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)
def run(traj_dir, conf_filename, project_filename, iext):
logger.info("Rebuilding project.")
file_list = glob.glob(traj_dir + "/trj*%s" % iext)
num_traj = len(file_list)
traj_lengths = np.zeros(num_traj, 'int')
traj_paths = []
if not os.path.exists(conf_filename):
raise(IOError("Cannot find conformation file %s" % conf_filename))
file_list = sorted(file_list, key=utils.keynat)
for i, filename in enumerate(file_list):
traj_lengths[i] = len(md.open(filename))
traj_paths.append(filename)
records = {
"conf_filename": conf_filename,
"traj_lengths": traj_lengths,
"traj_paths": traj_paths,
"traj_errors": [None for i in xrange(num_traj)],
"traj_converted_from": [[] for i in xrange(num_traj)]
}
p = Project(records)
p.save(project_filename)
logger.info("Wrote %s" % project_filename)
def run(traj_dir, conf_filename, project_filename):
logger.info("Rebuilding project.")
file_list = glob.glob(traj_dir + "/trj*.lh5")
num_traj = len(file_list)
traj_lengths = np.zeros(num_traj,'int')
traj_paths = []
file_list = sorted(file_list, key=utils.keynat)
for i,filename in enumerate(file_list):
traj_lengths[i] = Trajectory.load_trajectory_file(filename,JustInspect=True)[0]
traj_paths.append(filename)
records = {
"conf_filename":conf_filename,
"traj_lengths":traj_lengths,
"traj_paths":traj_paths,
"traj_errors": [None for i in xrange(num_traj)],
"traj_converted_from":[[] for i in xrange(num_traj)]
}
p = Project(records)
p.save(project_filename)
logger.info("Wrote %s" % project_filename)
parser = arglib.ArgumentParser()
parser.add_argument('traj_dir', help='Directory to find trajectory files.')
parser.add_argument('conf_fn', help='Conformation filename that has the same atom names and residue IDs, etc. as the trajectories.')
parser.add_argument('output', default='./ProjectInfo.yaml', help='Output filename [ ./ProjectInfo.yaml ]')
args = parser.parse_args()
traj_list = [ os.path.join(args.traj_dir, fn) for fn in os.listdir(args.traj_dir)]
traj_list.sort(key=utils.keynat) # = list.sort(traj_list, key=utils.keynat)
print traj_list
traj_lens = []
for i in xrange(len(traj_list)):
print i
shape = Trajectory.load_from_hdf(traj_list[i], JustInspect=True)
traj_lens.append(shape[0])
records = { 'conf_filename' : args.conf_fn,
'traj_lengths' : traj_lens,
'traj_paths' : traj_list,
'traj_converted_from' : [[] for fn in traj_list],
'traj_errors' : [None for fn in traj_list]
}
project = Project(records=records)
project.save(args.output)
not_too_short_inds = np.where( traj_lens >= ( args.min_length + args.trim_first ) )[0]
os.mkdir( os.path.join( args.write_dir, 'Trajectories' ) )
print "Will limit this project to %d trajectories." % len( not_too_short_inds )
for i in xrange( len( not_too_short_inds ) ):
print "Copying trajectory %d -> %d (length=%d)" % ( not_too_short_inds[i], i, Proj.traj_lengths[ not_too_short_inds[i] ] - args.trim_first )
trj0 = tables.openFile( Proj.traj_filename( not_too_short_inds[i] ) )
trj1 = tables.openFile( os.path.abspath( os.path.join( args.write_dir, 'Trajectories', '%s%d%s'% ('trj',i, '.lh5' ) ) ), 'w' )
#os.system( 'ln -s %s %s' % ( trj0, trj1 ) )
#os.symlink( trj0, trj1 )
for n0 in trj0.iterNodes('/'):
if n0.name != 'XYZList':
trj0.copyNode( where='/', name=n0.name, newparent=trj1.root )
else:
temp_ary = n0[ args.trim_first : ]
io.saveh( trj1, XYZList=temp_ary )
trj0.close()
trj1.close()
new_records = {'conf_filename': Proj.conf_filename.split('/')[-1],
'traj_lengths': Proj.traj_lengths[ not_too_short_inds ] - args.trim_first,
'traj_paths': Proj._traj_paths[ : len( not_too_short_inds ) ], # This works because they're named relatively and they are re-numbered
'traj_converted_from': Proj._traj_converted_from[ not_too_short_inds ],
'traj_errors': Proj._traj_errors[ not_too_short_inds ] }
new_proj_dir = args.write_dir
# Copy the trajectories
New_Proj = Project( new_records, project_dir = new_proj_dir )
New_Proj.save( os.path.join( args.write_dir, 'ProjectInfo.yaml' ) )
