#### Read in input topology, trajectory files, outTraj file
top_file = sys.argv[1]
traj_file = sys.argv[2]
out_traj_file = sys.argv[3]
if ("-crys" in sys.argv):
include_crys = True
else:
include_crys = False
#### load topology and trajectories
traj_molid = molecule.load('pdb', top_file)
molecule.read(traj_molid, 'netcdf', traj_file, beg=0, end=-1, waitfor=-1)
#### align all frames
refsel = atomsel("protein", molid=traj_molid, frame=0)
for i in range(molecule.numframes(traj_molid)):
molecule.set_frame(traj_molid, i)
b = atomsel("protein", molid=traj_molid, frame=i)
T = b.fit(refsel)
atomsel("all", molid=traj_molid, frame=i).move(T)
#### Read out file
if (include_crys == True):
molecule.write(traj_molid, 'dcd', out_traj_file, beg=0, end=-1)
else:
molecule.write(traj_molid, 'dcd', out_traj_file, beg=1, end=-1)
toc = time.clock()
print("Time for wrapAlign.py = " + str(toc - tic))
def setFrame(self, frame): """ Set the coordinate frame to the given value. Must be in the range [0, numFrames())""" molecule.set_frame(self.id, frame) return self
def setFrame(self, frame):
""" Set the coordinate frame to the given value. Must be in the range
[0, numFrames())"""
molecule.set_frame(self.id, frame)
return self