def test(self):
from msmbuilder.scripts.SaveStructures import save
project = get('ProjectInfo.yaml')
assignments = get('Assignments.h5')['arr_0']
which_states = [0, 1, 2]
list_of_trajs = project.get_random_confs_from_states(assignments,
which_states, num_confs=2, replacement=True,
random=np.random.RandomState(42))
assert isinstance(list_of_trajs, list)
assert isinstance(list_of_trajs[0], Trajectory)
eq(len(list_of_trajs), len(which_states))
for t in list_of_trajs:
eq(len(t), 2)
print list_of_trajs[0].keys()
# sep, tps, one
save(list_of_trajs, which_states, style='sep', format='lh5', outdir=self.td)
save(list_of_trajs, which_states, style='tps', format='lh5', outdir=self.td)
save(list_of_trajs, which_states, style='one', format='lh5', outdir=self.td)
names = ['State0-0.lh5', 'State0-1.lh5', 'State0.lh5', 'State1-0.lh5',
'State1-1.lh5', 'State1.lh5', 'State2-0.lh5', 'State2-1.lh5',
'State2.lh5']
for name in names:
t = Trajectory.load_trajectory_file(pjoin(self.td, name))
eq(t, get('save_structures/' + name))
def test(self):
from msmbuilder.scripts.SaveStructures import save
os.chdir(self.td)
project = get('ProjectInfo.yaml')
assignments = get('Assignments.h5')['arr_0']
which_states = [0, 1, 2]
list_of_trajs = project.get_random_confs_from_states(assignments,
which_states, num_confs=2, replacement=True,
random=np.random.RandomState(42))
assert isinstance(list_of_trajs, list)
assert isinstance(list_of_trajs[0], md.Trajectory)
eq(len(list_of_trajs), len(which_states))
for t in list_of_trajs:
eq(len(t), 2)
# sep, tps, one
save(list_of_trajs, which_states, style='sep', format='lh5', outdir=self.td)
save(list_of_trajs, which_states, style='tps', format='lh5', outdir=self.td)
save(list_of_trajs, which_states, style='one', format='lh5', outdir=self.td)
names = ['State0-0.lh5', 'State0-1.lh5', 'State0.lh5', 'State1-0.lh5',
'State1-1.lh5', 'State1.lh5', 'State2-0.lh5', 'State2-1.lh5',
'State2.lh5']
for name in names:
t = md.load(pjoin(self.td, name))
eq(t.xyz, get('save_structures/' + name).xyz) # Just checking coordinates because atom names / bonds in reference data are incompatible with MDTraj.