp(self):
download_test_data()
self.nstates = np.random.randint(3,100)
distraj_1 = np.random.randint(1,self.nstates+1, size=1000).tolist()
traj_1 = traj.TimeSeries(distraj= distraj_1, dt=1.)
distraj_2 = np.random.randint(1,self.nstates+1, size=1000).tolist()
traj_2 = traj.TimeSeries(distraj= distraj_2, dt=2.)
self.data = np.array([
traj_1,
traj_2
])
self.lagt = 10
self.keys = [i for i in range(1,self.nstates+1)]
msm_obj = msm.MSM(data=self.data, lagt=self.lagt, keys=self.keys, sym=True)
self.msm = msm_obj
def setUp(self):
download_test_data()
self.tr = traj.TimeSeries(top='test/data/alaTB.gro', \
traj=['test/data/protein_only.xtc'])
self.tr.discretize('rama', states=['A', 'E', 'O'])
self.tr.find_keys()
self.msm = msm.SuperMSM([self.tr])
def map_trajectory(self):
""" Maps trajectory onto the PCCA clusters
Returns
-------
mappedtraj : str
The mapped trajectory.
"""
print "\n Mapping trajectory onto macrostates..."
mappedtraj = []
keep_states = self.parent.keep_states
keep_keys = self.parent.keep_keys
mt_states = []
for data in self.parent.data:
for s in data.distraj:
try:
mt_states.append([k for k, v in self.macros.iteritems() \
if keep_keys.index(s) in v][0])
except ValueError:
#print " not in keep_keys"
try:
prev = mt_states[-1]
except IndexError:
pass
mt = traj.TimeSeries(distraj=mt_states, dt=data.dt)
mappedtraj.append(mt)
super(PCCA, self).__init__(mappedtraj, keys=range(self.N), lagt=self.parent.lagt)
def setUp(self):
download_test_data()
self.traj = md.load('test/data/protein_only.xtc', \
top='test/data/alaTB.gro')
self.topfn = 'test/data/alaTB.gro'
self.trajfn = 'test/data/protein_only.xtc'
self.tr = traj.TimeSeries(top='test/data/alaTB.gro', \
traj=['test/data/protein_only.xtc'])
def test_merge_trajs(self):
# create fake trajectory to merge
traj2 = traj.TimeSeries(distraj=['L', 'L', 'L', 'A'], dt = 2.0)
traj2.keys = ['L','A']
old_keys = self.msm.keys
self.msm.data = [self.tr, traj2]
new_keys = self.msm._merge_trajs()
self.assertEqual(len(new_keys), len(old_keys) + 1)
self.assertEqual(sorted(new_keys), ['A', 'E', 'L'])
def test_max_dt(self):
traj2 = traj.TimeSeries(distraj=['L', 'L', 'L', 'A'], dt=2.0)
old_dt = self.msm.dt
self.msm.data = [self.tr, traj2]
new_dt = self.msm._max_dt()
self.assertEqual(new_dt, 2.0)
def setUp(self):
self.tr = traj.TimeSeries(top='trajectory/tests/data/alaTB.gro', \
traj=['trajectory/tests/data/protein_only.xtc'])
pass