def save(self):
"Save the trajs as a n MSMBuilder project"
traj_dir = pjoin(self.project_dir, 'Trajectories')
if not os.path.exists(traj_dir):
os.makedirs(traj_dir)
t = Trajectory.load_trajectory_file(self.conf_filename)
traj_paths = []
for i, xyz in enumerate(self.trajectories):
t['IndexList'] = None # bug in msmbuilder
t['XYZList'] = xyz
traj_paths.append(pjoin(traj_dir, 'trj%d.lh5' % i))
t.save(traj_paths[-1])
p = Project(
{
'conf_filename': os.path.abspath(self.conf_filename),
'traj_lengths': self.n_frames * np.ones(self.n_trajs),
'traj_paths': [os.path.abspath(e) for e in traj_paths],
'traj_converted_from': [[] for i in range(self.n_trajs)],
'traj_errors': [None for i in range(self.n_trajs)],
},
project_dir=self.project_dir,
validate=True)
p.save(pjoin(self.project_dir, 'Project.yaml'))
# just check again
p = Project.load_from(pjoin(self.project_dir, 'Project.yaml'))
p._validate()
assert np.all(
(p.load_traj(0)['XYZList'] - self.trajectories[0])**2 < 1e-6)
def save(self):
"Save the trajs as a n MSMBuilder project"
traj_dir = pjoin(self.project_dir, 'Trajectories')
if not os.path.exists(traj_dir):
os.makedirs(traj_dir)
t = Trajectory.load_trajectory_file(self.conf_filename)
traj_paths = []
for i, xyz in enumerate(self.trajectories):
t['IndexList'] = None # bug in msmbuilder
t['XYZList'] = xyz
traj_paths.append(pjoin(traj_dir, 'trj%d.lh5' % i))
t.save(traj_paths[-1])
p = Project({'conf_filename': os.path.abspath(self.conf_filename),
'traj_lengths': self.n_frames*np.ones(self.n_trajs),
'traj_paths': [os.path.abspath(e) for e in traj_paths],
'traj_converted_from': [[] for i in range(self.n_trajs)],
'traj_errors': [None for i in range(self.n_trajs)],
}, project_dir=self.project_dir, validate=True)
p.save(pjoin(self.project_dir,'Project.yaml'))
# just check again
p = Project.load_from(pjoin(self.project_dir,'Project.yaml'))
p._validate()
assert np.all((p.load_traj(0)['XYZList'] - self.trajectories[0])**2 < 1e-6)
